22 files changed, 7820 insertions, 1458 deletions

diff --git a/biology/embassy/Makefile b/biology/embassy/Makefile
index 6c572598b54e..5d3ed872749a 100644
--- a/biology/embassy/Makefile
+++ b/biology/embassy/Makefile
@@ -7,18 +7,21 @@
 #
 
 PORTNAME=	embassy
-PORTVERSION=	2.10.0
+PORTVERSION=	3.0.0
 CATEGORIES=	biology
-MASTER_SITES=	ftp://ftp.uk.embnet.org/pub/EMBOSS/ \
+MASTER_SITES=	ftp://emboss.open-bio.org/pub/EMBOSS/ \
+		ftp://ftp.uk.embnet.org/pub/EMBOSS/ \
 		ftp://ftp.es.embnet.org/pub/software/emboss/EMBOSS/ \
 		ftp://ftp.ebi.ac.uk/pub/software/unix/EMBOSS/
-DIST_SUBDIR=	${PORTNAME}
+DIST_SUBDIR=	emboss
 
 MAINTAINER=	fernan@iib.unsam.edu.ar
 COMMENT=	A collection of contributed EMBOSS applications
 
-LIB_DEPENDS=	nucleus.1:${PORTSDIR}/biology/emboss
+LIB_DEPENDS=	nucleus.3:${PORTSDIR}/biology/emboss
 
+PREFIX?=	${LOCALBASE}/emboss
+NO_MTREE=	yes
 USE_SUBMAKE=	yes
 USE_ICONV=	yes
 USE_GMAKE=	yes
@@ -26,12 +29,17 @@ GNU_CONFIGURE=	yes
 USE_XLIB=	yes
 USE_MOTIF=	yes
 
-OPTIONS=	DOMAINATRIX	"Protein structure and domain apps" on \
+OPTIONS=	DOMAINATRIX	"Protein domain apps" on \
+		DOMALIGN	"Protein domain apps" on \
+		DOMSEARCH	"Protein domain apps" on \
+		SIGNATURE	"Protein domain apps" on \
+		STRUCTURE	"Protein domain apps" on \
 		EMNU		"EMBOSS simple menu" on \
 		ESIM4		"Align cDNA/EST to genome" on \
 		HMMER		"HMM alignment and searches" on \
 		MEME		"Motif detection" on \
 		MSE		"A multiple sequence screen editor" on \
+		MYEMBOSS	"Examples for developers of EMBOSS apps" on \
 		PHYLIP		"Phylogeny inference" on \
 		TOPO		"Transmembrane display" on
 
@@ -39,15 +47,21 @@ CONFIGURE_ENV+=	CPPFLAGS="-I${PREFIX}/include -I${LOCALBASE}/include" \
 		LDFLAGS="-L${PREFIX}/lib -L${LOCALBASE}/lib"
 
 EMBASSY_WRKDIR=		${WRKSRC}/EMBASSY
-DOMAINATRIX_VERSION=	1.0.0
+DOMAINATRIX_VERSION=	0.1.0
 EMNU_VERSION=		1.05
 ESIM4_VERSION=		1.0.0
 HMMER_VERSION=		2.1.1
 MEME_VERSION=		2.3.1
 MSE_VERSION=		1.0.0
 TOPO_VERSION=		1.0.0
-PHYLIP_VERSION=		3.57c
-EMBASSY_APPS=		DOMAINATRIX EMNU ESIM4 HMMER MEME MSE PHYLIP TOPO
+PHYLIP_VERSION=		3.6b
+DOMALIGN_VERSION=	0.1.0
+DOMSEARCH_VERSION=	0.1.0
+SIGNATURE_VERSION=	0.1.0
+STRUCTURE_VERSION=	0.1.0
+MYEMBOSS_VERSION=	3.0.0
+EMBASSY_APPS=		DOMAINATRIX EMNU ESIM4 HMMER MEME MSE PHYLIP TOPO \
+			DOMALIGN DOMSEARCH SIGNATURE STRUCTURE MYEMBOSS
 
 .include <bsd.port.pre.mk>
 
@@ -75,16 +89,6 @@ do-extract:
 	  fi
 .endfor
 
-.if !defined(WITHOUT_DOMAINATRIX)
-pre-configure::
-	@${PATCH} ${PATCH_ARGS} < ${PATCHDIR}/domainatrix-patch-Makefile.in
-.endif
-
-.if !defined(WITHOUT_EMNU)
-pre-configure::
-	@${PATCH} ${PATCH_ARGS} < ${PATCHDIR}/emnu-patch-Makefile.in
-.endif
-
 do-configure:
 .for app in ${APPLIST}
 	@ cd ${${app}_WRKSRC} && \
diff --git a/biology/embassy/distinfo b/biology/embassy/distinfo
index 62e43dd5e562..486dd95d3995 100644
--- a/biology/embassy/distinfo
+++ b/biology/embassy/distinfo
@@ -1,24 +1,39 @@
-MD5 (embassy/DOMAINATRIX-1.0.0.tar.gz) = 9deff6f5bf526408f0f02c002488ad59
-SHA256 (embassy/DOMAINATRIX-1.0.0.tar.gz) = 50abb58f3196f2f3d04af2649ace36457315c378fa73345cb635b51e913db8fc
-SIZE (embassy/DOMAINATRIX-1.0.0.tar.gz) = 471604
-MD5 (embassy/EMNU-1.05.tar.gz) = df29ae1e8201081f4413862d7f10edb5
-SHA256 (embassy/EMNU-1.05.tar.gz) = 4bcdc64c9ec2d818b3ba00eef34eee39e11ef99d87cf292a214b7be51bf6bf48
-SIZE (embassy/EMNU-1.05.tar.gz) = 339355
-MD5 (embassy/ESIM4-1.0.0.tar.gz) = 3b8137b3b8ff0e84bc6e1243c7343578
-SHA256 (embassy/ESIM4-1.0.0.tar.gz) = 6e24466905c457d3f464f3a7fb24680a01326cb22acf7d090b84a51da0382d2a
-SIZE (embassy/ESIM4-1.0.0.tar.gz) = 378342
-MD5 (embassy/HMMER-2.1.1.tar.gz) = 56816b26a43c8542f7d12f9069e77843
-SHA256 (embassy/HMMER-2.1.1.tar.gz) = 63f3d4e6a509b8d1a815a9dc7e74fe7c458a9478e4885608349eeb2aa8c2df87
-SIZE (embassy/HMMER-2.1.1.tar.gz) = 562855
-MD5 (embassy/MEME-2.3.1.tar.gz) = a9fb38886665f3f654da1244c2e1476f
-SHA256 (embassy/MEME-2.3.1.tar.gz) = 778589a63705e17db1aded3704b70a3cc3de4b1e41f90ccfcd8d86b7f6dab622
-SIZE (embassy/MEME-2.3.1.tar.gz) = 421914
-MD5 (embassy/MSE-1.0.0.tar.gz) = b666681aceb9f07f968585f2edc4a039
-SHA256 (embassy/MSE-1.0.0.tar.gz) = 13fca33f78cd83e2a53c0b08a0db97da2b9dd572e01a694e8acd6a87316b3fa7
-SIZE (embassy/MSE-1.0.0.tar.gz) = 411772
-MD5 (embassy/PHYLIP-3.57c.tar.gz) = 83201895898feb15dbbae6affabd3609
-SHA256 (embassy/PHYLIP-3.57c.tar.gz) = ff5385d0b5b6c5f42a8b7c53a682ede654e0309f4ab31859f5b907563a4a7b4f
-SIZE (embassy/PHYLIP-3.57c.tar.gz) = 858348
-MD5 (embassy/TOPO-1.0.0.tar.gz) = 0a8fcc84fdba071b20f3046de9fdb487
-SHA256 (embassy/TOPO-1.0.0.tar.gz) = d1e9e6c9c37b36f4bfca485fbda68d1c045c8fa1171eea94089773ed40bc11d3
-SIZE (embassy/TOPO-1.0.0.tar.gz) = 345938
+MD5 (emboss/DOMAINATRIX-0.1.0.tar.gz) = 655f6ec58e0b9dfdac111fd9481359cb
+SHA256 (emboss/DOMAINATRIX-0.1.0.tar.gz) = 6bc374c5275dead68ef09d8273bf4d73a03bc56990e795d6eddcee4de25c12a0
+SIZE (emboss/DOMAINATRIX-0.1.0.tar.gz) = 349882
+MD5 (emboss/EMNU-1.05.tar.gz) = b3a7fc11e46f7166ddeec11f2fe03d9b
+SHA256 (emboss/EMNU-1.05.tar.gz) = d7261d615d6547a9824d3d9e3f82ff756c0db5786e8356bc54cc5fa0c516b26f
+SIZE (emboss/EMNU-1.05.tar.gz) = 348924
+MD5 (emboss/ESIM4-1.0.0.tar.gz) = 835393b3246eb4543a694362c6f335ff
+SHA256 (emboss/ESIM4-1.0.0.tar.gz) = f8241c9e37ccc17dbd29df2d9c90063ba7caf4e64cc5c368b6878c3aa3895620
+SIZE (emboss/ESIM4-1.0.0.tar.gz) = 384396
+MD5 (emboss/HMMER-2.1.1.tar.gz) = 382594654e45a7e8d5872b4b1016a494
+SHA256 (emboss/HMMER-2.1.1.tar.gz) = 78647dfb7841e8b52b4c3de34400c68d17a877b698956ac9a5ee5e030569cca6
+SIZE (emboss/HMMER-2.1.1.tar.gz) = 561289
+MD5 (emboss/MEME-2.3.1.tar.gz) = 6f4e516e413582268a34e91fb12e21c3
+SHA256 (emboss/MEME-2.3.1.tar.gz) = bec2c8002b8b551ef9c639bcb58633499060cd8a1bfe4754db5ed201a6a0dffa
+SIZE (emboss/MEME-2.3.1.tar.gz) = 423966
+MD5 (emboss/MSE-1.0.0.tar.gz) = 3b9810e870937ec32220b5c9fe7a83cd
+SHA256 (emboss/MSE-1.0.0.tar.gz) = ddf9092721666d64c56733d9b6d04e749957848cafa8ba4ec6eee083a0ffcab3
+SIZE (emboss/MSE-1.0.0.tar.gz) = 415051
+MD5 (emboss/PHYLIP-3.6b.tar.gz) = 6f2c10438d788acf4a1dff23441b2a2c
+SHA256 (emboss/PHYLIP-3.6b.tar.gz) = 32aba94d0be011ee304e974657db11544297c008e53341cd000a1f412eb874e2
+SIZE (emboss/PHYLIP-3.6b.tar.gz) = 1136746
+MD5 (emboss/TOPO-1.0.0.tar.gz) = 7b3355570ba36f7daf57dcbc717215ce
+SHA256 (emboss/TOPO-1.0.0.tar.gz) = ff10378b4ecad69ddb374cd47a7d3c7fa5975d6695057f05ea264940258ebaa3
+SIZE (emboss/TOPO-1.0.0.tar.gz) = 351796
+MD5 (emboss/DOMALIGN-0.1.0.tar.gz) = 4332d7de49b27f257b58a90510223eb7
+SHA256 (emboss/DOMALIGN-0.1.0.tar.gz) = de66ddfdb72ccf7291be614c9a83fd8fc47363191cb2c045b372de5cc334a594
+SIZE (emboss/DOMALIGN-0.1.0.tar.gz) = 347672
+MD5 (emboss/DOMSEARCH-0.1.0.tar.gz) = c62f9b69a9ed9580d4489a8de9ea4863
+SHA256 (emboss/DOMSEARCH-0.1.0.tar.gz) = f4933b62e19ee6b23a78b70c3cf2d5a9a18eff1d7532f92e2d33b1d683877916
+SIZE (emboss/DOMSEARCH-0.1.0.tar.gz) = 352793
+MD5 (emboss/SIGNATURE-0.1.0.tar.gz) = 1e30e12048609a468b7b4d4affb177cf
+SHA256 (emboss/SIGNATURE-0.1.0.tar.gz) = c6bb252beaccac5256d99301933b15da6ef90af3f20d7f92fed1f78b271785ee
+SIZE (emboss/SIGNATURE-0.1.0.tar.gz) = 400125
+MD5 (emboss/STRUCTURE-0.1.0.tar.gz) = 6efc35eb2855738252e0537198f5225d
+SHA256 (emboss/STRUCTURE-0.1.0.tar.gz) = 7142e207987da46cd85c81088ea475abb866da90ff57e4c3ca1c63bd8f209b64
+SIZE (emboss/STRUCTURE-0.1.0.tar.gz) = 362563
+MD5 (emboss/MYEMBOSS-3.0.0.tar.gz) = 15d5bc7b0ce9dfb113777c06c4e18906
+SHA256 (emboss/MYEMBOSS-3.0.0.tar.gz) = 0a19ebbe52da849fb87799edaea2281a1bf235e6045725789b9b29e58f0a0dc5
+SIZE (emboss/MYEMBOSS-3.0.0.tar.gz) = 323628
diff --git a/biology/embassy/files/domainatrix-patch-Makefile.in b/biology/embassy/files/domainatrix-patch-Makefile.in
deleted file mode 100644
index d544a23f136b..000000000000
--- a/biology/embassy/files/domainatrix-patch-Makefile.in
+++ /dev/null
@@ -1,11 +0,0 @@
---- EMBASSY/DOMAINATRIX-1.0.0/src/Makefile.in.orig	Sat May 28 12:21:57 2005
-+++ EMBASSY/DOMAINATRIX-1.0.0/src/Makefile.in	Sat May 28 12:22:14 2005
-@@ -315,7 +315,7 @@
- @LOCALLINK_TRUE@	../../../plplot/libplplot.la \
- @LOCALLINK_TRUE@	$(am__DEPENDENCIES_1)
- DEFAULT_INCLUDES = -I. -I$(srcdir)
--depcomp = $(SHELL) $(top_srcdir)/../../depcomp
-+depcomp = $(SHELL) $(top_srcdir)/depcomp
- am__depfiles_maybe = depfiles
- COMPILE = $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) \
- 	$(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS)
diff --git a/biology/embassy/files/emnu-patch-Makefile.in b/biology/embassy/files/emnu-patch-Makefile.in
deleted file mode 100644
index 31688dfd589b..000000000000
--- a/biology/embassy/files/emnu-patch-Makefile.in
+++ /dev/null
@@ -1,11 +0,0 @@
---- EMBASSY/EMNU-1.05/source/Makefile.in.orig	Sat May 28 12:57:17 2005
-+++ EMBASSY/EMNU-1.05/source/Makefile.in	Sat May 28 13:03:33 2005
-@@ -63,7 +63,7 @@
- @LOCALLINK_TRUE@	../../../plplot/libplplot.la \
- @LOCALLINK_TRUE@	$(am__DEPENDENCIES_1)
- DEFAULT_INCLUDES = -I. -I$(srcdir)
--depcomp = $(SHELL) $(top_srcdir)/../../depcomp
-+depcomp = $(SHELL) $(top_srcdir)/depcomp
- am__depfiles_maybe = depfiles
- COMPILE = $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) \
- 	$(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS)
diff --git a/biology/embassy/pkg-plist b/biology/embassy/pkg-plist
index 22c88962c326..a1f0267522e1 100644
--- a/biology/embassy/pkg-plist
+++ b/biology/embassy/pkg-plist
@@ -1,148 +1,201 @@
-%%PLIST_DOMAINATRIX%%bin/allversusall
 %%PLIST_DOMAINATRIX%%bin/cathparse
-%%PLIST_DOMAINATRIX%%bin/contacts
-%%PLIST_DOMAINATRIX%%bin/domainalign
-%%PLIST_DOMAINATRIX%%bin/domainer
 %%PLIST_DOMAINATRIX%%bin/domainnr
-%%PLIST_DOMAINATRIX%%bin/domainrep
 %%PLIST_DOMAINATRIX%%bin/domainreso
 %%PLIST_DOMAINATRIX%%bin/domainseqs
 %%PLIST_DOMAINATRIX%%bin/domainsse
-%%PLIST_DOMAINATRIX%%bin/hetparse
-%%PLIST_DOMAINATRIX%%bin/interface
-%%PLIST_DOMAINATRIX%%bin/libgen
-%%PLIST_DOMAINATRIX%%bin/pdbparse
-%%PLIST_DOMAINATRIX%%bin/pdbplus
-%%PLIST_DOMAINATRIX%%bin/pdbtosp
-%%PLIST_DOMAINATRIX%%bin/rocon
-%%PLIST_DOMAINATRIX%%bin/rocplot
 %%PLIST_DOMAINATRIX%%bin/scopparse
-%%PLIST_DOMAINATRIX%%bin/seqalign
-%%PLIST_DOMAINATRIX%%bin/seqfraggle
-%%PLIST_DOMAINATRIX%%bin/seqnr
-%%PLIST_DOMAINATRIX%%bin/seqsearch
-%%PLIST_DOMAINATRIX%%bin/seqsort
-%%PLIST_DOMAINATRIX%%bin/seqwords
-%%PLIST_DOMAINATRIX%%bin/siggen
-%%PLIST_DOMAINATRIX%%bin/sigscan
-%%PLIST_DOMAINATRIX%%bin/sites
 %%PLIST_DOMAINATRIX%%bin/ssematch
+%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/cathparse.acd
+%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/domainnr.acd
+%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/domainreso.acd
+%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/domainseqs.acd
+%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/domainsse.acd
+%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/scopparse.acd
+%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/ssematch.acd
+%%PLIST_DOMALIGN%%bin/allversusall
+%%PLIST_DOMALIGN%%bin/domainalign
+%%PLIST_DOMALIGN%%bin/domainrep
+%%PLIST_DOMALIGN%%bin/seqalign
+%%PLIST_DOMALIGN%%share/EMBOSS/acd/allversusall.acd
+%%PLIST_DOMALIGN%%share/EMBOSS/acd/domainalign.acd
+%%PLIST_DOMALIGN%%share/EMBOSS/acd/domainrep.acd
+%%PLIST_DOMALIGN%%share/EMBOSS/acd/seqalign.acd
+%%PLIST_DOMSEARCH%%bin/seqfraggle
+%%PLIST_DOMSEARCH%%bin/seqnr
+%%PLIST_DOMSEARCH%%bin/seqsearch
+%%PLIST_DOMSEARCH%%bin/seqsort
+%%PLIST_DOMSEARCH%%bin/seqwords
+%%PLIST_DOMSEARCH%%share/EMBOSS/acd/seqfraggle.acd
+%%PLIST_DOMSEARCH%%share/EMBOSS/acd/seqnr.acd
+%%PLIST_DOMSEARCH%%share/EMBOSS/acd/seqsearch.acd
+%%PLIST_DOMSEARCH%%share/EMBOSS/acd/seqsort.acd
+%%PLIST_DOMSEARCH%%share/EMBOSS/acd/seqwords.acd
 %%PLIST_EMNU%%bin/emnu
-%%PLIST_ESIM4%%bin/esim4
-%%PLIST_MEME%%bin/meme
+%%PLIST_EMNU%%share/EMBOSS/acd/emnu.acd
+%%PLIST_HMMER%%bin/ealistat
+%%PLIST_HMMER%%bin/ehmmalign
+%%PLIST_HMMER%%bin/ehmmbuild
 %%PLIST_HMMER%%bin/ehmmcalibrate
 %%PLIST_HMMER%%bin/ehmmconvert
 %%PLIST_HMMER%%bin/ehmmemit
 %%PLIST_HMMER%%bin/ehmmfetch
 %%PLIST_HMMER%%bin/ehmmindex
-%%PLIST_HMMER%%bin/ehmmbuild
-%%PLIST_HMMER%%bin/ehmmalign
 %%PLIST_HMMER%%bin/ehmmpfam
 %%PLIST_HMMER%%bin/ehmmsearch
-%%PLIST_HMMER%%bin/ealistat
-%%PLIST_MSE%%bin/mse
-%%PLIST_PHYLIP%%bin/eclique
-%%PLIST_PHYLIP%%bin/econsense
-%%PLIST_PHYLIP%%bin/econtml
-%%PLIST_PHYLIP%%bin/econtrast
-%%PLIST_PHYLIP%%bin/ednacomp
-%%PLIST_PHYLIP%%bin/ednadist
-%%PLIST_PHYLIP%%bin/ednainvar
-%%PLIST_PHYLIP%%bin/ednaml
-%%PLIST_PHYLIP%%bin/ednamlk
-%%PLIST_PHYLIP%%bin/ednapars
-%%PLIST_PHYLIP%%bin/ednapenny
-%%PLIST_PHYLIP%%bin/edollop
-%%PLIST_PHYLIP%%bin/edolpenny
-%%PLIST_PHYLIP%%bin/efactor
-%%PLIST_PHYLIP%%bin/efitch
-%%PLIST_PHYLIP%%bin/egendist
-%%PLIST_PHYLIP%%bin/ekitsch
-%%PLIST_PHYLIP%%bin/emix
-%%PLIST_PHYLIP%%bin/epenny
-%%PLIST_PHYLIP%%bin/eprotdist
-%%PLIST_PHYLIP%%bin/eprotpars
-%%PLIST_PHYLIP%%bin/erestml
-%%PLIST_PHYLIP%%bin/eseqboot
-%%PLIST_PHYLIP%%bin/eneighbor
-%%PLIST_TOPO%%bin/topo
-%%PLIST_MEME%%lib/libmeme.so.2
-%%PLIST_MEME%%lib/libmeme.so
-%%PLIST_MEME%%lib/libmeme.la
-%%PLIST_MEME%%lib/libmeme.a
-%%PLIST_HMMER%%lib/libhmmer.so.2
-%%PLIST_HMMER%%lib/libhmmer.so
-%%PLIST_HMMER%%lib/libhmmer.la
 %%PLIST_HMMER%%lib/libhmmer.a
-%%PLIST_MSE%%lib/libckit.so.1
-%%PLIST_MSE%%lib/libckit.so
-%%PLIST_MSE%%lib/libckit.la
-%%PLIST_MSE%%lib/libckit.a
-%%PLIST_MSE%%share/EMBOSS/acd/mse.acd
-%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/allversusall.acd
-%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/cathparse.acd
-%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/contacts.acd
-%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/domainalign.acd
-%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/domainer.acd
-%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/domainnr.acd
-%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/domainrep.acd
-%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/domainreso.acd
-%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/domainseqs.acd
-%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/domainsse.acd
-%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/hetparse.acd
-%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/interface.acd
-%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/libgen.acd
-%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/pdbparse.acd
-%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/pdbplus.acd
-%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/pdbtosp.acd
-%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/rocon.acd
-%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/rocplot.acd
-%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/scopparse.acd
-%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/seqalign.acd
-%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/seqfraggle.acd
-%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/seqnr.acd
-%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/seqsearch.acd
-%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/seqsort.acd
-%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/seqwords.acd
-%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/siggen.acd
-%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/sigscan.acd
-%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/sites.acd
-%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/ssematch.acd
-%%PLIST_EMNU%%share/EMBOSS/acd/emnu.acd
-%%PLIST_ESIM4%%share/EMBOSS/acd/esim4.acd
-%%PLIST_MEME%%share/EMBOSS/acd/meme.acd
+%%PLIST_HMMER%%lib/libhmmer.la
+%%PLIST_HMMER%%lib/libhmmer.so
+%%PLIST_HMMER%%lib/libhmmer.so.2
+%%PLIST_HMMER%%share/EMBOSS/acd/ealistat.acd
+%%PLIST_HMMER%%share/EMBOSS/acd/ehmmalign.acd
+%%PLIST_HMMER%%share/EMBOSS/acd/ehmmbuild.acd
 %%PLIST_HMMER%%share/EMBOSS/acd/ehmmcalibrate.acd
 %%PLIST_HMMER%%share/EMBOSS/acd/ehmmconvert.acd
 %%PLIST_HMMER%%share/EMBOSS/acd/ehmmemit.acd
 %%PLIST_HMMER%%share/EMBOSS/acd/ehmmfetch.acd
 %%PLIST_HMMER%%share/EMBOSS/acd/ehmmindex.acd
-%%PLIST_HMMER%%share/EMBOSS/acd/ehmmbuild.acd
-%%PLIST_HMMER%%share/EMBOSS/acd/ehmmalign.acd
 %%PLIST_HMMER%%share/EMBOSS/acd/ehmmpfam.acd
 %%PLIST_HMMER%%share/EMBOSS/acd/ehmmsearch.acd
-%%PLIST_HMMER%%share/EMBOSS/acd/ealistat.acd
-%%PLIST_PHYLIP%%share/EMBOSS/acd/eclique.acd
-%%PLIST_PHYLIP%%share/EMBOSS/acd/econsense.acd
-%%PLIST_PHYLIP%%share/EMBOSS/acd/econtml.acd
-%%PLIST_PHYLIP%%share/EMBOSS/acd/econtrast.acd
-%%PLIST_PHYLIP%%share/EMBOSS/acd/ednacomp.acd
-%%PLIST_PHYLIP%%share/EMBOSS/acd/ednadist.acd
-%%PLIST_PHYLIP%%share/EMBOSS/acd/ednainvar.acd
-%%PLIST_PHYLIP%%share/EMBOSS/acd/ednaml.acd
-%%PLIST_PHYLIP%%share/EMBOSS/acd/ednamlk.acd
-%%PLIST_PHYLIP%%share/EMBOSS/acd/ednapars.acd
-%%PLIST_PHYLIP%%share/EMBOSS/acd/ednapenny.acd
-%%PLIST_PHYLIP%%share/EMBOSS/acd/edollop.acd
-%%PLIST_PHYLIP%%share/EMBOSS/acd/edolpenny.acd
-%%PLIST_PHYLIP%%share/EMBOSS/acd/efactor.acd
-%%PLIST_PHYLIP%%share/EMBOSS/acd/efitch.acd
-%%PLIST_PHYLIP%%share/EMBOSS/acd/egendist.acd
-%%PLIST_PHYLIP%%share/EMBOSS/acd/ekitsch.acd
-%%PLIST_PHYLIP%%share/EMBOSS/acd/emix.acd
-%%PLIST_PHYLIP%%share/EMBOSS/acd/eneighbor.acd
-%%PLIST_PHYLIP%%share/EMBOSS/acd/epenny.acd
-%%PLIST_PHYLIP%%share/EMBOSS/acd/eprotdist.acd
-%%PLIST_PHYLIP%%share/EMBOSS/acd/eprotpars.acd
-%%PLIST_PHYLIP%%share/EMBOSS/acd/erestml.acd
-%%PLIST_PHYLIP%%share/EMBOSS/acd/eseqboot.acd
+%%PLIST_MEME%%bin/meme
+%%PLIST_MEME%%lib/libmeme.a
+%%PLIST_MEME%%lib/libmeme.la
+%%PLIST_MEME%%lib/libmeme.so
+%%PLIST_MEME%%lib/libmeme.so.2
+%%PLIST_MEME%%share/EMBOSS/acd/meme.acd
+%%PLIST_MSE%%bin/mse
+%%PLIST_MSE%%lib/libckit.a
+%%PLIST_MSE%%lib/libckit.la
+%%PLIST_MSE%%lib/libckit.so
+%%PLIST_MSE%%lib/libckit.so.1
+%%PLIST_MSE%%share/EMBOSS/acd/mse.acd
+%%PLIST_MYEMBOSS%%bin/myseq
+%%PLIST_MYEMBOSS%%bin/mytest
+%%PLIST_MYEMBOSS%%share/EMBOSS/acd/myseq.acd
+%%PLIST_MYEMBOSS%%share/EMBOSS/acd/mytest.acd
+%%PLIST_PHYLIP%%bin/fclique
+%%PLIST_PHYLIP%%bin/fconsense
+%%PLIST_PHYLIP%%bin/fcontml
+%%PLIST_PHYLIP%%bin/fcontrast
+%%PLIST_PHYLIP%%bin/fdiscboot
+%%PLIST_PHYLIP%%bin/fdnacomp
+%%PLIST_PHYLIP%%bin/fdnadist
+%%PLIST_PHYLIP%%bin/fdnainvar
+%%PLIST_PHYLIP%%bin/fdnaml
+%%PLIST_PHYLIP%%bin/fdnamlk
+%%PLIST_PHYLIP%%bin/fdnamove
+%%PLIST_PHYLIP%%bin/fdnapars
+%%PLIST_PHYLIP%%bin/fdnapenny
+%%PLIST_PHYLIP%%bin/fdollop
+%%PLIST_PHYLIP%%bin/fdolmove
+%%PLIST_PHYLIP%%bin/fdolpenny
+%%PLIST_PHYLIP%%bin/fdrawgram
+%%PLIST_PHYLIP%%bin/fdrawtree
+%%PLIST_PHYLIP%%bin/ffactor
+%%PLIST_PHYLIP%%bin/ffitch
+%%PLIST_PHYLIP%%bin/ffreqboot
+%%PLIST_PHYLIP%%bin/fgendist
+%%PLIST_PHYLIP%%bin/fkitsch
+%%PLIST_PHYLIP%%bin/fmix
+%%PLIST_PHYLIP%%bin/fmove
+%%PLIST_PHYLIP%%bin/fneighbor
+%%PLIST_PHYLIP%%bin/fpars
+%%PLIST_PHYLIP%%bin/fpenny
+%%PLIST_PHYLIP%%bin/fproml
+%%PLIST_PHYLIP%%bin/fpromlk
+%%PLIST_PHYLIP%%bin/fprotdist
+%%PLIST_PHYLIP%%bin/fprotpars
+%%PLIST_PHYLIP%%bin/frestboot
+%%PLIST_PHYLIP%%bin/frestdist
+%%PLIST_PHYLIP%%bin/frestml
+%%PLIST_PHYLIP%%bin/fretree
+%%PLIST_PHYLIP%%bin/fseqboot
+%%PLIST_PHYLIP%%bin/fseqbootall
+%%PLIST_PHYLIP%%bin/ftreedist
+%%PLIST_PHYLIP%%bin/ftreedistpair
+%%PLIST_PHYLIP%%share/EMBOSS/acd/fclique.acd
+%%PLIST_PHYLIP%%share/EMBOSS/acd/fconsense.acd
+%%PLIST_PHYLIP%%share/EMBOSS/acd/fcontml.acd
+%%PLIST_PHYLIP%%share/EMBOSS/acd/fcontrast.acd
+%%PLIST_PHYLIP%%share/EMBOSS/acd/fdiscboot.acd
+%%PLIST_PHYLIP%%share/EMBOSS/acd/fdnacomp.acd
+%%PLIST_PHYLIP%%share/EMBOSS/acd/fdnadist.acd
+%%PLIST_PHYLIP%%share/EMBOSS/acd/fdnainvar.acd
+%%PLIST_PHYLIP%%share/EMBOSS/acd/fdnaml.acd
+%%PLIST_PHYLIP%%share/EMBOSS/acd/fdnamlk.acd
+%%PLIST_PHYLIP%%share/EMBOSS/acd/fdnamove.acd
+%%PLIST_PHYLIP%%share/EMBOSS/acd/fdnapars.acd
+%%PLIST_PHYLIP%%share/EMBOSS/acd/fdnapenny.acd
+%%PLIST_PHYLIP%%share/EMBOSS/acd/fdollop.acd
+%%PLIST_PHYLIP%%share/EMBOSS/acd/fdolmove.acd
+%%PLIST_PHYLIP%%share/EMBOSS/acd/fdolpenny.acd
+%%PLIST_PHYLIP%%share/EMBOSS/acd/fdrawgram.acd
+%%PLIST_PHYLIP%%share/EMBOSS/acd/fdrawtree.acd
+%%PLIST_PHYLIP%%share/EMBOSS/acd/ffactor.acd
+%%PLIST_PHYLIP%%share/EMBOSS/acd/ffitch.acd
+%%PLIST_PHYLIP%%share/EMBOSS/acd/ffreqboot.acd
+%%PLIST_PHYLIP%%share/EMBOSS/acd/fgendist.acd
+%%PLIST_PHYLIP%%share/EMBOSS/acd/fkitsch.acd
+%%PLIST_PHYLIP%%share/EMBOSS/acd/fmix.acd
+%%PLIST_PHYLIP%%share/EMBOSS/acd/fmove.acd
+%%PLIST_PHYLIP%%share/EMBOSS/acd/fneighbor.acd
+%%PLIST_PHYLIP%%share/EMBOSS/acd/fpars.acd
+%%PLIST_PHYLIP%%share/EMBOSS/acd/fpenny.acd
+%%PLIST_PHYLIP%%share/EMBOSS/acd/fproml.acd
+%%PLIST_PHYLIP%%share/EMBOSS/acd/fpromlk.acd
+%%PLIST_PHYLIP%%share/EMBOSS/acd/fprotdist.acd
+%%PLIST_PHYLIP%%share/EMBOSS/acd/fprotpars.acd
+%%PLIST_PHYLIP%%share/EMBOSS/acd/frestboot.acd
+%%PLIST_PHYLIP%%share/EMBOSS/acd/frestdist.acd
+%%PLIST_PHYLIP%%share/EMBOSS/acd/frestml.acd
+%%PLIST_PHYLIP%%share/EMBOSS/acd/fretree.acd
+%%PLIST_PHYLIP%%share/EMBOSS/acd/fseqboot.acd
+%%PLIST_PHYLIP%%share/EMBOSS/acd/fseqbootall.acd
+%%PLIST_PHYLIP%%share/EMBOSS/acd/ftreedist.acd
+%%PLIST_PHYLIP%%share/EMBOSS/acd/ftreedistpair.acd
+%%PLIST_PHYLIP%%share/PHYLIP/data/phylipnew/font1
+%%PLIST_PHYLIP%%share/PHYLIP/data/phylipnew/font2
+%%PLIST_PHYLIP%%share/PHYLIP/data/phylipnew/font3
+%%PLIST_PHYLIP%%share/PHYLIP/data/phylipnew/font4
+%%PLIST_PHYLIP%%share/PHYLIP/data/phylipnew/font5
+%%PLIST_PHYLIP%%share/PHYLIP/data/phylipnew/font6
+%%PLIST_PHYLIP%%@dirrm share/PHYLIP/data/phylipnew
+%%PLIST_PHYLIP%%@dirrm share/PHYLIP/data
+%%PLIST_PHYLIP%%@dirrm share/PHYLIP
+%%PLIST_SIGNATURE%%bin/libgen
+%%PLIST_SIGNATURE%%bin/matgen3d
+%%PLIST_SIGNATURE%%bin/rocon
+%%PLIST_SIGNATURE%%bin/rocplot
+%%PLIST_SIGNATURE%%bin/siggen
+%%PLIST_SIGNATURE%%bin/siggenlig
+%%PLIST_SIGNATURE%%bin/sigscan
+%%PLIST_SIGNATURE%%bin/sigscanlig
+%%PLIST_SIGNATURE%%share/EMBOSS/acd/libgen.acd
+%%PLIST_SIGNATURE%%share/EMBOSS/acd/matgen3d.acd
+%%PLIST_SIGNATURE%%share/EMBOSS/acd/rocon.acd
+%%PLIST_SIGNATURE%%share/EMBOSS/acd/rocplot.acd
+%%PLIST_SIGNATURE%%share/EMBOSS/acd/siggen.acd
+%%PLIST_SIGNATURE%%share/EMBOSS/acd/siggenlig.acd
+%%PLIST_SIGNATURE%%share/EMBOSS/acd/sigscan.acd
+%%PLIST_SIGNATURE%%share/EMBOSS/acd/sigscanlig.acd
+%%PLIST_ESIM4%%bin/esim4
+%%PLIST_ESIM4%%share/EMBOSS/acd/esim4.acd
+%%PLIST_STRUCTURE%%bin/contacts
+%%PLIST_STRUCTURE%%bin/domainer
+%%PLIST_STRUCTURE%%bin/hetparse
+%%PLIST_STRUCTURE%%bin/interface
+%%PLIST_STRUCTURE%%bin/pdbparse
+%%PLIST_STRUCTURE%%bin/pdbplus
+%%PLIST_STRUCTURE%%bin/pdbtosp
+%%PLIST_STRUCTURE%%bin/sites
+%%PLIST_STRUCTURE%%share/EMBOSS/acd/contacts.acd
+%%PLIST_STRUCTURE%%share/EMBOSS/acd/domainer.acd
+%%PLIST_STRUCTURE%%share/EMBOSS/acd/hetparse.acd
+%%PLIST_STRUCTURE%%share/EMBOSS/acd/interface.acd
+%%PLIST_STRUCTURE%%share/EMBOSS/acd/pdbparse.acd
+%%PLIST_STRUCTURE%%share/EMBOSS/acd/pdbplus.acd
+%%PLIST_STRUCTURE%%share/EMBOSS/acd/pdbtosp.acd
+%%PLIST_STRUCTURE%%share/EMBOSS/acd/sites.acd
+%%PLIST_TOPO%%bin/topo
 %%PLIST_TOPO%%share/EMBOSS/acd/topo.acd
+@dirrmtry share/EMBOSS/acd
+@dirrmtry share/EMBOSS
diff --git a/biology/emboss/Makefile b/biology/emboss/Makefile
index 27aa2db9b5ee..2fdecddae40f 100644
--- a/biology/emboss/Makefile
+++ b/biology/emboss/Makefile
@@ -6,14 +6,15 @@
 #
 
 PORTNAME=	emboss
-PORTVERSION=	2.10.0
-PORTREVISION=	1
+PORTVERSION=	3.0.0
 CATEGORIES=	biology
-MASTER_SITES=	ftp://ftp.uk.embnet.org/pub/EMBOSS/ \
+MASTER_SITES=	ftp://emboss.open-bio.org/pub/EMBOSS/ \
+		ftp://ftp.uk.embnet.org/pub/EMBOSS/ \
 		ftp://ftp.es.embnet.org/pub/software/emboss/EMBOSS/ \
 		ftp://ftp.ebi.ac.uk/pub/software/unix/EMBOSS/
 DISTNAME=	${PORTNAME:U}-${PORTVERSION}
 DISTFILES=	${PORTNAME:U}-${PORTVERSION}${EXTRACT_SUFX}
+DIST_SUBDIR=	${PORTNAME}
 
 MAINTAINER=	fernan@iib.unsam.edu.ar
 COMMENT=	A collection of open source tools for genetic sequence analysis
@@ -23,16 +24,19 @@ BUILD_DEPENDS=	clustalw:${PORTSDIR}/biology/clustalw \
 LIB_DEPENDS=	gd.4:${PORTSDIR}/graphics/gd \
 		png.5:${PORTSDIR}/graphics/png
 
-CONFLICTS=	qmail-ldap2-* digest-*
+CONFLICTS=	qmail-ldap-[0-9]* digest-[0-9]*
 
+PREFIX?=	${LOCALBASE}/emboss
+NO_MTREE=	yes
 USE_SUBMAKE=	yes
 USE_GMAKE=	yes
 GNU_CONFIGURE=	yes
+USE_AUTOTOOLS=	libtool:15
 INSTALLS_SHLIB=	yes
 USE_XLIB=	yes
 USE_MOTIF=	yes
-USE_REINPLACE=	yes
-PKGMESSAGE=	${WRKDIR}/pkg-message
+SUB_FILES=	pkg-message
+SUB_LIST=	PREFIX=${PREFIX} DATADIR=${DATADIR}
 
 DOCSDIR=	${PREFIX}/share/doc/${PORTNAME:U}
 DATADIR=	${PREFIX}/share/${PORTNAME:U}
@@ -43,20 +47,17 @@ CONFIG_FILE=	${WRKSRC}/emboss/emboss.default.template
 post-patch:
 .if !defined(NOPORTDOCS)
 .for DIR in ${DOC_DIRS}
-	${REINPLACE_CMD} -e \
+	@ ${REINPLACE_CMD} -e \
 	  's#$$(prefix)/share/$$(PACKAGE)/doc#$$(datadir)/doc/$$(PACKAGE)#' \
 	  ${WRKSRC}/${DIR}/Makefile.in
 .endfor
 .endif
 
+pre-install:
+	@ ${REINPLACE_CMD} -e 's#%%DATADIR%%#${DATADIR}#' ${CONFIG_FILE}
+
 post-install:
-	@ cd ${WRKSRC} && \
-	${SED} -e 's#%%PREFIX%%#${PREFIX}#' \
-	${CONFIG_FILE} > ${PREFIX}/etc/emboss.default.sample && \
-	${CHOWN} ${SHAREOWN}:${SHAREGRP} ${PREFIX}/etc/emboss.default.sample
-	@ ${SED} -e 's#%%PREFIX%%#${PREFIX}#' ${.CURDIR}/pkg-message > ${PKGMESSAGE}
-.if !defined(BATCH)
+	${CHOWN} ${SHAREOWN}:${SHAREGRP} ${DATADIR}/emboss.default.template
 	@ ${CAT} ${PKGMESSAGE}
-.endif
 
 .include <bsd.port.mk>
diff --git a/biology/emboss/distinfo b/biology/emboss/distinfo
index 5cf84b5d9e66..12a082f17df0 100644
--- a/biology/emboss/distinfo
+++ b/biology/emboss/distinfo
@@ -1,3 +1,3 @@
-MD5 (EMBOSS-2.10.0.tar.gz) = 4a48388ced7021a8ffece5166c40a364
-SHA256 (EMBOSS-2.10.0.tar.gz) = 1d3a8d84ff9c4f77d81b88c9e7c33517a232e7797eb2b761729f97898aa34a8f
-SIZE (EMBOSS-2.10.0.tar.gz) = 16262124
+MD5 (emboss/EMBOSS-3.0.0.tar.gz) = fa72feded9ab9272e3e731c09f545dcc
+SHA256 (emboss/EMBOSS-3.0.0.tar.gz) = 47a51ba7aeb9f6e7f4cd23c28cffad7c6d28432e92f37d6f08121791ef894dea
+SIZE (emboss/EMBOSS-3.0.0.tar.gz) = 16257908
diff --git a/biology/emboss/files/patch-ajindex.c b/biology/emboss/files/patch-ajindex.c
new file mode 100644
index 000000000000..410f90c1d2e2
--- /dev/null
+++ b/biology/emboss/files/patch-ajindex.c
@@ -0,0 +1,5134 @@
+--- ajax/ajindex.c.orig	Mon Jan 23 12:17:02 2006
++++ ajax/ajindex.c	Thu Dec 22 13:12:27 2005
+@@ -22,7 +22,6 @@
+ 
+ 
+ 
+-
+ static AjPBtpage  btreeCacheLocate(const AjPBtcache cache, ajlong page);
+ static AjPBtpage  btreeCacheLruUnlink(AjPBtcache cache);
+ static void       btreeCacheUnlink(AjPBtcache cache, AjPBtpage cpage);
+@@ -35,10 +34,14 @@
+ 				    AjBool isread);
+ static AjPBtpage  btreeFindINode(AjPBtcache cache, AjPBtpage page,
+ 				 const char *item);
++static AjPBtpage  btreeSecFindINode(AjPBtcache cache, AjPBtpage page,
++				    const char *item);
+ 
+ 
+ static AjPBtpage  btreePageFromKey(AjPBtcache cache, unsigned char *buf,
+ 				   const char *item);
++static AjPBtpage  btreeSecPageFromKey(AjPBtcache cache, unsigned char *buf,
++				      const char *item);
+ static ajint      btreeNumInBucket(AjPBtcache cache, ajlong pageno);
+ static AjPBucket  btreeReadBucket(AjPBtcache cache, ajlong pageno);
+ static void       btreeWriteBucket(AjPBtcache cache, const AjPBucket bucket,
+@@ -55,6 +58,7 @@
+ 				 AjPStr const *keys, const ajlong *ptrs,
+ 				 ajint nkeys);
+ static AjBool     btreeNodeIsFull(const AjPBtcache cache, AjPBtpage page);
++static AjBool     btreeNodeIsFullSec(const AjPBtcache cache, AjPBtpage page);
+ static void       btreeInsertNonFull(AjPBtcache cache, AjPBtpage page,
+ 				     const AjPStr key, ajlong less,
+ 				     ajlong greater);
+@@ -87,6 +91,8 @@
+ 
+ 
+ 
++
++
+ #if 0
+ static AjPBtpage  btreeTraverseLeaves(AjPBtcache cache, AjPBtpage thys);
+ static void       btreeJoinLeaves(AjPBtcache cache);
+@@ -168,6 +174,63 @@
+ static ajint         btreeDbnoCompare(const void *a, const void *b);
+ 
+ 
++static AjPBtMem      btreeAllocPriArray(AjPBtcache cache);
++static void          btreeDeallocPriArray(AjPBtcache cache, AjPBtMem node);
++static AjPBtMem      btreeAllocSecArray(AjPBtcache cache);
++static void          btreeDeallocSecArray(AjPBtcache cache, AjPBtMem node);
++
++
++
++static void          btreeAddToHybBucket(AjPBtcache cache, ajlong pageno,
++					 const AjPBtHybrid id);
++static AjPBtpage     btreeHybFindINode(AjPBtcache cache, AjPBtpage page,
++				       const char *item);
++static AjPBtpage     btreeHybPageFromKey(AjPBtcache cache,
++					 unsigned char *buf, const char *key);
++static ajlong        btreeHybInsertShift(AjPBtcache cache, AjPBtpage *retpage,
++					 const char *key);
++static AjBool        btreeHybReorderBuckets(AjPBtcache cache, AjPBtpage leaf);
++static AjPBtpage     btreeHybSplitLeaf(AjPBtcache cache, AjPBtpage spage);
++static void          btreeHybInsertKey(AjPBtcache cache, AjPBtpage page,
++				       const AjPStr key, ajlong less,
++				       ajlong greater);
++static void          btreeHybSplitRoot(AjPBtcache cache);
++static void          btreeHybDupInsert(AjPBtcache cache, AjPBtHybrid hyb,
++				       AjPBtId btid);
++static void          btreeGetNumKeys(AjPBtcache cache, unsigned char *buf,
++				     ajlong **keys, ajlong **ptrs);
++static void          btreeWriteNumNode(AjPBtcache cache, AjPBtpage spage,
++				       const ajlong *keys, const ajlong *ptrs,
++				       ajint nkeys);
++static AjPNumBucket  btreeReadNumBucket(AjPBtcache cache, ajlong pageno);
++static void          btreeNumBucketDel(AjPNumBucket *thys);
++static void          btreeAddToNumBucket(AjPBtcache cache, ajlong pageno,
++					 const AjPBtNumId num);
++static AjPBtpage     btreeNumFindINode(AjPBtcache cache, AjPBtpage page,
++				       const ajlong item);
++static AjPBtpage     btreeNumPageFromKey(AjPBtcache cache, unsigned char *buf,
++					 const ajlong key);
++static ajint         btreeNumInNumBucket(AjPBtcache cache, ajlong pageno);
++static AjBool        btreeReorderNumBuckets(AjPBtcache cache, AjPBtpage leaf);
++static AjPNumBucket  btreeNumBucketNew(ajint n);
++static ajint         btreeNumIdCompare(const void *a, const void *b);
++static AjBool        btreeNumNodeIsFull(const AjPBtcache cache,
++					AjPBtpage page);
++static void          btreeNumInsertNonFull(AjPBtcache cache, AjPBtpage page,
++					   const ajlong key, ajlong less,
++					   ajlong greater);
++static void          btreeNumInsertKey(AjPBtcache cache, AjPBtpage page,
++				       const ajlong key, ajlong less,
++				       ajlong greater);
++static void          btreeNumSplitRoot(AjPBtcache cache);
++static void          btreeNumKeyShift(AjPBtcache cache, AjPBtpage tpage);
++static ajlong        btreeNumInsertShift(AjPBtcache cache, AjPBtpage *retpage,
++					 ajlong key);
++static AjPBtpage     btreeNumSplitLeaf(AjPBtcache cache, AjPBtpage spage);
++
++
++
++
+ 
+ 
+ 
+@@ -196,11 +259,14 @@
+ {
+     FILE *fp;
+     AjPBtcache cache = NULL;
++#if 0
+ #if defined (HAVE64) && !defined(_OSF_SOURCE) && !defined(_AIX) && !defined(__hpux) && !defined(__ppc__) && !defined(__FreeBSD__)
+     struct stat64 buf;
+ #else
+     struct stat buf;
+ #endif
++#endif
++
+     ajlong filelen = 0L;
+ 
+     AjPStr fn = NULL;
+@@ -213,12 +279,18 @@
+ 	return NULL;
+ 
+ 
++    /* Commented out pending database updating */
++#if 0
++    if(strcmp(mode,"r"))
++    {
+ #if defined (HAVE64) && !defined(_OSF_SOURCE) && !defined(_AIX) && !defined(__hpux) && !defined(__ppc__) && !defined(__FreeBSD__)
+-    if(!stat64(file, &buf))
++	if(!stat64(fn->Ptr, &buf))
+ #else
+-    if(!stat(file, &buf))
++	    if(!stat(fn->Ptr, &buf))
+ #endif
+-	filelen = buf.st_size;
++		filelen = buf.st_size;
++    }
++#endif    
+ 
+     AJNEW0(cache);
+ 
+@@ -244,6 +316,13 @@
+     cache->totsize    = filelen;
+     cache->cachesize  = cachesize;
+ 
++    cache->bmem = NULL;
++    cache->tmem = NULL;
++
++    cache->bsmem = NULL;
++    cache->tsmem = NULL;
++
++
+     /* Add slevel, sorder and snperbucket ???? */
+ 
+     ajStrDel(&fn);
+@@ -808,7 +887,7 @@
+     root = btreeCacheLocate(cache,0L);
+ 
+     if(!root)
+-	ajFatal("Something has unlocked the PRI root cache page\n");
++	ajFatal("The PRI root cache page has been unlocked\n");
+     
+     if(!cache->level)
+ 	return root;
+@@ -863,6 +942,48 @@
+ 
+ 
+ 
++/* @funcstatic btreeSecFindINode *************************************************
++**
++** Recursive search for insert node in a secondary tree
++**
++** @param [u] cache [AjPBtcache] cache
++** @param [u] page [AjPBtpage] page
++** @param [r] item [const char*] key to search for 
++**
++** @return [AjPBtpage] leaf node where item should be inserted
++** @@
++******************************************************************************/
++
++static AjPBtpage btreeSecFindINode(AjPBtcache cache, AjPBtpage page,
++				 const char *item)
++{
++    AjPBtpage ret = NULL;
++    AjPBtpage pg  = NULL;
++
++    unsigned char *buf = NULL;
++    ajint status       = 0;
++    ajint ival         = 0;
++
++    /* ajDebug("In btreeSecFindINode\n"); */
++    
++    ret = page;
++    buf = page->buf;
++    GBT_NODETYPE(buf,&ival);
++    if(ival != BT_LEAF)
++    {
++	status = ret->dirty;
++	ret->dirty = BT_LOCK;	/* Lock in case of lots of overflow pages */
++	pg = btreeSecPageFromKey(cache,buf,item);
++	ret->dirty = status;
++	ret = btreeSecFindINode(cache,pg,item);
++    }
++    
++    return ret;
++}
++
++
++
++
+ /* @funcstatic btreePageFromKey *******************************************
+ **
+ ** Return next lower index page given a key
+@@ -928,6 +1049,71 @@
+ 
+ 
+ 
++/* @funcstatic btreeSecPageFromKey *******************************************
++**
++** Return next lower index page given a key in a secondary tree
++**
++** @param [u] cache [AjPBtcache] cache
++** @param [u] buf [unsigned char *] page buffer
++** @param [r] key [const char *] key to search for 
++**
++** @return [AjPBtpage] pointer to a page
++** @@
++******************************************************************************/
++
++static AjPBtpage btreeSecPageFromKey(AjPBtcache cache, unsigned char *buf,
++				     const char *key)
++{
++    unsigned char *rootbuf = NULL;
++    ajint nkeys = 0;
++    ajint order = 0;
++    ajint i;
++    
++    ajlong blockno = 0L;
++    AjPStr *karray = NULL;
++    ajlong *parray = NULL;
++    AjPBtpage page = NULL;
++    
++    /* ajDebug("In btreePageFromKey\n"); */
++    
++    rootbuf = buf;
++
++
++    GBT_NKEYS(rootbuf,&nkeys);
++    order = cache->sorder;
++
++    AJCNEW0(karray,order);
++    AJCNEW0(parray,order);
++    for(i=0;i<order;++i)
++	karray[i] = ajStrNew();
++
++    btreeGetKeys(cache,rootbuf,&karray,&parray);
++    i = 0;
++    while(i!=nkeys && strcmp(key,karray[i]->Ptr)>=0)
++	++i;
++    if(i==nkeys)
++    {
++	if(strcmp(key,karray[i-1]->Ptr)<0)
++	    blockno = parray[i-1];
++	else
++	    blockno = parray[i];
++    }
++    else
++	blockno = parray[i];
++
++    for(i=0;i<order;++i)
++	ajStrDel(&karray[i]);
++    AJFREE(karray);
++    AJFREE(parray);
++
++    page =  ajBtreeCacheRead(cache,blockno);
++
++    return page;
++}
++
++
++
++
+ /* @func ajBtreeIdNew *********************************************
+ **
+ ** Constructor for index bucket ID informationn
+@@ -1617,6 +1803,36 @@
+ 
+ 
+ 
++/* @funcstatic btreeNodeIsFullSec *****************************************
++**
++** Tests whether a secondary node is full of keys
++**
++** @param [r] cache [const AjPBtcache] cache
++** @param [u] page [AjPBtpage] original page
++**
++** @return [AjBool] true if full
++** @@
++******************************************************************************/
++
++static AjBool btreeNodeIsFullSec(const AjPBtcache cache, AjPBtpage page)
++{
++    unsigned char *buf = NULL;
++    ajint nkeys = 0;
++
++    /* ajDebug("In btreeNodeIsFull\n"); */
++
++    buf = page->buf;
++    GBT_NKEYS(buf,&nkeys);
++
++    if(nkeys == cache->sorder - 1)
++	return ajTrue;
++
++    return ajFalse;
++}
++
++
++
++
+ /* @funcstatic btreeInsertNonFull *****************************************
+ **
+ ** Insert a key into a non-full node
+@@ -2289,6 +2505,25 @@
+ 
+ 
+ 
++/* @funcstatic btreeNumIdCompare *******************************************
++**
++** Comparison function for ajListSort
++**
++** @param [r] a [const void*] ID 1
++** @param [r] b [const void*] ID 2
++**
++** @return [ajint] 0 = bases match
++** @@
++******************************************************************************/
++
++static ajint btreeNumIdCompare(const void *a, const void *b)
++{
++    return (*(AjPBtNumId*)a)->offset - (*(AjPBtNumId*)b)->offset;
++}
++
++
++
++
+ /* @funcstatic btreeWriteNode *******************************************
+ **
+ ** Write an internal node
+@@ -2999,8 +3234,7 @@
+     rno = totalkeys - lno;
+ 
+     maxnperbucket = nperbucket >> 1;
+-    if(!maxnperbucket)
+-	++maxnperbucket;
++    ++maxnperbucket;
+ 
+     cbucket = btreeBucketNew(maxnperbucket);
+ 
+@@ -5729,7 +5963,17 @@
+     {
+ 	bentries = buckets[i]->Nentries;
+ 	for(j=0;j<bentries;++j)
+-	    ajListPush(list,(void *)buckets[i]->Ids[j]);
++	{
++	    if(!buckets[i]->Ids[j]->dups)
++		ajListPush(list,(void *)buckets[i]->Ids[j]);
++	    else
++	    {
++		ajBtreeHybLeafList(cache,buckets[i]->Ids[j]->offset,
++				   buckets[i]->Ids[j]->id,list);
++		ajBtreeIdDel(&buckets[i]->Ids[j]);
++	    }
++	}
++	
+ 	AJFREE(buckets[i]->keylen);
+ 	AJFREE(buckets[i]->Ids);
+ 	AJFREE(buckets[i]);
+@@ -6273,6 +6517,7 @@
+ **
+ ** @param [r] filename [const char*] file name
+ ** @param [r] indexdir [const char*] index file directory
++** @param [r] directory [const char*] file directory
+ ** @param [w] seqfiles [AjPStr**] sequence file names
+ ** @param [w] reffiles [AjPStr**] reference file names (if any)
+ 
+@@ -6282,6 +6527,7 @@
+ ******************************************************************************/
+ 
+ ajint ajBtreeReadEntries(const char *filename, const char *indexdir,
++			 const char *directory,
+ 			 AjPStr **seqfiles, AjPStr **reffiles)
+ {
+     AjPStr line = NULL;
+@@ -6292,6 +6538,8 @@
+ 
+     AjPStr seqname = NULL;
+     AjPStr refname = NULL;
++    AjPStr tseqname = NULL;
++    AjPStr trefname = NULL;
+     
+     AjPFile inf   = NULL;
+     char p;
+@@ -6303,6 +6551,9 @@
+     line    = ajStrNew();
+     list    = ajListNew();
+     reflist = ajListNew();
++
++    tseqname = ajStrNew();
++    trefname = ajStrNew();
+     
+     fn = ajStrNew();
+     ajFmtPrintS(&fn,"%s/%s",indexdir,filename);
+@@ -6329,7 +6580,8 @@
+ 	while(ajFileReadLine(inf, &line))
+ 	{
+ 	    seqname = ajStrNew();
+-	    ajFmtScanS(line,"%S",&seqname);
++	    ajFmtScanS(line,"%S",&tseqname);
++	    ajFmtPrintS(&seqname,"%s/%S",directory,tseqname);
+ 	    ajListPushApp(list,(void *)seqname);
+ 	}
+ 
+@@ -6342,7 +6594,9 @@
+ 	{
+ 	    seqname = ajStrNew();
+ 	    refname = ajStrNew();
+-	    ajFmtScanS(line,"%S%S",&seqname,&refname);
++	    ajFmtScanS(line,"%S%S",&tseqname,&trefname);
++	    ajFmtPrintS(&seqname,"%s/%S",directory,tseqname);
++	    ajFmtPrintS(&refname,"%s/%S",directory,trefname);
+ 	    ajListPushApp(list,(void *)seqname);
+ 	    ajListPushApp(reflist,(void *)refname);
+ 	}
+@@ -6357,6 +6611,11 @@
+     ajListDel(&reflist);
+     ajStrDel(&line);
+     ajStrDel(&fn);
++
++    ajStrDel(&tseqname);
++    ajStrDel(&trefname);
++    
++
+     ajFileClose(&inf);
+ 
+     return entries;
+@@ -6967,7 +7226,7 @@
+ 	pripage = btreeCacheLocate(cache,0L);
+ 	pripage->dirty = BT_LOCK;
+ 
+-	ajDebug("Created secondary tree at block %d\n",(ajint)secrootpage);
++	/* ajDebug("Created 2ry tree at block %d\n",(ajint)secrootpage); */
+     }
+     else
+     {
+@@ -7776,8 +8035,7 @@
+     rno = totalkeys - lno;
+ 
+     maxnperbucket = nperbucket >> 1;
+-    if(!maxnperbucket)
+-	++maxnperbucket;
++    ++maxnperbucket;
+ 
+     cbucket = btreePriBucketNew(maxnperbucket);
+ 
+@@ -8230,11 +8488,13 @@
+ {
+     FILE *fp;
+     AjPBtcache cache = NULL;
++#if 0
+ #if defined (HAVE64) && !defined(_OSF_SOURCE) && !defined(_AIX) && !defined(__hpux) && !defined(__ppc__) && !defined(__FreeBSD__)
+     struct stat64 buf;
+ #else
+     struct stat buf;
+ #endif
++#endif
+     ajlong filelen = 0L;
+ 
+     AjPStr fn = NULL;
+@@ -8246,13 +8506,18 @@
+     if(!fp)
+ 	return NULL;
+ 
+-
++    /* Commented out pending database updating */
++#if 0
++    if(strcmp(mode,"r"))
++    {
+ #if defined (HAVE64) && !defined(_OSF_SOURCE) && !defined(_AIX) && !defined(__hpux) && !defined(__ppc__) && !defined(__FreeBSD__)
+-    if(!stat64(file, &buf))
++	if(!stat64(fn->Ptr, &buf))
+ #else
+-    if(!stat(file, &buf))
++	    if(!stat(fn->Ptr, &buf))
++#endif
++		filelen = buf.st_size;
++    }
+ #endif
+-	filelen = buf.st_size;
+ 
+     AJNEW0(cache);
+ 
+@@ -8283,6 +8548,12 @@
+     cache->snperbucket = sfill;
+     cache->count = count;
+     cache->kwlimit = kwlimit;
++
++    cache->bmem = NULL;
++    cache->tmem = NULL;
++
++    cache->bsmem = NULL;
++    cache->tsmem = NULL;
+     
+     ajStrDel(&fn);
+     
+@@ -8456,8 +8727,7 @@
+     rno = totalkeys - lno;
+ 
+     maxnperbucket = nperbucket >> 1;
+-    if(!maxnperbucket)
+-	++maxnperbucket;
++    ++maxnperbucket;
+ 
+     cbucket = btreeSecBucketNew(maxnperbucket);
+ 
+@@ -9070,7 +9340,7 @@
+     if(!cache->slevel)
+ 	return root;
+     
+-    ret = btreeFindINode(cache,root,key);
++    ret = btreeSecFindINode(cache,root,key);
+ 
+     return ret;
+ }
+@@ -9694,7 +9964,7 @@
+     
+     /* ajDebug("In btreeInsertKeySec\n"); */
+ 
+-    if(!btreeNodeIsFull(cache,page))
++    if(!btreeNodeIsFullSec(cache,page))
+     {
+ 	btreeInsertNonFullSec(cache,page,key,less,greater);
+ 	return;
+@@ -10572,7 +10842,7 @@
+ 
+     list = ajListNew();
+ 
+-    order = cache->order;
++    order = cache->sorder;
+ 
+     AJCNEW0(karray,order);
+     AJCNEW0(parray,order);
+@@ -11724,3 +11994,4580 @@
+     return (*(AjPBtId*)a)->dbno -
+ 		  (*(AjPBtId*)b)->dbno;
+ }
++
++
++
++
++
++
++
++
++/* @func ajBtreeHybNew *********************************************
++**
++** Constructor for index bucket ID informationn
++**
++**
++** @return [AjPBtHybrid] Index ID object
++** @@
++******************************************************************************/
++
++AjPBtHybrid ajBtreeHybNew(void)
++{
++    AjPBtHybrid Id = NULL;
++
++    /* ajDebug("In ajBtreeHybNew\n"); */
++
++    AJNEW0(Id);
++    Id->key1 = ajStrNew();
++    Id->dbno = 0;
++    Id->dups = 0;
++    Id->offset = 0L;
++    Id->refoffset = 0L;
++    Id->treeblock = 0L;    
++
++    return Id;
++}
++
++
++
++
++/* @func ajBtreeHybDel *********************************************
++**
++** Destructor for index bucket ID information
++**
++** @param [w] thys [AjPBtHybrid*] index ID object
++**
++** @return [void]
++** @@
++******************************************************************************/
++
++void ajBtreeHybDel(AjPBtHybrid *thys)
++{
++    AjPBtHybrid Id = NULL;
++
++    /* ajDebug("In ajBtreeIdDel\n"); */
++
++    if(!thys || !*thys)
++	return;
++    Id = *thys;
++    
++    ajStrDel(&Id->key1);
++    AJFREE(Id);
++    *thys = NULL;
++
++    return;
++}
++
++
++
++
++/* @funcstatic btreeAllocPriArray *******************************************
++**
++** Allocate karray and parray arrays for a primary key
++**
++** @param [rw] cache [AjPBtcache] cache
++**
++** @return [AjPBtMem] memory node
++** @@
++******************************************************************************/
++
++static AjPBtMem btreeAllocPriArray(AjPBtcache cache)
++{
++    AjPBtMem node = NULL;
++    ajint i;
++    ajint limit;
++    AjPBtMem p = NULL;
++
++    limit = cache->order;
++    if(!cache->bmem)
++    {
++        AJNEW0(node);
++        cache->bmem = node;
++        cache->tmem = node;
++        node->prev = NULL;
++        node->next = NULL;
++        node->used = ajTrue;
++        AJCNEW0(node->karray,limit);
++        AJCNEW0(node->parray,limit);
++        AJCNEW0(node->overflows,limit);
++        for(i=0;i<limit;++i)
++            node->karray[i] = ajStrNew();
++
++        return node;
++    }
++
++    if(!cache->bmem->used)
++    {
++        cache->bmem->used = ajTrue;
++
++        if(cache->bmem->next)
++        {
++            p = cache->bmem->next;
++
++            cache->tmem->next = cache->bmem;
++            cache->bmem->next = NULL;
++
++            cache->bmem->prev = cache->tmem;
++
++            cache->tmem = cache->bmem;
++
++            cache->bmem = p;
++            cache->bmem->prev = NULL;
++
++	    memset(cache->tmem->parray,0,sizeof(ajlong)*limit);
++	    
++	    return cache->tmem;
++        }
++
++	memset(cache->bmem->parray,0,sizeof(ajlong)*limit);
++	
++        return cache->bmem;
++    }
++
++
++    AJNEW0(node);
++    node->used = ajTrue;
++    node->next = NULL;
++    node->prev = cache->tmem;
++    cache->tmem->next = node;
++    cache->tmem = node;
++
++    AJCNEW0(node->karray,limit);
++    AJCNEW0(node->parray,limit);
++    AJCNEW0(node->overflows,limit);
++    for(i=0;i<limit;++i)
++        node->karray[i] = ajStrNew();
++
++    return node;
++}
++
++
++
++
++/* @funcstatic btreeDeallocPriArray *******************************************
++**
++** Deallocate karray and parray arrays for a primary key
++**
++** @param [rw] cache [AjPBtcache] cache
++** @param [rw] node [AjPBtMem] node
++**
++** @return [void]
++** @@
++******************************************************************************/
++
++static void btreeDeallocPriArray(AjPBtcache cache, AjPBtMem node)
++{
++    node->used = ajFalse;
++    if(!node->prev)
++        return;
++
++    node->prev->next = node->next;
++    if(node->next)
++        node->next->prev = node->prev;
++    else
++        cache->tmem = node->prev;
++
++    node->next = cache->bmem;
++    cache->bmem->prev = node;
++    cache->bmem = node;
++    node->prev = NULL;
++
++    return;
++}
++
++
++
++
++
++/* @funcstatic btreeAllocSecArray *******************************************
++**
++** Allocate karray and parray arrays for a primary key
++**
++** @param [rw] cache [AjPBtcache] cache
++**
++** @return [AjPBtMem] memory node
++** @@
++******************************************************************************/
++
++static AjPBtMem btreeAllocSecArray(AjPBtcache cache)
++{
++    AjPBtMem node = NULL;
++    ajint i;
++    ajint limit;
++    AjPBtMem p = NULL;
++
++    limit = cache->sorder;
++    if(!cache->bsmem)
++    {
++        AJNEW0(node);
++        cache->bsmem = node;
++        cache->tsmem = node;
++        node->prev = NULL;
++        node->next = NULL;
++        node->used = ajTrue;
++        AJCNEW0(node->karray,limit);
++        AJCNEW0(node->parray,limit);
++        AJCNEW0(node->overflows,limit);
++        for(i=0;i<limit;++i)
++            node->karray[i] = ajStrNew();
++
++        return node;
++    }
++
++    if(!cache->bsmem->used)
++    {
++        cache->bsmem->used = ajTrue;
++
++        if(cache->bsmem->next)
++        {
++            p = cache->bsmem->next;
++
++            cache->tsmem->next = cache->bsmem;
++            cache->bsmem->next = NULL;
++
++            cache->bsmem->prev = cache->tsmem;
++
++            cache->tsmem = cache->bsmem;
++
++            cache->bsmem = p;
++            cache->bsmem->prev = NULL;
++
++	    memset(cache->tsmem->parray,0,sizeof(ajlong)*limit);
++	    return cache->tsmem;
++        }
++
++	memset(cache->bsmem->parray,0,sizeof(ajlong)*limit);
++        return cache->bsmem;
++    }
++
++    AJNEW0(node);
++    node->used = ajTrue;
++    node->next = NULL;
++    node->prev = cache->tsmem;
++    cache->tsmem->next = node;
++    cache->tsmem = node;
++
++    AJCNEW0(node->karray,limit);
++    AJCNEW0(node->parray,limit);
++    AJCNEW0(node->overflows,limit);
++    for(i=0;i<limit;++i)
++        node->karray[i] = ajStrNew();
++
++    return node;
++}
++
++
++
++
++/* @funcstatic btreeDeallocSecArray *******************************************
++**
++** Deallocate karray and parray arrays for a primary key
++**
++** @param [rw] cache [AjPBtcache] cache
++** @param [rw] node [AjPBtMem] node
++**
++** @return [void]
++** @@
++******************************************************************************/
++
++static void btreeDeallocSecArray(AjPBtcache cache, AjPBtMem node)
++{
++    node->used = ajFalse;
++    if(!node->prev)
++        return;
++
++    node->prev->next = node->next;
++    if(node->next)
++        node->next->prev = node->prev;
++    else
++        cache->tsmem = node->prev;
++
++    node->next = cache->bsmem;
++    cache->bsmem->prev = node;
++    cache->bsmem = node;
++    node->prev = NULL;
++
++    return;
++}
++
++
++
++
++/* @funcstatic btreeAddToHybBucket *******************************************
++**
++** Add an ID to a bucket
++** Only called if there is room in the bucket
++**
++** @param [u] cache [AjPBtcache] cache
++** @param [r] pageno [ajlong] page number of bucket
++** @param [r] id [const AjPBtId] ID info
++**
++** @return [void]
++** @@
++******************************************************************************/
++
++static void btreeAddToHybBucket(AjPBtcache cache, ajlong pageno,
++				const AjPBtHybrid hyb)
++{
++    AjPBucket bucket = NULL;
++    AjPBtId   destid = NULL;
++    
++    ajint nentries;
++    
++    /* ajDebug("In btreeAddToHybBucket\n"); */
++
++    bucket   = btreeReadBucket(cache,pageno);
++    nentries = bucket->Nentries;
++
++
++    /* Reading a bucket always gives one extra ID position */
++    bucket->Ids[nentries] = ajBtreeIdNew();
++    destid = bucket->Ids[nentries];
++
++    ajStrAssS(&destid->id,hyb->key1);
++    destid->dbno      = hyb->dbno;
++    destid->offset    = hyb->offset;
++    destid->refoffset = hyb->refoffset;
++    destid->dups      = hyb->dups;
++    
++    ++bucket->Nentries;
++
++    btreeWriteBucket(cache,bucket,pageno);
++
++    btreeBucketDel(&bucket);
++    
++    return;
++}
++
++
++
++
++/* @func ajBtreeHybFindInsert ***********************************************
++**
++** Find the node that should contain a new key for insertion
++**
++** @param [u] cache [AjPBtcache] cache
++** @param [r] key [const char*] key to search for 
++**
++** @return [AjPBtpage] leaf node where item should be inserted
++** @@
++******************************************************************************/
++
++AjPBtpage ajBtreeHybFindInsert(AjPBtcache cache, const char *key)
++{
++    AjPBtpage root = NULL;
++    AjPBtpage ret  = NULL;
++
++    /* ajDebug("In ajBtreeHybFindInsert\n"); */
++
++    /* The root node should always be in the cache (BT_LOCKed) */
++    root = btreeCacheLocate(cache,0L);
++
++    if(!root)
++	ajFatal("The PRI root cache page has been unlocked\n");
++    
++    if(!cache->level)
++	return root;
++    
++    ret = btreeHybFindINode(cache,root,key);
++    
++    return ret;
++}
++
++
++
++
++/* @funcstatic btreeHybFindINode *********************************************
++**
++** Recursive search for insert node
++**
++** @param [u] cache [AjPBtcache] cache
++** @param [u] page [AjPBtpage] page
++** @param [r] item [const char*] key to search for 
++**
++** @return [AjPBtpage] leaf node where item should be inserted
++** @@
++******************************************************************************/
++
++static AjPBtpage btreeHybFindINode(AjPBtcache cache, AjPBtpage page,
++				 const char *item)
++{
++    AjPBtpage ret = NULL;
++    AjPBtpage pg  = NULL;
++
++    unsigned char *buf = NULL;
++    ajint status       = 0;
++    ajint ival         = 0;
++
++    /* ajDebug("In btreeHybFindINode\n"); */
++    
++    ret = page;
++    buf = page->buf;
++    GBT_NODETYPE(buf,&ival);
++    if(ival != BT_LEAF)
++    {
++	status = ret->dirty;
++	ret->dirty = BT_LOCK;	/* Lock in case of lots of overflow pages */
++	pg = btreeHybPageFromKey(cache,buf,item);
++	ret->dirty = status;
++	ret = btreeHybFindINode(cache,pg,item);
++    }
++    
++    return ret;
++}
++
++
++
++
++/* @funcstatic btreeHybPageFromKey *******************************************
++**
++** Return next lower index page given a key
++**
++** @param [u] cache [AjPBtcache] cache
++** @param [u] buf [unsigned char *] page buffer
++** @param [r] key [const char *] key to search for 
++**
++** @return [AjPBtpage] pointer to a page
++** @@
++******************************************************************************/
++
++static AjPBtpage btreeHybPageFromKey(AjPBtcache cache, unsigned char *buf,
++				     const char *key)
++{
++    unsigned char *rootbuf = NULL;
++    ajint nkeys = 0;
++    ajint order = 0;
++    ajint i;
++    
++    ajlong blockno = 0L;
++    AjPStr *karray = NULL;
++    ajlong *parray = NULL;
++    AjPBtpage page = NULL;
++    AjPBtMem arrays = NULL;
++    
++    /* ajDebug("In btreeHybPageFromKey\n"); */
++    
++    rootbuf = buf;
++
++
++    GBT_NKEYS(rootbuf,&nkeys);
++    order = cache->order;
++
++    arrays = btreeAllocPriArray(cache);
++    karray = arrays->karray;
++    parray = arrays->parray;
++
++    btreeGetKeys(cache,rootbuf,&karray,&parray);
++    i = 0;
++    while(i!=nkeys && strcmp(key,karray[i]->Ptr)>=0)
++	++i;
++    if(i==nkeys)
++    {
++	if(strcmp(key,karray[i-1]->Ptr)<0)
++	    blockno = parray[i-1];
++	else
++	    blockno = parray[i];
++    }
++    else
++	blockno = parray[i];
++
++    btreeDeallocPriArray(cache,arrays);
++
++    page =  ajBtreeCacheRead(cache,blockno);
++
++    return page;
++}
++
++
++
++
++/* @funcstatic btreeHybInsertShift ********************************************
++**
++** Rebalance buckets on insertion
++**
++** @param [u] cache [AjPBtcache] cache
++** @param [u] retpage [AjPBtpage*] page
++** @param [r] key [const char *] key
++**
++** @return [ajlong] bucket block or 0L if shift not posible 
++** @@
++******************************************************************************/
++
++static ajlong btreeHybInsertShift(AjPBtcache cache, AjPBtpage *retpage,
++				  const char *key)
++{
++    unsigned char *tbuf = NULL;
++    unsigned char *pbuf = NULL;
++    unsigned char *sbuf = NULL;
++
++    AjPBtpage ppage = NULL;
++    AjPBtpage spage = NULL;
++    AjPBtpage tpage = NULL;
++
++    ajint tkeys = 0;
++    ajint pkeys = 0;
++    ajint skeys = 0;
++    ajint order = 0;
++    
++    ajint i;
++    ajint n;
++    
++    ajlong parent  = 0L;
++    ajlong blockno = 0L;
++    
++    AjPStr *kTarray = NULL;
++    AjPStr *kParray = NULL;
++    AjPStr *kSarray = NULL;
++    ajlong *pTarray = NULL;
++    ajlong *pParray = NULL;
++    ajlong *pSarray = NULL;
++
++    AjPStr *karray = NULL;
++    ajlong *parray = NULL;
++
++    ajint ppos    = 0;
++    ajint pkeypos = 0;
++    ajint minsize = 0;
++
++    AjPBtMem arrays1 = NULL;
++    AjPBtMem arrays2 = NULL;
++    AjPBtMem arrays3 = NULL;
++    
++    /* ajDebug("In btreeHybInsertShift\n"); */
++
++
++    tpage = *retpage;
++
++    tbuf = tpage->buf;
++
++    GBT_PREV(tbuf,&parent);
++    GBT_NKEYS(tbuf,&tkeys);
++
++    order = cache->order;
++    minsize = order / 2;
++    if(order % 2)
++	++minsize;
++
++    if(tkeys <= minsize)
++	return 0L;
++
++    ppage = ajBtreeCacheRead(cache,parent);
++    
++    pbuf = ppage->buf;
++    GBT_NKEYS(pbuf,&pkeys);
++    
++
++    arrays1 = btreeAllocPriArray(cache);
++    kParray = arrays1->karray;
++    pParray = arrays1->parray;
++
++    arrays2 = btreeAllocPriArray(cache);
++    kSarray = arrays2->karray;
++    pSarray = arrays2->parray;
++
++    arrays3 = btreeAllocPriArray(cache);
++    kTarray = arrays3->karray;
++    pTarray = arrays3->parray;
++    
++
++    btreeGetKeys(cache,pbuf,&kParray,&pParray);
++
++    i=0;
++    while(i!=pkeys && strcmp(key,kParray[i]->Ptr)>=0)
++	++i;
++    pkeypos = i;
++    
++    if(i==pkeys)
++    {
++	if(strcmp(key,kParray[i-1]->Ptr)<0)
++	    ppos = i-1;
++	else
++	    ppos = i;
++    }
++    else
++	ppos = i;
++
++    
++    if(ppos) /* There is another leaf to the left */
++    {
++	spage = ajBtreeCacheRead(cache,pParray[ppos-1]);
++	sbuf = spage->buf;
++	GBT_NKEYS(sbuf,&skeys);
++    }
++
++    if(i && skeys != order-1) /* There is space in the left leaf */
++    {
++	/* ajDebug("Left shift\n"); */
++	btreeGetKeys(cache,tbuf,&kTarray,&pTarray);
++	if(skeys)
++	    btreeGetKeys(cache,sbuf,&kSarray,&pSarray);
++
++	i = 0;
++	while(pParray[i] != tpage->pageno)
++	    ++i;
++	--i;
++
++	pkeypos = i;
++
++	ajStrAssS(&kSarray[skeys],kParray[pkeypos]);
++	pSarray[skeys+1] = pTarray[0];
++	++skeys;
++	--tkeys;
++	ajStrAssS(&kParray[pkeypos],kTarray[0]);
++	for(i=0;i<tkeys;++i)
++	{
++	    ajStrAssS(&kTarray[i],kTarray[i+1]);
++	    pTarray[i] = pTarray[i+1];
++	}
++	pTarray[i] = pTarray[i+1];
++	pTarray[i+1] = 0L;
++	
++	btreeWriteNode(cache,spage,kSarray,pSarray,skeys);
++	btreeWriteNode(cache,tpage,kTarray,pTarray,tkeys);
++	btreeWriteNode(cache,ppage,kParray,pParray,pkeys);
++	if(!ppage->pageno)
++	    ppage->dirty = BT_LOCK;
++
++	i = 0;
++	while(i!=pkeys && strcmp(key,kParray[i]->Ptr)>=0)
++	    ++i;
++	if(i==pkeys)
++	{
++	    if(strcmp(key,kParray[i-1]->Ptr)<0)
++		blockno = pParray[i-1];
++	    else
++		blockno = pParray[i];
++	}
++	else
++	    blockno = pParray[i];
++
++	if(blockno == spage->pageno)
++	{
++	    *retpage = spage;
++	    karray = kSarray;
++	    parray = pSarray;
++	    n = skeys;
++	}
++	else
++	{
++	    karray = kTarray;
++	    parray = pTarray;
++	    n = tkeys;
++	}
++	
++
++	i = 0;
++	while(i!=n && strcmp(key,karray[i]->Ptr)>=0)
++	    ++i;
++	if(i==n)
++	{
++	    if(strcmp(key,karray[i-1]->Ptr)<0)
++		blockno = parray[i-1];
++	    else
++		blockno = parray[i];
++	}
++	else
++	    blockno = parray[i];
++
++	btreeDeallocPriArray(cache,arrays1);
++	btreeDeallocPriArray(cache,arrays2);
++	btreeDeallocPriArray(cache,arrays3);
++
++	/* ajDebug("... returns blockno (a) %Ld\n",blockno); */
++
++	return blockno;
++    }
++    
++
++    if(ppos != pkeys)	/* There is a right node */
++    {
++	spage = ajBtreeCacheRead(cache,pParray[ppos+1]);
++	sbuf = spage->buf;
++	GBT_NKEYS(sbuf,&skeys);
++    }
++
++
++    /* Space in the right leaf */
++    if(ppos != pkeys && skeys != order-1)
++    {
++	/* ajDebug("Right shift\n"); */
++	btreeGetKeys(cache,tbuf,&kTarray,&pTarray);
++	btreeGetKeys(cache,sbuf,&kSarray,&pSarray);
++
++	i = 0;
++	while(pParray[i] != tpage->pageno)
++	    ++i;
++	pkeypos = i;
++	
++	pSarray[skeys+1] = pSarray[skeys];
++	for(i=skeys-1;i>-1;--i)
++	{
++	    ajStrAssS(&kSarray[i+1],kSarray[i]);
++	    pSarray[i+1] = pSarray[i];
++	}
++	ajStrAssS(&kSarray[0],kParray[pkeypos]);
++	pSarray[0] = pTarray[tkeys];
++	ajStrAssS(&kParray[pkeypos],kTarray[tkeys-1]);
++	++skeys;
++	--tkeys;
++	pTarray[tkeys+1] = 0L;
++	
++	btreeWriteNode(cache,spage,kSarray,pSarray,skeys);
++	btreeWriteNode(cache,tpage,kTarray,pTarray,tkeys);
++	btreeWriteNode(cache,ppage,kParray,pParray,pkeys);
++	if(!ppage->pageno)
++	    ppage->dirty = BT_LOCK;
++
++	i = 0;
++	while(i!=pkeys && strcmp(key,kParray[i]->Ptr)>=0)
++	    ++i;
++	if(i==pkeys)
++	{
++	    if(strcmp(key,kParray[i-1]->Ptr)<0)
++		blockno = pParray[i-1];
++	    else
++		blockno = pParray[i];
++	}
++	else
++	    blockno = pParray[i];
++
++	if(blockno == spage->pageno)
++	{
++	    *retpage = spage;
++	    karray = kSarray;
++	    parray = pSarray;
++	    n = skeys;
++	}
++	else
++	{
++	    karray = kTarray;
++	    parray = pTarray;
++	    n = tkeys;
++	}
++	
++	i = 0;
++	while(i!=n && strcmp(key,karray[i]->Ptr)>=0)
++	    ++i;
++	if(i==n)
++	{
++	    if(strcmp(key,karray[i-1]->Ptr)<0)
++		blockno = parray[i-1];
++	    else
++		blockno = parray[i];
++	}
++	else
++	    blockno = parray[i];
++
++	btreeDeallocPriArray(cache,arrays1);
++	btreeDeallocPriArray(cache,arrays2);
++	btreeDeallocPriArray(cache,arrays3);
++
++	/* ajDebug("... returns blockno (b) %Ld\n",blockno); */
++	
++	return blockno;
++    }
++
++
++    btreeDeallocPriArray(cache,arrays1);
++    btreeDeallocPriArray(cache,arrays2);
++    btreeDeallocPriArray(cache,arrays3);
++
++    /* ajDebug("... returns 0L\n"); */
++
++    return 0L;
++}
++
++
++
++
++/* @funcstatic btreeHybReorderBuckets *****************************************
++**
++** Re-order leaf buckets
++** Must only be called if one of the buckets is full
++**
++** @param [u] cache [AjPBtcache] cache
++** @param [u] leaf [AjPBtpage] leaf page
++**
++** @return [AjBool] true if reorder was successful i.e. leaf not full
++** @@
++******************************************************************************/
++
++static AjBool btreeHybReorderBuckets(AjPBtcache cache, AjPBtpage leaf)
++{
++    ajint nkeys = 0;
++    unsigned char *lbuf = NULL;
++    AjPBucket *buckets  = NULL;
++    AjPStr *keys        = NULL;
++    ajlong *ptrs        = NULL;
++    ajlong *overflows   = NULL;
++    AjPBtMem arrays     = NULL;
++
++    ajint i = 0;
++    ajint j = 0;
++    
++    ajint order;
++    ajint bentries      = 0;
++    ajint totalkeys     = 0;
++    ajint nperbucket    = 0;
++    ajint maxnperbucket = 0;
++    ajint count         = 0;
++    ajint totkeylen     = 0;
++    ajint keylimit      = 0;
++    ajint bucketn       = 0;
++    ajint bucketlimit   = 0;
++    ajint nodetype      = 0;
++    
++    AjPList idlist    = NULL;
++    ajint   dirtysave = 0;
++    AjPBtId bid       = NULL;
++    AjPBucket cbucket = NULL;
++    AjPBtId cid       = NULL;
++
++    ajint   v = 0;
++    
++    /* ajDebug("In btreeHybReorderBuckets\n"); */
++
++    dirtysave = leaf->dirty;
++
++    leaf->dirty = BT_LOCK;
++    lbuf = leaf->buf;
++
++    GBT_NODETYPE(lbuf,&nodetype);
++
++    order = cache->order;
++    nperbucket = cache->nperbucket;
++    
++
++    /* Read keys/ptrs */
++    arrays    = btreeAllocPriArray(cache);
++    keys      = arrays->karray;
++    ptrs      = arrays->parray;
++    overflows = arrays->overflows;
++
++    btreeGetKeys(cache,lbuf,&keys,&ptrs);
++
++    GBT_NKEYS(lbuf,&nkeys);
++
++
++    if(!nkeys)
++	ajFatal("BucketReorder: Attempt to reorder empty leaf");
++
++    for(i=0;i<nkeys;++i)
++	totalkeys += btreeNumInBucket(cache,ptrs[i]);
++    totalkeys += btreeNumInBucket(cache,ptrs[i]);
++
++    /* Set the number of entries per bucket to approximately half full */
++    maxnperbucket = nperbucket >> 1;
++
++    if(!maxnperbucket)
++	++maxnperbucket;
++
++    /* Work out the number of new buckets needed */
++    bucketn = (totalkeys / maxnperbucket);
++    if(totalkeys % maxnperbucket)
++	++bucketn;
++    
++    if(bucketn > order)
++    {
++	btreeDeallocPriArray(cache,arrays);
++
++	leaf->dirty = dirtysave;
++	return ajFalse;
++    }
++    
++
++    /* Read buckets */
++    AJCNEW0(buckets,nkeys+1);
++    keylimit = nkeys + 1;
++    
++    for(i=0;i<keylimit;++i)
++	buckets[i] = btreeReadBucket(cache,ptrs[i]);
++
++
++    /* Read IDs from all buckets and push to list and sort (increasing id) */
++    idlist  = ajListNew();
++    
++    for(i=0;i<keylimit;++i)
++    {
++	overflows[i] = buckets[i]->Overflow;
++	bentries = buckets[i]->Nentries;
++	for(j=0;j<bentries;++j)
++	    ajListPush(idlist,(void *)buckets[i]->Ids[j]);
++	
++	AJFREE(buckets[i]->keylen);
++	AJFREE(buckets[i]->Ids);
++	AJFREE(buckets[i]);
++    }
++    ajListSort(idlist,btreeIdCompare);
++    AJFREE(buckets);
++
++    cbucket = btreeBucketNew(maxnperbucket);
++    bucketlimit = bucketn - 1;
++    
++    for(i=0;i<bucketlimit;++i)
++    {
++	cbucket->Overflow = overflows[i];
++	cbucket->Nentries = 0;
++
++	count = 0;
++	while(count!=maxnperbucket)
++	{
++	    ajListPop(idlist,(void **)&bid);
++	    
++	    cid = cbucket->Ids[count];
++	    ajStrAssS(&cid->id,bid->id);
++	    cid->dbno = bid->dbno;
++	    cid->dups = bid->dups;
++	    cid->offset = bid->offset;
++	    cid->refoffset = bid->refoffset;
++	    
++	    cbucket->keylen[count] = BT_BUCKIDLEN(bid->id);
++	    ++cbucket->Nentries;
++	    ++count;
++	    ajBtreeIdDel(&bid);
++	}
++
++
++	ajListPeek(idlist,(void **)&bid);
++	ajStrAssS(&keys[i],bid->id);
++
++	totkeylen += ajStrLen(bid->id);
++
++	if(!ptrs[i])
++	    ptrs[i] = cache->totsize;
++	btreeWriteBucket(cache,cbucket,ptrs[i]);
++    }
++
++
++    /* Deal with greater-than bucket */
++
++    cbucket->Overflow = overflows[i];
++    cbucket->Nentries = 0;
++
++    count = 0;
++    while(ajListPop(idlist,(void **)&bid))
++    {
++	cid = cbucket->Ids[count];
++	ajStrAssS(&cid->id,bid->id);
++	cid->dbno = bid->dbno;
++	cid->dups = bid->dups;
++	cid->offset = bid->offset;
++	cid->refoffset = bid->refoffset;
++	
++	++cbucket->Nentries;
++	++count;
++	ajBtreeIdDel(&bid);
++    }
++    
++    
++    if(!ptrs[i])
++	ptrs[i] = cache->totsize;
++    btreeWriteBucket(cache,cbucket,ptrs[i]);
++
++    cbucket->Nentries = maxnperbucket;
++    btreeBucketDel(&cbucket);
++
++    /* Now write out a modified leaf with new keys/ptrs */
++
++    nkeys = bucketn - 1;
++    v = nkeys;
++    SBT_NKEYS(lbuf,v);
++    v = totkeylen;
++    SBT_TOTLEN(lbuf,v);
++
++    btreeWriteNode(cache,leaf,keys,ptrs,nkeys);
++
++    leaf->dirty = BT_DIRTY;
++    if(nodetype == BT_ROOT)
++	leaf->dirty = BT_LOCK;
++
++    btreeDeallocPriArray(cache,arrays);
++    
++    btreeBucketDel(&cbucket);
++    ajListDel(&idlist);
++
++    return ajTrue;
++}
++
++
++
++
++/* @funcstatic btreeHybSplitLeaf *********************************************
++**
++** Split a leaf and propagate up if necessary
++**
++** @param [u] cache [AjPBtcache] cache
++** @param [u] spage [AjPBtpage] page
++**
++** @return [AjPBtpage] pointer to a parent page
++** @@
++******************************************************************************/
++
++static AjPBtpage btreeHybSplitLeaf(AjPBtcache cache, AjPBtpage spage)
++{
++    ajint nkeys     = 0;
++    ajint order     = 0;
++    ajint totalkeys = 0;
++    ajint bentries  = 0;
++    ajint keylimit  = 0;
++    ajint nodetype  = 0;
++
++    ajint rootnodetype  = 0;
++    
++    ajint i;
++    ajint j;
++    
++    AjPBtpage lpage = NULL;
++    AjPBtpage rpage = NULL;
++    AjPBtpage page  = NULL;
++    
++    AjPStr mediankey  = NULL;
++    ajlong mediangtr  = 0L;
++    ajlong medianless = 0L;
++    
++
++    AjPBtId bid = NULL;
++    AjPBtId cid = NULL;
++
++    unsigned char *buf  = NULL;
++    unsigned char *lbuf = NULL;
++    unsigned char *rbuf = NULL;
++
++    AjPList idlist = NULL;
++
++    AjPBucket *buckets = NULL;
++    AjPBucket cbucket  = NULL;
++    
++    AjPStr *karray = NULL;
++    ajlong *parray = NULL;
++    AjPBtMem arrays     = NULL;
++    
++    ajint keypos = 0;
++    ajint lno    = 0;
++    ajint rno    = 0;
++
++    ajint bucketlimit   = 0;
++    ajint maxnperbucket = 0;
++    ajint nperbucket    = 0;
++    ajint bucketn       = 0;
++    ajint count         = 0;
++    ajint totkeylen     = 0;
++    
++    ajlong lblockno = 0L;
++    ajlong rblockno = 0L;
++    ajlong prev     = 0L;
++    ajlong overflow = 0L;
++    ajlong prevsave = 0L;
++
++    ajlong zero = 0L;
++    ajlong join = 0L;
++    
++    ajlong lv = 0L;
++    ajint  v  = 0;
++    
++    /* ajDebug("In btreeHybSplitLeaf\n"); */
++
++    order = cache->order;
++    nperbucket = cache->nperbucket;
++
++    mediankey = ajStrNew();
++
++    arrays    = btreeAllocPriArray(cache);
++    karray    = arrays->karray;
++    parray    = arrays->parray;
++
++
++    buf = spage->buf;
++    lbuf = buf;
++
++    GBT_NKEYS(buf,&nkeys);
++
++    for(i=nkeys+1; i<order; ++i)
++	parray[i] = 0L;
++
++    GBT_NODETYPE(buf,&rootnodetype);
++
++    if(rootnodetype == BT_ROOT)
++    {
++	/* ajDebug("Splitting root node\n"); */
++	lblockno = cache->totsize;
++	lpage = ajBtreeCacheWrite(cache,lblockno);
++	lpage->pageno = cache->totsize;
++	cache->totsize += cache->pagesize;
++	lbuf = lpage->buf;
++	lv = prev;
++	SBT_PREV(lbuf,lv);
++    }
++    else
++    {
++	lblockno = spage->pageno;
++	lpage = spage;
++    }
++
++    lpage->dirty = BT_LOCK;
++
++
++    rblockno = cache->totsize;
++    rpage = ajBtreeCacheWrite(cache,rblockno);
++    rpage->pageno = cache->totsize;
++    rpage->dirty = BT_LOCK;
++    cache->totsize += cache->pagesize;
++    rbuf = rpage->buf;
++
++
++    if(rootnodetype == BT_ROOT)
++    {
++	lv = zero;
++	SBT_RIGHT(rbuf,lv);
++	lv = zero;
++	SBT_LEFT(lbuf,lv);
++    }
++    else
++    {
++	GBT_RIGHT(lbuf,&join);
++	lv = join;
++	SBT_RIGHT(rbuf,lv);
++    }
++    lv = lblockno;
++    SBT_LEFT(rbuf,lv);
++    lv = rblockno;
++    SBT_RIGHT(lbuf,lv);
++
++
++    btreeGetKeys(cache,buf,&karray,&parray);
++
++
++    keylimit = nkeys+1;
++    AJCNEW0(buckets,keylimit);
++    for(i=0;i<keylimit;++i)
++	buckets[i] = btreeReadBucket(cache,parray[i]);
++
++    idlist = ajListNew();
++    for(i=0;i<keylimit;++i)
++    {
++	bentries = buckets[i]->Nentries;
++	for(j=0;j<bentries;++j)
++	    ajListPush(idlist,(void *)buckets[i]->Ids[j]);
++	AJFREE(buckets[i]->keylen);
++	AJFREE(buckets[i]->Ids);
++	AJFREE(buckets[i]);
++    }
++    ajListSort(idlist,btreeIdCompare);
++    AJFREE(buckets);
++
++
++    totalkeys = ajListLength(idlist);
++
++    keypos = totalkeys / 2;
++
++    lno = keypos;
++    rno = totalkeys - lno;
++
++    maxnperbucket = nperbucket >> 1;
++    ++maxnperbucket;
++
++    cbucket = btreeBucketNew(maxnperbucket);
++
++    bucketn = lno / maxnperbucket;
++    if(lno % maxnperbucket)
++	++bucketn;
++    bucketlimit = bucketn - 1;
++
++
++    totkeylen = 0;
++    count = 0;
++    for(i=0;i<bucketlimit;++i)
++    {
++	cbucket->Nentries = 0;
++	for(j=0;j<maxnperbucket;++j)
++	{
++	    ajListPop(idlist,(void **)&bid);
++	    
++	    cid = cbucket->Ids[j];
++	    ajStrAssS(&cid->id,bid->id);
++	    cid->dbno = bid->dbno;
++	    cid->dups = bid->dups;
++	    cid->offset = bid->offset;
++	    cid->refoffset = bid->refoffset;
++	    
++	    cbucket->keylen[j] = BT_BUCKIDLEN(bid->id);
++	    ++count;
++	    ++cbucket->Nentries;
++	    ajBtreeIdDel(&bid);
++	}
++	ajListPeek(idlist,(void **)&bid);
++	
++	ajStrAssS(&karray[i],bid->id);
++	totkeylen += ajStrLen(bid->id);
++
++	if(!parray[i])
++	    parray[i] = cache->totsize;
++	btreeWriteBucket(cache,cbucket,parray[i]);
++    }
++
++    cbucket->Nentries = 0;
++
++    j = 0;
++    while(count != lno)
++    {
++	ajListPop(idlist,(void **)&bid);
++	cid = cbucket->Ids[j];
++	++j;
++	++count;
++
++	ajStrAssS(&cid->id,bid->id);
++	cid->dbno = bid->dbno;
++	cid->dups = bid->dups;
++	cid->offset = bid->offset;
++	cid->refoffset = bid->refoffset;
++	
++	++cbucket->Nentries;
++	ajBtreeIdDel(&bid);
++    }
++
++    if(!parray[i])
++	parray[i] = cache->totsize;
++    btreeWriteBucket(cache,cbucket,parray[i]);
++
++    nkeys = bucketn - 1;
++    v = nkeys;
++    SBT_NKEYS(lbuf,v);
++    v = totkeylen;
++    SBT_TOTLEN(lbuf,v);
++    nodetype = BT_LEAF;
++    v = nodetype;
++    SBT_NODETYPE(lbuf,v);
++    lpage->dirty = BT_DIRTY;
++
++    GBT_PREV(lbuf,&prevsave);
++
++    btreeWriteNode(cache,lpage,karray,parray,nkeys);
++
++    ajListPeek(idlist,(void **)&bid);
++    ajStrAssS(&mediankey,bid->id);
++
++    totkeylen = 0;
++    bucketn = rno / maxnperbucket;
++    if(rno % maxnperbucket)
++	++bucketn;
++    bucketlimit = bucketn - 1;
++
++    for(i=0;i<bucketlimit;++i)
++    {
++	cbucket->Nentries = 0;
++	for(j=0;j<maxnperbucket;++j)
++	{
++	    ajListPop(idlist,(void **)&bid);
++	    
++	    cid = cbucket->Ids[j];
++	    ajStrAssS(&cid->id,bid->id);
++	    cid->dbno = bid->dbno;
++	    cid->dups = bid->dups;
++	    cid->offset = bid->offset;
++	    cid->refoffset = bid->refoffset;
++	    
++	    cbucket->keylen[j] = BT_BUCKIDLEN(bid->id);
++	    ++cbucket->Nentries;
++	    ajBtreeIdDel(&bid);
++	}
++
++	ajListPeek(idlist,(void **)&bid);
++	ajStrAssS(&karray[i],bid->id);
++	totkeylen += ajStrLen(bid->id);
++
++	parray[i] = cache->totsize;
++	btreeWriteBucket(cache,cbucket,parray[i]);
++    }
++
++    cbucket->Nentries = 0;
++
++    j = 0;
++    while(ajListPop(idlist,(void**)&bid))
++    {
++	cid = cbucket->Ids[j];
++	++j;
++
++	ajStrAssS(&cid->id,bid->id);
++	cid->dbno = bid->dbno;
++	cid->dups = bid->dups;
++	cid->offset = bid->offset;
++	cid->refoffset = bid->refoffset;
++	
++	++cbucket->Nentries;
++	ajBtreeIdDel(&bid);
++    }
++    
++    parray[i] = cache->totsize;
++    btreeWriteBucket(cache,cbucket,parray[i]);
++
++    nkeys = bucketn - 1;
++
++    v = nkeys;
++    SBT_NKEYS(rbuf,v);
++    v = totkeylen;
++    SBT_TOTLEN(rbuf,v);
++    nodetype = BT_LEAF;
++    v = nodetype;
++    SBT_NODETYPE(rbuf,v);
++    lv = prevsave;
++    SBT_PREV(rbuf,lv);
++    lv = overflow;
++    SBT_OVERFLOW(rbuf,lv);
++
++    btreeWriteNode(cache,rpage,karray,parray,nkeys);
++    rpage->dirty = BT_DIRTY;
++
++    cbucket->Nentries = maxnperbucket;
++    btreeBucketDel(&cbucket);
++    ajListDel(&idlist);
++
++
++
++    medianless = lblockno;
++    mediangtr  = rblockno;
++
++
++    if(rootnodetype == BT_ROOT)
++    {
++	ajStrAssS(&karray[0],mediankey);
++	parray[0]=lblockno;
++	parray[1]=rblockno;
++	nkeys = 1;
++	btreeWriteNode(cache,spage,karray,parray,nkeys);	
++	spage->dirty = BT_LOCK;
++
++	btreeDeallocPriArray(cache,arrays);
++
++	ajStrDel(&mediankey);
++	++cache->level;
++	return spage;
++    }
++
++
++    btreeDeallocPriArray(cache,arrays);
++
++    page = ajBtreeCacheRead(cache,prevsave);
++    btreeHybInsertKey(cache,page,mediankey,medianless,mediangtr);
++    ajStrDel(&mediankey);
++
++    page = ajBtreeCacheRead(cache,prevsave);
++
++    return page;
++}
++
++
++
++
++/* @funcstatic btreeHybInsertKey *****************************************
++**
++** Insert a key into a potentially full node
++**
++** @param [u] cache [AjPBtcache] cache
++** @param [u] page [AjPBtpage] original page
++** @param [r] key [const AjPStr] key to insert
++** @param [r] less [ajlong] less-than pointer
++** @param [r] greater [ajlong] greater-than pointer
++**
++** @return [void]
++** @@
++******************************************************************************/
++
++static void btreeHybInsertKey(AjPBtcache cache, AjPBtpage page,
++			      const AjPStr key, ajlong less, ajlong greater)
++{
++    unsigned char *lbuf = NULL;
++    unsigned char *rbuf = NULL;
++    unsigned char *tbuf = NULL;
++    AjPStr *karray      = NULL;
++    ajlong *parray      = NULL;
++    AjPStr *tkarray     = NULL;
++    ajlong *tparray     = NULL;
++
++    AjPBtMem arrays1    = NULL;
++    AjPBtMem arrays2    = NULL;
++
++    ajint nkeys    = 0;
++    ajint order    = 0;
++    ajint keypos   = 0;
++    ajint rkeyno   = 0;
++    
++    ajint i = 0;
++    ajint n = 0;
++    
++    ajint nodetype  = 0;
++    AjPBtpage ipage = NULL;
++    AjPBtpage lpage = NULL;
++    AjPBtpage rpage = NULL;
++    AjPBtpage tpage = NULL;
++
++    ajlong blockno  = 0L;
++    ajlong rblockno = 0L;
++    ajlong lblockno = 0L;
++    AjPStr mediankey  = NULL;
++    ajlong medianless = 0L;
++    ajlong mediangtr  = 0L;
++    ajlong overflow   = 0L;
++    ajlong prev       = 0L;
++    ajint  totlen     = 0;
++    
++    ajlong lv = 0L;
++    ajint  v  = 0;
++    
++    /* ajDebug("In btreeHybInsertKey\n"); */
++
++    if(!btreeNodeIsFull(cache,page))
++    {
++	btreeInsertNonFull(cache,page,key,less,greater);
++	return;
++    }
++    
++    order = cache->order;
++    lbuf = page->buf;
++    GBT_NODETYPE(lbuf,&nodetype);
++    page->dirty = BT_LOCK;
++
++    if(nodetype == BT_ROOT)
++    {
++	arrays1   = btreeAllocPriArray(cache);
++	karray    = arrays1->karray;
++	parray    = arrays1->parray;
++
++	btreeHybSplitRoot(cache);
++
++	if(page->pageno)
++	    page->dirty = BT_DIRTY;
++	btreeGetKeys(cache,lbuf,&karray,&parray);
++
++	if(strcmp(key->Ptr,karray[0]->Ptr)<0)
++	    blockno = parray[0];
++	else
++	    blockno = parray[1];
++	ipage = ajBtreeCacheRead(cache,blockno);
++	btreeInsertNonFull(cache,ipage,key,less,greater);
++
++	btreeDeallocPriArray(cache,arrays1);
++	return;
++    }
++
++
++    arrays1   = btreeAllocPriArray(cache);
++    karray    = arrays1->karray;
++    parray    = arrays1->parray;
++
++    arrays2   = btreeAllocPriArray(cache);
++    tkarray   = arrays2->karray;
++    tparray   = arrays2->parray;
++
++    mediankey = ajStrNew();
++    
++    lpage = page;
++    lbuf = lpage->buf;
++    
++    btreeGetKeys(cache,lbuf,&karray,&parray);
++
++    GBT_BLOCKNUMBER(lbuf,&lblockno);
++    rblockno = cache->totsize;
++    rpage = ajBtreeCacheWrite(cache,rblockno);
++    rpage->dirty = BT_LOCK;
++    rpage->pageno = cache->totsize;
++    cache->totsize += cache->pagesize;
++    rbuf = rpage->buf;
++    lv = rblockno;
++    SBT_BLOCKNUMBER(rbuf,lv);
++
++    
++    GBT_PREV(lbuf,&prev);
++    lv = prev;
++    SBT_PREV(rbuf,lv);
++
++    nkeys = order - 1;
++    keypos = nkeys / 2;
++    if(!(nkeys % 2))
++	--keypos;
++
++    ajStrAssS(&mediankey,karray[keypos]);
++    medianless = lblockno;
++    mediangtr  = rblockno;
++
++
++    GBT_NODETYPE(lbuf,&nodetype);
++    v = nodetype;
++    SBT_NODETYPE(rbuf,v);
++    lv = overflow;
++    SBT_OVERFLOW(rbuf,lv);
++
++
++    totlen = 0;
++    for(i=0;i<keypos;++i)
++    {
++	ajStrAssS(&tkarray[i],karray[i]);
++	totlen += ajStrLen(karray[i]);
++	tparray[i] = parray[i];
++    }
++    tparray[i] = parray[i];
++    v = totlen;
++    SBT_TOTLEN(lbuf,v);
++    n = i;
++    v = n;
++    SBT_NKEYS(lbuf,v);
++    btreeWriteNode(cache,lpage,tkarray,tparray,i);
++
++
++
++    for(i=0;i<n+1;++i)
++    {
++	tpage = ajBtreeCacheRead(cache,tparray[i]);
++	tbuf = tpage->buf;
++	lv = lblockno;
++	SBT_PREV(tbuf,lv);
++	tpage->dirty = BT_DIRTY;
++    }
++
++
++    totlen = 0;
++    for(i=keypos+1;i<nkeys;++i)
++    {
++	ajStrAssS(&tkarray[i-(keypos+1)],karray[i]);
++	totlen += ajStrLen(karray[i]);
++	tparray[i-(keypos+1)] = parray[i];
++    }
++    tparray[i-(keypos+1)] = parray[i];
++    v = totlen;
++    SBT_TOTLEN(rbuf,v);
++    rkeyno = (nkeys-keypos) - 1;
++    v = rkeyno;
++    SBT_NKEYS(rbuf,v);
++    rpage->dirty = BT_DIRTY;
++    btreeWriteNode(cache,rpage,tkarray,tparray,rkeyno);
++
++
++    for(i=0;i<rkeyno+1;++i)
++    {
++	tpage = ajBtreeCacheRead(cache,tparray[i]);
++	tbuf = tpage->buf;
++	lv = rblockno;
++	SBT_PREV(tbuf,lv);
++	tpage->dirty = BT_DIRTY;
++    }
++
++
++    ipage = rpage;
++    if(strcmp(key->Ptr,mediankey->Ptr)<0)
++	ipage = lpage;
++
++    btreeInsertNonFull(cache,ipage,key,less,greater);
++
++
++    btreeDeallocPriArray(cache,arrays1);
++    btreeDeallocPriArray(cache,arrays2);
++
++    ipage = ajBtreeCacheRead(cache,prev);
++
++    btreeHybInsertKey(cache,ipage,mediankey,medianless,mediangtr);
++    ajStrDel(&mediankey);
++
++    return;
++}
++
++
++
++
++/* @funcstatic btreeHybSplitRoot *****************************************
++**
++** Split the root node
++**
++** @param [u] cache [AjPBtcache] cache
++**
++** @return [void]
++** @@
++******************************************************************************/
++
++static void btreeHybSplitRoot(AjPBtcache cache)
++{
++    AjPBtpage rootpage = NULL;
++    AjPBtpage rpage    = NULL;
++    AjPBtpage lpage    = NULL;
++    AjPBtpage tpage    = NULL;
++
++    AjPStr *karray     = NULL;
++    AjPStr *tkarray    = NULL;
++    ajlong *parray     = NULL;
++    ajlong *tparray    = NULL;
++    AjPBtMem arrays1   = NULL;
++    AjPBtMem arrays2   = NULL;
++
++    ajint order     = 0;
++    ajint nkeys     = 0;
++    ajint keypos    = 0;
++    
++    ajlong rblockno = 0L;
++    ajlong lblockno = 0L;
++    
++    AjPStr key = NULL;
++    ajint  i;
++
++    unsigned char *rootbuf = NULL;
++    unsigned char *rbuf    = NULL;
++    unsigned char *lbuf    = NULL;
++    unsigned char *tbuf    = NULL;
++    
++    ajint nodetype  = 0;
++    ajlong overflow = 0L;
++    ajlong zero     = 0L;
++    ajint totlen    = 0;
++    ajint rkeyno    = 0;
++    ajint n         = 0;
++
++    ajlong lv = 0L;
++    ajint  v  = 0;
++    
++    
++    /* ajDebug("In btreeHybSplitRoot\n"); */
++
++    order = cache->order;
++
++    arrays1   = btreeAllocPriArray(cache);
++    karray    = arrays1->karray;
++    parray    = arrays1->parray;
++
++    arrays2   = btreeAllocPriArray(cache);
++    tkarray   = arrays2->karray;
++    tparray   = arrays2->parray;
++
++    key = ajStrNew();
++
++    rootpage = btreeCacheLocate(cache,0L);
++    if(!rootpage)
++	ajFatal("Root page has been unlocked 1");
++    
++    rootbuf = rootpage->buf;
++
++    nkeys = order - 1;
++
++    keypos = nkeys / 2;
++    if(!(nkeys % 2))
++	--keypos;
++
++
++    rblockno = cache->totsize;
++    rpage = ajBtreeCacheWrite(cache,rblockno);
++    rpage->dirty = BT_LOCK;
++    rpage->pageno = cache->totsize;
++    cache->totsize += cache->pagesize;
++
++    lblockno = cache->totsize;
++    lpage = ajBtreeCacheWrite(cache,lblockno);
++    lpage->pageno = cache->totsize;
++    cache->totsize += cache->pagesize;
++
++    lv = rblockno;
++    SBT_BLOCKNUMBER(rpage->buf,lv);
++    lv = lblockno;
++    SBT_BLOCKNUMBER(lpage->buf,lv);
++
++    if(!cache->level)
++    {
++	lv = zero;
++	SBT_LEFT(lpage->buf,lv);
++	lv = rblockno;
++	SBT_RIGHT(lpage->buf,lv);
++	lv = lblockno;
++	SBT_LEFT(rpage->buf,lv);
++	lv = zero;
++	SBT_RIGHT(rpage->buf,lv);
++    }
++
++    btreeGetKeys(cache,rootbuf,&karray,&parray);
++
++    /* Get key for root node and write new root node */
++    ajStrAssS(&tkarray[0],karray[keypos]);
++    tparray[0] = lblockno;
++    tparray[1] = rblockno;
++    
++
++    n = 1;
++    v = n;
++    SBT_NKEYS(rootbuf,v);
++    btreeWriteNode(cache,rootpage,tkarray,tparray,1);
++    rootpage->dirty = BT_LOCK;
++
++    rbuf = rpage->buf;
++    lbuf = lpage->buf;
++    
++    if(cache->level)
++	nodetype = BT_INTERNAL;
++    else
++	nodetype = BT_LEAF;
++
++    v = nodetype;
++    SBT_NODETYPE(rbuf,v);
++    v = nodetype;
++    SBT_NODETYPE(lbuf,v);
++    lv = overflow;
++    SBT_OVERFLOW(rbuf,lv);
++    lv = overflow;
++    SBT_PREV(rbuf,lv);
++    lv = overflow;
++    SBT_OVERFLOW(lbuf,lv);
++    lv = overflow;
++    SBT_PREV(lbuf,lv);
++
++    totlen = 0;
++    for(i=0;i<keypos;++i)
++    {
++	ajStrAssS(&tkarray[i],karray[i]);
++	totlen += ajStrLen(karray[i]);
++	tparray[i] = parray[i];
++    }
++    tparray[i] = parray[i];
++    v = totlen;
++    SBT_TOTLEN(lbuf,v);
++    n = i;
++    v = n;
++    SBT_NKEYS(lbuf,v);
++    btreeWriteNode(cache,lpage,tkarray,tparray,i);
++
++    for(i=0;i<n+1;++i)
++    {
++	tpage = ajBtreeCacheRead(cache,tparray[i]);
++	tbuf = tpage->buf;
++	lv = lblockno;
++	SBT_PREV(tbuf,lv);
++	tpage->dirty = BT_DIRTY;
++    }
++
++    totlen = 0;
++    for(i=keypos+1;i<nkeys;++i)
++    {
++	ajStrAssS(&tkarray[i-(keypos+1)],karray[i]);
++	totlen += ajStrLen(karray[i]);
++	tparray[i-(keypos+1)] = parray[i];
++    }
++    tparray[i-(keypos+1)] = parray[i];
++    v = totlen;
++    SBT_TOTLEN(rbuf,v);
++    rkeyno = (nkeys-keypos) - 1;
++    v = rkeyno;
++    SBT_NKEYS(rbuf,v);
++    rpage->dirty = BT_DIRTY;
++    btreeWriteNode(cache,rpage,tkarray,tparray,rkeyno);
++
++    for(i=0;i<rkeyno+1;++i)
++    {
++	tpage = ajBtreeCacheRead(cache,tparray[i]);
++	tbuf = tpage->buf;
++	lv = rblockno;
++	SBT_PREV(tbuf,lv);
++	tpage->dirty = BT_DIRTY;
++    }
++
++
++    btreeDeallocPriArray(cache,arrays1);
++    btreeDeallocPriArray(cache,arrays2);
++
++    ++cache->level;
++
++    ajStrDel(&key);
++    
++    return;
++}
++
++
++
++
++/* @func ajBtreeHybInsertId *********************************************
++**
++** Insert an ID structure into the tree
++**
++** @param [u] cache [AjPBtcache] cache
++** @param [r] id [const AjPBtId] Id object
++**
++** @return [void] pointer to a page
++** @@
++******************************************************************************/
++
++void ajBtreeHybInsertId(AjPBtcache cache, AjPBtHybrid hyb)
++{
++    AjPBtpage spage   = NULL;
++    AjPBtpage parent  = NULL;
++    AjPStr key        = NULL;
++    const char *ckey  = NULL;
++    AjPBucket lbucket = NULL;
++    AjPBucket rbucket = NULL;
++    AjPBucket bucket  = NULL;
++    ajlong lblockno = 0L;
++    ajlong rblockno = 0L;
++    ajlong blockno  = 0L;
++    ajlong shift    = 0L;
++
++    ajint nkeys = 0;
++    ajint order = 0;
++
++    ajint nodetype = 0;
++    ajint nentries = 0;
++    
++    AjPStr *karray = NULL;
++    ajlong *parray = NULL;
++    AjPBtMem arrays = NULL;
++    AjBool found = ajFalse;
++    AjPBtId btid = NULL;
++    
++    ajint i;
++    ajint n;
++    
++    unsigned char *buf = NULL;
++
++    /* ajDebug("In ajBtreeHybInsertId\n"); */
++
++    key = ajStrNew();
++    
++
++    ajStrAssS(&key,hyb->key1);
++    if(!ajStrLen(key))
++    {
++	ajStrDel(&key);
++	return;
++    }
++
++    ckey = ajStrStr(key);
++    spage = ajBtreeHybFindInsert(cache,ckey);
++    buf = spage->buf;
++
++    GBT_NKEYS(buf,&nkeys);
++    GBT_NODETYPE(buf,&nodetype);
++    
++    order = cache->order;
++
++    arrays = btreeAllocPriArray(cache);
++    karray = arrays->karray;
++    parray = arrays->parray;
++    
++    if(!nkeys)
++    {
++	lbucket  = btreeBucketNew(0);
++	rbucket  = btreeBucketNew(0);
++
++	lblockno = cache->totsize;
++	btreeWriteBucket(cache,lbucket,lblockno);
++
++	rblockno = cache->totsize;
++	btreeWriteBucket(cache,rbucket,rblockno);	
++
++	parray[0] = lblockno;
++	parray[1] = rblockno;
++	ajStrAssS(karray,key);
++	
++	btreeWriteNode(cache,spage,karray,parray,1);
++
++	btreeBucketDel(&lbucket);
++	btreeBucketDel(&rbucket);
++
++	btreeAddToHybBucket(cache,rblockno,hyb);
++
++	btreeDeallocPriArray(cache,arrays);
++
++	ajStrDel(&key);
++
++	return;
++    }
++
++
++    /* Search to see whether entry exists */
++    
++    btreeGetKeys(cache,buf,&karray,&parray);
++
++    i=0;
++    while(i!=nkeys && strcmp(key->Ptr,karray[i]->Ptr)>=0)
++	++i;
++    if(i==nkeys)
++    {
++	if(strcmp(key->Ptr,karray[i-1]->Ptr)<0)
++	    blockno = parray[i-1];
++	else
++	    blockno = parray[i];
++    }
++    else
++	blockno = parray[i];
++
++
++    bucket = btreeReadBucket(cache,blockno);
++    
++    nentries = bucket->Nentries;
++    
++    found = ajFalse;
++
++    for(i=0;i<nentries;++i)
++	if(!strcmp(hyb->key1->Ptr,bucket->Ids[i]->id->Ptr))
++	{
++	    found = ajTrue;
++	    break;
++	}
++    
++
++    if(found)
++    {
++	btid = bucket->Ids[i];
++
++	btreeHybDupInsert(cache,hyb,btid);
++
++	btreeWriteBucket(cache,bucket,blockno);
++	btreeBucketDel(&bucket);
++
++	btreeDeallocPriArray(cache,arrays);
++
++	ajStrDel(&key);
++	
++	return;
++    }
++    else
++	btreeBucketDel(&bucket);
++
++    if(nodetype != BT_ROOT)
++	if((shift = btreeHybInsertShift(cache,&spage,key->Ptr)))
++	    blockno = shift;
++
++    buf = spage->buf;
++
++    n = btreeNumInBucket(cache,blockno);
++
++    if(n == cache->nperbucket)
++    {
++	if(btreeHybReorderBuckets(cache,spage))
++	{
++	    GBT_NKEYS(buf,&nkeys);	    
++	    btreeGetKeys(cache,buf,&karray,&parray);
++
++	    i=0;
++	    while(i!=nkeys && strcmp(key->Ptr,karray[i]->Ptr)>=0)
++		++i;
++
++	    if(i==nkeys)
++	    {
++		if(strcmp(key->Ptr,karray[i-1]->Ptr)<0)
++		    blockno = parray[i-1];
++		else
++		    blockno = parray[i];
++	    }
++	    else
++		blockno = parray[i];
++	}
++	else
++	{
++	    parent = btreeHybSplitLeaf(cache,spage);
++	    spage  = ajBtreeHybFindInsert(cache,ckey);
++	    buf = spage->buf;
++
++	    btreeGetKeys(cache,buf,&karray,&parray);
++
++	    GBT_NKEYS(buf,&nkeys);
++	    i=0;
++	    while(i!=nkeys && strcmp(key->Ptr,karray[i]->Ptr)>=0)
++		++i;
++
++	    if(i==nkeys)
++	    {
++		if(strcmp(key->Ptr,karray[i-1]->Ptr)<0)
++		    blockno = parray[i-1];
++		else
++		    blockno = parray[i];
++	    }
++	    else
++		blockno = parray[i];
++
++	}
++    }
++
++
++    btreeAddToHybBucket(cache,blockno,hyb);
++
++    ++cache->count;
++
++    btreeDeallocPriArray(cache,arrays);
++
++    ajStrDel(&key);
++
++    return;
++}
++
++
++
++
++static void btreeHybDupInsert(AjPBtcache cache, AjPBtHybrid hyb,
++			      AjPBtId btid)
++{
++    AjPBtpage page;
++    AjPBtpage rpage;
++    ajlong secrootpage = 0L;
++    unsigned char *buf;
++    ajlong right = 0L;
++    AjPBtNumId num = NULL;
++
++    /* ajDebug("In btreeHybDupInsert\n"); */
++
++    if(!btid->dups)
++    {
++	btid->dups = 1;
++	AJNEW0(num);
++	
++	num->offset    = btid->offset;
++	num->refoffset = btid->refoffset;
++	num->dbno      = btid->dbno;
++
++	secrootpage = cache->totsize;
++
++	btid->offset = secrootpage;
++
++	ajBtreeCreateRootNode(cache,secrootpage);
++	cache->secrootblock = secrootpage;
++	page = ajBtreeCacheWrite(cache,secrootpage);
++	page->dirty = BT_DIRTY;
++	ajBtreeCacheSync(cache,secrootpage);
++	page->dirty = BT_LOCK;
++	
++	rpage = btreeCacheLocate(cache, 0L);
++	rpage->dirty = BT_LOCK;
++
++	cache->slevel = 0;
++
++	ajBtreeInsertNum(cache,num,page);
++
++	num->offset    = hyb->offset;
++	num->refoffset = hyb->refoffset;
++	num->dbno      = hyb->dbno;
++
++	ajBtreeInsertNum(cache,num,page);
++	++btid->dups;
++
++	AJFREE(num);
++
++	return;
++    }
++    else
++    {
++	cache->secrootblock = btid->offset;
++	page = ajBtreeCacheWrite(cache,cache->secrootblock);
++	page->dirty = BT_LOCK;
++	buf = page->buf;
++	GBT_RIGHT(buf,&right);
++	cache->slevel = (ajint) right;
++
++	AJNEW0(num);
++	
++	num->offset    = hyb->offset;
++	num->refoffset = hyb->refoffset;
++	num->dbno      = hyb->dbno;
++	
++	ajBtreeInsertNum(cache,num,page);
++
++	AJFREE(num);
++	
++	++btid->dups;
++    }
++    
++
++    page->dirty = BT_DIRTY;
++
++    return;
++}
++
++
++
++
++/* @funcstatic btreeGetNumKeys *********************************************
++**
++** Get Keys and Pointers from an internal node
++**
++** @param [u] cache [AjPBtcache] cache
++** @param [u] buf [unsigned char *] page buffer
++** @param [w] keys [ajlong **] keys
++** @param [w] ptrs [ajlong**] ptrs
++**
++** @return [void]
++** @@
++******************************************************************************/
++
++static void btreeGetNumKeys(AjPBtcache cache, unsigned char *buf,
++			    ajlong **keys, ajlong **ptrs)
++{
++    ajlong *karray = NULL;
++    ajlong *parray = NULL;
++    
++    ajint nkeys = 0;
++    unsigned char *pptr = NULL;
++    ajint    i;
++
++    /* ajDebug("In btreeGetNumKeys\n"); */
++
++
++    karray = *keys;
++    parray = *ptrs;
++
++    pptr = PBT_KEYLEN(buf);
++    GBT_NKEYS(buf,&nkeys);
++    if(!nkeys)
++	ajFatal("GetNumKeys: No keys in node");
++
++    for(i=0;i<nkeys;++i)
++    {
++	BT_GETAJLONG(pptr,&karray[i]);
++	pptr += sizeof(ajlong);
++    }
++
++    for(i=0;i<nkeys;++i)
++    {
++	BT_GETAJLONG(pptr,&parray[i]);
++	pptr += sizeof(ajlong);
++    }
++    
++    BT_GETAJLONG(pptr,&parray[i]);
++
++    return;
++}
++
++
++
++
++/* @funcstatic btreeWriteNumNode *******************************************
++**
++** Write an internal node
++**
++** @param [u] cache [AjPBtcache] cache
++** @param [u] spage [AjPBtpage] buffer
++** @param [r] keys [AjPStr const *] keys
++** @param [r] ptrs [const ajlong*] page pointers
++** @param [r] nkeys [ajint] number of keys
++
++**
++** @return [void]
++** @@
++******************************************************************************/
++
++static void btreeWriteNumNode(AjPBtcache cache, AjPBtpage spage,
++			      const ajlong *keys, const ajlong *ptrs,
++			      ajint nkeys)
++{
++    unsigned char *pptr   = NULL;
++    unsigned char *buf;
++    
++    ajint tnkeys = 0;
++
++    ajlong aspace   = 0L;
++    ajlong lv       = 0L;
++    ajlong overflow = 0L;
++    ajint i;
++
++
++    /* ajDebug("In btreeWriteNumNode\n"); */
++
++    buf = spage->buf;
++
++    tnkeys = nkeys;
++    SBT_NKEYS(buf,tnkeys);
++
++    pptr = PBT_KEYLEN(buf);
++    aspace = 2 * nkeys * sizeof(ajlong) + sizeof(ajlong);
++    if((pptr+aspace)-buf > cache->pagesize)
++	ajFatal("WriteNumNode: too many keys for available pagesize");
++
++    for(i=0;i<nkeys;++i)
++    {
++	lv = keys[i];
++	BT_SETAJLONG(pptr,lv);
++	pptr += sizeof(ajlong);
++    }
++
++    for(i=0;i<nkeys;++i)
++    {
++	lv = ptrs[i];
++	BT_SETAJLONG(pptr,lv);
++	pptr += sizeof(ajlong);
++    }
++    
++    lv = ptrs[i];
++    BT_SETAJLONG(pptr,lv);
++
++    spage->dirty = BT_DIRTY;
++
++    overflow = 0L;
++    SBT_OVERFLOW(buf,overflow);
++
++
++    return;
++}
++
++
++
++
++/* @funcstatic btreeWriteNumBucket *******************************************
++**
++** Write index bucket object to the cache given a disc page number
++**
++** @param [u] cache [AjPBtcache] cache
++** @param [r] bucket [const AjPBucket] bucket
++** @param [r] pageno [ajlong] page number
++**
++** @return [void]
++** @@
++******************************************************************************/
++
++static void btreeWriteNumBucket(AjPBtcache cache, const AjPNumBucket bucket,
++			     ajlong pageno)
++{
++    AjPBtpage page      = NULL;
++    unsigned char *buf  = NULL;
++    unsigned char *pptr = NULL;
++
++    ajint   v   = 0;
++    ajint   i   = 0;
++    ajlong lv   = 0L;
++    ajint  nentries = 0;
++    ajlong overflow = 0L;
++
++    /* ajDebug("In btreeWriteNumBucket\n"); */
++
++    if(pageno == cache->totsize)
++    {
++	page = ajBtreeCacheWrite(cache,pageno);
++	page->pageno = cache->totsize;
++	cache->totsize += cache->pagesize;
++	buf = page->buf;
++	overflow = 0L;
++	lv = overflow;
++	SBT_BUCKOVERFLOW(buf,lv);
++    }
++    else
++    {
++	page = ajBtreeCacheRead(cache,pageno);
++	buf = page->buf;
++	GBT_BUCKOVERFLOW(buf,&overflow);
++    }
++
++    v = BT_BUCKET;
++    SBT_BUCKNODETYPE(buf,v);
++    page->dirty = BT_LOCK;
++
++    nentries = bucket->Nentries;
++    v = nentries;
++    SBT_BUCKNENTRIES(buf,v);
++    
++    pptr = PBT_BUCKKEYLEN(buf);
++
++    for(i=0;i<nentries;++i)
++    {
++	lv = bucket->NumId[i]->offset;
++	BT_SETAJLONG(pptr,lv);
++	pptr += sizeof(ajlong);
++	lv = bucket->NumId[i]->refoffset;
++	BT_SETAJLONG(pptr,lv);
++	pptr += sizeof(ajlong);
++	v = bucket->NumId[i]->dbno;
++	BT_SETAJINT(pptr,v);
++	pptr += sizeof(ajint);
++    }
++    
++    lv = 0L;
++    SBT_BUCKOVERFLOW(buf,lv);
++    page->dirty = BT_DIRTY;
++
++    return;
++}
++
++
++
++
++/* @funcstatic btreeReadNumBucket *********************************************
++**
++** Constructor for index bucket given a disc page number
++** Creates one empty key slot for possible addition
++**
++** @param [u] cache [AjPBtcache] cache
++** @param [r] pageno [ajlong] page number
++**
++** @return [AjPNumBucket] bucket
++** @@
++******************************************************************************/
++
++static AjPNumBucket btreeReadNumBucket(AjPBtcache cache, ajlong pageno)
++{
++    AjPNumBucket bucket    = NULL;
++    AjPBtpage page      = NULL;
++    unsigned char *buf  = NULL;
++    unsigned char *pptr = NULL;
++    ajint  nodetype  = 0;
++    ajint  nentries  = 0;
++    ajlong overflow  = 0L;
++    ajint  dirtysave = 0;
++    
++    ajint  i;
++    
++    /* ajDebug("In btreeReadNumBucket\n"); */
++
++    if(pageno == cache->secrootblock)
++	ajFatal("ReadNumBucket: cannot read bucket from a root page");
++
++    page = ajBtreeCacheRead(cache,pageno);
++    dirtysave = page->dirty;
++    page->dirty = BT_LOCK;
++    buf = page->buf;
++
++    GBT_BUCKNODETYPE(buf,&nodetype);
++    if(nodetype != BT_BUCKET)
++	ajFatal("ReadNumBucket: Nodetype mismatch. Not bucket (%d)",nodetype);
++
++    GBT_BUCKNENTRIES(buf,&nentries);
++    if(nentries > cache->snperbucket)
++	ajFatal("ReadNumBucket: Bucket too full");
++
++    GBT_BUCKOVERFLOW(buf,&overflow);
++
++    AJNEW0(bucket);
++    bucket->NodeType = nodetype;
++    bucket->Nentries = nentries;
++    bucket->Overflow = overflow;
++
++    AJCNEW0(bucket->NumId,nentries+1);
++    for(i=0;i<nentries;++i)
++	AJNEW0(bucket->NumId[i]);
++    
++
++    pptr = PBT_BUCKKEYLEN(buf);
++
++    for(i=0;i<nentries;++i)
++    {
++	BT_GETAJLONG(pptr,&bucket->NumId[i]->offset);
++	pptr += sizeof(ajlong);
++	BT_GETAJLONG(pptr,&bucket->NumId[i]->refoffset);
++	pptr += sizeof(ajlong);
++	BT_GETAJINT(pptr,&bucket->NumId[i]->dbno);
++	pptr += sizeof(ajint);
++    }
++    
++    page->dirty = dirtysave;
++
++    return bucket;
++}
++
++
++
++
++/* @funcstatic btreeNumBucketDel *********************************************
++**
++** Delete a bucket object
++**
++** @param [w] thys [AjPNumBucket*] bucket
++**
++** @return [void]
++** @@
++******************************************************************************/
++
++static void btreeNumBucketDel(AjPNumBucket *thys)
++{
++    AjPNumBucket pthis = NULL;
++    int i;
++    
++    
++    /* ajDebug("In btreeNumBucketDel\n"); */
++
++    if(!thys || !*thys)
++	return;
++
++    pthis = *thys;
++
++    if(pthis->Nentries)
++    {
++	for(i=0;i<pthis->Nentries;++i)
++	    AJFREE(pthis->NumId[i]);
++    
++	AJFREE(pthis->NumId);
++    }
++    
++    
++    AJFREE(pthis);
++
++    *thys = NULL;
++
++    return;
++}
++
++
++
++
++/* @func ajBtreeNumFindInsert ***********************************************
++**
++** Find the node that should contain a new key for insertion
++**
++** @param [u] cache [AjPBtcache] cache
++** @param [r] key [const ajlong] key to search for 
++**
++** @return [AjPBtpage] leaf node where item should be inserted
++** @@
++******************************************************************************/
++
++AjPBtpage ajBtreeNumFindInsert(AjPBtcache cache, const ajlong key)
++{
++    AjPBtpage root = NULL;
++    AjPBtpage ret  = NULL;
++
++    /* ajDebug("In ajBtreeNumFindInsert\n"); */
++
++    /* The root node should always be in the cache (BT_LOCKed) */
++    root = btreeCacheLocate(cache,cache->secrootblock);
++
++    /* ajDebug("cache->slevel = %d root=%d\n",cache->slevel,(ajint)root); */
++    
++
++    if(!cache->slevel)
++	return root;
++    
++    ret = btreeNumFindINode(cache,root,key);
++
++    return ret;
++}
++
++
++
++
++/* @funcstatic btreeNumFindINode **********************************************
++**
++** Recursive search for insert node in a secondary tree
++**
++** @param [u] cache [AjPBtcache] cache
++** @param [u] page [AjPBtpage] page
++** @param [r] item [const ajlong] key to search for 
++**
++** @return [AjPBtpage] leaf node where item should be inserted
++** @@
++******************************************************************************/
++
++static AjPBtpage btreeNumFindINode(AjPBtcache cache, AjPBtpage page,
++				   const ajlong item)
++{
++    AjPBtpage ret = NULL;
++    AjPBtpage pg  = NULL;
++
++    unsigned char *buf = NULL;
++    ajint status       = 0;
++    ajint ival         = 0;
++
++    /* ajDebug("In btreeNumFindINode\n"); */
++    
++    ret = page;
++    buf = page->buf;
++    GBT_NODETYPE(buf,&ival);
++    if(ival != BT_LEAF)
++    {
++	status = ret->dirty;
++	ret->dirty = BT_LOCK;	/* Lock in case of lots of overflow pages */
++	pg = btreeNumPageFromKey(cache,buf,item);
++	ret->dirty = status;
++	ret = btreeNumFindINode(cache,pg,item);
++    }
++    
++    return ret;
++}
++
++
++
++
++/* @funcstatic btreeNumPageFromKey *******************************************
++**
++** Return next lower index page given a key in a secondary tree
++**
++** @param [u] cache [AjPBtcache] cache
++** @param [u] buf [unsigned char *] page buffer
++** @param [r] key [const ajlong] key to search for 
++**
++** @return [AjPBtpage] pointer to a page
++** @@
++******************************************************************************/
++
++static AjPBtpage btreeNumPageFromKey(AjPBtcache cache, unsigned char *buf,
++				     const ajlong key)
++{
++    unsigned char *rootbuf = NULL;
++    ajint nkeys = 0;
++    ajint order = 0;
++    ajint i;
++    
++    ajlong blockno = 0L;
++    ajlong *karray = NULL;
++    ajlong *parray = NULL;
++    AjPBtpage page = NULL;
++    AjPBtMem array = NULL;
++
++    /* ajDebug("In btreeNumPageFromKey\n"); */
++    
++    rootbuf = buf;
++
++
++    GBT_NKEYS(rootbuf,&nkeys);
++    order = cache->sorder;
++
++    array = btreeAllocSecArray(cache);
++    karray = array->overflows;
++    parray = array->parray;
++    
++    btreeGetNumKeys(cache,rootbuf,&karray,&parray);
++    i = 0;
++    while(i!=nkeys && key >= karray[i])
++	++i;
++    if(i==nkeys)
++    {
++	if(key < karray[i-1])
++	    blockno = parray[i-1];
++	else
++	    blockno = parray[i];
++    }
++    else
++	blockno = parray[i];
++
++    btreeDeallocSecArray(cache,array);
++
++    page =  ajBtreeCacheRead(cache,blockno);
++
++    return page;
++}
++
++
++
++
++/* @funcstatic btreeAddToNumBucket *******************************************
++**
++** Add offset info to a bucket
++** Only called if there is room in the bucket
++**
++** @param [u] cache [AjPBtcache] cache
++** @param [r] pageno [ajlong] page number of bucket
++** @param [r] num [const AjPBtNumId] ID info
++**
++** @return [void]
++** @@
++******************************************************************************/
++
++static void btreeAddToNumBucket(AjPBtcache cache, ajlong pageno,
++				const AjPBtNumId num)
++{
++    AjPNumBucket bucket = NULL;
++    ajint nentries;
++    
++    /* ajDebug("In btreeAddToNumBucket\n"); */
++
++    bucket   = btreeReadNumBucket(cache,pageno);
++
++    nentries = bucket->Nentries;
++
++    /* Reading a bucket always gives one extra ID position */
++
++    AJNEW0(bucket->NumId[nentries]);
++    bucket->NumId[nentries]->offset    = num->offset;
++    bucket->NumId[nentries]->refoffset = num->refoffset;
++    bucket->NumId[nentries]->dbno      = num->dbno;
++
++    
++    ++bucket->Nentries;
++
++    btreeWriteNumBucket(cache,bucket,pageno);
++
++    btreeNumBucketDel(&bucket);
++    
++    return;
++}
++
++
++
++
++/* @funcstatic btreeNumInNumBucket *******************************************
++**
++** Return number of entries in a bucket
++**
++** @param [u] cache [AjPBtcache] cache
++** @param [r] pageno [ajlong] page number
++**
++** @return [ajint] Number of entries in bucket
++** @@
++******************************************************************************/
++
++static ajint btreeNumInNumBucket(AjPBtcache cache, ajlong pageno)
++{
++    AjPBtpage page     = NULL;
++    unsigned char *buf = NULL;
++    ajint  nodetype    = 0;
++    ajint  nentries    = 0;
++    
++    /* ajDebug("In btreeNumInNumBucket\n"); */
++    
++    if(pageno == cache->secrootblock)
++	ajFatal("NumInNumBucket: Attempt to read bucket from root page\n");
++
++    page  = ajBtreeCacheRead(cache,pageno);
++
++    buf = page->buf;
++
++    GBT_BUCKNODETYPE(buf,&nodetype);
++    if(nodetype != BT_BUCKET)
++	ajFatal("NumInNumBucket: NodeType mismatch. Not bucket (%d)",
++		nodetype);
++    
++    GBT_BUCKNENTRIES(buf,&nentries);
++
++    return nentries;
++}
++
++
++
++
++/* @funcstatic btreeNumBucketNew *********************************************
++**
++** Construct a bucket object
++**
++** @param [r] n [ajint] Number of IDs
++**
++** @return [AjPBucket] initialised disc block cache structure
++** @@
++******************************************************************************/
++
++static AjPNumBucket btreeNumBucketNew(ajint n)
++{
++    AjPNumBucket bucket = NULL;
++    ajint i;
++
++    /* ajDebug("In btreeNumBucketNew\n"); */
++    
++    AJNEW0(bucket);
++
++    if(n)
++    {
++	AJCNEW0(bucket->NumId,n);
++	for(i=0;i<n;++i)
++	    AJNEW0(bucket->NumId[i]);
++    }
++
++    bucket->NodeType = BT_BUCKET;
++    bucket->Nentries = n;
++    bucket->Overflow = 0L;
++    
++    return bucket;
++}
++
++
++
++
++/* @funcstatic btreeReorderNumBuckets *****************************************
++**
++** Re-order leaf buckets
++** Must only be called if one of the buckets is full
++**
++** @param [u] cache [AjPBtcache] cache
++** @param [u] leaf [AjPBtpage] leaf page
++**
++** @return [AjBool] true if reorder was successful i.e. leaf not full
++** @@
++******************************************************************************/
++
++static AjBool btreeReorderNumBuckets(AjPBtcache cache, AjPBtpage leaf)
++{
++    ajint nkeys = 0;
++    unsigned char *lbuf = NULL;
++
++    ajlong *keys        = NULL;
++    ajlong *ptrs        = NULL;
++
++    AjPNumBucket *buckets  = NULL;
++    
++    ajint i = 0;
++    ajint j = 0;
++    
++    ajint order;
++    ajint bentries      = 0;
++    ajint totalkeys     = 0;
++    ajint nperbucket    = 0;
++    ajint maxnperbucket = 0;
++    ajint count         = 0;
++    ajint keylimit      = 0;
++    ajint bucketn       = 0;
++    ajint bucketlimit   = 0;
++    ajint nodetype      = 0;
++    
++    AjPList idlist    = NULL;
++    ajint   dirtysave = 0;
++    AjPBtNumId bid       = NULL;
++    AjPNumBucket cbucket = NULL;
++    AjPBtNumId cid       = NULL;
++
++    ajint   v = 0;
++    AjPBtMem array = NULL;
++    
++    /* ajDebug("In btreeReorderNumBuckets\n"); */
++
++    dirtysave = leaf->dirty;
++
++    leaf->dirty = BT_LOCK;
++    lbuf = leaf->buf;
++
++    GBT_NODETYPE(lbuf,&nodetype);
++
++    order = cache->sorder;
++    nperbucket = cache->snperbucket;
++    
++
++    array = btreeAllocSecArray(cache);
++    keys  = array->overflows;
++    ptrs  = array->parray;
++
++    /* Read keys/ptrs */
++
++    btreeGetNumKeys(cache,lbuf,&keys,&ptrs);
++
++    GBT_NKEYS(lbuf,&nkeys);
++
++
++    if(!nkeys)
++	ajFatal("NumBucketReorder: Attempt to reorder empty leaf");
++
++    for(i=0;i<nkeys;++i)
++	totalkeys += btreeNumInNumBucket(cache,ptrs[i]);
++    totalkeys += btreeNumInNumBucket(cache,ptrs[i]);
++
++    /* Set the number of entries per bucket to approximately half full */
++    maxnperbucket = nperbucket >> 1;
++
++    if(!maxnperbucket)
++	++maxnperbucket;
++
++    /* Work out the number of new buckets needed */
++    bucketn = (totalkeys / maxnperbucket);
++    if(totalkeys % maxnperbucket)
++	++bucketn;
++    
++    if(bucketn > order)
++    {
++	btreeDeallocSecArray(cache,array);
++	
++	leaf->dirty = dirtysave;
++	return ajFalse;
++    }
++    
++
++    /* Read buckets */
++    AJCNEW0(buckets,nkeys+1);
++    keylimit = nkeys + 1;
++    
++    for(i=0;i<keylimit;++i)
++	buckets[i] = btreeReadNumBucket(cache,ptrs[i]);
++
++
++    /* Read IDs from all buckets and push to list and sort (increasing id) */
++    idlist  = ajListNew();
++    
++    for(i=0;i<keylimit;++i)
++    {
++	bentries = buckets[i]->Nentries;
++	for(j=0;j<bentries;++j)
++	    ajListPush(idlist,(void *)buckets[i]->NumId[j]);
++	
++	AJFREE(buckets[i]->NumId);
++	AJFREE(buckets[i]);
++    }
++    ajListSort(idlist,btreeNumIdCompare);
++    AJFREE(buckets);
++
++    cbucket = btreeNumBucketNew(maxnperbucket);
++    bucketlimit = bucketn - 1;
++    
++    for(i=0;i<bucketlimit;++i)
++    {
++	cbucket->Nentries = 0;
++
++	count = 0;
++	while(count!=maxnperbucket)
++	{
++	    ajListPop(idlist,(void **)&bid);
++	    
++	    cid = cbucket->NumId[count];
++	    cid->dbno = bid->dbno;
++	    cid->offset = bid->offset;
++	    cid->refoffset = bid->refoffset;
++	    
++	    ++cbucket->Nentries;
++	    ++count;
++	    AJFREE(bid);
++	}
++
++
++	ajListPeek(idlist,(void **)&bid);
++	keys[i] = bid->offset;
++
++	if(!ptrs[i])
++	    ptrs[i] = cache->totsize;
++	btreeWriteNumBucket(cache,cbucket,ptrs[i]);
++    }
++
++
++    /* Deal with greater-than bucket */
++
++    cbucket->Nentries = 0;
++
++    count = 0;
++    while(ajListPop(idlist,(void **)&bid))
++    {
++	cid = cbucket->NumId[count];
++	cid->dbno = bid->dbno;
++	cid->offset = bid->offset;
++	cid->refoffset = bid->refoffset;
++	
++	++cbucket->Nentries;
++	++count;
++	AJFREE(bid);
++    }
++    
++    
++    if(!ptrs[i])
++	ptrs[i] = cache->totsize;
++    btreeWriteNumBucket(cache,cbucket,ptrs[i]);
++
++    cbucket->Nentries = maxnperbucket;
++    btreeNumBucketDel(&cbucket);
++
++    /* Now write out a modified leaf with new keys/ptrs */
++
++    nkeys = bucketn - 1;
++    v = nkeys;
++    SBT_NKEYS(lbuf,v);
++
++    btreeWriteNumNode(cache,leaf,keys,ptrs,nkeys);
++
++    leaf->dirty = BT_DIRTY;
++    if(nodetype == BT_ROOT)
++	leaf->dirty = BT_LOCK;
++    
++    btreeDeallocSecArray(cache,array);
++
++    ajListDel(&idlist);
++
++    return ajTrue;
++}
++
++
++
++
++/* @funcstatic btreeNumNodeIsFull *****************************************
++**
++** Tests whether a node is full of keys
++**
++** @param [r] cache [const AjPBtcache] cache
++** @param [u] page [AjPBtpage] original page
++**
++** @return [AjBool] true if full
++** @@
++******************************************************************************/
++
++static AjBool btreeNumNodeIsFull(const AjPBtcache cache, AjPBtpage page)
++{
++    unsigned char *buf = NULL;
++    ajint nkeys = 0;
++
++    /* ajDebug("In btreeNumNodeIsFull\n"); */
++
++    buf = page->buf;
++    GBT_NKEYS(buf,&nkeys);
++
++    if(nkeys == cache->sorder - 1)
++	return ajTrue;
++
++    return ajFalse;
++}
++
++
++
++
++/* @funcstatic btreeNumInsertNonFull *****************************************
++**
++** Insert a key into a non-full node
++**
++** @param [u] cache [AjPBtcache] cache
++** @param [u] page [AjPBtpage] original page
++** @param [r] key [const ajlong] key to insert
++** @param [r] less [ajlong] less-than pointer
++** @param [r] greater [ajlong] greater-than pointer
++**
++** @return [void]
++** @@
++******************************************************************************/
++
++static void btreeNumInsertNonFull(AjPBtcache cache, AjPBtpage page,
++				  const ajlong key, ajlong less,
++				  ajlong greater)
++{
++    unsigned char *buf = NULL;
++    ajlong *karray     = NULL;
++    ajlong *parray     = NULL;
++    ajint nkeys  = 0;
++    ajint order  = 0;
++    ajint ipos   = 0;
++    ajint i;
++    ajint count  = 0;
++
++    ajlong lv = 0L;
++    ajint  v  = 0;
++    AjPBtMem array = NULL;    
++
++    AjPBtpage ppage = NULL;
++    ajlong pageno   = 0L;
++
++    ajint nodetype = 0;
++    
++    /* ajDebug("In btreeNumInsertNonFull\n"); */
++
++    order = cache->sorder;
++
++    array = btreeAllocSecArray(cache);
++    karray  = array->overflows;
++    parray  = array->parray;
++
++
++    buf = page->buf;
++    GBT_NKEYS(buf,&nkeys);
++    GBT_NODETYPE(buf,&nodetype);
++    
++    btreeGetNumKeys(cache,buf,&karray,&parray);
++
++    i = 0;
++    while(i!=nkeys && key >= karray[i])
++	++i;
++
++    ipos = i;
++
++    count = nkeys - ipos;
++    
++
++    if(ipos == nkeys)
++    {
++	karray[ipos] = key;
++	parray[ipos+1] = greater;
++	parray[ipos]   = less;
++    }
++    else
++    {
++	parray[nkeys+1] = parray[nkeys];
++
++	for(i=nkeys-1; count>0; --count, --i)
++	{
++	    karray[i+1] = karray[i];
++	    parray[i+1] = parray[i];
++	}
++
++	karray[ipos] = key;
++	parray[ipos] = less;
++	parray[ipos+1] = greater;
++    }
++
++    ++nkeys;
++    v = nkeys;
++    SBT_NKEYS(buf,v);
++
++    btreeWriteNumNode(cache,page,karray,parray,nkeys);
++    if(nodetype == BT_ROOT)
++	page->dirty = BT_LOCK;
++
++    pageno = page->pageno;
++    ppage = ajBtreeCacheRead(cache,less);
++    lv = pageno;
++    SBT_PREV(ppage->buf,lv);
++    ppage->dirty = BT_DIRTY;
++    ppage = ajBtreeCacheRead(cache,greater);
++    lv = pageno;
++    SBT_PREV(ppage->buf,lv);
++    ppage->dirty = BT_DIRTY;
++    
++
++    btreeDeallocSecArray(cache,array);
++
++    if(nodetype != BT_ROOT)
++	btreeNumKeyShift(cache,page);
++
++    return;
++}
++
++
++
++
++/* @funcstatic btreeNumInsertKey **********************************************
++**
++** Insert a key into a potentially full node
++**
++** @param [u] cache [AjPBtcache] cache
++** @param [u] page [AjPBtpage] original page
++** @param [r] key [const ajlong] key to insert
++** @param [r] less [ajlong] less-than pointer
++** @param [r] greater [ajlong] greater-than pointer
++**
++** @return [void]
++** @@
++******************************************************************************/
++
++static void btreeNumInsertKey(AjPBtcache cache, AjPBtpage page,
++			      const ajlong key, ajlong less, ajlong greater)
++{
++    unsigned char *lbuf = NULL;
++    unsigned char *rbuf = NULL;
++    unsigned char *tbuf = NULL;
++    ajlong *karray      = NULL;
++    ajlong *parray      = NULL;
++    ajlong *tkarray     = NULL;
++    ajlong *tparray     = NULL;
++    ajint nkeys    = 0;
++    ajint order    = 0;
++    ajint keypos   = 0;
++    ajint rkeyno   = 0;
++    
++    ajint i = 0;
++    ajint n = 0;
++    
++    ajint nodetype  = 0;
++    AjPBtpage ipage = NULL;
++    AjPBtpage lpage = NULL;
++    AjPBtpage rpage = NULL;
++    AjPBtpage tpage = NULL;
++
++    ajlong blockno  = 0L;
++    ajlong rblockno = 0L;
++    ajlong lblockno = 0L;
++    ajlong mediankey  = 0L;
++    ajlong medianless = 0L;
++    ajlong mediangtr  = 0L;
++    ajlong overflow   = 0L;
++    ajlong prev       = 0L;
++    ajint  totlen     = 0;
++    
++    ajlong lv = 0L;
++    ajint  v  = 0;
++    AjPBtMem array  = NULL;    
++    AjPBtMem array2 = NULL;    
++    
++    /* ajDebug("In btreeNumInsertKey\n"); */
++
++    if(!btreeNumNodeIsFull(cache,page))
++    {
++	btreeNumInsertNonFull(cache,page,key,less,greater);
++	return;
++    }
++    
++    order = cache->sorder;
++    lbuf = page->buf;
++    GBT_NODETYPE(lbuf,&nodetype);
++    page->dirty = BT_LOCK;
++
++    if(nodetype == BT_ROOT)
++    {
++	array = btreeAllocSecArray(cache);
++	karray  = array->overflows;
++	parray  = array->parray;
++
++	btreeNumSplitRoot(cache);
++
++	if(page->pageno)
++	    page->dirty = BT_DIRTY;
++	btreeGetNumKeys(cache,lbuf,&karray,&parray);
++
++	if(key < karray[0])
++	    blockno = parray[0];
++	else
++	    blockno = parray[1];
++	ipage = ajBtreeCacheRead(cache,blockno);
++	btreeNumInsertNonFull(cache,ipage,key,less,greater);
++
++	btreeDeallocSecArray(cache,array);
++	return;
++    }
++
++
++    array = btreeAllocSecArray(cache);
++    karray  = array->overflows;
++    parray  = array->parray;
++    
++    array2 = btreeAllocSecArray(cache);
++    tkarray  = array2->overflows;
++    tparray  = array2->parray;
++
++    
++    lpage = page;
++    lbuf = lpage->buf;
++    
++    btreeGetNumKeys(cache,lbuf,&karray,&parray);
++
++    GBT_BLOCKNUMBER(lbuf,&lblockno);
++    rblockno = cache->totsize;
++    rpage = ajBtreeCacheWrite(cache,rblockno);
++    rpage->dirty = BT_LOCK;
++    rpage->pageno = cache->totsize;
++    cache->totsize += cache->pagesize;
++    rbuf = rpage->buf;
++    lv = rblockno;
++    SBT_BLOCKNUMBER(rbuf,lv);
++
++    
++    GBT_PREV(lbuf,&prev);
++    lv = prev;
++    SBT_PREV(rbuf,lv);
++
++    nkeys = order - 1;
++    keypos = nkeys / 2;
++    if(!(nkeys % 2))
++	--keypos;
++
++    mediankey = karray[keypos];
++    medianless = lblockno;
++    mediangtr  = rblockno;
++
++
++    GBT_NODETYPE(lbuf,&nodetype);
++    v = nodetype;
++    SBT_NODETYPE(rbuf,v);
++    lv = overflow;
++    SBT_OVERFLOW(rbuf,lv);
++
++
++    totlen = 0;
++    for(i=0;i<keypos;++i)
++    {
++	tkarray[i] = karray[i];
++	tparray[i] = parray[i];
++    }
++    tparray[i] = parray[i];
++
++    n = i;
++    v = n;
++    SBT_NKEYS(lbuf,v);
++    btreeWriteNumNode(cache,lpage,tkarray,tparray,i);
++
++
++
++    for(i=0;i<n+1;++i)
++    {
++	tpage = ajBtreeCacheRead(cache,tparray[i]);
++	tbuf = tpage->buf;
++	lv = lblockno;
++	SBT_PREV(tbuf,lv);
++	tpage->dirty = BT_DIRTY;
++    }
++
++
++    totlen = 0;
++    for(i=keypos+1;i<nkeys;++i)
++    {
++	tkarray[i-(keypos+1)] = karray[i];
++	tparray[i-(keypos+1)] = parray[i];
++    }
++    tparray[i-(keypos+1)] = parray[i];
++
++    rkeyno = (nkeys-keypos) - 1;
++    v = rkeyno;
++    SBT_NKEYS(rbuf,v);
++    rpage->dirty = BT_DIRTY;
++    btreeWriteNumNode(cache,rpage,tkarray,tparray,rkeyno);
++
++
++    for(i=0;i<rkeyno+1;++i)
++    {
++	tpage = ajBtreeCacheRead(cache,tparray[i]);
++	tbuf = tpage->buf;
++	lv = rblockno;
++	SBT_PREV(tbuf,lv);
++	tpage->dirty = BT_DIRTY;
++    }
++
++
++    ipage = rpage;
++    if(key < mediankey)
++	ipage = lpage;
++
++    btreeNumInsertNonFull(cache,ipage,key,less,greater);
++
++
++    btreeDeallocSecArray(cache,array);
++    btreeDeallocSecArray(cache,array2);
++
++    ipage = ajBtreeCacheRead(cache,prev);
++
++    btreeNumInsertKey(cache,ipage,mediankey,medianless,mediangtr);
++
++    return;
++}
++
++
++
++
++/* @funcstatic btreeNumSplitRoot *****************************************
++**
++** Split s secondary root node
++**
++** @param [u] cache [AjPBtcache] cache
++**
++** @return [void]
++** @@
++******************************************************************************/
++
++static void btreeNumSplitRoot(AjPBtcache cache)
++{
++    AjPBtpage rootpage = NULL;
++    AjPBtpage rpage    = NULL;
++    AjPBtpage lpage    = NULL;
++    AjPBtpage tpage    = NULL;
++
++    ajlong *karray  = NULL;
++    ajlong *tkarray = NULL;
++    ajlong *parray  = NULL;
++    ajlong *tparray = NULL;
++
++    ajint order  = 0;
++    ajint nkeys  = 0;
++    ajint keypos = 0;
++    
++    ajlong rblockno = 0L;
++    ajlong lblockno = 0L;
++
++    ajlong right;
++    
++    ajint  i;
++
++    unsigned char *rootbuf = NULL;
++    unsigned char *rbuf    = NULL;
++    unsigned char *lbuf    = NULL;
++    unsigned char *tbuf    = NULL;
++    
++    ajint nodetype  = 0;
++    ajlong overflow = 0L;
++    ajlong zero     = 0L;
++    ajint rkeyno    = 0;
++    ajint n         = 0;
++
++    ajlong lv = 0L;
++    ajint  v  = 0;
++
++    AjPBtMem array  = NULL;    
++    AjPBtMem array2 = NULL;    
++    
++    
++    /* ajDebug("In btreeNumSplitRoot\n"); */
++
++    order = cache->sorder;
++
++    array = btreeAllocSecArray(cache);
++    karray  = array->overflows;
++    parray  = array->parray;
++    
++    array2 = btreeAllocSecArray(cache);
++    tkarray  = array2->overflows;
++    tparray  = array2->parray;
++
++
++    rootpage = btreeCacheLocate(cache,cache->secrootblock);
++    rootbuf = rootpage->buf;
++
++    nkeys = order - 1;
++
++    keypos = nkeys / 2;
++    if(!(nkeys % 2))
++	--keypos;
++
++
++    rblockno = cache->totsize;
++    rpage = ajBtreeCacheWrite(cache,rblockno);
++    rpage->pageno = cache->totsize;
++    cache->totsize += cache->pagesize;
++    rpage->dirty = BT_LOCK;
++    
++    lblockno = cache->totsize;
++    lpage = ajBtreeCacheWrite(cache,lblockno);
++    lpage->pageno = cache->totsize;
++    cache->totsize += cache->pagesize;
++
++    lv = rblockno;
++    SBT_BLOCKNUMBER(rpage->buf,lv);
++    lv = lblockno;
++    SBT_BLOCKNUMBER(lpage->buf,lv);
++
++    /* Comment this next block out after the beta test */
++    if(!cache->slevel)
++    {
++	fprintf(stderr,"btreeSplitRootSec: Shouldn't get here\n");
++	exit(0);
++	lv = zero;
++	SBT_LEFT(lpage->buf,lv);
++	lv = rblockno;
++	SBT_RIGHT(lpage->buf,lv);
++	lv = lblockno;
++	SBT_LEFT(rpage->buf,lv);
++	lv = zero;
++	SBT_RIGHT(rpage->buf,lv);
++    }
++
++    btreeGetNumKeys(cache,rootbuf,&karray,&parray);
++
++    /* Get key for root node and write new root node */
++    tkarray[0] = karray[keypos];
++    tparray[0] = lblockno;
++    tparray[1] = rblockno;
++    
++
++    n = 1;
++    v = n;
++    SBT_NKEYS(rootbuf,v);
++    btreeWriteNumNode(cache,rootpage,tkarray,tparray,1);
++    right = (ajlong)(cache->slevel + 1);
++    SBT_RIGHT(rootbuf,right);
++
++    rootpage->dirty = BT_LOCK;
++
++    rbuf = rpage->buf;
++    lbuf = lpage->buf;
++    
++    if(cache->slevel)
++	nodetype = BT_INTERNAL;
++    else
++	nodetype = BT_LEAF;
++
++    v = nodetype;
++    SBT_NODETYPE(rbuf,v);
++    v = nodetype;
++    SBT_NODETYPE(lbuf,v);
++    lv = overflow;
++    SBT_OVERFLOW(rbuf,lv);
++    lv = cache->secrootblock;
++    SBT_PREV(rbuf,lv);
++    lv = overflow;
++    SBT_OVERFLOW(lbuf,lv);
++    lv = cache->secrootblock;
++    SBT_PREV(lbuf,lv);
++
++    for(i=0;i<keypos;++i)
++    {
++	tkarray[i] = karray[i];
++	tparray[i] = parray[i];
++    }
++    tparray[i] = parray[i];
++
++    n = i;
++    v = n;
++    SBT_NKEYS(lbuf,v);
++    btreeWriteNumNode(cache,lpage,tkarray,tparray,i);
++
++    for(i=0;i<n+1;++i)
++    {
++	tpage = ajBtreeCacheRead(cache,tparray[i]);
++	tbuf = tpage->buf;
++	lv = lblockno;
++	SBT_PREV(tbuf,lv);
++	tpage->dirty = BT_DIRTY;
++    }
++
++    for(i=keypos+1;i<nkeys;++i)
++    {
++	tkarray[i-(keypos+1)] = karray[i];
++	tparray[i-(keypos+1)] = parray[i];
++    }
++    tparray[i-(keypos+1)] = parray[i];
++
++    rkeyno = (nkeys-keypos) - 1;
++    v = rkeyno;
++    SBT_NKEYS(rbuf,v);
++    rpage->dirty = BT_DIRTY;
++    btreeWriteNumNode(cache,rpage,tkarray,tparray,rkeyno);
++
++    for(i=0;i<rkeyno+1;++i)
++    {
++	tpage = ajBtreeCacheRead(cache,tparray[i]);
++	tbuf = tpage->buf;
++	lv = rblockno;
++	SBT_PREV(tbuf,lv);
++	tpage->dirty = BT_DIRTY;
++    }
++
++
++    ++cache->slevel;
++
++    btreeDeallocSecArray(cache,array);
++    btreeDeallocSecArray(cache,array2);
++    
++    return;
++}
++
++
++
++
++/* @funcstatic btreeNumKeyShift ********************************************
++**
++** Rebalance Nodes on insertion
++**
++** @param [u] cache [AjPBtcache] cache
++** @param [u] tpage [AjPBtpage] page
++**
++** @return [void]
++** @@
++******************************************************************************/
++
++static void btreeNumKeyShift(AjPBtcache cache, AjPBtpage tpage)
++{
++    unsigned char *tbuf = NULL;
++    unsigned char *pbuf = NULL;
++    unsigned char *sbuf = NULL;
++    unsigned char *buf  = NULL;
++
++    AjPBtpage ppage = NULL;
++    AjPBtpage spage = NULL;
++    AjPBtpage page  = NULL;
++
++    ajint tkeys = 0;
++    ajint pkeys = 0;
++    ajint skeys = 0;
++    ajint order = 0;
++    
++    ajint i;
++    
++    ajlong parent  = 0L;
++    
++    ajlong *kTarray = NULL;
++    ajlong *kParray = NULL;
++    ajlong *kSarray = NULL;
++    ajlong *pTarray = NULL;
++    ajlong *pParray = NULL;
++    ajlong *pSarray = NULL;
++
++    ajint pkeypos = 0;
++    ajint minsize = 0;
++
++    ajlong lv = 0L;
++
++    AjPBtMem array  = NULL;    
++    AjPBtMem array2 = NULL;    
++    AjPBtMem array3 = NULL;    
++    
++    /* ajDebug("In btreeNumKeyShift\n"); */
++    
++    tbuf = tpage->buf;
++
++    GBT_PREV(tbuf,&parent);
++    GBT_NKEYS(tbuf,&tkeys);
++
++    order = cache->sorder;
++    minsize = order / 2;
++    if(order % 2)
++	++minsize;
++
++    if(tkeys <= minsize)
++	return;
++
++    
++    ppage = ajBtreeCacheRead(cache,parent);
++    pbuf = ppage->buf;
++    GBT_NKEYS(pbuf,&pkeys);
++    
++    array = btreeAllocSecArray(cache);
++    kParray  = array->overflows;
++    pParray  = array->parray;
++    
++    array2 = btreeAllocSecArray(cache);
++    kSarray  = array2->overflows;
++    pSarray  = array2->parray;
++
++    array3 = btreeAllocSecArray(cache);
++    kTarray  = array3->overflows;
++    pTarray  = array3->parray;
++
++
++    btreeGetNumKeys(cache,tbuf,&kTarray,&pTarray);
++    GBT_NKEYS(tbuf,&tkeys);
++
++
++    btreeGetNumKeys(cache,pbuf,&kParray,&pParray);
++    i=0;
++    while(pParray[i] != tpage->pageno)
++	++i;
++
++    if(i) /* There is another leaf to the left */
++    {
++	pkeypos = i-1;
++	spage = ajBtreeCacheRead(cache,pParray[pkeypos]);
++	sbuf = spage->buf;
++	GBT_NKEYS(sbuf,&skeys);
++	
++    }
++
++    if(i && skeys != order-1) /* There is space in the left leaf */
++    {
++	if(skeys)
++	    btreeGetNumKeys(cache,sbuf,&kSarray,&pSarray);
++
++	kSarray[skeys] = kParray[pkeypos];
++	pSarray[skeys+1] = pTarray[0];
++	++skeys;
++	--tkeys;
++	kParray[pkeypos] = kTarray[0];
++	for(i=0;i<tkeys;++i)
++	{
++	    kTarray[i] = kTarray[i+1];
++	    pTarray[i] = pTarray[i+1];
++	}
++	pTarray[i] = pTarray[i+1];
++	pTarray[i+1] = 0L;
++	
++	btreeWriteNumNode(cache,spage,kSarray,pSarray,skeys);
++	btreeWriteNumNode(cache,tpage,kTarray,pTarray,tkeys);
++	btreeWriteNumNode(cache,ppage,kParray,pParray,pkeys);
++	if(!ppage->pageno)
++	    ppage->dirty = BT_LOCK;
++
++	page = ajBtreeCacheRead(cache,pSarray[skeys]);
++	buf = page->buf;
++	lv = spage->pageno;
++	SBT_PREV(buf,lv);
++	page->dirty = BT_DIRTY;
++
++
++	btreeDeallocSecArray(cache,array);
++	btreeDeallocSecArray(cache,array2);
++	btreeDeallocSecArray(cache,array3);
++
++	return;
++    }
++
++
++
++    if(i != pkeys)	/* There is a right node */
++    {
++	pkeypos = i;
++	spage = ajBtreeCacheRead(cache,pParray[pkeypos+1]);
++	sbuf = spage->buf;
++	GBT_NKEYS(sbuf,&skeys);
++    }
++
++
++    if(i != pkeys && skeys != order-1) /* Space in the right node */
++    {
++	if(skeys)
++	    btreeGetNumKeys(cache,sbuf,&kSarray,&pSarray);
++
++	pSarray[skeys+1] = pSarray[skeys];
++	for(i=skeys-1;i>-1;--i)
++	{
++	    kSarray[i+1] = kSarray[i];
++	    pSarray[i+1] = pSarray[i];
++	}
++	kSarray[0] = kParray[pkeypos];
++	pSarray[0] = pTarray[tkeys];
++	kParray[pkeypos] = kTarray[tkeys-1];
++	++skeys;
++	--tkeys;
++	pTarray[tkeys+1] = 0L;
++	
++	btreeWriteNumNode(cache,spage,kSarray,pSarray,skeys);
++	btreeWriteNumNode(cache,tpage,kTarray,pTarray,tkeys);
++	btreeWriteNumNode(cache,ppage,kParray,pParray,pkeys);
++	if(!ppage->pageno)
++	    ppage->dirty = BT_LOCK;
++
++	page = ajBtreeCacheRead(cache,pSarray[0]);
++	buf = page->buf;
++	lv = spage->pageno;
++	SBT_PREV(buf,lv);
++	page->dirty = BT_DIRTY;
++
++	btreeDeallocSecArray(cache,array);
++	btreeDeallocSecArray(cache,array2);
++	btreeDeallocSecArray(cache,array3);
++
++	return;
++    }
++
++
++    btreeDeallocSecArray(cache,array);
++    btreeDeallocSecArray(cache,array2);
++    btreeDeallocSecArray(cache,array3);
++
++    return;
++}
++
++
++
++
++/* @funcstatic btreeNumInsertShift ********************************************
++**
++** Rebalance buckets on insertion
++**
++** @param [u] cache [AjPBtcache] cache
++** @param [u] retpage [AjPBtpage*] page
++** @param [r] key [const ajlong] key
++**
++** @return [ajlong] bucket block or 0L if shift not posible 
++** @@
++******************************************************************************/
++
++static ajlong btreeNumInsertShift(AjPBtcache cache, AjPBtpage *retpage,
++				  ajlong key)
++{
++    unsigned char *tbuf = NULL;
++    unsigned char *pbuf = NULL;
++    unsigned char *sbuf = NULL;
++
++    AjPBtpage ppage = NULL;
++    AjPBtpage spage = NULL;
++    AjPBtpage tpage = NULL;
++
++    ajint tkeys = 0;
++    ajint pkeys = 0;
++    ajint skeys = 0;
++    ajint order = 0;
++    
++    ajint i;
++    ajint n;
++    
++    ajlong parent  = 0L;
++    ajlong blockno = 0L;
++    
++    ajlong *kTarray = NULL;
++    ajlong *kParray = NULL;
++    ajlong *kSarray = NULL;
++    ajlong *pTarray = NULL;
++    ajlong *pParray = NULL;
++    ajlong *pSarray = NULL;
++
++    ajlong *karray = NULL;
++    ajlong *parray = NULL;
++
++    ajint ppos    = 0;
++    ajint pkeypos = 0;
++    ajint minsize = 0;
++
++    AjPBtMem array  = NULL;    
++    AjPBtMem array2 = NULL;    
++    AjPBtMem array3 = NULL;    
++
++
++    
++    /* ajDebug("In btreeNumInsertShift\n"); */
++
++
++    tpage = *retpage;
++
++    tbuf = tpage->buf;
++
++    GBT_PREV(tbuf,&parent);
++    GBT_NKEYS(tbuf,&tkeys);
++
++
++    order = cache->sorder;
++    minsize = order / 2;
++    if(order % 2)
++	++minsize;
++
++    if(tkeys <= minsize)
++	return 0L;
++
++    ppage = ajBtreeCacheRead(cache,parent);
++
++
++    
++    pbuf = ppage->buf;
++    GBT_NKEYS(pbuf,&pkeys);
++
++    
++    array = btreeAllocSecArray(cache);
++    kParray  = array->overflows;
++    pParray  = array->parray;
++    
++    array2 = btreeAllocSecArray(cache);
++    kSarray  = array2->overflows;
++    pSarray  = array2->parray;
++
++    array3 = btreeAllocSecArray(cache);
++    kTarray  = array3->overflows;
++    pTarray  = array3->parray;
++
++
++    btreeGetNumKeys(cache,pbuf,&kParray,&pParray);
++
++    i=0;
++    while(i!=pkeys && key >= kParray[i])
++	++i;
++    pkeypos = i;
++    
++    if(i==pkeys)
++    {
++	if(key < kParray[i-1])
++	    ppos = i-1;
++	else
++	    ppos = i;
++    }
++    else
++	ppos = i;
++
++    
++    if(ppos) /* There is another leaf to the left */
++    {
++	spage = ajBtreeCacheRead(cache,pParray[ppos-1]);
++	sbuf = spage->buf;
++	GBT_NKEYS(sbuf,&skeys);
++    }
++
++    if(i && skeys != order-1) /* There is space in the left leaf */
++    {
++	/* ajDebug("Left shift\n"); */
++	btreeGetNumKeys(cache,tbuf,&kTarray,&pTarray);
++	if(skeys)
++	    btreeGetNumKeys(cache,sbuf,&kSarray,&pSarray);
++
++	i = 0;
++	while(pParray[i] != tpage->pageno)
++	    ++i;
++	--i;
++
++	pkeypos = i;
++
++	kSarray[skeys] = kParray[pkeypos];
++	pSarray[skeys+1] = pTarray[0];
++	++skeys;
++	--tkeys;
++	kParray[pkeypos] = kTarray[0];
++	for(i=0;i<tkeys;++i)
++	{
++	    kTarray[i] = kTarray[i+1];
++	    pTarray[i] = pTarray[i+1];
++	}
++	pTarray[i] = pTarray[i+1];
++	pTarray[i+1] = 0L;
++	
++	btreeWriteNumNode(cache,spage,kSarray,pSarray,skeys);
++	btreeWriteNumNode(cache,tpage,kTarray,pTarray,tkeys);
++	btreeWriteNumNode(cache,ppage,kParray,pParray,pkeys);
++	if(!ppage->pageno)
++	    ppage->dirty = BT_LOCK;
++
++	i = 0;
++	while(i!=pkeys && key >= kParray[i])
++	    ++i;
++	if(i==pkeys)
++	{
++	    if(key < kParray[i-1])
++		blockno = pParray[i-1];
++	    else
++		blockno = pParray[i];
++	}
++	else
++	    blockno = pParray[i];
++
++	if(blockno == spage->pageno)
++	{
++	    *retpage = spage;
++	    karray = kSarray;
++	    parray = pSarray;
++	    n = skeys;
++	}
++	else
++	{
++	    karray = kTarray;
++	    parray = pTarray;
++	    n = tkeys;
++	}
++	
++
++	i = 0;
++	while(i!=n && key >= karray[i])
++	    ++i;
++	if(i==n)
++	{
++	    if(key < karray[i-1])
++		blockno = parray[i-1];
++	    else
++		blockno = parray[i];
++	}
++	else
++	    blockno = parray[i];
++
++	btreeDeallocSecArray(cache,array);
++	btreeDeallocSecArray(cache,array2);
++	btreeDeallocSecArray(cache,array3);
++
++	/* ajDebug("... returns blockno (a) %Ld\n",blockno); */
++
++	return blockno;
++    }
++    
++
++    if(ppos != pkeys)	/* There is a right node */
++    {
++	spage = ajBtreeCacheRead(cache,pParray[ppos+1]);
++	sbuf = spage->buf;
++	GBT_NKEYS(sbuf,&skeys);
++    }
++
++
++    /* Space in the right leaf */
++    if(ppos != pkeys && skeys != order-1)
++    {
++	/* ajDebug("Right shift\n"); */
++	btreeGetNumKeys(cache,tbuf,&kTarray,&pTarray);
++	btreeGetNumKeys(cache,sbuf,&kSarray,&pSarray);
++
++	i = 0;
++	while(pParray[i] != tpage->pageno)
++	    ++i;
++	pkeypos = i;
++	
++	pSarray[skeys+1] = pSarray[skeys];
++	for(i=skeys-1;i>-1;--i)
++	{
++	    kSarray[i+1] = kSarray[i];
++	    pSarray[i+1] = pSarray[i];
++	}
++	kSarray[0] = kParray[pkeypos];
++	pSarray[0] = pTarray[tkeys];
++	kParray[pkeypos] = kTarray[tkeys-1];
++	++skeys;
++	--tkeys;
++	pTarray[tkeys+1] = 0L;
++	
++	btreeWriteNumNode(cache,spage,kSarray,pSarray,skeys);
++	btreeWriteNumNode(cache,tpage,kTarray,pTarray,tkeys);
++	btreeWriteNumNode(cache,ppage,kParray,pParray,pkeys);
++	if(!ppage->pageno)
++	    ppage->dirty = BT_LOCK;
++
++	i = 0;
++	while(i!=pkeys && key >= kParray[i])
++	    ++i;
++	if(i==pkeys)
++	{
++	    if(key < kParray[i-1])
++		blockno = pParray[i-1];
++	    else
++		blockno = pParray[i];
++	}
++	else
++	    blockno = pParray[i];
++
++	if(blockno == spage->pageno)
++	{
++	    *retpage = spage;
++	    karray = kSarray;
++	    parray = pSarray;
++	    n = skeys;
++	}
++	else
++	{
++	    karray = kTarray;
++	    parray = pTarray;
++	    n = tkeys;
++	}
++	
++	i = 0;
++	while(i!=n && key >= karray[i])
++	    ++i;
++	if(i==n)
++	{
++	    if(key < karray[i-1])
++		blockno = parray[i-1];
++	    else
++		blockno = parray[i];
++	}
++	else
++	    blockno = parray[i];
++
++	btreeDeallocSecArray(cache,array);
++	btreeDeallocSecArray(cache,array2);
++	btreeDeallocSecArray(cache,array3);
++
++	/* ajDebug("... returns blockno (b) %Ld\n",blockno); */
++	
++	return blockno;
++    }
++
++
++    btreeDeallocSecArray(cache,array);
++    btreeDeallocSecArray(cache,array2);
++    btreeDeallocSecArray(cache,array3);
++
++    /* ajDebug("... returns 0L\n"); */
++
++    return 0L;
++}
++
++
++
++
++void ajBtreeInsertNum(AjPBtcache cache, AjPBtNumId num, AjPBtpage page)
++{
++    unsigned char *buf = NULL;
++    ajint order;
++    AjPBtMem array = NULL;
++    ajlong key;
++    AjPBtpage spage  = NULL;
++    AjPBtpage parent = NULL;
++    ajint nkeys = 0;
++    ajint nodetype = 0;
++    ajlong *karray = NULL;
++    ajlong *parray = NULL;
++    AjPNumBucket lbucket = NULL;
++    AjPNumBucket rbucket = NULL;
++    ajlong lblockno;
++    ajlong rblockno;
++    ajlong blockno;
++    ajlong shift;
++    ajint n;
++    ajint i;
++
++    /* ajDebug("In ajBtreeInsertNum\n"); */
++
++    key = num->offset;
++
++    spage = ajBtreeNumFindInsert(cache,key);
++    buf = spage->buf;
++
++    GBT_NKEYS(buf,&nkeys);
++    GBT_NODETYPE(buf,&nodetype);
++
++    order = cache->sorder;
++
++    array = btreeAllocSecArray(cache);
++    karray = array->overflows;
++    parray = array->parray;
++
++    if(!nkeys)
++    {
++	lbucket = btreeNumBucketNew(0);
++	rbucket = btreeNumBucketNew(0);
++
++	lblockno = cache->totsize;
++	btreeWriteNumBucket(cache,lbucket,lblockno);
++	rblockno = cache->totsize;
++	btreeWriteNumBucket(cache,rbucket,rblockno);
++
++	parray[0] = lblockno;
++	parray[1] = rblockno;
++	karray[0] = key;
++
++	btreeWriteNumNode(cache,spage,karray,parray,1);
++
++	btreeNumBucketDel(&lbucket);
++	btreeNumBucketDel(&rbucket);
++
++	btreeAddToNumBucket(cache,rblockno,num);
++
++	btreeDeallocSecArray(cache,array);
++
++	return;
++    }
++
++
++    btreeGetNumKeys(cache,buf,&karray,&parray);
++    i=0;
++    while(i != nkeys && key >= karray[i])
++	++i;
++    if(i==nkeys)
++    {
++	if(key < karray[i-1])
++	    blockno = parray[i-1];
++	else
++	    blockno = parray[i];
++    }
++    else
++	blockno = parray[i];
++
++    if(nodetype != BT_ROOT)
++	if((shift = btreeNumInsertShift(cache,&spage,key)))
++	    blockno = shift;
++
++
++    buf = spage->buf;
++    n = btreeNumInNumBucket(cache,blockno);
++
++    if(n == cache->snperbucket)
++    {
++	if(btreeReorderNumBuckets(cache,spage))
++	{
++	    GBT_NKEYS(buf,&nkeys);
++	    btreeGetNumKeys(cache,buf,&karray,&parray);
++	    i=0;
++	    while(i != nkeys && key >= karray[i])
++		++i;
++	    if(i==nkeys)
++	    {
++		if(key < karray[i-1])
++		    blockno = parray[i-1];
++		else
++		    blockno = parray[i];
++	    }
++	    else
++		blockno = parray[i];
++	}
++	else
++	{
++	    parent = btreeNumSplitLeaf(cache,spage);
++	    spage = ajBtreeNumFindInsert(cache,key);
++	    buf = spage->buf;
++
++	    btreeGetNumKeys(cache,buf,&karray,&parray);
++	    GBT_NKEYS(buf,&nkeys);
++	
++	    i=0;
++	    while(i != nkeys && key >= karray[i])
++		++i;
++	    if(i==nkeys)
++	    {
++		if(key < karray[i-1])
++		    blockno = parray[i-1];
++		else
++		    blockno = parray[i];
++	    }
++	    else
++		blockno = parray[i];
++	}
++    }
++
++    btreeAddToNumBucket(cache,blockno,num);
++
++    btreeDeallocSecArray(cache,array);
++
++    ++cache->count;
++
++    return;
++}
++
++
++
++
++/* @funcstatic btreeNumSplitLeaf *********************************************
++**
++** Split a leaf and propagate up if necessary
++**
++** @param [u] cache [AjPBtcache] cache
++** @param [u] spage [AjPBtpage] page
++**
++** @return [AjPBtpage] pointer to a parent page
++** @@
++******************************************************************************/
++
++static AjPBtpage btreeNumSplitLeaf(AjPBtcache cache, AjPBtpage spage)
++{
++    ajint nkeys     = 0;
++    ajint order     = 0;
++    ajint totalkeys = 0;
++    ajint bentries  = 0;
++    ajint keylimit  = 0;
++    ajint nodetype  = 0;
++
++    ajint rootnodetype = 0;
++    
++    ajint i;
++    ajint j;
++    
++    AjPBtpage lpage = NULL;
++    AjPBtpage rpage = NULL;
++    AjPBtpage page  = NULL;
++    
++    ajlong mediankey  = 0L;
++    ajlong mediangtr  = 0L;
++    ajlong medianless = 0L;
++
++    AjPBtNumId bid = NULL;
++
++    unsigned char *buf  = NULL;
++    unsigned char *lbuf = NULL;
++    unsigned char *rbuf = NULL;
++
++    AjPList idlist = NULL;
++
++    AjPNumBucket *buckets = NULL;
++    AjPNumBucket cbucket  = NULL;
++    
++    ajlong *karray = NULL;
++    ajlong *parray = NULL;
++    
++    ajint keypos = 0;
++    ajint lno    = 0;
++    ajint rno    = 0;
++
++    ajint bucketlimit   = 0;
++    ajint maxnperbucket = 0;
++    ajint nperbucket    = 0;
++    ajint bucketn       = 0;
++    ajint count         = 0;
++    
++    ajlong lblockno = 0L;
++    ajlong rblockno = 0L;
++    ajlong overflow = 0L;
++    ajlong prevsave = 0L;
++    
++    ajlong zero = 0L;
++    ajlong join = 0L;
++    
++    ajlong lv = 0L;
++    ajint  v  = 0;
++
++    AjPBtMem array = NULL;
++    
++    
++    /* ajDebug("In btreeNumSplitLeaf\n"); */
++
++    order = cache->sorder;
++    nperbucket = cache->snperbucket;
++
++    array = btreeAllocSecArray(cache);
++    karray = array->overflows;
++    parray = array->parray;
++
++    buf = spage->buf;
++    lbuf = buf;
++
++    GBT_NKEYS(buf,&nkeys);
++    GBT_NODETYPE(buf,&rootnodetype);
++
++    if(rootnodetype == BT_ROOT)
++    {
++	/* ajDebug("Root leaf splitting\n"); */
++	lblockno = cache->totsize;
++	lpage = ajBtreeCacheWrite(cache,lblockno);
++	lpage->pageno = cache->totsize;
++	cache->totsize += cache->pagesize;
++	lbuf = lpage->buf;
++	lv = cache->secrootblock;
++	SBT_PREV(lbuf,lv);
++    }
++    else
++    {
++	lblockno = spage->pageno;
++	lpage = spage;
++    }
++
++    lpage->dirty = BT_LOCK;
++
++    rblockno = cache->totsize;
++    rpage = ajBtreeCacheWrite(cache,rblockno);
++    rpage->pageno = cache->totsize;
++    cache->totsize += cache->pagesize;
++    rbuf = rpage->buf;
++    rpage->dirty = BT_LOCK;
++
++    if(rootnodetype == BT_ROOT)
++    {
++	lv = zero;
++	SBT_RIGHT(rbuf,lv);
++	lv = zero;
++	SBT_LEFT(lbuf,lv);
++    }
++    else
++    {
++	GBT_RIGHT(lbuf,&join);
++	lv = join;
++	SBT_RIGHT(rbuf,lv);
++    }
++    lv = lblockno;
++    SBT_LEFT(rbuf,lv);
++    lv = rblockno;
++    SBT_RIGHT(lbuf,lv);
++
++
++    btreeGetNumKeys(cache,buf,&karray,&parray);
++
++
++    keylimit = nkeys+1;
++    AJCNEW0(buckets,keylimit);
++    for(i=0;i<keylimit;++i)
++	buckets[i] = btreeReadNumBucket(cache,parray[i]);
++
++    idlist = ajListNew();
++    for(i=0;i<keylimit;++i)
++    {
++	bentries = buckets[i]->Nentries;
++	for(j=0;j<bentries;++j)
++	    ajListPush(idlist,(void *)buckets[i]->NumId[j]);
++	AJFREE(buckets[i]->NumId);
++	AJFREE(buckets[i]);
++    }
++
++
++
++    ajListSort(idlist,btreeNumIdCompare);
++    AJFREE(buckets);
++
++    totalkeys = ajListLength(idlist);
++
++    keypos = totalkeys / 2;
++
++    lno = keypos;
++    rno = totalkeys - lno;
++
++    maxnperbucket = nperbucket >> 1;
++    ++maxnperbucket;
++
++    cbucket = btreeNumBucketNew(maxnperbucket);
++
++    bucketn = lno / maxnperbucket;
++    if(lno % maxnperbucket)
++	++bucketn;
++    bucketlimit = bucketn - 1;
++
++
++    count = 0;
++    for(i=0;i<bucketlimit;++i)
++    {
++	cbucket->Nentries = 0;
++	for(j=0;j<maxnperbucket;++j)
++	{
++	    ajListPop(idlist,(void **)&bid);
++
++	    cbucket->NumId[j]->offset    = bid->offset;
++	    cbucket->NumId[j]->refoffset = bid->refoffset;
++	    cbucket->NumId[j]->dbno      = bid->dbno;
++	    
++	    ++count;
++	    ++cbucket->Nentries;
++	    AJFREE(bid);
++	}
++	ajListPeek(idlist,(void **)&bid);
++
++	karray[i] = bid->offset;
++
++	if(!parray[i])
++	    parray[i] = cache->totsize;
++	btreeWriteNumBucket(cache,cbucket,parray[i]);
++    }
++
++    cbucket->Nentries = 0;
++
++    j = 0;
++    while(count != lno)
++    {
++	ajListPop(idlist,(void **)&bid);
++
++	cbucket->NumId[j]->offset    = bid->offset;
++	cbucket->NumId[j]->refoffset = bid->refoffset;
++	cbucket->NumId[j]->dbno      = bid->dbno;
++
++	++j;
++	++count;
++
++
++	++cbucket->Nentries;
++	AJFREE(bid);
++    }
++
++    if(!parray[i])
++	parray[i] = cache->totsize;
++    btreeWriteNumBucket(cache,cbucket,parray[i]);
++
++    nkeys = bucketn - 1;
++    v = nkeys;
++    SBT_NKEYS(lbuf,v);
++    nodetype = BT_LEAF;
++    v = nodetype;
++    SBT_NODETYPE(lbuf,v);
++    GBT_PREV(lbuf,&prevsave);
++    lpage->dirty = BT_DIRTY;
++    btreeWriteNumNode(cache,lpage,karray,parray,nkeys);
++
++    ajListPeek(idlist,(void **)&bid);
++    mediankey = bid->offset;
++
++    bucketn = rno / maxnperbucket;
++    if(rno % maxnperbucket)
++	++bucketn;
++    bucketlimit = bucketn - 1;
++
++    for(i=0;i<bucketlimit;++i)
++    {
++	cbucket->Nentries = 0;
++	for(j=0;j<maxnperbucket;++j)
++	{
++	    ajListPop(idlist,(void **)&bid);
++	    
++	    cbucket->NumId[j]->offset    = bid->offset;
++	    cbucket->NumId[j]->refoffset = bid->refoffset;
++	    cbucket->NumId[j]->dbno      = bid->dbno;
++	    
++	    ++cbucket->Nentries;
++	    AJFREE(bid);
++	}
++
++	ajListPeek(idlist,(void **)&bid);
++	karray[i] = bid->offset;
++
++	parray[i] = cache->totsize;
++	btreeWriteNumBucket(cache,cbucket,parray[i]);
++    }
++
++    cbucket->Nentries = 0;
++
++    j = 0;
++    while(ajListPop(idlist,(void**)&bid))
++    {
++	cbucket->NumId[j]->offset    = bid->offset;
++	cbucket->NumId[j]->refoffset = bid->refoffset;
++	cbucket->NumId[j]->dbno      = bid->dbno;
++	++j;
++
++
++	++cbucket->Nentries;
++	AJFREE(bid);
++    }
++    
++    parray[i] = cache->totsize;
++    btreeWriteNumBucket(cache,cbucket,parray[i]);
++
++    nkeys = bucketn - 1;
++
++    v = nkeys;
++    SBT_NKEYS(rbuf,v);
++    nodetype = BT_LEAF;
++    v = nodetype;
++    SBT_NODETYPE(rbuf,v);
++    lv = prevsave;
++    SBT_PREV(rbuf,lv);
++    lv = overflow;
++    SBT_OVERFLOW(rbuf,lv);
++    
++    btreeWriteNumNode(cache,rpage,karray,parray,nkeys);
++    rpage->dirty = BT_DIRTY;
++
++    cbucket->Nentries = maxnperbucket;
++    btreeNumBucketDel(&cbucket);
++    ajListDel(&idlist);
++
++
++
++    medianless = lblockno;
++    mediangtr  = rblockno;
++
++
++    if(rootnodetype == BT_ROOT)
++    {
++	karray[0] = mediankey;
++	parray[0]=lblockno;
++	parray[1]=rblockno;
++	nkeys = 1;
++	spage->dirty = BT_DIRTY;
++	btreeWriteNumNode(cache,spage,karray,parray,nkeys);	
++
++	++cache->slevel;
++	lv = cache->slevel;
++	SBT_RIGHT(buf,lv);
++	spage->dirty = BT_LOCK;
++
++	btreeDeallocSecArray(cache,array);
++
++	return spage;
++    }
++
++    btreeDeallocSecArray(cache,array);
++
++
++    page = ajBtreeCacheRead(cache,prevsave);
++    btreeNumInsertKey(cache,page,mediankey,medianless,mediangtr);
++
++
++    page = ajBtreeCacheRead(cache,prevsave);
++
++    return page;
++}
++
++
++
++
++/* @func ajBtreeFreePriArray *******************************************
++**
++** Free karray and parray arrays for a primary key
++**
++** @param [rw] cache [AjPBtcache] cache
++**
++** @return [void]
++** @@
++******************************************************************************/
++
++void ajBtreeFreePriArray(AjPBtcache cache)
++{
++    AjPBtMem p;
++    AjPBtMem next;
++    ajint i;
++
++    /* ajDebug("In ajBtreeFreePriArray\n"); */
++    
++    if(!cache->bmem)
++	return;
++
++    p = cache->bmem;
++    next = p->next;
++    
++    while(next)
++    {
++	AJFREE(p->parray);
++	AJFREE(p->overflows);
++	for(i=0;i<cache->order;++i)
++	    ajStrDel(&p->karray[i]);
++	AJFREE(p->karray);
++	AJFREE(p);
++	p = next;
++	next = p->next;
++    }
++    
++
++    AJFREE(p->parray);
++    AJFREE(p->overflows);
++    for(i=0;i<cache->order;++i)
++	ajStrDel(&p->karray[i]);
++    AJFREE(p->karray);
++    AJFREE(p);
++    
++    cache->bmem = NULL;
++    cache->tmem = NULL;
++
++    return;
++}
++
++
++
++
++/* @func ajBtreeFreeSecArray *******************************************
++**
++** Free karray and parray arrays for a secondary key
++**
++** @param [rw] cache [AjPBtcache] cache
++**
++** @return [void]
++** @@
++******************************************************************************/
++
++void ajBtreeFreeSecArray(AjPBtcache cache)
++{
++    AjPBtMem p;
++    AjPBtMem next;
++    ajint i;
++
++    /* ajDebug("In ajBtreeFreeSecArray\n"); */
++    
++    if(!cache->bsmem)
++	return;
++
++    p = cache->bsmem;
++    next = p->next;
++    
++    while(next)
++    {
++	AJFREE(p->parray);
++	AJFREE(p->overflows);
++	for(i=0;i<cache->sorder;++i)
++	    ajStrDel(&p->karray[i]);
++	AJFREE(p->karray);
++	AJFREE(p);
++	
++	p = next;
++	next = p->next;
++    }
++    
++
++    AJFREE(p->parray);
++    AJFREE(p->overflows);
++    for(i=0;i<cache->sorder;++i)
++	ajStrDel(&p->karray[i]);
++    AJFREE(p->karray);
++    AJFREE(p);
++
++    cache->bsmem = NULL;
++    cache->tsmem = NULL;
++
++    return;
++}
++
++
++
++
++/* @func ajBtreeHybLeafList ********************************************
++**
++** Read the leaves of a secondary hybrid tree
++**
++** @param [u] cache [AjPBtcache] cache
++** @param [r] rootblock [ajlong] root page of secondary tree
++** @param [r] idname [AjPStr] id name
++** @param [r] list [AjPList] list to add BtIDs to
++**
++** @return [void]
++** @@
++******************************************************************************/
++
++void ajBtreeHybLeafList(AjPBtcache cache, ajlong rootblock, AjPStr idname,
++			AjPList list)
++{
++    AjPBtId id = NULL;
++    
++    ajint order;
++    ajlong *karray;
++    ajlong *parray;
++    AjPBtpage page;
++    unsigned char *buf;
++    ajint nodetype;
++    ajint i;
++    ajint j;
++    ajlong level = 0L;
++    
++    AjPNumBucket bucket;
++    ajint nkeys;
++    ajlong right;
++    AjPBtMem array = NULL;
++
++    order = cache->sorder;
++
++    array = btreeAllocSecArray(cache);
++    karray = array->overflows;
++    parray = array->parray;
++
++    page = ajBtreeCacheRead(cache, rootblock);
++    buf = page->buf;
++
++    GBT_RIGHT(buf,&level);
++    cache->slevel = (ajint) level;
++
++    btreeGetNumKeys(cache,buf,&karray,&parray);
++    GBT_NODETYPE(buf,&nodetype);
++
++    while(nodetype != BT_LEAF && cache->slevel != 0)
++    {
++	page = ajBtreeCacheRead(cache,parray[0]);
++	buf = page->buf;
++	btreeGetNumKeys(cache,buf,&karray,&parray);
++	GBT_NODETYPE(buf,&nodetype);
++    }
++
++    do
++    {
++	GBT_NKEYS(buf,&nkeys);
++	for(i=0;i<nkeys+1;++i)
++	{
++	    bucket = btreeReadNumBucket(cache,parray[i]);
++	    for(j=0;j<bucket->Nentries;++j)
++	    {
++		id = ajBtreeIdNew();
++		ajStrAssS(&id->id,idname);
++		id->offset = bucket->NumId[j]->offset;
++		id->refoffset = bucket->NumId[j]->refoffset;
++		id->dbno = bucket->NumId[j]->dbno;
++		ajListPush(list, (void*)id);
++	    }
++	    btreeNumBucketDel(&bucket);
++	}
++
++	right = 0L;
++	if(cache->slevel)
++	{
++	    GBT_RIGHT(buf,&right);
++	    if(right)
++	    {
++		page = ajBtreeCacheRead(cache,right);
++		buf = page->buf;
++		btreeGetNumKeys(cache,buf,&karray,&parray);
++	    }
++	}
++    } while(right);
++
++    btreeDeallocSecArray(cache,array);
++
++    return;
++}
++
diff --git a/biology/emboss/files/patch-ajindex.h b/biology/emboss/files/patch-ajindex.h
new file mode 100644
index 000000000000..bcd3faa62f17
--- /dev/null
+++ b/biology/emboss/files/patch-ajindex.h
@@ -0,0 +1,170 @@
+--- ajax/ajindex.h.orig	Mon Jan 23 12:17:10 2006
++++ ajax/ajindex.h	Thu Dec 22 13:12:32 2005
+@@ -67,6 +67,23 @@
+ } AjOBtNode;
+ #define AjPBtNode AjOBtNode*
+ 
++
++
++
++typedef struct AjSBtMem
++{
++    struct AjSBtMem *next;
++    struct AjSBtMem *prev;
++    AjPStr *karray;
++    ajlong *parray;
++    ajlong *overflows;
++    AjBool used;
++} AjOBtMem;
++#define AjPBtMem AjOBtMem*
++
++
++
++
+ /* @data AjPBtId ***************************************************
+ **
+ ** Btree ID
+@@ -137,6 +154,54 @@
+ 
+ 
+ 
++/* @data AjPBtNumId ***************************************************
++**
++** Btree ID
++**
++** @attr id [AjPStr] Unique ID
++** @attr dbno [ajint] Database file number
++** @attr dups [ajint] Duplicates
++** @attr offset [ajlong] Offset within database file (ftello)
++** @attr refoffset [ajlong] Offset within reference database file (ftello)
++******************************************************************************/
++
++typedef struct AjSBtNumId
++{
++    ajint  dbno;
++    ajlong offset;
++    ajlong refoffset;
++} AjOBtNumId;
++#define AjPBtNumId AjOBtNumId*
++
++
++
++
++/* @data AjPNumBucket ***************************************************
++**
++** Offset bucket structure on disc
++**
++** Key, filenumber, ftell ID, subkey page (char*, ajint, ajlong, ajlong)
++**
++** @attr NodeType [ajint] Node type
++** @attr Nentries [ajint] Number of entries
++** @attr Overflow [ajlong] Offset to overflow block
++** @attr offset [ajlong*] file offsets
++** @attr refoffset [ajlong*] ref file offsets
++** @attr offset [ajint*] database numbers
++******************************************************************************/
++
++typedef struct AjSNumBucket
++{
++    ajint    NodeType;
++    ajint    Nentries;
++    ajlong   Overflow;
++    AjPBtNumId *NumId;
++} AjONumBucket;
++#define AjPNumBucket AjONumBucket*
++
++
++
++
+ /* Database file name structure
+ **
+ ** ajint        order			Order of B+tree
+@@ -387,6 +452,10 @@
+ ** @attr snperbucket [ajint] Undocumented
+ ** @attr secrootblock [ajlong] secondary tree root block
+ ** @attr kwlimit [ajint] Max length of secondary key
++** @attr bmem [AjPBtMem] primary memory allocation MRU bottom
++** @attr bsmem [AjPBtMem] secondary memory allocation MRU bottom
++** @attr tmem [AjPBtMem] primary memory allocation MRU top
++** @attr tsmem [AjPBtMem] secondary memory allocation MRU top
+ ******************************************************************************/
+ 
+ typedef struct AjSBtCache
+@@ -409,6 +478,12 @@
+     ajint snperbucket;
+     ajlong secrootblock;
+     ajint  kwlimit;
++
++    AjPBtMem bmem;
++    AjPBtMem tmem;
++    AjPBtMem bsmem;
++    AjPBtMem tsmem;
++
+ } AjOBtcache;
+ #define AjPBtcache AjOBtcache*
+ 
+@@ -511,6 +586,32 @@
+ 
+ 
+ 
++/* @data AjPBtHybrid ***************************************************
++**
++** Btree ID
++**
++** @attr key1 [AjPStr] Unique ID
++** @attr dbno [ajint] Database file number
++** @attr dups [ajint] Duplicates
++** @attr offset [ajlong] Offset within database file (ftello)** @attr refoffset [ajlong] Offset within reference database file (ftello)
++** @attr refoffset [ajlong] Offset within reference database file (ftello)
++** @attr treeblock [ajlong] Secondary tree root page
++******************************************************************************/
++
++typedef struct AjSBtHybrid
++{
++    AjPStr key1;
++    ajint  dbno;
++    ajint  dups;
++    ajlong offset;
++    ajlong refoffset;
++    ajlong treeblock;
++} AjOBtHybrid;
++#define AjPBtHybrid AjOBtHybrid*
++
++
++
++
+ AjPBtcache ajBtreeCacheNewC(const char *file, const char *ext,
+ 			    const char *idir, const char *mode,
+ 			    ajint pagesize, ajint order, ajint fill,
+@@ -553,7 +654,8 @@
+ AjBool     ajBtreeReplaceId(AjPBtcache cache, const AjPBtId rid);
+ 
+ ajint      ajBtreeReadEntries(const char *filename, const char *indexdir,
+-		   	      AjPStr **seqfiles, AjPStr **reffiles);
++			      const char *directory,
++			      AjPStr **seqfiles, AjPStr **reffiles);
+ void       ajBtreeInsertDupId(AjPBtcache cache, AjPBtId id);
+ AjPList    ajBtreeDupFromKey(AjPBtcache cache, const char *key);
+ 
+@@ -580,6 +682,21 @@
+ void       ajBtreeInsertKeyword(AjPBtcache cache, const AjPBtPri pri);
+ 
+ void       ajBtreeLockTest(AjPBtcache cache);
++
++
++
++AjPBtpage   ajBtreeHybFindInsert(AjPBtcache cache, const char *key);
++AjPBtpage   ajBtreeNumFindInsert(AjPBtcache cache, const ajlong key);
++
++void        ajBtreeInsertNum(AjPBtcache cache, AjPBtNumId num, AjPBtpage page);
++void        ajBtreeHybInsertId(AjPBtcache cache, AjPBtHybrid hyb);
++AjPBtHybrid ajBtreeHybNew(void);
++void        ajBtreeHybDel(AjPBtHybrid *thys);
++void        ajBtreeFreePriArray(AjPBtcache cache);
++void        ajBtreeFreeSecArray(AjPBtcache cache);
++void 	    ajBtreeHybLeafList(AjPBtcache cache, ajlong rootblock,
++			       AjPStr idname, AjPList list);
++
+ 
+ #endif
+ 
diff --git a/biology/emboss/files/patch-ajpdb.c b/biology/emboss/files/patch-ajpdb.c
new file mode 100644
index 000000000000..39b7300f56c0
--- /dev/null
+++ b/biology/emboss/files/patch-ajpdb.c
@@ -0,0 +1,67 @@
+--- ajax/ajpdb.c.orig	Mon Jan 23 12:19:22 2006
++++ ajax/ajpdb.c	Fri Aug 19 13:49:12 2005
+@@ -1198,7 +1198,7 @@
+     osstr = ajStrNew();
+     xstr  = ajStrNew();
+ 
+-    /* Start of main application loop */
++    /* Start of main loop */
+     while(ajFileReadLine(inf,&line))
+     {
+ 	if(ajStrPrefixC(line,"XX"))
+@@ -1313,6 +1313,8 @@
+ 	    
+ 	    (ret)->Nchn = ncha;
+ 	    (ret)->Ngp  = ngrp;
++
++	    continue;
+ 	}
+ 	
+ 
+@@ -1382,7 +1384,11 @@
+ 	    ajStrToken(&token,&handle,NULL);
+ 	    ajStrToInt(token,&mod);
+ 	    if((mode == 0) && (mod!=1))
+-		break;
++	      {
++		/* break; */
++		/* Discard remaining AT lines */
++		while(ajFileReadLine(inf,&line) && ajStrPrefixC(line,"AT"));
++	      }
+ 
+ 	    /* Chain number */
+ 	    ajStrToken(&token,&handle,NULL);
+@@ -1463,7 +1469,10 @@
+ 			    "jison@hgmp.mrc.ac.uk");
+ 	    }
+ 	    else
++	      {
+ 		ajListPushApp((ret)->Chains[chn-1]->Atoms,(void *)atom);
++	      }
++	    continue;
+ 	}
+ 	
+ 	/* Parse residue line */
+@@ -1479,8 +1488,11 @@
+ 	    ajStrToken(&token,&handle,NULL);
+ 	    ajStrToInt(token,&mod);
+ 	    if((mode == 0) && (mod!=1))
+-		break;
+-
++	      {
++		/* break;*/
++		/* Discard remaining RE lines */
++		while(ajFileReadLine(inf,&line) && ajStrPrefixC(line,"RE"));
++	      }
+ 	    /* Chain number */
+ 	    ajStrToken(&token,&handle,NULL);
+ 	    ajStrToInt(token,&chn);
+@@ -1585,6 +1597,8 @@
+             ajStrToFloat(token,&residue->pol_rel);
+ 
+ 	    ajListPushApp((ret)->Chains[chn-1]->Residues,(void *)residue);  
++
++	    continue;
+ 	}
+     }
+     /* End of main application loop */
diff --git a/biology/emboss/files/patch-ajseqdb.c b/biology/emboss/files/patch-ajseqdb.c
new file mode 100644
index 000000000000..236f96035a0a
--- /dev/null
+++ b/biology/emboss/files/patch-ajseqdb.c
@@ -0,0 +1,195 @@
+--- ajax/ajseqdb.c.orig	Mon Jan 23 12:20:25 2006
++++ ajax/ajseqdb.c	Thu Dec 22 13:12:57 2005
+@@ -27,8 +27,7 @@
+ ******************************************************************************/
+ 
+ #include "ajax.h"
+-#include "ajmem.h"
+-#include "ajfile.h"
++
+ #include "limits.h"
+ #include <stdarg.h>
+ #include <sys/types.h>
+@@ -3055,13 +3054,13 @@
+ 
+ 
+     if(qryd->do_id)
+-        seqEmbossOpenCache(qry,ID_EXTENSION,&qryd->idcache);
++        seqEmbossOpenSecCache(qry,ID_EXTENSION,&qryd->idcache);
+ 
+     if(qryd->do_ac)
+-	seqEmbossOpenCache(qry,AC_EXTENSION,&qryd->accache);
++	seqEmbossOpenSecCache(qry,AC_EXTENSION,&qryd->accache);
+ 
+     if(qryd->do_sv)
+-	seqEmbossOpenCache(qry,SV_EXTENSION,&qryd->svcache);
++	seqEmbossOpenSecCache(qry,SV_EXTENSION,&qryd->svcache);
+ 
+     if(qryd->do_kw)
+     {
+@@ -3073,14 +3072,14 @@
+     if(qryd->do_de)
+     {
+ 	if(!qryd->idcache)
+-	    seqEmbossOpenCache(qry,ID_EXTENSION,&qryd->idcache);	
++	    seqEmbossOpenSecCache(qry,ID_EXTENSION,&qryd->idcache);	
+ 	seqEmbossOpenSecCache(qry,DE_EXTENSION,&qryd->decache);
+     }
+ 
+     if(qryd->do_tx)
+     {
+ 	if(!qryd->idcache)
+-	    seqEmbossOpenCache(qry,ID_EXTENSION,&qryd->idcache);	
++	    seqEmbossOpenSecCache(qry,ID_EXTENSION,&qryd->idcache);	
+ 	seqEmbossOpenSecCache(qry,TX_EXTENSION,&qryd->txcache);
+     }
+ 
+@@ -3149,6 +3148,7 @@
+     if(qryd->nentries == -1)
+ 	qryd->nentries = ajBtreeReadEntries(ajStrStr(qry->DbAlias),
+ 					    ajStrStr(qry->IndexDir),
++					    ajStrStr(qry->Directory),
+ 					    &qryd->files,&qryd->reffiles);
+ 
+     *cache = ajBtreeCacheNewC(ajStrStr(qry->DbAlias),ext,
+@@ -3209,6 +3209,7 @@
+     if(qryd->nentries == -1)
+ 	qryd->nentries = ajBtreeReadEntries(ajStrStr(qry->DbAlias),
+ 					    ajStrStr(qry->IndexDir),
++					    ajStrStr(qry->Directory),
+ 					    &qryd->files,&qryd->reffiles);
+     
+     
+@@ -3270,6 +3271,7 @@
+ 
+ 
+     n = ajBtreeReadEntries(qry->DbAlias->Ptr,qry->IndexDir->Ptr,
++			   qry->Directory->Ptr,
+ 			   &filestrings,&reffilestrings);
+ 
+ 
+@@ -3365,7 +3367,13 @@
+     {
+ 	    entry = ajBtreeIdFromKey(qryd->idcache,ajStrStr(qry->Id));
+ 	    if(entry)
+-		ajListPushApp(qryd->List,(void *)entry);
++	    {
++		if(!entry->dups)
++		    ajListPushApp(qryd->List,(void *)entry);
++		else
++		    ajBtreeHybLeafList(qryd->idcache,entry->offset,
++				       entry->id,qryd->List);
++	    }
+     }
+     
+ 
+@@ -3373,14 +3381,26 @@
+     {
+ 	    entry = ajBtreeIdFromKey(qryd->accache,ajStrStr(qry->Acc));
+ 	    if(entry)
+-		ajListPushApp(qryd->List,(void *)entry);
++	    {
++		if(!entry->dups)
++		    ajListPushApp(qryd->List,(void *)entry);
++		else
++		    ajBtreeHybLeafList(qryd->accache,entry->offset,
++				       entry->id,qryd->List);
++	    }
+     }
+ 
+     if((qryd->do_sv && !entry) && (qryd->do_sv && qryd->svcache))
+     {
+ 	    entry = ajBtreeIdFromKey(qryd->svcache,ajStrStr(qry->Gi));
+ 	    if(entry)
+-		ajListPushApp(qryd->List,(void *)entry);
++	    {
++		if(!entry->dups)
++		    ajListPushApp(qryd->List,(void *)entry);
++		else
++		    ajBtreeHybLeafList(qryd->svcache,entry->offset,
++				       entry->id,qryd->List);
++	    }
+     }
+ 
+     if(!ajListLength(qryd->List))
+@@ -3512,13 +3532,25 @@
+     qryd = qry->QryData;
+ 
+     if(qryd->do_id && qryd->idcache)
++    {
++	ajBtreeFreeSecArray(qryd->idcache);
+ 	ajBtreeCacheDel(&qryd->idcache);
++    }
++    
+ 
+     if(qryd->do_ac && qryd->accache)
++    {
++	ajBtreeFreeSecArray(qryd->accache);	
+ 	ajBtreeCacheDel(&qryd->accache);
++    }
++    
+ 
+     if(qryd->do_sv && qryd->svcache)
++    {
++	ajBtreeFreeSecArray(qryd->svcache);	
+ 	ajBtreeCacheDel(&qryd->svcache);
++    }
++
+ 
+     if(qryd->do_kw && qryd->kwcache)
+ 	ajBtreeCacheDel(&qryd->kwcache);
+@@ -3608,7 +3640,14 @@
+ 		    ajStrToLower(&kwid);
+ 		    id = ajBtreeIdFromKey(qryd->idcache,ajStrStr(kwid));
+ 		    if(id)
+-			ajListPushApp(qryd->List,(void *)id);
++		    {
++			if(!id->dups)
++			    ajListPushApp(qryd->List,(void *)id);
++			else
++			    ajBtreeHybLeafList(qryd->idcache,id->offset,
++					       id->id,qryd->List);
++		    }
++		    ajStrDel(&kwid);
+ 		}
+ 		ajListDel(&tlist);
+ 		ajBtreePriDel(&pri);
+@@ -3637,7 +3676,13 @@
+ 		    ajStrToLower(&kwid);
+ 		    id = ajBtreeIdFromKey(qryd->idcache,ajStrStr(kwid));
+ 		    if(id)
+-			ajListPushApp(qryd->List,(void *)id);
++		    {
++			if(!id->dups)
++			    ajListPushApp(qryd->List,(void *)id);
++			else
++			    ajBtreeHybLeafList(qryd->idcache,id->offset,
++					       id->id,qryd->List);
++		    }
+ 		    ajStrDel(&kwid);
+ 		}
+ 		ajListDel(&tlist);
+@@ -3667,7 +3712,14 @@
+ 		    ajStrToLower(&kwid);
+ 		    id = ajBtreeIdFromKey(qryd->idcache,ajStrStr(kwid));
+ 		    if(id)
+-			ajListPushApp(qryd->List,(void *)id);
++		    {
++			if(!id->dups)
++			    ajListPushApp(qryd->List,(void *)id);
++			else
++			    ajBtreeHybLeafList(qryd->idcache,id->offset,
++					       id->id,qryd->List);
++		    }
++		    ajStrDel(&kwid);
+ 		}
+ 		ajListDel(&tlist);
+ 		ajBtreePriDel(&pri);
+@@ -3832,6 +3884,7 @@
+ 	qryd = qry->QryData;
+ 	i = -1;
+ 	ajBtreeReadEntries(qry->DbAlias->Ptr,qry->IndexDir->Ptr,
++			   qry->Directory->Ptr,
+ 			   &qryd->files,&qryd->reffiles);
+ 
+ 	seqin->Single = ajTrue;
diff --git a/biology/emboss/files/patch-dbxfasta.c b/biology/emboss/files/patch-dbxfasta.c
new file mode 100644
index 000000000000..66f97c17c6df
--- /dev/null
+++ b/biology/emboss/files/patch-dbxfasta.c
@@ -0,0 +1,89 @@
+--- emboss/dbxfasta.c.orig	Mon Jan 23 12:22:12 2006
++++ emboss/dbxfasta.c	Wed Jan  4 16:31:37 2006
+@@ -2,7 +2,7 @@
+ **
+ ** Index flatfile databases
+ **
+-** @author: Copyright (C) Alan Bleasby (ableasby@hgmp.mrc.ac.uk)
++** @author Copyright (C) Alan Bleasby (ableasby@hgmp.mrc.ac.uk)
+ ** @@
+ **
+ ** This program is free software; you can redistribute it and/or
+@@ -77,6 +77,7 @@
+     
+     AjPBtId  idobj  = NULL;
+     AjPBtPri priobj = NULL;
++    AjPBtHybrid hyb = NULL;
+     
+ 
+     AjPRegexp typeexp = NULL;
+@@ -102,7 +103,8 @@
+     
+     idobj   = ajBtreeIdNew();
+     priobj  = ajBtreePriNew();
+-
++    hyb     = ajBtreeHybNew();
++    
+ 
+     nfields = embBtreeSetFields(entry,fieldarray);
+     embBtreeSetDbInfo(entry,dbname,dbrs,datestr,release,dbtype,directory,
+@@ -134,22 +136,22 @@
+ 	    if(entry->do_id)
+ 	    {
+ 		ajStrToLower(&entry->id);
+-		ajStrAssS(&idobj->id,entry->id);
+-		idobj->dbno = i;
+-		idobj->offset = entry->fpos;
+-		idobj->dups = 0;
+-		ajBtreeInsertId(entry->idcache,idobj);
++		ajStrAssS(&hyb->key1,entry->id);
++		hyb->dbno = i;
++		hyb->offset = entry->fpos;
++		hyb->dups = 0;
++		ajBtreeHybInsertId(entry->idcache,hyb);
+ 	    }
+ 
+ 	    if(entry->do_accession)
+                 while(ajListPop(entry->ac,(void **)&word))
+                 {
+ 		    ajStrToLower(&word);
+-                    ajStrAssS(&idobj->id,word);
+-                    idobj->dbno = i;
+-		    idobj->offset = entry->fpos;
+-		    idobj->dups = 0;
+-		    ajBtreeInsertId(entry->accache,idobj);
++                    ajStrAssS(&hyb->key1,word);
++                    hyb->dbno = i;
++		    hyb->offset = entry->fpos;
++		    hyb->dups = 0;
++		    ajBtreeHybInsertId(entry->accache,hyb);
+ 		    ajStrDel(&word);
+                 }
+ 
+@@ -157,11 +159,11 @@
+                 while(ajListPop(entry->sv,(void **)&word))
+                 {
+ 		    ajStrToLower(&word);
+-                    ajStrAssS(&idobj->id,word);
+-                    idobj->dbno = i;
+-		    idobj->offset = entry->fpos;
+-		    idobj->dups = 0;
+-		    ajBtreeInsertId(entry->svcache,idobj);
++                    ajStrAssS(&hyb->key1,word);
++                    hyb->dbno = i;
++		    hyb->offset = entry->fpos;
++		    hyb->dups = 0;
++		    ajBtreeHybInsertId(entry->svcache,hyb);
+ 		    ajStrDel(&word);
+                 }
+ 
+@@ -197,7 +199,8 @@
+ 
+     ajBtreeIdDel(&idobj);
+     ajBtreePriDel(&priobj);
+-
++    ajBtreeHybDel(&hyb);
++    
+     ajExit();
+ 
+     return 0;
diff --git a/biology/emboss/files/patch-dbxflat.c b/biology/emboss/files/patch-dbxflat.c
new file mode 100644
index 000000000000..f89837097c0e
--- /dev/null
+++ b/biology/emboss/files/patch-dbxflat.c
@@ -0,0 +1,146 @@
+--- emboss/dbxflat.c.orig	Mon Jan 23 12:22:23 2006
++++ emboss/dbxflat.c	Sun Jan  1 07:29:09 2006
+@@ -2,7 +2,7 @@
+ **
+ ** Index flatfile databases
+ **
+-** @author: Copyright (C) Alan Bleasby (ableasby@hgmp.mrc.ac.uk)
++** @author Copyright (C) Alan Bleasby (ableasby@hgmp.mrc.ac.uk)
+ ** @@
+ **
+ ** This program is free software; you can redistribute it and/or
+@@ -106,6 +106,7 @@
+     
+     AjPBtId  idobj  = NULL;
+     AjPBtPri priobj = NULL;
++    AjPBtHybrid hyb = NULL;
+     
+ 
+     embInit("dbxflat", argc, argv);
+@@ -126,7 +127,8 @@
+     
+     idobj   = ajBtreeIdNew();
+     priobj  = ajBtreePriNew();
+-
++    hyb     = ajBtreeHybNew();
++    
+ 
+     nfields = embBtreeSetFields(entry,fieldarray);
+     embBtreeSetDbInfo(entry,dbname,dbrs,datestr,release,dbtype,directory,
+@@ -156,11 +158,11 @@
+ 	    if(entry->do_id)
+ 	    {
+ 		ajStrToLower(&entry->id);
+-		ajStrAssS(&idobj->id,entry->id);
+-		idobj->dbno = i;
+-		idobj->offset = entry->fpos;
+-		idobj->dups = 0;
+-		ajBtreeInsertId(entry->idcache,idobj);
++		ajStrAssS(&hyb->key1,entry->id);
++		hyb->dbno = i;
++		hyb->offset = entry->fpos;
++		hyb->dups = 0;
++		ajBtreeHybInsertId(entry->idcache,hyb);
+ 	    }
+ 
+ 	    if(entry->do_accession)
+@@ -168,11 +170,11 @@
+                 while(ajListPop(entry->ac,(void **)&word))
+                 {
+ 		    ajStrToLower(&word);
+-                    ajStrAssS(&idobj->id,word);
+-                    idobj->dbno = i;
+-		    idobj->offset = entry->fpos;
+-		    idobj->dups = 0;
+-		    ajBtreeInsertId(entry->accache,idobj);
++                    ajStrAssS(&hyb->key1,word);
++                    hyb->dbno = i;
++		    hyb->offset = entry->fpos;
++		    hyb->dups = 0;
++		    ajBtreeHybInsertId(entry->accache,hyb);
+ 		    ajStrDel(&word);
+                 }
+ 	    }
+@@ -182,11 +184,11 @@
+                 while(ajListPop(entry->sv,(void **)&word))
+                 {
+ 		    ajStrToLower(&word);
+-                    ajStrAssS(&idobj->id,word);
+-                    idobj->dbno = i;
+-		    idobj->offset = entry->fpos;
+-		    idobj->dups = 0;
+-		    ajBtreeInsertId(entry->svcache,idobj);
++                    ajStrAssS(&hyb->key1,word);
++                    hyb->dbno = i;
++		    hyb->offset = entry->fpos;
++		    hyb->dups = 0;
++		    ajBtreeHybInsertId(entry->svcache,hyb);
+ 		    ajStrDel(&word);
+                 }
+ 	    }
+@@ -231,15 +233,11 @@
+ 	    }
+ 	}
+ 	
+-
+-
+-
+-
+-
+ 	ajFileClose(&inf);
+     }
+     
+ 
++
+     embBtreeDumpParameters(entry);
+     embBtreeCloseCaches(entry);
+     
+@@ -256,7 +254,8 @@
+ 
+     ajBtreeIdDel(&idobj);
+     ajBtreePriDel(&priobj);
+-
++    ajBtreeHybDel(&hyb);
++    
+     ajExit();
+ 
+     return 0;
+@@ -306,11 +305,13 @@
+ 	}
+ 
+ 	if(entry->do_sv)
+-	    if(ajStrPrefixC(line,"SV"))
++	    if(ajStrPrefixC(line,"SV") ||
++	       ajStrPrefixC(line,"IV"))	/* emblcds database format */
+ 		embBtreeEmblAC(line,entry->sv);
+ 
+ 	if(entry->do_accession)
+-	    if(ajStrPrefixC(line,"AC"))
++	    if(ajStrPrefixC(line,"AC") ||
++	       ajStrPrefixC(line,"PA"))	/* emblcds database format */
+ 		embBtreeEmblAC(line,entry->ac);
+ 	
+ 	if(entry->do_keyword)
+@@ -356,12 +357,10 @@
+     
+     line = ajStrNewC("");
+     sumline = ajStrNew();
++
+     
+     while(!ajStrPrefixC(line,"//") && ret)
+     {
+-	pos = ajFileTell(inf);
+-	
+-	
+ 	if(ajStrPrefixC(line,"LOCUS"))
+ 	{
+ 	    entry->fpos = pos;
+@@ -423,7 +422,7 @@
+ 	    }
+ 	
+ 
+-
++	pos = ajFileTell(inf);
+ 
+ 	if(!ajFileReadLine(inf,&line))
+ 	    ret = ajFalse;
diff --git a/biology/emboss/files/patch-dbxgcg.c b/biology/emboss/files/patch-dbxgcg.c
new file mode 100644
index 000000000000..5856843c57e8
--- /dev/null
+++ b/biology/emboss/files/patch-dbxgcg.c
@@ -0,0 +1,96 @@
+--- emboss/dbxgcg.c.orig	Mon Jan 23 12:22:30 2006
++++ emboss/dbxgcg.c	Thu Dec 22 13:13:18 2005
+@@ -2,7 +2,7 @@
+ **
+ ** Index flatfile databases
+ **
+-** @author: Copyright (C) Alan Bleasby (ableasby@hgmp.mrc.ac.uk)
++** @author Copyright (C) Alan Bleasby (ableasby@hgmp.mrc.ac.uk)
+ ** @@
+ **
+ ** This program is free software; you can redistribute it and/or
+@@ -136,6 +136,7 @@
+     
+     AjPBtId  idobj  = NULL;
+     AjPBtPri priobj = NULL;
++    AjPBtHybrid hyb = NULL;
+     
+ 
+     embInit("dbxgcg", argc, argv);
+@@ -156,7 +157,8 @@
+     
+     idobj   = ajBtreeIdNew();
+     priobj  = ajBtreePriNew();
+-
++    hyb     = ajBtreeHybNew();
++    
+ 
+     nfields = embBtreeSetFields(entry,fieldarray);
+     embBtreeSetDbInfo(entry,dbname,dbrs,datestr,release,dbtype,directory,
+@@ -204,12 +206,12 @@
+ 	    if(entry->do_id)
+ 	    {
+ 		ajStrToLower(&entry->id);
+-		ajStrAssS(&idobj->id,entry->id);
+-		idobj->dbno = i;
+-		idobj->offset = entry->fpos;
+-		idobj->refoffset = entry->reffpos;
+-		idobj->dups = 0;
+-		ajBtreeInsertId(entry->idcache,idobj);
++		ajStrAssS(&hyb->key1,entry->id);
++		hyb->dbno = i;
++		hyb->offset = entry->fpos;
++		hyb->refoffset = entry->reffpos;
++		hyb->dups = 0;
++		ajBtreeHybInsertId(entry->idcache,hyb);
+ 	    }
+ 
+ 	    if(entry->do_accession)
+@@ -217,12 +219,12 @@
+                 while(ajListPop(entry->ac,(void **)&word))
+                 {
+ 		    ajStrToLower(&word);
+-                    ajStrAssS(&idobj->id,word);
+-                    idobj->dbno = i;
+-		    idobj->offset = entry->fpos;
+-		    idobj->refoffset = entry->reffpos;
+-		    idobj->dups = 0;
+-		    ajBtreeInsertId(entry->accache,idobj);
++                    ajStrAssS(&hyb->key1,word);
++                    hyb->dbno = i;
++		    hyb->offset = entry->fpos;
++		    hyb->refoffset = entry->reffpos;
++		    hyb->dups = 0;
++		    ajBtreeHybInsertId(entry->accache,hyb);
+ 		    ajStrDel(&word);
+                 }
+ 	    }
+@@ -232,12 +234,12 @@
+                 while(ajListPop(entry->sv,(void **)&word))
+                 {
+ 		    ajStrToLower(&word);
+-                    ajStrAssS(&idobj->id,word);
+-                    idobj->dbno = i;
+-		    idobj->offset = entry->fpos;
+-		    idobj->refoffset = entry->reffpos;
+-		    idobj->dups = 0;
+-		    ajBtreeInsertId(entry->svcache,idobj);
++                    ajStrAssS(&hyb->key1,word);
++                    hyb->dbno = i;
++		    hyb->offset = entry->fpos;
++		    hyb->refoffset = entry->reffpos;
++		    hyb->dups = 0;
++		    ajBtreeHybInsertId(entry->svcache,hyb);
+ 		    ajStrDel(&word);
+                 }
+ 	    }
+@@ -303,7 +305,8 @@
+ 
+     ajBtreeIdDel(&idobj);
+     ajBtreePriDel(&priobj);
+-
++    ajBtreeHybDel(&hyb);
++    
+     ajExit();
+ 
+     return 0;
diff --git a/biology/emboss/files/patch-embindex.c b/biology/emboss/files/patch-embindex.c
new file mode 100644
index 000000000000..25569485eca7
--- /dev/null
+++ b/biology/emboss/files/patch-embindex.c
@@ -0,0 +1,115 @@
+--- nucleus/embindex.c.orig	Mon Jan 23 12:24:54 2006
++++ nucleus/embindex.c	Thu Dec 22 13:12:38 2005
+@@ -973,15 +973,14 @@
+ 	if(!do_ref)
+ 	{
+ 	    ajListPop(entry->files,(void **)&tmpstr);
+-	    ajFmtPrintF(entfile,"%S%S\n",entry->directory,tmpstr);
++	    ajFmtPrintF(entfile,"%S\n",tmpstr);
+ 	    ajListPushApp(entry->files,(void *)tmpstr);
+ 	}
+ 	else
+ 	{
+ 	    ajListPop(entry->files,(void **)&tmpstr);
+ 	    ajListPop(entry->reffiles,(void **)&refstr);
+-	    ajFmtPrintF(entfile,"%S%S %S%S\n",entry->directory,tmpstr,
+-			entry->directory,refstr);
++	    ajFmtPrintF(entfile,"%S %S\n",tmpstr, refstr);
+ 	    ajListPushApp(entry->files,(void *)tmpstr);
+ 	    ajListPushApp(entry->reffiles,(void *)refstr);
+ 	}
+@@ -1150,7 +1149,15 @@
+     entry->desecfill  = (entry->pagesize - 16) / (entry->idlen + 4);
+     entry->txsecfill  = (entry->pagesize - 16) / (entry->idlen + 4);
+ 
++    entry->idsecorder = (entry->pagesize - 60) / 24;
++    entry->idsecfill  = (entry->pagesize - 60) / 20;
+ 
++    entry->acsecorder = (entry->pagesize - 60) / 24;
++    entry->acsecfill  = (entry->pagesize - 60) / 20;
++
++    entry->svsecorder = (entry->pagesize - 60) / 24;
++    entry->svsecfill  = (entry->pagesize - 60) / 20;
++    
+     ajStrDel(&value);
+ 
+     return;
+@@ -1183,28 +1190,38 @@
+ 
+     if(entry->do_id)
+     {
+-	entry->idcache = ajBtreeCacheNewC(basenam,ID_EXTENSION,idir,"w+",
+-					  entry->pagesize, entry->idorder,
+-					  entry->idfill, level,
+-					  entry->cachesize);
++	entry->idcache = ajBtreeSecCacheNewC(basenam,ID_EXTENSION,idir,"w+",
++					     entry->pagesize, entry->idorder,
++					     entry->idfill, level,
++					     entry->cachesize,
++					     entry->idsecorder, slevel,
++					     entry->idsecfill, count,
++					     entry->kwlen);
+ 	ajBtreeCreateRootNode(entry->idcache,0L);
+     }
+ 
+     if(entry->do_accession)
+     {
+-	entry->accache = ajBtreeCacheNewC(basenam,AC_EXTENSION,idir,"w+",
+-					  entry->pagesize, entry->acorder,
+-					  entry->acfill, level,
+-					  entry->cachesize);
++	entry->accache = ajBtreeSecCacheNewC(basenam,AC_EXTENSION,idir,"w+",
++					     entry->pagesize,
++					     entry->acorder, entry->acfill,
++					     level,
++					     entry->cachesize,
++					     entry->acsecorder, slevel,
++					     entry->acsecfill, count,
++					     entry->kwlen);
+ 	ajBtreeCreateRootNode(entry->accache,0L);
+     }
+ 
+     if(entry->do_sv)
+     {
+-	entry->svcache = ajBtreeCacheNewC(basenam,SV_EXTENSION,idir,"w+",
+-					  entry->pagesize, entry->svorder,
+-					  entry->svfill, level,
+-					  entry->cachesize);
++	entry->svcache = ajBtreeSecCacheNewC(basenam,SV_EXTENSION,idir,"w+",
++					     entry->pagesize, entry->svorder,
++					     entry->svfill, level,
++					     entry->cachesize,
++					     entry->svsecorder, slevel,
++					     entry->svsecfill, count,
++					     entry->kwlen);
+ 	ajBtreeCreateRootNode(entry->svcache,0L);
+     }
+ 
+@@ -1270,18 +1287,27 @@
+ 
+     if(entry->do_id)
+     {
++	ajBtreeFreePriArray(entry->idcache);
++	ajBtreeFreeSecArray(entry->idcache);
++
+ 	ajBtreeCacheSync(entry->idcache,0L);
+ 	ajBtreeCacheDel(&entry->idcache);
+     }
+ 
+     if(entry->do_accession)
+     {
++	ajBtreeFreePriArray(entry->accache);
++	ajBtreeFreeSecArray(entry->accache);
++
+ 	ajBtreeCacheSync(entry->accache,0L);
+ 	ajBtreeCacheDel(&entry->accache);
+     }
+ 
+     if(entry->do_sv)
+     {
++	ajBtreeFreePriArray(entry->svcache);
++	ajBtreeFreeSecArray(entry->svcache);
++
+ 	ajBtreeCacheSync(entry->svcache,0L);
+ 	ajBtreeCacheDel(&entry->svcache);
+     }
diff --git a/biology/emboss/files/patch-embindex.h b/biology/emboss/files/patch-embindex.h
new file mode 100644
index 000000000000..3714ede97e10
--- /dev/null
+++ b/biology/emboss/files/patch-embindex.h
@@ -0,0 +1,96 @@
+--- nucleus/embindex.h.orig	Mon Jan 23 12:24:46 2006
++++ nucleus/embindex.h	Thu Dec 22 13:12:44 2005
+@@ -16,6 +16,76 @@
+ #define BTREE_DEF_CACHESIZE 100
+ #define BTREE_DEF_PAGESIZE  2048
+ 
++/* @data EmbPBtreeEntry *******************************************************
++**
++** Index tree entries
++**
++** @alias EmbSBtreeEntry
++**
++** @attr do_id [AjBool] Undocumented
++** @attr do_accession [AjBool] Undocumented
++** @attr do_sv [AjBool] Undocumented
++** @attr do_description [AjBool] Undocumented
++** @attr do_keyword [AjBool] Undocumented
++** @attr do_taxonomy [AjBool] Undocumented
++** @attr dbname [AjPStr] Undocumented
++** @attr dbrs [AjPStr] Undocumented
++** @attr release [AjPStr] Undocumented
++** @attr date [AjPStr] Undocumented
++** @attr dbtype [AjPStr] Undocumented
++** @attr directory [AjPStr] Undocumented
++** @attr idirectory [AjPStr] Undocumented
++** @attr files [AjPList] Undocumented
++** @attr reffiles [AjPList] Undocumented
++** @attr nfiles [ajint] Undocumented
++** @attr cachesize [ajint] Undocumented
++** @attr pagesize [ajint] Undocumented
++** @attr idlen [ajint] Undocumented
++** @attr aclen [ajint] Undocumented
++** @attr svlen [ajint] Undocumented
++** @attr kwlen [ajint] Undocumented
++** @attr delen [ajint] Undocumented
++** @attr txlen [ajint] Undocumented
++** @attr idorder [ajint] Undocumented
++** @attr idfill [ajint] Undocumented
++** @attr idsecorder [ajint] Undocumented
++** @attr idsecfill [ajint] Undocumented
++** @attr acorder [ajint] Undocumented
++** @attr acfill [ajint] Undocumented
++** @attr acsecorder [ajint] Undocumented
++** @attr acsecfill [ajint] Undocumented
++** @attr svorder [ajint] Undocumented
++** @attr svfill [ajint] Undocumented
++** @attr svsecorder [ajint] Undocumented
++** @attr svsecfill [ajint] Undocumented
++** @attr kworder [ajint] Undocumented
++** @attr kwfill [ajint] Undocumented
++** @attr kwsecorder [ajint] Undocumented
++** @attr kwsecfill [ajint] Undocumented
++** @attr deorder [ajint] Undocumented
++** @attr defill [ajint] Undocumented
++** @attr desecorder [ajint] Undocumented
++** @attr desecfill [ajint] Undocumented
++** @attr txorder [ajint] Undocumented
++** @attr txfill [ajint] Undocumented
++** @attr txsecorder [ajint] Undocumented
++** @attr txsecfill [ajint] Undocumented
++** @attr idcache [AjPBtcache] Undocumented
++** @attr accache [AjPBtcache] Undocumented
++** @attr svcache [AjPBtcache] Undocumented
++** @attr kwcache [AjPBtcache] Undocumented
++** @attr decache [AjPBtcache] Undocumented
++** @attr txcache [AjPBtcache] Undocumented
++** @attr fpos [ajlong] Undocumented
++** @attr reffpos [ajlong] Undocumented
++** @attr id [AjPStr] Undocumented
++** @attr ac [AjPList] Undocumented
++** @attr sv [AjPList] Undocumented
++** @attr tx [AjPList] Undocumented
++** @attr kw [AjPList] Undocumented
++** @attr de [AjPList] Undocumented
++******************************************************************************/
++
+ typedef struct EmbSBtreeEntry
+ {
+     AjBool do_id;
+@@ -48,10 +118,16 @@
+ 
+     ajint idorder;
+     ajint idfill;
++    ajint idsecorder;
++    ajint idsecfill;
+     ajint acorder;
+     ajint acfill;
++    ajint acsecorder;
++    ajint acsecfill;
+     ajint svorder;
+     ajint svfill;
++    ajint svsecorder;
++    ajint svsecfill;
+ 
+     ajint kworder;
+     ajint kwfill;
diff --git a/biology/emboss/files/patch-emboss.default.template b/biology/emboss/files/patch-emboss.default.template
new file mode 100644
index 000000000000..04ee586b4bfb
--- /dev/null
+++ b/biology/emboss/files/patch-emboss.default.template
@@ -0,0 +1,20 @@
+--- emboss/emboss.default.template.orig	Wed Feb  8 00:43:42 2006
++++ emboss/emboss.default.template	Wed Feb  8 00:40:34 2006
+@@ -4,7 +4,7 @@
+ # By default this is /usr/local/share/EMBOSS/test but the directory can
+ # be changed with --prefix when you configure EMBOSS.
+ 
+-# SET emboss_tempdata path_to_directory_$EMBOSS/test
++# SET emboss_tempdata %%DATADIR%%/test
+ 
+ # Proxy - set this if any databases are accessed through a proxy web server.
+ # Turn off in the DB definition with proxy: ":" for any
+@@ -15,7 +15,7 @@
+ # Logfile - set this to a file that any user can append to
+ # and EMBOSS applications will automatically write log information
+ 
+-# SET emboss_logfile /packages/emboss/emboss/log
++# SET emboss_logfile /var/log/emboss.log
+ 
+ # Pagesize - this is the size of disc page blocks and is
+ # required by the 'dbx' indexing programs and 'method: emboss'
diff --git a/biology/emboss/files/patch-marscan.c b/biology/emboss/files/patch-marscan.c
new file mode 100644
index 000000000000..85481fedfe78
--- /dev/null
+++ b/biology/emboss/files/patch-marscan.c
@@ -0,0 +1,72 @@
+--- emboss/marscan.c.orig	Mon Jan 23 11:36:36 2006
++++ emboss/marscan.c	Mon Jan 23 08:56:35 2006
+@@ -1,7 +1,7 @@
+ /* @source marscan application
+ **
+ ** Finds MAR/SAR sites in nucleic sequences
+-** @author: Copyright (C) Gary Williams (gwilliam@hgmp.mrc.ac.uk)
++** @author Copyright (C) Gary Williams (gwilliam@hgmp.mrc.ac.uk)
+ ** @@
+ **
+ ** This program is free software; you can redistribute it and/or
+@@ -249,33 +249,41 @@
+ 			 amino8rev, carboxyl8rev, buf8rev, off8rev,
+ 			 sotable8rev, solimit8rev, regexp8rev, skipm8rev,
+ 			 &hits8rev, m8rev, &tidy8rev);
++	ajDebug("Marscan '%S' hits %d:%d %d:%d\n", seqname,
++		hits16, hits16rev,
++		hits8, hits8rev);
++
++	/* initialise the output feature table */
++	tab = ajFeattableNewDna(seqname);
++
++	/*
++	**  append reverse lists to forward lists and sort them by match
++	**  position
++	*/
+ 
+-	if((hits16 || hits16rev) && (hits8 || hits8rev))
++	if(hits8 || hits8rev)
+ 	{
+-	    /*
+-	    **  append reverse lists to forward lists and sort them by match
+-	    **  position
+-	    */
+ 	    ajListPushList(l8, &l8rev);
+ 	    ajListSort(l8, embPatRestrictStartCompare);
+-
++	}
++	if((hits16 || hits16rev))
++	{
+ 	    ajListPushList(l16, &l16rev);
+ 	    ajListSort(l16, embPatRestrictStartCompare);
+ 
+-	    /* initialise the output feature table */
+-	    if(!tab)
+-		tab = ajFeattableNewDna(seqname);
+-
+-	    /*
+-	    **  find pairs of hits within the required distance and output
+-	    **  the results
+-	    */
+-	    marscan_stepdown(l16, l8, &tab);
+-
+-	    /* write features and tidy up */
+-	    ajReportWrite(report, tab, seq);
+-	    ajFeattableDel(&tab);
+ 	}
++
++
++	/*
++	**  find pairs of hits within the required distance and output
++	**  the results
++	*/
++	marscan_stepdown(l16, l8, &tab);
++
++	ajDebug("Marscan reportwrite '%S'\n", seqname);
++	/* write features and tidy up */
++	ajReportWrite(report, tab, seq);
++	ajFeattableDel(&tab);
+ 
+         while(ajListPop(l16,(void **)&aptr))
+             embMatMatchDel(&aptr);
diff --git a/biology/emboss/files/pkg-message.in b/biology/emboss/files/pkg-message.in
new file mode 100644
index 000000000000..cdedc5082b5c
--- /dev/null
+++ b/biology/emboss/files/pkg-message.in
@@ -0,0 +1,27 @@
+=============================================================================
+
+ The EMBOSS suite has been successfully installed under
+ %%PREFIX%%
+
+ To run EMBOSS programs make sure that %%PREFIX%%/bin is in your PATH.
+
+ In order to see graphical output from some EMBOSS programs, you will 
+ need to set the following environment variable in your shell:
+
+ set PLPLOT_LIB to: "%%PREFIX%%/share/EMBOSS"
+
+ A sample configuration file has been installed in
+ %%DATADIR%%/emboss.default.template
+
+ This must be renamed to emboss.default and edited to suit your site 
+ and requirements.
+
+ A .embossrc file in a user's home directory overrides settings in the
+ system-wide emboss.default.
+
+ Additional third party applications for EMBOSS can be installed from the
+ biology/embassy port. Remember, though that if you installed EMBOSS in a 
+ PREFIX other than the default, you will have to install EMBASSY into this 
+ same PREFIX.
+
+=============================================================================
diff --git a/biology/emboss/files/pre-install.in b/biology/emboss/files/pre-install.in
new file mode 100644
index 000000000000..e39e4d0c3b21
--- /dev/null
+++ b/biology/emboss/files/pre-install.in
@@ -0,0 +1,21 @@
+===============================================================================
+
+ ATENTION!!!
+
+ The EMBOSS port is currently affected by a CONFLICTS condition.
+ If you install the port in the default prefix
+ PREFIX = LOCALBASE = %%LOCALBASE%%
+ it will conflict with other ports that install applications with the 
+ same name, in the same places. 
+
+ It is highly recommended that you install EMBOSS to a different prefix,
+ for example PREFIX=%%LOCALBASE%%/emboss
+ In this case, all of the documentation and examples will be installed 
+ within this PREFIX. 
+
+ If you still choose to install EMBOSS on the default prefix, do note 
+ that documentation, examples and shared data will not be installed 
+ in the usual places for a FreeBSD port (i.e. docs in
+ PREFIX/share/EMBOSS/doc instead of in PREFIX/share/doc/EMBOSS).
+
+===============================================================================
diff --git a/biology/emboss/pkg-message b/biology/emboss/pkg-message
deleted file mode 100644
index 1c36c80c0b39..000000000000
--- a/biology/emboss/pkg-message
+++ /dev/null
@@ -1,22 +0,0 @@
---------------------------------------------------------------------------
-
-The EMBOSS suite has been successfully installed.
-
-In order to see graphical output from some EMBOSS programs, you will need to
-set the following environment variable in your shell startup file:
-
-- set PLPLOT_LIB to:     "%%PREFIX%%/share/EMBOSS"
-
-NB:  A sample configuration file has been installed to %%PREFIX%%/etc as
-emboss.default.sample.  This must be renamed to emboss.default and edited
-to suit your site and its requirements.
-
-A .embossrc in a user's home directory overrides settings in the
-system-wide emboss.default.
-
-Online EMBOSS documentation is available at:
-	http://www.uk.embnet.org/Software/EMBOSS/userdoc.html
-	http://www.uk.embnet.org/Software/EMBOSS/Doc/
-  http://emboss.sourceforge.net/docs/
-
---------------------------------------------------------------------------
diff --git a/biology/emboss/pkg-plist b/biology/emboss/pkg-plist
index 9154aea12af3..ea98778089e1 100644
--- a/biology/emboss/pkg-plist
+++ b/biology/emboss/pkg-plist
@@ -17,6 +17,7 @@ bin/checktrans
 bin/chips
 bin/cirdna
 bin/codcmp
+bin/codcopy
 bin/coderet
 bin/compseq
 bin/cons
@@ -24,12 +25,15 @@ bin/cpgplot
 bin/cpgreport
 bin/cusp
 bin/cutgextract
-bin/cutseq
 bin/dan
+bin/cutseq
 bin/dbiblast
 bin/dbifasta
 bin/dbiflat
 bin/dbigcg
+bin/dbxfasta
+bin/dbxflat
+bin/dbxgcg
 bin/degapseq
 bin/descseq
 bin/diffseq
@@ -119,7 +123,6 @@ bin/remap
 bin/restover
 bin/restrict
 bin/revseq
-bin/runJemboss.csh
 bin/seealso
 bin/seqmatchall
 bin/seqret
@@ -135,11 +138,11 @@ bin/silent
 bin/sirna
 bin/sixpack
 bin/skipseq
+bin/syco
 bin/splitter
 bin/stretcher
 bin/stssearch
 bin/supermatcher
-bin/syco
 bin/tcode
 bin/textsearch
 bin/tfextract
@@ -160,18 +163,30 @@ bin/wordcount
 bin/wordmatch
 bin/wossname
 bin/yank
-etc/emboss.default.sample
+bin/runJemboss.csh
+include/drivers.h
+include/pdf.h
+include/plcore.h
+include/plevent.h
+include/plplotP.h
+include/plxwd.h
+include/metadefs.h
+include/plConfig.h
+include/pldebug.h
+include/plplot.h
+include/plstrm.h
+include/plDevs.h
+include/ajax.h
+include/ajarch.h
+include/ajdefine.h
 include/ajacd.h
 include/ajalign.h
-include/ajarch.h
 include/ajarr.h
 include/ajassert.h
-include/ajax.h
 include/ajbase.h
 include/ajcall.h
 include/ajcod.h
 include/ajdan.h
-include/ajdefine.h
 include/ajdmx.h
 include/ajdomain.h
 include/ajexcept.h
@@ -180,8 +195,8 @@ include/ajfeatdata.h
 include/ajfile.h
 include/ajfmt.h
 include/ajgraph.h
-include/ajgraphstruct.h
 include/ajgraphxml.h
+include/ajgraphstruct.h
 include/ajhist.h
 include/ajindex.h
 include/ajjava.h
@@ -214,7 +229,14 @@ include/ajtranslate.h
 include/ajtree.h
 include/ajutil.h
 include/ajvector.h
-include/drivers.h
+include/pcre.h
+include/pcre_chartables.c
+include/pcre_config.h
+include/pcre_get.c
+include/pcre_printint.c
+include/pcre_internal.h
+include/pcreposix.h
+include/emboss.h
 include/embaln.h
 include/embcom.h
 include/embcons.h
@@ -232,48 +254,817 @@ include/embmat.h
 include/embmisc.h
 include/embmol.h
 include/embnmer.h
-include/emboss.h
 include/embpat.h
-include/embpdb.h
 include/embprop.h
+include/embpdb.h
 include/embread.h
-include/embshow.h
 include/embsig.h
+include/embshow.h
 include/embword.h
-include/metadefs.h
-include/pcre.h
-include/pcre_chartables.c
-include/pcre_config.h
-include/pcre_get.c
-include/pcre_internal.h
-include/pcre_printint.c
-include/pcreposix.h
-include/pdf.h
-include/plConfig.h
-include/plDevs.h
-include/plcore.h
-include/pldebug.h
-include/plevent.h
-include/plplot.h
-include/plplotP.h
-include/plstrm.h
-include/plxwd.h
-lib/libajax.a
-lib/libajax.la
+lib/libplplot.so.5
+lib/libplplot.so
+lib/libplplot.la
+lib/libplplot.a
+lib/libajax.so.3
 lib/libajax.so
-lib/libajax.so.1
-lib/libajaxg.a
-lib/libajaxg.la
+lib/libajax.la
+lib/libajax.a
+lib/libajaxg.so.3
 lib/libajaxg.so
-lib/libajaxg.so.1
-lib/libnucleus.a
-lib/libnucleus.la
+lib/libajaxg.la
+lib/libajaxg.a
+lib/libnucleus.so.3
 lib/libnucleus.so
-lib/libnucleus.so.1
-lib/libplplot.a
-lib/libplplot.la
-lib/libplplot.so
-lib/libplplot.so.5
+lib/libnucleus.la
+lib/libnucleus.a
+%%PORTDOCS%%%%DOCSDIR%%/manuals/admin.sty
+%%PORTDOCS%%%%DOCSDIR%%/manuals/admin.tex
+%%PORTDOCS%%%%DOCSDIR%%/manuals/admin.aux
+%%PORTDOCS%%%%DOCSDIR%%/manuals/admin.dvi
+%%PORTDOCS%%%%DOCSDIR%%/manuals/admin.log
+%%PORTDOCS%%%%DOCSDIR%%/manuals/admin.pdf
+%%PORTDOCS%%%%DOCSDIR%%/manuals/admin.ps
+%%PORTDOCS%%%%DOCSDIR%%/manuals/admin.toc
+%%PORTDOCS%%%%DOCSDIR%%/manuals/adminguide.tar.gz
+%%PORTDOCS%%%%DOCSDIR%%/manuals/domainatrix.doc
+%%PORTDOCS%%%%DOCSDIR%%/manuals/program.ps.gz
+%%PORTDOCS%%%%DOCSDIR%%/manuals/EMBOSS-FreeBSD-HOWTO.txt
+%%PORTDOCS%%%%DOCSDIR%%/manuals/emboss_qg.pdf
+%%PORTDOCS%%%%DOCSDIR%%/manuals/emboss_qg.ps
+%%PORTDOCS%%%%DOCSDIR%%/manuals/emboss.sty
+%%PORTDOCS%%%%DOCSDIR%%/manuals/fdl.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/lindna.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/listor.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/marscan.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/maskfeat.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/maskseq.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/matcher.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/matgen3d.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/megamerger.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/meme.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/menus_group.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/merger.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/msbar.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/mse.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/mwcontam.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/mwfilter.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/myseq.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/nawalign.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/nawalignrunner.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/needle.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/needlerunner.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/newcpgreport.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/newcpgseek.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/newseq.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/noreturn.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/notseq.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/nthseq.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/nucleic_2d_structure_group.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/nucleic_codon_usage_group.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/nucleic_codon_usage_nucleic_gene_finding_group.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/nucleic_composition_group.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/nucleic_cpg_islands_group.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/nucleic_gene_finding_group.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/nucleic_motifs_group.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/nucleic_mutation_group.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/nucleic_primers_group.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/nucleic_profiles_group.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/nucleic_repeats_group.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/nucleic_restriction_group.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/nucleic_transcription_group.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/nucleic_translation_group.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/octanol.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/oddcomp.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/palindrome.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/pasteseq.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/patmatdb.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/patmatmotifs.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/pdbparse.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/pdbplus.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/pdbtosp.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/pepcoil.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/pepinfo.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/pepnet.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/pepstats.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/pepwheel.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/pepwindow.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/pepwindowall.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/phylogeny_consensus_group.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/phylogeny_continuous_characters_group.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/phylogeny_discrete_characters_group.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/phylogeny_distance_matrix_group.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/phylogeny_gene_frequencies_group.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/phylogeny_group.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/phylogeny_molecular_sequence_group.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/phylogeny_tree_drawing_group.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/plotcon.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/plotorf.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/polydot.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/preg.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/prettyplot.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/prettyseq.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/primersearch.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/printsextract.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/profit.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/prophecy.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/prophet.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/prosextract.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/protein_2d_structure_group.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/protein_3d_structure_group.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/protein_composition_group.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/protein_motifs_group.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/protein_mutation_group.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/protein_profiles_group.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/protein_sequence_alignment_group.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/pscan.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/psiphi.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/rebaseextract.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/recoder.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/redata.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/remap.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/restover.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/restrict.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/revseq.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/rocon.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/rocplot.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/scope.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/scopparse.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/scorecmapdir.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/scorer.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/scorerrunner.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/seealso.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/seqalign.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/seqfraggle.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/seqmatchall.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/seqnr.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/seqret.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/seqretsplit.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/seqsearch.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/seqsort.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/seqwords.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/showalign.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/showdb.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/showfeat.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/showorf.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/showseq.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/shuffleseq.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/sigcleave.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/siggen.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/siggenlig.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/sigscan.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/sigscanlig.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/silent.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/sirna.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/sites.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/sixpack.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/skipseq.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/splitter.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/ssematch.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/stretcher.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/stssearch.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/substitute.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/substituterunner.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/supermatcher.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/syco.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/tcode.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/template.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/test_group.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/textsearch.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/tfextract.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/tfm.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/tfscan.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/tmap.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/topo.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/tranalign.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/transeq.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/trimest.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/trimseq.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/twofeat.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/union.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/utils_database_creation_group.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/utils_database_indexing_group.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/utils_misc_group.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/vectorstrip.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/water.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/whichdb.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/wobble.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/wordcount.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/wordmatch.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/wossname.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/yank.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/emboss_icon.jpg
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/abiview.1.abiview.gif
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/chaos.1.chaos.gif
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/cirdna.1.cirdna.gif
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/cpgplot.1.cpgplot.gif
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/dan.2.dan.gif
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/dotmatcher.1.dotmatcher.gif
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/dotpath.1.dotpath.gif
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/dottup.1.dottup.gif
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/emboss_icon.gif
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/findkm.1.findkm.gif
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/isochore.1.isochore.gif
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/lindna.1.lindna.gif
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/octanol.1.octanol.gif
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/pepinfo.1.pepinfo.gif
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/pepnet.1.pepnet.gif
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/pepwheel.1.pepwheel.gif
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/pepwindow.1.pepwindow.gif
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/pepwindowall.1.pepwindowall.gif
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/plotcon.1.plotcon.gif
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/plotorf.1.plotorf.gif
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/plotorf.2.plotorf.gif
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/polydot.1.polydot.gif
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/prettyplot.1.prettyplot.gif
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/prettyplot.2.prettyplot.gif
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/syco.1.syco.gif
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/tmap.1.tmap.gif
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/topo.gif
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/wobble.1.wobble.gif
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/aaindexextract.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/abiview.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/acd_group.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/acdc.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/acdlog.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/acdpretty.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/acdtable.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/acdtrace.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/acdvalid.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/ajtest.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/alignment_consensus_group.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/alignment_differences_group.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/alignment_dot_plots_group.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/antigenic.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/alignment_global_group.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/alignment_local_group.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/alignment_multiple_group.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/alignrunner.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/allversusall.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/backtranseq.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/banana.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/biosed.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/btwisted.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/cai.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/cathparse.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/chaos.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/charge.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/checktrans.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/chips.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/cirdna.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/codcmp.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/codcopy.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/coderet.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/comparator.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/compseq.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/cons.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/contactalign.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/contacts.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/cpgplot.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/cpgreport.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/crystalball.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/cusp.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/cutgextract.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/cutseq.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/dan.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/dbiblast.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/dbifasta.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/dbiflat.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/dbigcg.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/dbxfasta.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/dbxflat.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/dbxgcg.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/degapseq.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/degapseqrunner.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/descseq.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/diffseq.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/digest.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/display_group.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/distmat.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/domainalign.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/domainer.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/domainnr.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/domainrep.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/domainreso.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/domainseqs.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/domainsse.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/dotmatcher.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/dotpath.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/dottup.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/dreg.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/ealistat.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/eclique.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/econsense.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/econtml.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/econtrast.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/edit_group.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/ednacomp.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/ednadist.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/ednainvar.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/ednaml.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/ednamlk.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/ednapars.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/ednapenny.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/edollop.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/edolpenny.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/efactor.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/efitch.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/egendist.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/ehmmalign.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/ehmmbuild.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/ehmmcalibrate.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/ehmmconvert.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/ehmmemit.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/ehmmfetch.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/ehmmindex.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/ehmmpfam.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/ehmmsearch.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/einverted.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/ekitsch.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/embossdata.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/embossversion.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/emix.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/emma.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/emnu.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/emowse.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/eneighbor.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/entret.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/enzyme_kinetics_group.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/epenny.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/epestfind.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/eprimer3.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/eprotdist.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/eprotpars.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/equicktandem.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/erestml.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/eseqboot.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/esim4.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/est2genome.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/etandem.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/extractfeat.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/extractseq.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/fclique.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/fconsense.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/fcontml.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/fcontrast.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/fdiscboot.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/fdnacomp.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/fdnadist.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/fdnainvar.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/fdnaml.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/fdnamlk.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/fdnamove.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/fdnapars.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/fdnapenny.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/fdollop.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/fdolmove.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/fdolpenny.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/fdrawgram.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/fdrawtree.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/feature_tables_group.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/ffactor.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/ffitch.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/ffreqboot.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/fgendist.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/findkm.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/fkitsch.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/fmix.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/fmove.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/fneighbor.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/fpars.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/fpenny.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/fproml.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/fpromlk.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/fprotdist.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/fprotpars.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/freak.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/frestboot.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/frestdist.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/frestml.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/fretree.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/fseqboot.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/fseqbootall.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/ftreedist.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/ftreedistpair.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/fuzznuc.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/fuzzpro.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/fuzztran.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/garnier.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/geecee.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/getorf.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/groups.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/helixturnhelix.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/hetparse.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/hmm_group.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/hmoment.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/iep.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/index.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/infoalign.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/information_group.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/infoseq.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/interface.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/isochore.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/jembossctl.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/libgen.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/html/libscan.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/jembossctl.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/libgen.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/libscan.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/lindna.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/listor.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/marscan.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/maskfeat.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/maskseq.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/matcher.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/matgen3d.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/megamerger.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/meme.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/merger.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/msbar.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/mse.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/mwcontam.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/mwfilter.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/myseq.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/nawalign.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/nawalignrunner.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/needle.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/needlerunner.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/newcpgreport.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/newcpgseek.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/newseq.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/noreturn.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/notseq.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/nthseq.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/octanol.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/oddcomp.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/palindrome.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/pasteseq.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/patmatdb.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/patmatmotifs.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/pdbparse.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/pdbplus.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/pdbtosp.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/pepcoil.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/pepinfo.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/pepnet.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/pepstats.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/pepwheel.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/pepwindow.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/pepwindowall.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/plotcon.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/plotorf.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/polydot.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/preg.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/prettyplot.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/prettyseq.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/primersearch.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/printsextract.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/profit.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/prophecy.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/prophet.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/prosextract.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/pscan.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/psiphi.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/rebaseextract.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/recoder.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/redata.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/remap.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/restover.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/restrict.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/revseq.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/rocon.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/rocplot.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/scope.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/scopparse.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/scorecmapdir.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/scorer.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/scorerrunner.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/seealso.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/seqalign.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/seqfraggle.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/seqmatchall.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/seqnr.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/seqret.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/seqretsplit.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/seqsearch.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/seqsort.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/seqwords.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/showalign.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/showdb.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/showfeat.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/showorf.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/showseq.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/shuffleseq.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/sigcleave.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/siggen.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/siggenlig.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/sigscan.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/sigscanlig.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/silent.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/sirna.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/SITE-DIRECTED.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/sites.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/sixpack.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/skipseq.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/splitter.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/ssematch.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/stretcher.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/stssearch.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/substitute.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/substituterunner.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/supermatcher.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/syco.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/tcode.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/textsearch.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/tfextract.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/tfm.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/tfscan.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/tmap.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/topo.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/tranalign.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/transeq.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/trimest.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/trimseq.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/twofeat.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/union.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/vectorstrip.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/water.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/whichdb.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/wobble.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/wordcount.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/wordmatch.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/wossname.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/yank.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/aaindexextract.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/abiview.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/acdc.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/acdlog.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/acdpretty.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/acdtable.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/cai.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/acdtrace.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/acdvalid.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/alignrunner.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/allversusall.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/antigenic.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/backtranseq.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/banana.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/biosed.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/btwisted.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/cathparse.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/chaos.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/charge.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/checktrans.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/chips.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/cirdna.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/codcmp.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/codcopy.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/coderet.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/comparator.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/complex.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/compseq.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/cons.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/contactalign.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/contacts.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/cpgplot.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/cpgreport.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/crystalball.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/cusp.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/cutgextract.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/cutseq.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/dan.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/dbiblast.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/dbifasta.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/dbiflat.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/dbigcg.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/dbxfasta.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/dbxflat.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/dbxgcg.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/degapseq.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/degapseqrunner.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/descseq.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/diffseq.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/digest.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/distmat.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/domainalign.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/domainer.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/domainnr.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/domainrep.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/domainreso.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/domainseqs.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/domainsse.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/dotmatcher.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/dotpath.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/dottup.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/dreg.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/ealistat.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/eclique.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/econsense.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/econtml.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/econtrast.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/ednacomp.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/ednadist.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/ednainvar.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/ednaml.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/ednamlk.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/ednapars.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/ednapenny.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/edollop.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/iep.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/edolpenny.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/efactor.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/efitch.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/egendist.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/ehmmalign.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/ehmmbuild.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/ehmmcalibrate.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/ehmmconvert.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/ehmmemit.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/ehmmfetch.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/ehmmindex.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/ehmmpfam.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/ehmmsearch.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/einverted.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/ekitsch.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/embossdata.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/embossversion.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/emix.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/emma.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/emnu.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/emowse.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/eneighbor.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/entret.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/epenny.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/epestfind.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/eprimer3.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/eprotdist.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/eprotpars.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/equicktandem.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/erestml.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/eseqboot.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/esim4.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/est2genome.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/etandem.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/extractfeat.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/extractseq.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/fclique.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/fconsense.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/fcontml.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/fcontrast.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/fdiscboot.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/fdnacomp.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/fdnadist.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/fdnainvar.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/fdnaml.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/fdnamlk.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/fdnamove.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/fdnapars.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/fdnapenny.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/fdollop.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/fdolmove.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/fdolpenny.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/fdrawgram.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/fdrawtree.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/ffactor.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/ffitch.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/ffreqboot.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/fgendist.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/findkm.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/fkitsch.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/fmix.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/fmove.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/fneighbor.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/fpars.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/fpenny.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/fproml.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/fpromlk.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/fprotdist.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/fprotpars.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/freak.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/frestboot.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/frestdist.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/frestml.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/fretree.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/fseqboot.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/fseqbootall.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/ftreedist.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/ftreedistpair.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/fuzznuc.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/fuzzpro.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/fuzztran.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/garnier.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/geecee.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/getorf.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/helixturnhelix.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/hetparse.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/hmoment.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/infoalign.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/infoseq.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/interface.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/isochore.txt
+%%PORTDOCS%%%%DOCSDIR%%/tutorials/emboss-gcg.ppt
+%%PORTDOCS%%%%DOCSDIR%%/tutorials/emboss-interfaces.ppt
+%%PORTDOCS%%%%DOCSDIR%%/tutorials/emboss-talk.ppt
+%%PORTDOCS%%%%DOCSDIR%%/tutorials/emboss_tut.tar.gz
+%%DATADIR%%/plstnd5.fnt
+%%DATADIR%%/plxtnd5.fnt
+%%DATADIR%%/acd/needle.acd
+%%DATADIR%%/acd/newcoils.acd
+%%DATADIR%%/acd/newcpgreport.acd
+%%DATADIR%%/acd/newcpgseek.acd
+%%DATADIR%%/acd/newseq.acd
+%%DATADIR%%/acd/noreturn.acd
+%%DATADIR%%/acd/notseq.acd
+%%DATADIR%%/acd/nthseq.acd
+%%DATADIR%%/acd/octanol.acd
+%%DATADIR%%/acd/oddcomp.acd
+%%DATADIR%%/acd/palindrome.acd
+%%DATADIR%%/acd/pasteseq.acd
+%%DATADIR%%/acd/patmatdb.acd
+%%DATADIR%%/acd/patmatmotifs.acd
+%%DATADIR%%/acd/patmattest.acd
+%%DATADIR%%/acd/pepcoil.acd
+%%DATADIR%%/acd/pepinfo.acd
+%%DATADIR%%/acd/pepnet.acd
+%%DATADIR%%/acd/pepstats.acd
+%%DATADIR%%/acd/pepwheel.acd
+%%DATADIR%%/acd/pepwindow.acd
+%%DATADIR%%/acd/pepwindowall.acd
+%%DATADIR%%/acd/plotcon.acd
+%%DATADIR%%/acd/plotorf.acd
+%%DATADIR%%/acd/polydot.acd
+%%DATADIR%%/acd/preg.acd
+%%DATADIR%%/acd/prettyplot.acd
+%%DATADIR%%/acd/prettyseq.acd
+%%DATADIR%%/acd/prima.acd
+%%DATADIR%%/acd/primers.acd
+%%DATADIR%%/acd/primersearch.acd
+%%DATADIR%%/acd/printsextract.acd
+%%DATADIR%%/acd/profit.acd
+%%DATADIR%%/acd/prophecy.acd
+%%DATADIR%%/acd/prophet.acd
+%%DATADIR%%/acd/prosextract.acd
+%%DATADIR%%/acd/pscan.acd
+%%DATADIR%%/acd/psiphi.acd
+%%DATADIR%%/acd/rebaseextract.acd
+%%DATADIR%%/acd/recoder.acd
+%%DATADIR%%/acd/redata.acd
+%%DATADIR%%/acd/remap.acd
+%%DATADIR%%/acd/restover.acd
+%%DATADIR%%/acd/revseq.acd
+%%DATADIR%%/acd/restrict.acd
+%%DATADIR%%/acd/seealso.acd
+%%DATADIR%%/acd/seqinfo.acd
+%%DATADIR%%/acd/seqmatchall.acd
+%%DATADIR%%/acd/seqret.acd
+%%DATADIR%%/acd/seqretall.acd
+%%DATADIR%%/acd/seqretallfeat.acd
+%%DATADIR%%/acd/seqretset.acd
+%%DATADIR%%/acd/seqretsingle.acd
+%%DATADIR%%/acd/seqretsplit.acd
+%%DATADIR%%/acd/seqrettype.acd
+%%DATADIR%%/acd/showalign.acd
+%%DATADIR%%/acd/showdb.acd
+%%DATADIR%%/acd/showfeat.acd
+%%DATADIR%%/acd/showorf.acd
+%%DATADIR%%/acd/showseq.acd
+%%DATADIR%%/acd/shuffleseq.acd
+%%DATADIR%%/acd/sigcleave.acd
+%%DATADIR%%/acd/silent.acd
+%%DATADIR%%/acd/sirna.acd
+%%DATADIR%%/acd/sixpack.acd
+%%DATADIR%%/acd/skipseq.acd
+%%DATADIR%%/acd/tfm.acd
+%%DATADIR%%/acd/splitter.acd
+%%DATADIR%%/acd/stretcher.acd
+%%DATADIR%%/acd/stssearch.acd
+%%DATADIR%%/acd/supermatcher.acd
+%%DATADIR%%/acd/syco.acd
+%%DATADIR%%/acd/tcode.acd
+%%DATADIR%%/acd/testplot.acd
+%%DATADIR%%/acd/textsearch.acd
+%%DATADIR%%/acd/tfextract.acd
+%%DATADIR%%/acd/tfscan.acd
+%%DATADIR%%/acd/tmap.acd
+%%DATADIR%%/acd/tranalign.acd
+%%DATADIR%%/acd/transeq.acd
+%%DATADIR%%/acd/treetypedisplay.acd
+%%DATADIR%%/acd/trimest.acd
+%%DATADIR%%/acd/trimseq.acd
+%%DATADIR%%/acd/twofeat.acd
+%%DATADIR%%/acd/union.acd
+%%DATADIR%%/acd/vectorstrip.acd
+%%DATADIR%%/acd/water.acd
+%%DATADIR%%/acd/whichdb.acd
+%%DATADIR%%/acd/wobble.acd
+%%DATADIR%%/acd/wordcount.acd
+%%DATADIR%%/acd/wordmatch.acd
+%%DATADIR%%/acd/wossname.acd
+%%DATADIR%%/acd/yank.acd
+%%DATADIR%%/acd/codes.english
+%%DATADIR%%/acd/groups.standard
+%%DATADIR%%/acd/knowntypes.standard
+%%DATADIR%%/acd/sections.standard
+%%DATADIR%%/acd/variables.standard
 %%DATADIR%%/acd/aaindexextract.acd
 %%DATADIR%%/acd/abiview.acd
 %%DATADIR%%/acd/acdc.acd
@@ -287,18 +1078,18 @@ lib/libplplot.so.5
 %%DATADIR%%/acd/ajtest.acd
 %%DATADIR%%/acd/antigenic.acd
 %%DATADIR%%/acd/backtranseq.acd
+%%DATADIR%%/acd/cai.acd
 %%DATADIR%%/acd/banana.acd
 %%DATADIR%%/acd/biosed.acd
 %%DATADIR%%/acd/btwisted.acd
-%%DATADIR%%/acd/cai.acd
 %%DATADIR%%/acd/chaos.acd
 %%DATADIR%%/acd/charge.acd
 %%DATADIR%%/acd/checktrans.acd
 %%DATADIR%%/acd/chips.acd
 %%DATADIR%%/acd/cirdna.acd
 %%DATADIR%%/acd/codcmp.acd
+%%DATADIR%%/acd/codcopy.acd
 %%DATADIR%%/acd/coderet.acd
-%%DATADIR%%/acd/codes.english
 %%DATADIR%%/acd/complex.acd
 %%DATADIR%%/acd/compseq.acd
 %%DATADIR%%/acd/cons.acd
@@ -313,6 +1104,9 @@ lib/libplplot.so.5
 %%DATADIR%%/acd/dbifasta.acd
 %%DATADIR%%/acd/dbiflat.acd
 %%DATADIR%%/acd/dbigcg.acd
+%%DATADIR%%/acd/dbxfasta.acd
+%%DATADIR%%/acd/dbxflat.acd
+%%DATADIR%%/acd/dbxgcg.acd
 %%DATADIR%%/acd/degapseq.acd
 %%DATADIR%%/acd/demoalign.acd
 %%DATADIR%%/acd/demofeatures.acd
@@ -331,6 +1125,7 @@ lib/libplplot.so.5
 %%DATADIR%%/acd/dreg.acd
 %%DATADIR%%/acd/einverted.acd
 %%DATADIR%%/acd/embossdata.acd
+%%DATADIR%%/acd/iep.acd
 %%DATADIR%%/acd/embossversion.acd
 %%DATADIR%%/acd/emma.acd
 %%DATADIR%%/acd/emowse.acd
@@ -352,18 +1147,15 @@ lib/libplplot.so.5
 %%DATADIR%%/acd/geecee.acd
 %%DATADIR%%/acd/getorf.acd
 %%DATADIR%%/acd/giep.acd
-%%DATADIR%%/acd/groups.standard
 %%DATADIR%%/acd/helixturnhelix.acd
-%%DATADIR%%/acd/histogramtest.acd
 %%DATADIR%%/acd/hmoment.acd
-%%DATADIR%%/acd/iep.acd
+%%DATADIR%%/acd/histogramtest.acd
 %%DATADIR%%/acd/infoalign.acd
 %%DATADIR%%/acd/infoseq.acd
 %%DATADIR%%/acd/intconv.acd
 %%DATADIR%%/acd/isochore.acd
 %%DATADIR%%/acd/kmrsplitter.acd
 %%DATADIR%%/acd/kmrunion.acd
-%%DATADIR%%/acd/knowntypes.standard
 %%DATADIR%%/acd/lindna.acd
 %%DATADIR%%/acd/listor.acd
 %%DATADIR%%/acd/marscan.acd
@@ -375,107 +1167,120 @@ lib/libplplot.so.5
 %%DATADIR%%/acd/msbar.acd
 %%DATADIR%%/acd/mwcontam.acd
 %%DATADIR%%/acd/mwfilter.acd
-%%DATADIR%%/acd/needle.acd
-%%DATADIR%%/acd/newcoils.acd
-%%DATADIR%%/acd/newcpgreport.acd
-%%DATADIR%%/acd/newcpgseek.acd
-%%DATADIR%%/acd/newseq.acd
-%%DATADIR%%/acd/noreturn.acd
-%%DATADIR%%/acd/notseq.acd
-%%DATADIR%%/acd/nthseq.acd
-%%DATADIR%%/acd/octanol.acd
-%%DATADIR%%/acd/oddcomp.acd
-%%DATADIR%%/acd/palindrome.acd
-%%DATADIR%%/acd/pasteseq.acd
-%%DATADIR%%/acd/patmatdb.acd
-%%DATADIR%%/acd/patmatmotifs.acd
-%%DATADIR%%/acd/patmattest.acd
-%%DATADIR%%/acd/pepcoil.acd
-%%DATADIR%%/acd/pepinfo.acd
-%%DATADIR%%/acd/pepnet.acd
-%%DATADIR%%/acd/pepstats.acd
-%%DATADIR%%/acd/pepwheel.acd
-%%DATADIR%%/acd/pepwindow.acd
-%%DATADIR%%/acd/pepwindowall.acd
-%%DATADIR%%/acd/plotcon.acd
-%%DATADIR%%/acd/plotorf.acd
-%%DATADIR%%/acd/polydot.acd
-%%DATADIR%%/acd/preg.acd
-%%DATADIR%%/acd/prettyplot.acd
-%%DATADIR%%/acd/prettyseq.acd
-%%DATADIR%%/acd/prima.acd
-%%DATADIR%%/acd/primers.acd
-%%DATADIR%%/acd/primersearch.acd
-%%DATADIR%%/acd/printsextract.acd
-%%DATADIR%%/acd/profit.acd
-%%DATADIR%%/acd/prophecy.acd
-%%DATADIR%%/acd/prophet.acd
-%%DATADIR%%/acd/prosextract.acd
-%%DATADIR%%/acd/pscan.acd
-%%DATADIR%%/acd/psiphi.acd
-%%DATADIR%%/acd/rebaseextract.acd
-%%DATADIR%%/acd/recoder.acd
-%%DATADIR%%/acd/redata.acd
-%%DATADIR%%/acd/remap.acd
-%%DATADIR%%/acd/restover.acd
-%%DATADIR%%/acd/restrict.acd
-%%DATADIR%%/acd/revseq.acd
-%%DATADIR%%/acd/sections.standard
-%%DATADIR%%/acd/seealso.acd
-%%DATADIR%%/acd/seqinfo.acd
-%%DATADIR%%/acd/seqmatchall.acd
-%%DATADIR%%/acd/seqret.acd
-%%DATADIR%%/acd/seqretall.acd
-%%DATADIR%%/acd/seqretallfeat.acd
-%%DATADIR%%/acd/seqretset.acd
-%%DATADIR%%/acd/seqretsingle.acd
-%%DATADIR%%/acd/seqretsplit.acd
-%%DATADIR%%/acd/seqrettype.acd
-%%DATADIR%%/acd/showalign.acd
-%%DATADIR%%/acd/showdb.acd
-%%DATADIR%%/acd/showfeat.acd
-%%DATADIR%%/acd/showorf.acd
-%%DATADIR%%/acd/showseq.acd
-%%DATADIR%%/acd/shuffleseq.acd
-%%DATADIR%%/acd/sigcleave.acd
-%%DATADIR%%/acd/silent.acd
-%%DATADIR%%/acd/sirna.acd
-%%DATADIR%%/acd/sixpack.acd
-%%DATADIR%%/acd/skipseq.acd
-%%DATADIR%%/acd/splitter.acd
-%%DATADIR%%/acd/stretcher.acd
-%%DATADIR%%/acd/stssearch.acd
-%%DATADIR%%/acd/supermatcher.acd
-%%DATADIR%%/acd/syco.acd
-%%DATADIR%%/acd/tcode.acd
-%%DATADIR%%/acd/testplot.acd
-%%DATADIR%%/acd/textsearch.acd
-%%DATADIR%%/acd/tfextract.acd
-%%DATADIR%%/acd/tfm.acd
-%%DATADIR%%/acd/tfscan.acd
-%%DATADIR%%/acd/tmap.acd
-%%DATADIR%%/acd/tranalign.acd
-%%DATADIR%%/acd/transeq.acd
-%%DATADIR%%/acd/treetypedisplay.acd
-%%DATADIR%%/acd/trimest.acd
-%%DATADIR%%/acd/trimseq.acd
-%%DATADIR%%/acd/twofeat.acd
-%%DATADIR%%/acd/union.acd
-%%DATADIR%%/acd/variables.standard
-%%DATADIR%%/acd/vectorstrip.acd
-%%DATADIR%%/acd/water.acd
-%%DATADIR%%/acd/whichdb.acd
-%%DATADIR%%/acd/wobble.acd
-%%DATADIR%%/acd/wordcount.acd
-%%DATADIR%%/acd/wordmatch.acd
-%%DATADIR%%/acd/wossname.acd
-%%DATADIR%%/acd/yank.acd
 %%DATADIR%%/data/AAINDEX/dummyfile
+%%DATADIR%%/data/CODONS/Cut.index
+%%DATADIR%%/data/CODONS/Eacica.cut
+%%DATADIR%%/data/CODONS/Eagrtu.cut
+%%DATADIR%%/data/CODONS/Eanasp.cut
+%%DATADIR%%/data/CODONS/Earath.cut
+%%DATADIR%%/data/CODONS/Eazovi.cut
+%%DATADIR%%/data/CODONS/Ebacme.cut
+%%DATADIR%%/data/CODONS/Ebacst.cut
+%%DATADIR%%/data/CODONS/Ebacsu.cut
+%%DATADIR%%/data/CODONS/Ebacsu_high.cut
+%%DATADIR%%/data/CODONS/Ebommo.cut
+%%DATADIR%%/data/CODONS/Ebovin.cut
+%%DATADIR%%/data/CODONS/Ebpphx.cut
+%%DATADIR%%/data/CODONS/Ebraja.cut
+%%DATADIR%%/data/CODONS/Ebrana.cut
+%%DATADIR%%/data/CODONS/Ebrare.cut
+%%DATADIR%%/data/CODONS/Ecaeel.cut
+%%DATADIR%%/data/CODONS/Ecanal.cut
+%%DATADIR%%/data/CODONS/Ecanfa.cut
+%%DATADIR%%/data/CODONS/Ecaucr.cut
+%%DATADIR%%/data/CODONS/Echick.cut
+%%DATADIR%%/data/CODONS/Echlre.cut
+%%DATADIR%%/data/CODONS/Echltr.cut
+%%DATADIR%%/data/CODONS/Ecloab.cut
+%%DATADIR%%/data/CODONS/Ecrigr.cut
+%%DATADIR%%/data/CODONS/Ecyapa.cut
+%%DATADIR%%/data/CODONS/Edayhoff.cut
+%%DATADIR%%/data/CODONS/Edicdi.cut
+%%DATADIR%%/data/CODONS/Edicdi_high.cut
+%%DATADIR%%/data/CODONS/Edrome.cut
+%%DATADIR%%/data/CODONS/Edrome_high.cut
+%%DATADIR%%/data/CODONS/Eecoli.cut
+%%DATADIR%%/data/CODONS/Eecoli_high.cut
+%%DATADIR%%/data/CODONS/Eemeni.cut
+%%DATADIR%%/data/CODONS/Eemeni_mit.cut
+%%DATADIR%%/data/CODONS/Eemeni_high.cut
+%%DATADIR%%/data/CODONS/Eerwct.cut
+%%DATADIR%%/data/CODONS/Ehaein.cut
+%%DATADIR%%/data/CODONS/Ehalma.cut
+%%DATADIR%%/data/CODONS/Ehalsa.cut
+%%DATADIR%%/data/CODONS/Ehorvu.cut
+%%DATADIR%%/data/CODONS/Ehuman.cut
+%%DATADIR%%/data/CODONS/Eklepn.cut
+%%DATADIR%%/data/CODONS/Eklula.cut
+%%DATADIR%%/data/CODONS/Elacdl.cut
+%%DATADIR%%/data/CODONS/Elyces.cut
+%%DATADIR%%/data/CODONS/Emacfa.cut
+%%DATADIR%%/data/CODONS/Emaize.cut
+%%DATADIR%%/data/CODONS/Emaize_chl.cut
+%%DATADIR%%/data/CODONS/Emammal_high.cut
+%%DATADIR%%/data/CODONS/Emanse.cut
+%%DATADIR%%/data/CODONS/Emarpo_chl.cut
+%%DATADIR%%/data/CODONS/Emedsa.cut
+%%DATADIR%%/data/CODONS/Emetth.cut
+%%DATADIR%%/data/CODONS/Emouse.cut
+%%DATADIR%%/data/CODONS/Emyctu.cut
+%%DATADIR%%/data/CODONS/Eneigo.cut
+%%DATADIR%%/data/CODONS/Eneucr.cut
+%%DATADIR%%/data/CODONS/Eoncmy.cut
+%%DATADIR%%/data/CODONS/Eorysa.cut
+%%DATADIR%%/data/CODONS/Eorysa_chl.cut
+%%DATADIR%%/data/CODONS/Epea.cut
+%%DATADIR%%/data/CODONS/Epethy.cut
+%%DATADIR%%/data/CODONS/Ephavu.cut
+%%DATADIR%%/data/CODONS/Epig.cut
+%%DATADIR%%/data/CODONS/Eplafa.cut
+%%DATADIR%%/data/CODONS/Eprovu.cut
+%%DATADIR%%/data/CODONS/Epseae.cut
+%%DATADIR%%/data/CODONS/Epsepu.cut
+%%DATADIR%%/data/CODONS/Epsesm.cut
+%%DATADIR%%/data/CODONS/Erabit.cut
+%%DATADIR%%/data/CODONS/Erat.cut
+%%DATADIR%%/data/CODONS/Erhile.cut
+%%DATADIR%%/data/CODONS/Erhime.cut
+%%DATADIR%%/data/CODONS/Erhoca.cut
+%%DATADIR%%/data/CODONS/Erhosh.cut
+%%DATADIR%%/data/CODONS/Esalsa.cut
+%%DATADIR%%/data/CODONS/Esalty.cut
+%%DATADIR%%/data/CODONS/Eschma.cut
+%%DATADIR%%/data/CODONS/Eschpo.cut
+%%DATADIR%%/data/CODONS/Eschpo_cai.cut
+%%DATADIR%%/data/CODONS/Eschpo_high.cut
+%%DATADIR%%/data/CODONS/Eserma.cut
+%%DATADIR%%/data/CODONS/Esheep.cut
+%%DATADIR%%/data/CODONS/Esoltu.cut
+%%DATADIR%%/data/CODONS/Esoybn.cut
+%%DATADIR%%/data/CODONS/Espiol.cut
+%%DATADIR%%/data/CODONS/Estaau.cut
+%%DATADIR%%/data/CODONS/Estrco.cut
+%%DATADIR%%/data/CODONS/Estrmu.cut
+%%DATADIR%%/data/CODONS/Estrpn.cut
+%%DATADIR%%/data/CODONS/Estrpu.cut
+%%DATADIR%%/data/CODONS/Esyncy.cut
+%%DATADIR%%/data/CODONS/Esynco.cut
+%%DATADIR%%/data/CODONS/Etetth.cut
+%%DATADIR%%/data/CODONS/Etheth.cut
+%%DATADIR%%/data/CODONS/Etobac.cut
+%%DATADIR%%/data/CODONS/Etobac_chl.cut
+%%DATADIR%%/data/CODONS/Etrybr.cut
+%%DATADIR%%/data/CODONS/Etrycr.cut
+%%DATADIR%%/data/CODONS/Evibch.cut
+%%DATADIR%%/data/CODONS/Ewheat.cut
+%%DATADIR%%/data/CODONS/Exenla.cut
+%%DATADIR%%/data/CODONS/Eyeast.cut
+%%DATADIR%%/data/CODONS/Eyeast_cai.cut
+%%DATADIR%%/data/CODONS/Eyeast_high.cut
+%%DATADIR%%/data/CODONS/Eyeast_mit.cut
+%%DATADIR%%/data/CODONS/Eyeren.cut
+%%DATADIR%%/data/CODONS/Eyerpe.cut
 %%DATADIR%%/data/CODONS/Eacc.cut
 %%DATADIR%%/data/CODONS/Eadenovirus5.cut
 %%DATADIR%%/data/CODONS/Eadenovirus7.cut
 %%DATADIR%%/data/CODONS/Eaidlav.cut
-%%DATADIR%%/data/CODONS/Eanasp.cut
 %%DATADIR%%/data/CODONS/Eani.cut
 %%DATADIR%%/data/CODONS/Eani_h.cut
 %%DATADIR%%/data/CODONS/Eanidmit.cut
@@ -483,6 +1288,7 @@ lib/libplplot.so.5
 %%DATADIR%%/data/CODONS/Eath.cut
 %%DATADIR%%/data/CODONS/Eatu.cut
 %%DATADIR%%/data/CODONS/Eavi.cut
+%%DATADIR%%/data/CODONS/Ef1.cut
 %%DATADIR%%/data/CODONS/Ebja.cut
 %%DATADIR%%/data/CODONS/Ebly.cut
 %%DATADIR%%/data/CODONS/Ebme.cut
@@ -510,7 +1316,6 @@ lib/libplplot.so.5
 %%DATADIR%%/data/CODONS/Ecre.cut
 %%DATADIR%%/data/CODONS/Ecrisp.cut
 %%DATADIR%%/data/CODONS/Ectr.cut
-%%DATADIR%%/data/CODONS/Edayhoff.cut
 %%DATADIR%%/data/CODONS/Eddi.cut
 %%DATADIR%%/data/CODONS/Eddi_h.cut
 %%DATADIR%%/data/CODONS/Edog.cut
@@ -520,8 +1325,6 @@ lib/libplplot.so.5
 %%DATADIR%%/data/CODONS/Eeca.cut
 %%DATADIR%%/data/CODONS/Eeco.cut
 %%DATADIR%%/data/CODONS/Eeco_h.cut
-%%DATADIR%%/data/CODONS/Eecoli.cut
-%%DATADIR%%/data/CODONS/Ef1.cut
 %%DATADIR%%/data/CODONS/Efish.cut
 %%DATADIR%%/data/CODONS/Efmdvpolyp.cut
 %%DATADIR%%/data/CODONS/Eham.cut
@@ -529,15 +1332,12 @@ lib/libplplot.so.5
 %%DATADIR%%/data/CODONS/Ehin.cut
 %%DATADIR%%/data/CODONS/Ehma.cut
 %%DATADIR%%/data/CODONS/Ehum.cut
-%%DATADIR%%/data/CODONS/Ehuman.cut
 %%DATADIR%%/data/CODONS/Ekla.cut
 %%DATADIR%%/data/CODONS/Ekpn.cut
 %%DATADIR%%/data/CODONS/Ella.cut
 %%DATADIR%%/data/CODONS/Emac.cut
-%%DATADIR%%/data/CODONS/Emaize.cut
 %%DATADIR%%/data/CODONS/Emam_h.cut
 %%DATADIR%%/data/CODONS/Emixlg.cut
-%%DATADIR%%/data/CODONS/Emouse.cut
 %%DATADIR%%/data/CODONS/Emsa.cut
 %%DATADIR%%/data/CODONS/Emse.cut
 %%DATADIR%%/data/CODONS/Emta.cut
@@ -552,13 +1352,11 @@ lib/libplplot.so.5
 %%DATADIR%%/data/CODONS/Engo.cut
 %%DATADIR%%/data/CODONS/Eoncsp.cut
 %%DATADIR%%/data/CODONS/Epae.cut
-%%DATADIR%%/data/CODONS/Epea.cut
 %%DATADIR%%/data/CODONS/Epet.cut
 %%DATADIR%%/data/CODONS/Epfa.cut
 %%DATADIR%%/data/CODONS/Ephix174.cut
 %%DATADIR%%/data/CODONS/Ephv.cut
 %%DATADIR%%/data/CODONS/Ephy.cut
-%%DATADIR%%/data/CODONS/Epig.cut
 %%DATADIR%%/data/CODONS/Epolyomaa2.cut
 %%DATADIR%%/data/CODONS/Epombe.cut
 %%DATADIR%%/data/CODONS/Epombecai.cut
@@ -570,7 +1368,6 @@ lib/libplplot.so.5
 %%DATADIR%%/data/CODONS/Erab.cut
 %%DATADIR%%/data/CODONS/Erabbit.cut
 %%DATADIR%%/data/CODONS/Erabsp.cut
-%%DATADIR%%/data/CODONS/Erat.cut
 %%DATADIR%%/data/CODONS/Eratsp.cut
 %%DATADIR%%/data/CODONS/Erca.cut
 %%DATADIR%%/data/CODONS/Erhm.cut
@@ -613,7 +1410,6 @@ lib/libplplot.so.5
 %%DATADIR%%/data/CODONS/Ewht.cut
 %%DATADIR%%/data/CODONS/Exel.cut
 %%DATADIR%%/data/CODONS/Exenopus.cut
-%%DATADIR%%/data/CODONS/Eyeast.cut
 %%DATADIR%%/data/CODONS/Eyeastcai.cut
 %%DATADIR%%/data/CODONS/Eyen.cut
 %%DATADIR%%/data/CODONS/Eysc.cut
@@ -622,6 +1418,9 @@ lib/libplplot.so.5
 %%DATADIR%%/data/CODONS/Eysp.cut
 %%DATADIR%%/data/CODONS/Ezebrafish.cut
 %%DATADIR%%/data/CODONS/Ezma.cut
+%%DATADIR%%/data/REBASE/dummyfile
+%%DATADIR%%/data/PRINTS/dummyfile
+%%DATADIR%%/data/PROSITE/dummyfile
 %%DATADIR%%/data/EBLOSUM30
 %%DATADIR%%/data/EBLOSUM35
 %%DATADIR%%/data/EBLOSUM40
@@ -658,6 +1457,8 @@ lib/libplplot.so.5
 %%DATADIR%%/data/EGC.5
 %%DATADIR%%/data/EGC.6
 %%DATADIR%%/data/EGC.9
+%%DATADIR%%/data/EGC.index
+%%DATADIR%%/data/EGC.txt
 %%DATADIR%%/data/ENUC.4.2
 %%DATADIR%%/data/ENUC.4.4
 %%DATADIR%%/data/EPAM10
@@ -732,10 +1533,7 @@ lib/libplplot.so.5
 %%DATADIR%%/data/Ehet.dat
 %%DATADIR%%/data/Ehth.dat
 %%DATADIR%%/data/Ehth87.dat
-%%DATADIR%%/data/Emass.dat
-%%DATADIR%%/data/Emassmod.dat
 %%DATADIR%%/data/Ememe.dat
-%%DATADIR%%/data/Emwfilter.dat
 %%DATADIR%%/data/Enakai.dat
 %%DATADIR%%/data/Epepcoil.dat
 %%DATADIR%%/data/Epk.dat
@@ -754,38 +1552,215 @@ lib/libplplot.so.5
 %%DATADIR%%/data/Etcode.dat
 %%DATADIR%%/data/Evdw.dat
 %%DATADIR%%/data/Ewhite-wimley.dat
-%%DATADIR%%/data/PRINTS/dummyfile
-%%DATADIR%%/data/PROSITE/dummyfile
-%%DATADIR%%/data/REBASE/dummyfile
 %%DATADIR%%/data/embossre.equ
+%%DATADIR%%/data/Emwfilter.dat
+%%DATADIR%%/data/Emass.dat
+%%DATADIR%%/data/Emassmod.dat
+%%DATADIR%%/data/Matrices.nucleotide
+%%DATADIR%%/data/Matrices.protein
+%%DATADIR%%/data/Matrices.proteinstructure
 %%DATADIR%%/emboss.default.template
-%%DATADIR%%/jemboss/LICENSE
-%%DATADIR%%/jemboss/README
-%%DATADIR%%/jemboss/api/allclasses-frame.html
-%%DATADIR%%/jemboss/api/deprecated-list.html
-%%DATADIR%%/jemboss/api/getClasses.pl
-%%DATADIR%%/jemboss/api/help-doc.html
-%%DATADIR%%/jemboss/api/index-all.html
-%%DATADIR%%/jemboss/api/index.html
-%%DATADIR%%/jemboss/api/makeDocs.csh
-%%DATADIR%%/jemboss/api/org/emboss/jemboss/Jemboss.html
-%%DATADIR%%/jemboss/api/org/emboss/jemboss/Jemboss.winExit.html
-%%DATADIR%%/jemboss/api/org/emboss/jemboss/JembossLogo.html
-%%DATADIR%%/jemboss/api/org/emboss/jemboss/JembossParams.html
-%%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/BuildProgramMenu.html
-%%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/ResultsMenuBar.html
-%%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/SetUpMenuBar.html
-%%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/ShowResultSet.html
-%%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/ShowSavedResults.html
-%%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/SwingWorker.html
+%%DATADIR%%/test/data/aaindex1.test
+%%DATADIR%%/test/data/prosite.dat
+%%DATADIR%%/test/data/prosite.doc
+%%DATADIR%%/test/data/prints.test
+%%DATADIR%%/test/data/withrefm
+%%DATADIR%%/test/data/site.dat
+%%DATADIR%%/test/data/cutg.codon
+%%DATADIR%%/test/data/dna.acedb
+%%DATADIR%%/test/data/dna.aln
+%%DATADIR%%/test/data/dna.asn1
+%%DATADIR%%/test/data/dna.codata
+%%DATADIR%%/test/data/dna.embl
+%%DATADIR%%/test/data/dna.fasta
+%%DATADIR%%/test/data/dna.fitch
+%%DATADIR%%/test/data/dna.gcg
+%%DATADIR%%/test/data/dna.gcg8
+%%DATADIR%%/test/data/dna.genbank
+%%DATADIR%%/test/data/dna.ig
+%%DATADIR%%/test/data/dna.m-acedb
+%%DATADIR%%/test/data/dna.m-codata
+%%DATADIR%%/test/data/dna.m-embl
+%%DATADIR%%/test/data/dna.m-fasta
+%%DATADIR%%/test/data/dna.m-fasta-long
+%%DATADIR%%/test/data/dna.m-ncbi
+%%DATADIR%%/test/data/dna.m-strider
+%%DATADIR%%/test/data/dna.msf
+%%DATADIR%%/test/data/dna.msf8
+%%DATADIR%%/test/data/dna.ncbi
+%%DATADIR%%/test/data/dna.phylip
+%%DATADIR%%/test/data/dna.phylip3
+%%DATADIR%%/test/data/dna.staden
+%%DATADIR%%/test/data/dna.strider
+%%DATADIR%%/test/data/dna.text
+%%DATADIR%%/test/data/feat.emft
+%%DATADIR%%/test/data/feat.fasta
+%%DATADIR%%/test/data/feat.pir
+%%DATADIR%%/test/data/mw1.dat
+%%DATADIR%%/test/data/mw2.dat
+%%DATADIR%%/test/data/mw3.dat
+%%DATADIR%%/test/data/paamir.pep
+%%DATADIR%%/test/data/pax6_cdna.fasta
+%%DATADIR%%/test/data/prot.acedb
+%%DATADIR%%/test/data/prot.codata
+%%DATADIR%%/test/data/prot.fasta
+%%DATADIR%%/test/data/prot.gcg
+%%DATADIR%%/test/data/prot.gcg8
+%%DATADIR%%/test/data/prot.ig
+%%DATADIR%%/test/data/prot.m-acedb
+%%DATADIR%%/test/data/prot.m-codata
+%%DATADIR%%/test/data/prot.m-fasta
+%%DATADIR%%/test/data/prot.m-nbrf
+%%DATADIR%%/test/data/prot.m-ncbi
+%%DATADIR%%/test/data/prot.m-swiss
+%%DATADIR%%/test/data/prot.nbrf
+%%DATADIR%%/test/data/prot.ncbi
+%%DATADIR%%/test/data/prot.swiss
+%%DATADIR%%/test/data/prot.text
+%%DATADIR%%/test/data/z83307.seq
+%%DATADIR%%/test/data/aligna.dna
+%%DATADIR%%/test/data/alignapart.dna
+%%DATADIR%%/test/data/alignb.dna
+%%DATADIR%%/test/data/aligna.prot
+%%DATADIR%%/test/data/alignapart.prot
+%%DATADIR%%/test/data/alignb.prot
+%%DATADIR%%/test/data/tranalign.pep
+%%DATADIR%%/test/data/tranalign.seq
+%%DATADIR%%/test/embl/acnum.hit
+%%DATADIR%%/test/embl/acnum.trg
+%%DATADIR%%/test/embl/division.lkp
+%%DATADIR%%/test/embl/entrynam.idx
+%%DATADIR%%/test/embl/seqvn.hit
+%%DATADIR%%/test/embl/seqvn.trg
+%%DATADIR%%/test/embl/des.hit
+%%DATADIR%%/test/embl/des.trg
+%%DATADIR%%/test/embl/keyword.hit
+%%DATADIR%%/test/embl/keyword.trg
+%%DATADIR%%/test/embl/taxon.hit
+%%DATADIR%%/test/embl/taxon.trg
+%%DATADIR%%/test/embl/est.dat
+%%DATADIR%%/test/embl/fun.dat
+%%DATADIR%%/test/embl/hum1.dat
+%%DATADIR%%/test/embl/inv.dat
+%%DATADIR%%/test/embl/pln.dat
+%%DATADIR%%/test/embl/pro.dat
+%%DATADIR%%/test/embl/rod.dat
+%%DATADIR%%/test/embl/sts.dat
+%%DATADIR%%/test/embl/vrl.dat
+%%DATADIR%%/test/embl/vrt.dat
+%%DATADIR%%/test/genbank/acnum.hit
+%%DATADIR%%/test/genbank/acnum.trg
+%%DATADIR%%/test/genbank/division.lkp
+%%DATADIR%%/test/genbank/entrynam.idx
+%%DATADIR%%/test/genbank/seqvn.hit
+%%DATADIR%%/test/genbank/seqvn.trg
+%%DATADIR%%/test/genbank/des.hit
+%%DATADIR%%/test/genbank/des.trg
+%%DATADIR%%/test/genbank/keyword.hit
+%%DATADIR%%/test/genbank/keyword.trg
+%%DATADIR%%/test/genbank/taxon.hit
+%%DATADIR%%/test/genbank/taxon.trg
+%%DATADIR%%/test/genbank/gbbct1.seq
+%%DATADIR%%/test/genbank/gbest1.seq
+%%DATADIR%%/test/genbank/gbinv1.seq
+%%DATADIR%%/test/genbank/gbpln1.seq
+%%DATADIR%%/test/genbank/gbpln2.seq
+%%DATADIR%%/test/genbank/gbpri1.seq
+%%DATADIR%%/test/genbank/gbrod1.seq
+%%DATADIR%%/test/genbank/gbsts1.seq
+%%DATADIR%%/test/genbank/gbvrl1.seq
+%%DATADIR%%/test/genbank/gbvrt.seq
+%%DATADIR%%/test/gb/acnum.hit
+%%DATADIR%%/test/gb/acnum.trg
+%%DATADIR%%/test/gb/division.lkp
+%%DATADIR%%/test/gb/entrynam.idx
+%%DATADIR%%/test/gb/seqvn.hit
+%%DATADIR%%/test/gb/seqvn.trg
+%%DATADIR%%/test/gb/des.hit
+%%DATADIR%%/test/gb/des.trg
+%%DATADIR%%/test/gb/keyword.hit
+%%DATADIR%%/test/gb/keyword.trg
+%%DATADIR%%/test/gb/taxon.hit
+%%DATADIR%%/test/gb/taxon.trg
+%%DATADIR%%/test/gb/ba.ref
+%%DATADIR%%/test/gb/ba.seq
+%%DATADIR%%/test/gb/htg.ref
+%%DATADIR%%/test/gb/htg.seq
+%%DATADIR%%/test/pir/acnum.hit
+%%DATADIR%%/test/pir/acnum.trg
+%%DATADIR%%/test/pir/division.lkp
+%%DATADIR%%/test/pir/entrynam.idx
+%%DATADIR%%/test/pir/des.hit
+%%DATADIR%%/test/pir/des.trg
+%%DATADIR%%/test/pir/keyword.hit
+%%DATADIR%%/test/pir/keyword.trg
+%%DATADIR%%/test/pir/taxon.hit
+%%DATADIR%%/test/pir/taxon.trg
+%%DATADIR%%/test/pir/pir1.header
+%%DATADIR%%/test/pir/pir1.names
+%%DATADIR%%/test/pir/pir1.numbers
+%%DATADIR%%/test/pir/pir1.offset
+%%DATADIR%%/test/pir/pir1.ref
+%%DATADIR%%/test/pir/pir1.seq
+%%DATADIR%%/test/pir/pir2.header
+%%DATADIR%%/test/pir/pir2.names
+%%DATADIR%%/test/pir/pir2.numbers
+%%DATADIR%%/test/pir/pir2.offset
+%%DATADIR%%/test/pir/pir2.ref
+%%DATADIR%%/test/pir/pir2.seq
+%%DATADIR%%/test/pir/pir3.header
+%%DATADIR%%/test/pir/pir3.names
+%%DATADIR%%/test/pir/pir3.numbers
+%%DATADIR%%/test/pir/pir3.offset
+%%DATADIR%%/test/pir/pir3.ref
+%%DATADIR%%/test/pir/pir3.seq
+%%DATADIR%%/test/pir/pir4.header
+%%DATADIR%%/test/pir/pir4.names
+%%DATADIR%%/test/pir/pir4.numbers
+%%DATADIR%%/test/pir/pir4.offset
+%%DATADIR%%/test/pir/pir4.ref
+%%DATADIR%%/test/pir/pir4.seq
+%%DATADIR%%/test/swiss/seq.dat
+%%DATADIR%%/test/swiss/acnum.hit
+%%DATADIR%%/test/swiss/acnum.trg
+%%DATADIR%%/test/swiss/division.lkp
+%%DATADIR%%/test/swiss/entrynam.idx
+%%DATADIR%%/test/swiss/seqvn.hit
+%%DATADIR%%/test/swiss/seqvn.trg
+%%DATADIR%%/test/swiss/des.hit
+%%DATADIR%%/test/swiss/des.trg
+%%DATADIR%%/test/swiss/keyword.hit
+%%DATADIR%%/test/swiss/keyword.trg
+%%DATADIR%%/test/swiss/taxon.hit
+%%DATADIR%%/test/swiss/taxon.trg
+%%DATADIR%%/test/swnew/acnum.hit
+%%DATADIR%%/test/swnew/acnum.trg
+%%DATADIR%%/test/swnew/division.lkp
+%%DATADIR%%/test/swnew/entrynam.idx
+%%DATADIR%%/test/swnew/seqvn.hit
+%%DATADIR%%/test/swnew/seqvn.trg
+%%DATADIR%%/test/swnew/des.hit
+%%DATADIR%%/test/swnew/des.trg
+%%DATADIR%%/test/swnew/keyword.hit
+%%DATADIR%%/test/swnew/keyword.trg
+%%DATADIR%%/test/swnew/taxon.hit
+%%DATADIR%%/test/swnew/taxon.trg
+%%DATADIR%%/test/swnew/new_seq.dat
+%%DATADIR%%/test/swnew/upd_ann.dat
+%%DATADIR%%/test/swnew/upd_seq.dat
+%%DATADIR%%/test/wormpep/wormpep
+%%DATADIR%%/test/wormpep/acnum.hit
+%%DATADIR%%/test/wormpep/acnum.trg
+%%DATADIR%%/test/wormpep/division.lkp
+%%DATADIR%%/test/wormpep/entrynam.idx
+%%DATADIR%%/test/wormpep/des.hit
+%%DATADIR%%/test/wormpep/des.trg
 %%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/filetree/DragTree.html
 %%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/filetree/FileEditorDisplay.PopupListener.html
 %%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/filetree/FileEditorDisplay.html
 %%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/filetree/FileNode.html
 %%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/filetree/FileSaving.html
 %%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/form/BuildJembossForm.html
-%%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/form/JembossComboPopup.html
-%%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/form/JembossComboPopup.myComboUI.html
 %%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/form/ListFilePanel.html
 %%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/form/SectionPanel.html
 %%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/form/SetInFileCard.html
@@ -795,6 +1770,8 @@ lib/libplplot.so.5
 %%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/form/TextFieldInt.WholeNumberDocument.html
 %%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/form/TextFieldInt.html
 %%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/form/TextFieldSink.html
+%%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/form/JembossComboPopup.html
+%%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/form/JembossComboPopup.myComboUI.html
 %%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/sequenceChooser/CutNPasteTextArea.html
 %%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/sequenceChooser/FileChooser.html
 %%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/sequenceChooser/InputSequenceAttributes.html
@@ -805,13 +1782,19 @@ lib/libplplot.so.5
 %%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/startup/ProgList.HorizontalMenu.html
 %%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/startup/ProgList.html
 %%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/startup/Splash.html
+%%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/BuildProgramMenu.html
+%%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/ResultsMenuBar.html
+%%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/SetUpMenuBar.html
+%%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/ShowResultSet.html
+%%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/ShowSavedResults.html
+%%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/SwingWorker.html
+%%DATADIR%%/jemboss/api/org/emboss/jemboss/parser/acd/ApplicationFields.html
+%%DATADIR%%/jemboss/api/org/emboss/jemboss/parser/acd/ApplicationParam.html
 %%DATADIR%%/jemboss/api/org/emboss/jemboss/parser/AcdFunResolve.html
 %%DATADIR%%/jemboss/api/org/emboss/jemboss/parser/AcdVarResolve.html
 %%DATADIR%%/jemboss/api/org/emboss/jemboss/parser/Ajax.html
 %%DATADIR%%/jemboss/api/org/emboss/jemboss/parser/Dependent.html
 %%DATADIR%%/jemboss/api/org/emboss/jemboss/parser/ParseAcd.html
-%%DATADIR%%/jemboss/api/org/emboss/jemboss/parser/acd/ApplicationFields.html
-%%DATADIR%%/jemboss/api/org/emboss/jemboss/parser/acd/ApplicationParam.html
 %%DATADIR%%/jemboss/api/org/emboss/jemboss/programs/JembossProcess.html
 %%DATADIR%%/jemboss/api/org/emboss/jemboss/programs/ListFile.html
 %%DATADIR%%/jemboss/api/org/emboss/jemboss/programs/ResultList.html
@@ -824,6 +1807,17 @@ lib/libplplot.so.5
 %%DATADIR%%/jemboss/api/org/emboss/jemboss/soap/PendingResults.html
 %%DATADIR%%/jemboss/api/org/emboss/jemboss/soap/PrivateRequest.html
 %%DATADIR%%/jemboss/api/org/emboss/jemboss/soap/ResListView.html
+%%DATADIR%%/jemboss/api/org/emboss/jemboss/Jemboss.html
+%%DATADIR%%/jemboss/api/org/emboss/jemboss/Jemboss.winExit.html
+%%DATADIR%%/jemboss/api/org/emboss/jemboss/JembossLogo.html
+%%DATADIR%%/jemboss/api/org/emboss/jemboss/JembossParams.html
+%%DATADIR%%/jemboss/api/allclasses-frame.html
+%%DATADIR%%/jemboss/api/deprecated-list.html
+%%DATADIR%%/jemboss/api/getClasses.pl
+%%DATADIR%%/jemboss/api/help-doc.html
+%%DATADIR%%/jemboss/api/index-all.html
+%%DATADIR%%/jemboss/api/index.html
+%%DATADIR%%/jemboss/api/makeDocs.csh
 %%DATADIR%%/jemboss/api/overview-tree.html
 %%DATADIR%%/jemboss/api/package-list
 %%DATADIR%%/jemboss/api/packages.html
@@ -839,9 +1833,6 @@ lib/libplplot.so.5
 %%DATADIR%%/jemboss/images/Job_manager_button.gif
 %%DATADIR%%/jemboss/images/Refresh_button.gif
 %%DATADIR%%/jemboss/images/Refresh_button2.gif
-%%DATADIR%%/jemboss/lib/JembossPrintAlignment.jar
-%%DATADIR%%/jemboss/lib/README
-%%DATADIR%%/jemboss/lib/activation.jar
 %%DATADIR%%/jemboss/lib/axis/axis-ant.jar
 %%DATADIR%%/jemboss/lib/axis/axis.jar
 %%DATADIR%%/jemboss/lib/axis/commons-discovery.jar
@@ -851,101 +1842,83 @@ lib/libplplot.so.5
 %%DATADIR%%/jemboss/lib/axis/saaj.jar
 %%DATADIR%%/jemboss/lib/axis/servlet.jar
 %%DATADIR%%/jemboss/lib/axis/wsdl4j.jar
-%%DATADIR%%/jemboss/lib/grout.jar
+%%DATADIR%%/jemboss/lib/README
+%%DATADIR%%/jemboss/lib/activation.jar
 %%DATADIR%%/jemboss/lib/jakarta-regexp-1.2.jar
-%%DATADIR%%/jemboss/lib/jalview.jar
 %%DATADIR%%/jemboss/lib/mail.jar
 %%DATADIR%%/jemboss/lib/xerces.jar
-%%DATADIR%%/jemboss/org/emboss/jemboss/Jemboss.java
-%%DATADIR%%/jemboss/org/emboss/jemboss/JembossJarUtil.java
-%%DATADIR%%/jemboss/org/emboss/jemboss/JembossLogo.java
-%%DATADIR%%/jemboss/org/emboss/jemboss/JembossParams.java
-%%DATADIR%%/jemboss/org/emboss/jemboss/draw/Block.java
-%%DATADIR%%/jemboss/org/emboss/jemboss/draw/DNADraw.java
-%%DATADIR%%/jemboss/org/emboss/jemboss/draw/EmbossCirdnaReader.java
-%%DATADIR%%/jemboss/org/emboss/jemboss/draw/GeneticMarker.java
-%%DATADIR%%/jemboss/org/emboss/jemboss/draw/LineAttribute.java
-%%DATADIR%%/jemboss/org/emboss/jemboss/draw/PrintDNAImage.java
-%%DATADIR%%/jemboss/org/emboss/jemboss/draw/RestrictionEnzyme.java
-%%DATADIR%%/jemboss/org/emboss/jemboss/draw/Ticks.java
-%%DATADIR%%/jemboss/org/emboss/jemboss/draw/Wizard.java
+%%DATADIR%%/jemboss/lib/jalview.jar
+%%DATADIR%%/jemboss/lib/JembossPrintAlignment.jar
+%%DATADIR%%/jemboss/lib/grout.jar
 %%DATADIR%%/jemboss/org/emboss/jemboss/editor/AlignApplet.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/editor/GroutSequenceJPanel.java
 %%DATADIR%%/jemboss/org/emboss/jemboss/editor/AlignJFrame.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/editor/Matrix.java
 %%DATADIR%%/jemboss/org/emboss/jemboss/editor/ColourJFrame.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/editor/MatrixJFrame.java
 %%DATADIR%%/jemboss/org/emboss/jemboss/editor/ColourMenu.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/editor/PatternJFrame.java
 %%DATADIR%%/jemboss/org/emboss/jemboss/editor/ColourPanel.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/editor/PlotConsensus.java
 %%DATADIR%%/jemboss/org/emboss/jemboss/editor/Consensus.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/editor/PrettyPlotJFrame.java
 %%DATADIR%%/jemboss/org/emboss/jemboss/editor/ConsensusOptions.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/editor/PrintAlignmentImage.java
 %%DATADIR%%/jemboss/org/emboss/jemboss/editor/GraphicSequenceCollection.java
-%%DATADIR%%/jemboss/org/emboss/jemboss/editor/GroutAlignJFrame.java
-%%DATADIR%%/jemboss/org/emboss/jemboss/editor/GroutAlignJFrameEvent.java
-%%DATADIR%%/jemboss/org/emboss/jemboss/editor/GroutAlignJFrameListener.java
-%%DATADIR%%/jemboss/org/emboss/jemboss/editor/GroutGraphicSequenceCollection.java
-%%DATADIR%%/jemboss/org/emboss/jemboss/editor/GroutGraphicSequenceCollectionEvent.java
-%%DATADIR%%/jemboss/org/emboss/jemboss/editor/GroutGraphicSequenceCollectionListener.java
-%%DATADIR%%/jemboss/org/emboss/jemboss/editor/GroutSequence.java
-%%DATADIR%%/jemboss/org/emboss/jemboss/editor/GroutSequenceJPanel.java
-%%DATADIR%%/jemboss/org/emboss/jemboss/editor/IDTableJFrame.java
-%%DATADIR%%/jemboss/org/emboss/jemboss/editor/Matrix.java
-%%DATADIR%%/jemboss/org/emboss/jemboss/editor/MatrixJFrame.java
-%%DATADIR%%/jemboss/org/emboss/jemboss/editor/Paste.java
-%%DATADIR%%/jemboss/org/emboss/jemboss/editor/PatternJFrame.java
-%%DATADIR%%/jemboss/org/emboss/jemboss/editor/PlotConsensus.java
-%%DATADIR%%/jemboss/org/emboss/jemboss/editor/PrettyPlotJFrame.java
 %%DATADIR%%/jemboss/org/emboss/jemboss/editor/PrintAlignment.java
-%%DATADIR%%/jemboss/org/emboss/jemboss/editor/PrintAlignmentImage.java
-%%DATADIR%%/jemboss/org/emboss/jemboss/editor/PrintableJTable.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/editor/Paste.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/editor/GroutAlignJFrameEvent.java
 %%DATADIR%%/jemboss/org/emboss/jemboss/editor/Sequence.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/editor/GroutAlignJFrame.java
 %%DATADIR%%/jemboss/org/emboss/jemboss/editor/SequenceJPanel.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/editor/GroutAlignJFrameListener.java
 %%DATADIR%%/jemboss/org/emboss/jemboss/editor/SequenceNameJButton.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/editor/GroutGraphicSequenceCollectionEvent.java
 %%DATADIR%%/jemboss/org/emboss/jemboss/editor/SequenceProperties.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/editor/GroutGraphicSequenceCollection.java
 %%DATADIR%%/jemboss/org/emboss/jemboss/editor/SequenceReader.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/editor/GroutGraphicSequenceCollectionListener.java
 %%DATADIR%%/jemboss/org/emboss/jemboss/editor/SequenceSaver.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/editor/GroutSequence.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/editor/IDTableJFrame.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/editor/PrintableJTable.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/draw/Block.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/draw/PrintDNAImage.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/draw/DNADraw.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/draw/RestrictionEnzyme.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/draw/EmbossCirdnaReader.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/draw/Ticks.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/draw/GeneticMarker.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/draw/Wizard.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/draw/LineAttribute.java
 %%DATADIR%%/jemboss/org/emboss/jemboss/graphics/Graph2DPlot.java
 %%DATADIR%%/jemboss/org/emboss/jemboss/graphics/PrintPlot.java
-%%DATADIR%%/jemboss/org/emboss/jemboss/gui/AdvancedOptions.java
-%%DATADIR%%/jemboss/org/emboss/jemboss/gui/Browser.java
-%%DATADIR%%/jemboss/org/emboss/jemboss/gui/BuildProgramMenu.java
-%%DATADIR%%/jemboss/org/emboss/jemboss/gui/Favorites.java
-%%DATADIR%%/jemboss/org/emboss/jemboss/gui/ImageIconJPanel.java
-%%DATADIR%%/jemboss/org/emboss/jemboss/gui/KeywordSearch.java
-%%DATADIR%%/jemboss/org/emboss/jemboss/gui/LaunchJalView.java
-%%DATADIR%%/jemboss/org/emboss/jemboss/gui/MemoryComboBox.java
-%%DATADIR%%/jemboss/org/emboss/jemboss/gui/ResultsMenuBar.java
-%%DATADIR%%/jemboss/org/emboss/jemboss/gui/ScrollPanel.java
-%%DATADIR%%/jemboss/org/emboss/jemboss/gui/SequenceData.java
-%%DATADIR%%/jemboss/org/emboss/jemboss/gui/SequenceList.java
-%%DATADIR%%/jemboss/org/emboss/jemboss/gui/SetUpMenuBar.java
-%%DATADIR%%/jemboss/org/emboss/jemboss/gui/ShowResultSet.java
-%%DATADIR%%/jemboss/org/emboss/jemboss/gui/ShowSavedResults.java
-%%DATADIR%%/jemboss/org/emboss/jemboss/gui/SplashThread.java
-%%DATADIR%%/jemboss/org/emboss/jemboss/gui/SwingWorker.java
 %%DATADIR%%/jemboss/org/emboss/jemboss/gui/filetree/DragTree.java
 %%DATADIR%%/jemboss/org/emboss/jemboss/gui/filetree/FileEditorDisplay.java
 %%DATADIR%%/jemboss/org/emboss/jemboss/gui/filetree/FileNode.java
 %%DATADIR%%/jemboss/org/emboss/jemboss/gui/filetree/FileSave.java
 %%DATADIR%%/jemboss/org/emboss/jemboss/gui/filetree/FileSaving.java
-%%DATADIR%%/jemboss/org/emboss/jemboss/gui/filetree/LocalAndRemoteFileTreeFrame.java
-%%DATADIR%%/jemboss/org/emboss/jemboss/gui/filetree/LocalTreeToolBar.java
 %%DATADIR%%/jemboss/org/emboss/jemboss/gui/filetree/RemoteDragTree.java
 %%DATADIR%%/jemboss/org/emboss/jemboss/gui/filetree/RemoteFileNode.java
 %%DATADIR%%/jemboss/org/emboss/jemboss/gui/filetree/RemoteFileTreePanel.java
-%%DATADIR%%/jemboss/org/emboss/jemboss/gui/form/AlignFormat.java
-%%DATADIR%%/jemboss/org/emboss/jemboss/gui/form/ApplicationNamePanel.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/gui/filetree/LocalAndRemoteFileTreeFrame.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/gui/filetree/LocalTreeToolBar.java
 %%DATADIR%%/jemboss/org/emboss/jemboss/gui/form/BuildJembossForm.java
-%%DATADIR%%/jemboss/org/emboss/jemboss/gui/form/JembossComboPopup.java
-%%DATADIR%%/jemboss/org/emboss/jemboss/gui/form/LabelTextBox.java
 %%DATADIR%%/jemboss/org/emboss/jemboss/gui/form/ListFilePanel.java
-%%DATADIR%%/jemboss/org/emboss/jemboss/gui/form/MultiLineToolTipUI.java
-%%DATADIR%%/jemboss/org/emboss/jemboss/gui/form/PlafMacros.java
-%%DATADIR%%/jemboss/org/emboss/jemboss/gui/form/ReportFormat.java
 %%DATADIR%%/jemboss/org/emboss/jemboss/gui/form/SectionPanel.java
-%%DATADIR%%/jemboss/org/emboss/jemboss/gui/form/Separator.java
 %%DATADIR%%/jemboss/org/emboss/jemboss/gui/form/SetInFileCard.java
 %%DATADIR%%/jemboss/org/emboss/jemboss/gui/form/SetOutFileCard.java
 %%DATADIR%%/jemboss/org/emboss/jemboss/gui/form/TextFieldFloat.java
 %%DATADIR%%/jemboss/org/emboss/jemboss/gui/form/TextFieldInt.java
 %%DATADIR%%/jemboss/org/emboss/jemboss/gui/form/TextFieldSink.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/gui/form/JembossComboPopup.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/gui/form/MultiLineToolTipUI.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/gui/form/PlafMacros.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/gui/form/ReportFormat.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/gui/form/AlignFormat.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/gui/form/ApplicationNamePanel.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/gui/form/LabelTextBox.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/gui/form/Separator.java
 %%DATADIR%%/jemboss/org/emboss/jemboss/gui/sequenceChooser/CutNPasteTextArea.java
 %%DATADIR%%/jemboss/org/emboss/jemboss/gui/sequenceChooser/FileChooser.java
 %%DATADIR%%/jemboss/org/emboss/jemboss/gui/sequenceChooser/InputSequenceAttributes.java
@@ -954,15 +1927,32 @@ lib/libplplot.so.5
 %%DATADIR%%/jemboss/org/emboss/jemboss/gui/sequenceChooser/TextAreaSink.java
 %%DATADIR%%/jemboss/org/emboss/jemboss/gui/startup/Database.java
 %%DATADIR%%/jemboss/org/emboss/jemboss/gui/startup/ProgList.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/gui/AdvancedOptions.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/gui/ResultsMenuBar.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/gui/ShowResultSet.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/gui/BuildProgramMenu.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/gui/SequenceData.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/gui/ShowSavedResults.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/gui/LaunchJalView.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/gui/SequenceList.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/gui/SwingWorker.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/gui/MemoryComboBox.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/gui/SetUpMenuBar.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/gui/Browser.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/gui/SplashThread.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/gui/ScrollPanel.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/gui/ImageIconJPanel.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/gui/Favorites.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/gui/KeywordSearch.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/parser/acd/ApplicationFields.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/parser/acd/ApplicationParam.java
 %%DATADIR%%/jemboss/org/emboss/jemboss/parser/AcdFunResolve.java
-%%DATADIR%%/jemboss/org/emboss/jemboss/parser/AcdVarResolve.java
 %%DATADIR%%/jemboss/org/emboss/jemboss/parser/AcdVariableResolve.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/parser/AcdVarResolve.java
 %%DATADIR%%/jemboss/org/emboss/jemboss/parser/Ajax.java
 %%DATADIR%%/jemboss/org/emboss/jemboss/parser/AjaxUtil.java
 %%DATADIR%%/jemboss/org/emboss/jemboss/parser/Dependent.java
 %%DATADIR%%/jemboss/org/emboss/jemboss/parser/ParseAcd.java
-%%DATADIR%%/jemboss/org/emboss/jemboss/parser/acd/ApplicationFields.java
-%%DATADIR%%/jemboss/org/emboss/jemboss/parser/acd/ApplicationParam.java
 %%DATADIR%%/jemboss/org/emboss/jemboss/programs/BatchUpdateTimer.java
 %%DATADIR%%/jemboss/org/emboss/jemboss/programs/JembossProcess.java
 %%DATADIR%%/jemboss/org/emboss/jemboss/programs/ListFile.java
@@ -970,1017 +1960,112 @@ lib/libplplot.so.5
 %%DATADIR%%/jemboss/org/emboss/jemboss/programs/ResultsUpdateTimer.java
 %%DATADIR%%/jemboss/org/emboss/jemboss/programs/RunEmbossApplication.java
 %%DATADIR%%/jemboss/org/emboss/jemboss/programs/RunEmbossApplication2.java
-%%DATADIR%%/jemboss/org/emboss/jemboss/server/AppendToLogFileThread.java
-%%DATADIR%%/jemboss/org/emboss/jemboss/server/JembossAuthServer.java
-%%DATADIR%%/jemboss/org/emboss/jemboss/server/JembossFileAuthServer.java
-%%DATADIR%%/jemboss/org/emboss/jemboss/server/JembossFileServer.java
 %%DATADIR%%/jemboss/org/emboss/jemboss/server/JembossServer.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/server/JembossFileServer.java
 %%DATADIR%%/jemboss/org/emboss/jemboss/server/JembossThread.java
-%%DATADIR%%/jemboss/org/emboss/jemboss/server/TestPrivateServer.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/server/JembossAuthServer.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/server/JembossFileAuthServer.java
 %%DATADIR%%/jemboss/org/emboss/jemboss/server/TestPublicServer.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/server/TestPrivateServer.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/server/AppendToLogFileThread.java
 %%DATADIR%%/jemboss/org/emboss/jemboss/soap/AuthPopup.java
-%%DATADIR%%/jemboss/org/emboss/jemboss/soap/CallAjax.java
-%%DATADIR%%/jemboss/org/emboss/jemboss/soap/FileList.java
-%%DATADIR%%/jemboss/org/emboss/jemboss/soap/FileRoots.java
-%%DATADIR%%/jemboss/org/emboss/jemboss/soap/GetACD.java
-%%DATADIR%%/jemboss/org/emboss/jemboss/soap/GetHelp.java
-%%DATADIR%%/jemboss/org/emboss/jemboss/soap/GetWossname.java
-%%DATADIR%%/jemboss/org/emboss/jemboss/soap/JembossRun.java
 %%DATADIR%%/jemboss/org/emboss/jemboss/soap/JembossSoapException.java
-%%DATADIR%%/jemboss/org/emboss/jemboss/soap/MakeFileSafe.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/soap/CallAjax.java
 %%DATADIR%%/jemboss/org/emboss/jemboss/soap/PendingResults.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/soap/GetWossname.java
 %%DATADIR%%/jemboss/org/emboss/jemboss/soap/PrivateRequest.java
-%%DATADIR%%/jemboss/org/emboss/jemboss/soap/PublicRequest.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/soap/JembossRun.java
 %%DATADIR%%/jemboss/org/emboss/jemboss/soap/ServerSetup.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/soap/FileRoots.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/soap/FileList.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/soap/PublicRequest.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/soap/GetACD.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/soap/GetHelp.java
 %%DATADIR%%/jemboss/org/emboss/jemboss/soap/ShowDB.java
-%%DATADIR%%/jemboss/readme.html
-%%DATADIR%%/jemboss/resources/filemgr.html
+%%DATADIR%%/jemboss/org/emboss/jemboss/soap/MakeFileSafe.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/Jemboss.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/JembossLogo.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/JembossParams.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/JembossJarUtil.java
 %%DATADIR%%/jemboss/resources/jemboss.properties
 %%DATADIR%%/jemboss/resources/readme.html
 %%DATADIR%%/jemboss/resources/readmeAlign.html
 %%DATADIR%%/jemboss/resources/readmeDNADraw.html
 %%DATADIR%%/jemboss/resources/results.html
-%%DATADIR%%/jemboss/resources/seqList.html
 %%DATADIR%%/jemboss/resources/version
-%%DATADIR%%/jemboss/runJemboss.sh
-%%DATADIR%%/jemboss/utils/README
+%%DATADIR%%/jemboss/resources/filemgr.html
+%%DATADIR%%/jemboss/resources/seqList.html
 %%DATADIR%%/jemboss/utils/install-jemboss-server.sh
 %%DATADIR%%/jemboss/utils/keys.sh
-%%DATADIR%%/jemboss/utils/makeFileManagerJNLP.sh
-%%DATADIR%%/jemboss/utils/makeJNLP.sh
 %%DATADIR%%/jemboss/utils/makeJar.csh
+%%DATADIR%%/jemboss/utils/makeJNLP.sh
+%%DATADIR%%/jemboss/utils/makeFileManagerJNLP.sh
 %%DATADIR%%/jemboss/utils/template.html
-%%DATADIR%%/plstnd5.fnt
-%%DATADIR%%/plxtnd5.fnt
-%%DATADIR%%/test/data/aaindex1.test
-%%DATADIR%%/test/data/aligna.dna
-%%DATADIR%%/test/data/aligna.prot
-%%DATADIR%%/test/data/alignapart.dna
-%%DATADIR%%/test/data/alignapart.prot
-%%DATADIR%%/test/data/alignb.dna
-%%DATADIR%%/test/data/alignb.prot
-%%DATADIR%%/test/data/cutg.codon
-%%DATADIR%%/test/data/dna.acedb
-%%DATADIR%%/test/data/dna.aln
-%%DATADIR%%/test/data/dna.asn1
-%%DATADIR%%/test/data/dna.codata
-%%DATADIR%%/test/data/dna.embl
-%%DATADIR%%/test/data/dna.fasta
-%%DATADIR%%/test/data/dna.fitch
-%%DATADIR%%/test/data/dna.gcg
-%%DATADIR%%/test/data/dna.gcg8
-%%DATADIR%%/test/data/dna.genbank
-%%DATADIR%%/test/data/dna.ig
-%%DATADIR%%/test/data/dna.m-acedb
-%%DATADIR%%/test/data/dna.m-codata
-%%DATADIR%%/test/data/dna.m-embl
-%%DATADIR%%/test/data/dna.m-fasta
-%%DATADIR%%/test/data/dna.m-fasta-long
-%%DATADIR%%/test/data/dna.m-ncbi
-%%DATADIR%%/test/data/dna.m-strider
-%%DATADIR%%/test/data/dna.msf
-%%DATADIR%%/test/data/dna.msf8
-%%DATADIR%%/test/data/dna.ncbi
-%%DATADIR%%/test/data/dna.phylip
-%%DATADIR%%/test/data/dna.phylip3
-%%DATADIR%%/test/data/dna.staden
-%%DATADIR%%/test/data/dna.strider
-%%DATADIR%%/test/data/dna.text
-%%DATADIR%%/test/data/feat.emft
-%%DATADIR%%/test/data/feat.fasta
-%%DATADIR%%/test/data/feat.pir
-%%DATADIR%%/test/data/mw1.dat
-%%DATADIR%%/test/data/mw2.dat
-%%DATADIR%%/test/data/mw3.dat
-%%DATADIR%%/test/data/paamir.pep
-%%DATADIR%%/test/data/pax6_cdna.fasta
-%%DATADIR%%/test/data/prints.test
-%%DATADIR%%/test/data/prosite.dat
-%%DATADIR%%/test/data/prosite.doc
-%%DATADIR%%/test/data/prot.acedb
-%%DATADIR%%/test/data/prot.codata
-%%DATADIR%%/test/data/prot.fasta
-%%DATADIR%%/test/data/prot.gcg
-%%DATADIR%%/test/data/prot.gcg8
-%%DATADIR%%/test/data/prot.ig
-%%DATADIR%%/test/data/prot.m-acedb
-%%DATADIR%%/test/data/prot.m-codata
-%%DATADIR%%/test/data/prot.m-fasta
-%%DATADIR%%/test/data/prot.m-nbrf
-%%DATADIR%%/test/data/prot.m-ncbi
-%%DATADIR%%/test/data/prot.m-swiss
-%%DATADIR%%/test/data/prot.nbrf
-%%DATADIR%%/test/data/prot.ncbi
-%%DATADIR%%/test/data/prot.swiss
-%%DATADIR%%/test/data/prot.text
-%%DATADIR%%/test/data/site.dat
-%%DATADIR%%/test/data/tranalign.pep
-%%DATADIR%%/test/data/tranalign.seq
-%%DATADIR%%/test/data/withrefm
-%%DATADIR%%/test/data/z83307.seq
-%%DATADIR%%/test/embl/acnum.hit
-%%DATADIR%%/test/embl/acnum.trg
-%%DATADIR%%/test/embl/des.hit
-%%DATADIR%%/test/embl/des.trg
-%%DATADIR%%/test/embl/division.lkp
-%%DATADIR%%/test/embl/entrynam.idx
-%%DATADIR%%/test/embl/est.dat
-%%DATADIR%%/test/embl/fun.dat
-%%DATADIR%%/test/embl/hum1.dat
-%%DATADIR%%/test/embl/inv.dat
-%%DATADIR%%/test/embl/keyword.hit
-%%DATADIR%%/test/embl/keyword.trg
-%%DATADIR%%/test/embl/pln.dat
-%%DATADIR%%/test/embl/pro.dat
-%%DATADIR%%/test/embl/rod.dat
-%%DATADIR%%/test/embl/seqvn.hit
-%%DATADIR%%/test/embl/seqvn.trg
-%%DATADIR%%/test/embl/sts.dat
-%%DATADIR%%/test/embl/taxon.hit
-%%DATADIR%%/test/embl/taxon.trg
-%%DATADIR%%/test/embl/vrl.dat
-%%DATADIR%%/test/embl/vrt.dat
-%%DATADIR%%/test/gb/acnum.hit
-%%DATADIR%%/test/gb/acnum.trg
-%%DATADIR%%/test/gb/ba.ref
-%%DATADIR%%/test/gb/ba.seq
-%%DATADIR%%/test/gb/des.hit
-%%DATADIR%%/test/gb/des.trg
-%%DATADIR%%/test/gb/division.lkp
-%%DATADIR%%/test/gb/entrynam.idx
-%%DATADIR%%/test/gb/htg.ref
-%%DATADIR%%/test/gb/htg.seq
-%%DATADIR%%/test/gb/keyword.hit
-%%DATADIR%%/test/gb/keyword.trg
-%%DATADIR%%/test/gb/seqvn.hit
-%%DATADIR%%/test/gb/seqvn.trg
-%%DATADIR%%/test/gb/taxon.hit
-%%DATADIR%%/test/gb/taxon.trg
-%%DATADIR%%/test/genbank/acnum.hit
-%%DATADIR%%/test/genbank/acnum.trg
-%%DATADIR%%/test/genbank/des.hit
-%%DATADIR%%/test/genbank/des.trg
-%%DATADIR%%/test/genbank/division.lkp
-%%DATADIR%%/test/genbank/entrynam.idx
-%%DATADIR%%/test/genbank/gbbct1.seq
-%%DATADIR%%/test/genbank/gbest1.seq
-%%DATADIR%%/test/genbank/gbinv1.seq
-%%DATADIR%%/test/genbank/gbpln1.seq
-%%DATADIR%%/test/genbank/gbpln2.seq
-%%DATADIR%%/test/genbank/gbpri1.seq
-%%DATADIR%%/test/genbank/gbrod1.seq
-%%DATADIR%%/test/genbank/gbsts1.seq
-%%DATADIR%%/test/genbank/gbvrl1.seq
-%%DATADIR%%/test/genbank/gbvrt.seq
-%%DATADIR%%/test/genbank/keyword.hit
-%%DATADIR%%/test/genbank/keyword.trg
-%%DATADIR%%/test/genbank/seqvn.hit
-%%DATADIR%%/test/genbank/seqvn.trg
-%%DATADIR%%/test/genbank/taxon.hit
-%%DATADIR%%/test/genbank/taxon.trg
-%%DATADIR%%/test/pir/acnum.hit
-%%DATADIR%%/test/pir/acnum.trg
-%%DATADIR%%/test/pir/des.hit
-%%DATADIR%%/test/pir/des.trg
-%%DATADIR%%/test/pir/division.lkp
-%%DATADIR%%/test/pir/entrynam.idx
-%%DATADIR%%/test/pir/keyword.hit
-%%DATADIR%%/test/pir/keyword.trg
-%%DATADIR%%/test/pir/pir1.header
-%%DATADIR%%/test/pir/pir1.names
-%%DATADIR%%/test/pir/pir1.numbers
-%%DATADIR%%/test/pir/pir1.offset
-%%DATADIR%%/test/pir/pir1.ref
-%%DATADIR%%/test/pir/pir1.seq
-%%DATADIR%%/test/pir/pir2.header
-%%DATADIR%%/test/pir/pir2.names
-%%DATADIR%%/test/pir/pir2.numbers
-%%DATADIR%%/test/pir/pir2.offset
-%%DATADIR%%/test/pir/pir2.ref
-%%DATADIR%%/test/pir/pir2.seq
-%%DATADIR%%/test/pir/pir3.header
-%%DATADIR%%/test/pir/pir3.names
-%%DATADIR%%/test/pir/pir3.numbers
-%%DATADIR%%/test/pir/pir3.offset
-%%DATADIR%%/test/pir/pir3.ref
-%%DATADIR%%/test/pir/pir3.seq
-%%DATADIR%%/test/pir/pir4.header
-%%DATADIR%%/test/pir/pir4.names
-%%DATADIR%%/test/pir/pir4.numbers
-%%DATADIR%%/test/pir/pir4.offset
-%%DATADIR%%/test/pir/pir4.ref
-%%DATADIR%%/test/pir/pir4.seq
-%%DATADIR%%/test/pir/taxon.hit
-%%DATADIR%%/test/pir/taxon.trg
-%%DATADIR%%/test/swiss/acnum.hit
-%%DATADIR%%/test/swiss/acnum.trg
-%%DATADIR%%/test/swiss/des.hit
-%%DATADIR%%/test/swiss/des.trg
-%%DATADIR%%/test/swiss/division.lkp
-%%DATADIR%%/test/swiss/entrynam.idx
-%%DATADIR%%/test/swiss/keyword.hit
-%%DATADIR%%/test/swiss/keyword.trg
-%%DATADIR%%/test/swiss/seq.dat
-%%DATADIR%%/test/swiss/seqvn.hit
-%%DATADIR%%/test/swiss/seqvn.trg
-%%DATADIR%%/test/swiss/taxon.hit
-%%DATADIR%%/test/swiss/taxon.trg
-%%DATADIR%%/test/swnew/acnum.hit
-%%DATADIR%%/test/swnew/acnum.trg
-%%DATADIR%%/test/swnew/des.hit
-%%DATADIR%%/test/swnew/des.trg
-%%DATADIR%%/test/swnew/division.lkp
-%%DATADIR%%/test/swnew/entrynam.idx
-%%DATADIR%%/test/swnew/keyword.hit
-%%DATADIR%%/test/swnew/keyword.trg
-%%DATADIR%%/test/swnew/new_seq.dat
-%%DATADIR%%/test/swnew/seqvn.hit
-%%DATADIR%%/test/swnew/seqvn.trg
-%%DATADIR%%/test/swnew/taxon.hit
-%%DATADIR%%/test/swnew/taxon.trg
-%%DATADIR%%/test/swnew/upd_ann.dat
-%%DATADIR%%/test/swnew/upd_seq.dat
-%%DATADIR%%/test/wormpep/acnum.hit
-%%DATADIR%%/test/wormpep/acnum.trg
-%%DATADIR%%/test/wormpep/des.hit
-%%DATADIR%%/test/wormpep/des.trg
-%%DATADIR%%/test/wormpep/division.lkp
-%%DATADIR%%/test/wormpep/entrynam.idx
-%%DATADIR%%/test/wormpep/wormpep
-%%PORTDOCS%%%%DOCSDIR%%/manuals/EMBOSS-FreeBSD-HOWTO.txt
-%%PORTDOCS%%%%DOCSDIR%%/manuals/admin.aux
-%%PORTDOCS%%%%DOCSDIR%%/manuals/admin.dvi
-%%PORTDOCS%%%%DOCSDIR%%/manuals/admin.log
-%%PORTDOCS%%%%DOCSDIR%%/manuals/admin.pdf
-%%PORTDOCS%%%%DOCSDIR%%/manuals/admin.ps
-%%PORTDOCS%%%%DOCSDIR%%/manuals/admin.sty
-%%PORTDOCS%%%%DOCSDIR%%/manuals/admin.tex
-%%PORTDOCS%%%%DOCSDIR%%/manuals/admin.toc
-%%PORTDOCS%%%%DOCSDIR%%/manuals/adminguide.tar.gz
-%%PORTDOCS%%%%DOCSDIR%%/manuals/domainatrix.doc
-%%PORTDOCS%%%%DOCSDIR%%/manuals/emboss.sty
-%%PORTDOCS%%%%DOCSDIR%%/manuals/emboss_qg.pdf
-%%PORTDOCS%%%%DOCSDIR%%/manuals/emboss_qg.ps
-%%PORTDOCS%%%%DOCSDIR%%/manuals/fdl.txt
-%%PORTDOCS%%%%DOCSDIR%%/manuals/program.ps.gz
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/aaindexextract.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/abiview.1.abiview.gif
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/abiview.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/acd_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/acdc.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/acdlog.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/acdpretty.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/acdtable.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/acdtrace.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/acdvalid.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/ajtest.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/alignment_consensus_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/alignment_differences_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/alignment_dot_plots_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/alignment_global_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/alignment_local_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/alignment_multiple_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/alignrunner.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/allversusall.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/antigenic.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/backtranseq.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/banana.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/biosed.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/btwisted.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/cai.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/cathparse.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/chaos.1.chaos.gif
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/chaos.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/charge.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/checktrans.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/chips.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/cirdna.1.cirdna.gif
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/cirdna.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/clique.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/codcmp.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/coderet.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/compseq.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/cons.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/consense.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/contactalign.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/contactcount.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/contacts.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/contml.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/contrast.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/cpgplot.1.cpgplot.gif
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/cpgplot.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/cpgreport.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/crystalball.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/cusp.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/cutgextract.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/cutseq.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/dan.2.dan.gif
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/dan.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/dbiblast.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/dbifasta.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/dbiflat.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/dbigcg.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/degapseq.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/degapseqrunner.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/descseq.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/diffseq.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/digest.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/display_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/distmat.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/dnacomp.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/dnadist.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/dnainvar.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/dnaml.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/dnamlk.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/dnapars.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/dnapenny.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/dollop.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/dolpenny.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/domainalign.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/domainer.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/domainnr.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/domainrep.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/domainreso.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/domainseqs.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/domainsse.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/dotmatcher.1.dotmatcher.gif
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/dotmatcher.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/dotpath.1.dotpath.gif
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/dotpath.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/dottup.1.dottup.gif
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/dottup.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/dreg.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/ealistat.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/eclique.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/econsense.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/econtml.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/econtrast.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/edit_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/ednacomp.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/ednadist.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/ednainvar.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/ednaml.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/ednamlk.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/ednapars.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/ednapenny.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/edollop.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/edolpenny.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/efactor.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/efitch.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/egendist.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/ehmmalign.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/ehmmbuild.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/ehmmcalibrate.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/ehmmconvert.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/ehmmemit.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/ehmmfetch.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/ehmmindex.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/ehmmpfam.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/ehmmsearch.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/einverted.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/ekitsch.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/emboss_icon.gif
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/emboss_icon.jpg
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/embossdata.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/embossversion.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/emix.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/emma.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/emnu.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/emowse.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/eneighbor.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/entret.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/enzyme_kinetics_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/epenny.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/epestfind.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/eprimer3.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/eprotdist.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/eprotpars.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/equicktandem.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/erestml.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/eseqboot.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/esim4.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/est2genome.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/etandem.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/extractfeat.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/extractseq.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/factor.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/fclique.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/fconsense.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/fcontml.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/fcontrast.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/fdiscboot.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/fdnacomp.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/fdnadist.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/fdnainvar.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/fdnaml.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/fdnamlk.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/fdnamove.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/fdnapars.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/fdnapenny.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/fdollop.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/fdolmove.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/fdolpenny.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/fdrawgram.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/fdrawtree.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/feature_tables_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/ffactor.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/ffitch.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/ffreqboot.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/fgendist.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/findkm.1.findkm.gif
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/findkm.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/fitch.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/fkitsch.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/fmix.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/fmove.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/fneighbor.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/fpars.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/fpenny.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/fproml.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/fpromlk.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/fprotdist.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/fprotpars.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/freak.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/frestboot.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/frestdist.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/frestml.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/fretree.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/fseqboot.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/fseqbootall.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/ftreedist.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/ftreedistpair.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/fuzznuc.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/fuzzpro.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/fuzztran.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/garnier.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/geecee.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/gendist.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/getorf.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/groups.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/helixturnhelix.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/hetparse.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/hmm_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/hmoment.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/iep.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/index.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/infoalign.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/information_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/infoseq.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/interface.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/isochore.1.isochore.gif
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/isochore.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/jembossctl.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/kitsch.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/libgen.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/libscan.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/lindna.1.lindna.gif
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/lindna.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/listor.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/marscan.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/maskfeat.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/maskseq.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/matcher.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/megamerger.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/meme.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/menus_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/merger.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/mix.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/msbar.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/mse.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/mwcontam.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/mwfilter.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/myseq.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/nawalign.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/nawalignrunner.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/needle.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/needlerunner.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/neighbor.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/newcpgreport.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/newcpgseek.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/newseq.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/noreturn.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/notseq.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/nthseq.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/nucleic_2d_structure_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/nucleic_codon_usage_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/nucleic_codon_usage_nucleic_gene_finding_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/nucleic_composition_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/nucleic_cpg_islands_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/nucleic_gene_finding_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/nucleic_motifs_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/nucleic_mutation_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/nucleic_primers_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/nucleic_profiles_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/nucleic_repeats_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/nucleic_restriction_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/nucleic_transcription_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/nucleic_translation_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/octanol.1.octanol.gif
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/octanol.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/oddcomp.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/palindrome.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/pasteseq.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/patmatdb.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/patmatmotifs.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/pdbparse.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/pdbplus.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/pdbtosp.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/penny.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/pepcoil.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/pepinfo.1.pepinfo.gif
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/pepinfo.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/pepnet.1.pepnet.gif
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/pepnet.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/pepstats.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/pepwheel.1.pepwheel.gif
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/pepwheel.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/pepwindow.1.pepwindow.gif
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/pepwindow.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/pepwindowall.1.pepwindowall.gif
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/pepwindowall.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/pestfind.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/phylogeny_consensus_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/phylogeny_continuous_characters_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/phylogeny_discrete_characters_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/phylogeny_distance_matrix_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/phylogeny_gene_frequencies_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/phylogeny_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/phylogeny_molecular_sequence_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/phylogeny_tree_drawing_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/plotcon.1.plotcon.gif
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/plotcon.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/plotorf.1.plotorf.gif
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/plotorf.2.plotorf.gif
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/plotorf.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/polydot.1.polydot.gif
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/polydot.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/preg.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/prettyplot.1.prettyplot.gif
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/prettyplot.2.prettyplot.gif
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/prettyplot.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/prettyseq.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/primersearch.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/printsextract.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/profit.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/prophecy.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/prophet.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/prosextract.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/protdist.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/protein_2d_structure_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/protein_3d_structure_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/protein_composition_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/protein_motifs_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/protein_mutation_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/protein_profiles_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/protein_sequence_alignment_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/pscan.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/psiphi.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/rebaseextract.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/recoder.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/redata.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/remap.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/restml.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/restover.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/restrict.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/revseq.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/rocon.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/rocplot.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/scope.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/scopparse.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/scorer.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/scorerrunner.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/seealso.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/seqalign.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/seqboot.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/seqfraggle.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/seqmatchall.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/seqnr.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/seqret.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/seqretsplit.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/seqsearch.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/seqsort.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/seqwords.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/showalign.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/showdb.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/showfeat.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/showorf.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/showseq.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/shuffleseq.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/sigcleave.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/siggen.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/sigscan.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/silent.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/sirna.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/sites.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/sixpack.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/skipseq.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/splitter.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/ssematch.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/stretcher.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/stssearch.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/substitute.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/substituterunner.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/supermatcher.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/syco.1.syco.gif
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/syco.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/tcode.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/template.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/test_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/textsearch.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/tfextract.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/tfm.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/tfscan.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/tmap.1.tmap.gif
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/tmap.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/topo.gif
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/topo.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/tranalign.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/transeq.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/trimest.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/trimseq.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/twofeat.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/union.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/utils_database_creation_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/utils_database_indexing_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/utils_misc_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/vectorstrip.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/water.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/whichdb.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/wobble.1.wobble.gif
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/wobble.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/wordcount.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/wordmatch.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/wossname.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/yank.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/aaindexextract.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/abiview.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/acdc.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/acdlog.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/acdpretty.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/acdtable.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/acdtrace.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/acdvalid.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/alignrunner.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/allversusall.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/antigenic.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/backtranseq.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/banana.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/biosed.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/btwisted.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/cai.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/cathparse.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/chaos.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/charge.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/checktrans.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/chips.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/cirdna.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/clique.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/codcmp.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/coderet.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/complex.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/compseq.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/cons.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/consense.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/contactalign.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/contactcount.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/contacts.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/contml.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/contrast.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/cpgplot.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/cpgreport.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/crystalball.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/cusp.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/cutgextract.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/cutseq.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/dan.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/dbiblast.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/dbifasta.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/dbiflat.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/dbigcg.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/degapseq.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/degapseqrunner.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/descseq.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/diffseq.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/digest.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/distmat.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/dnacomp.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/dnadist.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/dnainvar.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/dnaml.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/dnamlk.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/dnapars.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/dnapenny.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/dollop.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/dolpenny.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/domainalign.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/domainer.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/domainnr.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/domainrep.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/domainreso.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/domainseqs.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/domainsse.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/dotmatcher.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/dotpath.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/dottup.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/dreg.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/ealistat.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/eclique.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/econsense.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/econtml.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/econtrast.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/ednacomp.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/ednadist.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/ednainvar.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/ednaml.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/ednamlk.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/ednapars.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/ednapenny.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/edollop.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/edolpenny.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/efactor.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/efitch.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/egendist.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/ehmmalign.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/ehmmbuild.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/ehmmcalibrate.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/ehmmconvert.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/ehmmemit.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/ehmmfetch.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/ehmmindex.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/ehmmpfam.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/ehmmsearch.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/einverted.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/ekitsch.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/embossdata.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/embossversion.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/emix.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/emma.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/emnu.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/emowse.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/eneighbor.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/entret.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/epenny.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/epestfind.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/eprimer3.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/eprotdist.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/eprotpars.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/equicktandem.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/erestml.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/eseqboot.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/esim4.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/est2genome.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/etandem.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/extractfeat.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/extractseq.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/factor.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/fclique.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/fconsense.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/fcontml.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/fcontrast.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/fdiscboot.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/fdnacomp.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/fdnadist.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/fdnainvar.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/fdnaml.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/fdnamlk.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/fdnamove.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/fdnapars.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/fdnapenny.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/fdollop.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/fdolmove.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/fdolpenny.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/fdrawgram.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/fdrawtree.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/ffactor.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/ffitch.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/ffreqboot.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/fgendist.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/findkm.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/fitch.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/fkitsch.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/fmix.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/fmove.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/fneighbor.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/fpars.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/fpenny.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/fproml.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/fpromlk.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/fprotdist.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/fprotpars.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/freak.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/frestboot.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/frestdist.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/frestml.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/fretree.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/fseqboot.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/fseqbootall.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/ftreedist.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/ftreedistpair.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/fuzznuc.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/fuzzpro.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/fuzztran.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/garnier.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/geecee.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/gendist.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/getorf.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/helixturnhelix.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/hetparse.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/hmoment.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/iep.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/infoalign.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/infoseq.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/interface.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/isochore.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/jembossctl.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/kitsch.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/libgen.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/libscan.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/lindna.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/listor.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/marscan.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/maskfeat.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/maskseq.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/matcher.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/megamerger.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/meme.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/merger.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/mix.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/msbar.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/mse.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/mwcontam.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/mwfilter.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/myseq.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/nawalign.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/nawalignrunner.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/needle.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/needlerunner.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/neighbor.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/newcpgreport.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/newcpgseek.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/newseq.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/noreturn.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/notseq.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/nthseq.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/octanol.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/oddcomp.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/palindrome.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/pasteseq.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/patmatdb.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/patmatmotifs.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/pdbparse.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/pdbplus.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/pdbtosp.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/penny.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/pepcoil.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/pepinfo.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/pepnet.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/pepstats.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/pepwheel.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/pepwindow.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/pepwindowall.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/pestfind.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/plotcon.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/plotorf.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/polydot.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/preg.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/prettyplot.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/prettyseq.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/primersearch.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/printsextract.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/profit.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/prophecy.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/prophet.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/prosextract.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/protdist.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/pscan.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/psiphi.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/rebaseextract.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/recoder.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/redata.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/remap.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/restml.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/restover.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/restrict.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/revseq.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/rocon.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/rocplot.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/scope.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/scopparse.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/scorer.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/scorerrunner.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/seealso.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/seqalign.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/seqboot.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/seqfraggle.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/seqmatchall.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/seqnr.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/seqret.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/seqretsplit.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/seqsearch.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/seqsort.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/seqwords.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/showalign.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/showdb.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/showfeat.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/showorf.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/showseq.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/shuffleseq.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/sigcleave.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/siggen.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/sigscan.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/silent.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/sirna.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/sites.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/sixpack.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/skipseq.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/splitter.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/ssematch.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/stretcher.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/stssearch.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/substitute.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/substituterunner.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/supermatcher.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/syco.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/tcode.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/textsearch.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/tfextract.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/tfm.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/tfscan.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/tmap.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/topo.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/tranalign.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/transeq.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/trimest.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/trimseq.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/twofeat.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/union.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/vectorstrip.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/water.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/whichdb.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/wobble.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/wordcount.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/wordmatch.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/wossname.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/yank.txt
-%%PORTDOCS%%%%DOCSDIR%%/tutorials/emboss-gcg.ppt
-%%PORTDOCS%%%%DOCSDIR%%/tutorials/emboss-interfaces.ppt
-%%PORTDOCS%%%%DOCSDIR%%/tutorials/emboss-talk.ppt
-%%PORTDOCS%%%%DOCSDIR%%/tutorials/emboss_tut.tar.gz
-%%PORTDOCS%%@dirrm %%DOCSDIR%%/tutorials
-%%PORTDOCS%%@dirrm %%DOCSDIR%%/programs/text
+%%DATADIR%%/jemboss/utils/README
+%%DATADIR%%/jemboss/LICENSE
+%%DATADIR%%/jemboss/readme.html
+%%DATADIR%%/jemboss/runJemboss.sh
+%%DATADIR%%/jemboss/README
+%%PORTDOCS%%@dirrm %%DOCSDIR%%/manuals
 %%PORTDOCS%%@dirrm %%DOCSDIR%%/programs/html
+%%PORTDOCS%%@dirrm %%DOCSDIR%%/programs/text
 %%PORTDOCS%%@dirrm %%DOCSDIR%%/programs
-%%PORTDOCS%%@dirrm %%DOCSDIR%%/manuals
+%%PORTDOCS%%@dirrm %%DOCSDIR%%/tutorials
 %%PORTDOCS%%@dirrm %%DOCSDIR%%
-@dirrm %%DATADIR%%/test/wormpep
-@dirrm %%DATADIR%%/test/swnew
-@dirrm %%DATADIR%%/test/swiss
-@dirrm %%DATADIR%%/test/pir
+@dirrm %%DATADIR%%/acd
+@dirrm %%DATADIR%%/data/AAINDEX
+@dirrm %%DATADIR%%/data/CODONS
+@dirrm %%DATADIR%%/data/REBASE
+@dirrm %%DATADIR%%/data/PRINTS
+@dirrm %%DATADIR%%/data/PROSITE
+@dirrmtry %%DATADIR%%/data
+@dirrm %%DATADIR%%/test/data
+@dirrm %%DATADIR%%/test/embl
 @dirrm %%DATADIR%%/test/genbank
 @dirrm %%DATADIR%%/test/gb
-@dirrm %%DATADIR%%/test/embl
-@dirrm %%DATADIR%%/test/data
+@dirrm %%DATADIR%%/test/pir
+@dirrm %%DATADIR%%/test/swiss
+@dirrm %%DATADIR%%/test/swnew
+@dirrm %%DATADIR%%/test/wormpep
 @dirrm %%DATADIR%%/test
-@dirrm %%DATADIR%%/jemboss/utils
-@dirrm %%DATADIR%%/jemboss/resources
-@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/soap
-@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/server
-@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/programs
-@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/parser/acd
-@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/parser
-@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/gui/startup
-@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/gui/sequenceChooser
-@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/gui/form
-@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/gui/filetree
-@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/gui
-@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/graphics
-@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/editor
-@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/draw
-@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss
-@dirrm %%DATADIR%%/jemboss/org/emboss
-@dirrm %%DATADIR%%/jemboss/org
-@dirrm %%DATADIR%%/jemboss/lib/axis
-@dirrm %%DATADIR%%/jemboss/lib
-@dirrm %%DATADIR%%/jemboss/images
-@dirrm %%DATADIR%%/jemboss/api/org/emboss/jemboss/soap
-@dirrm %%DATADIR%%/jemboss/api/org/emboss/jemboss/programs
-@dirrm %%DATADIR%%/jemboss/api/org/emboss/jemboss/parser/acd
-@dirrm %%DATADIR%%/jemboss/api/org/emboss/jemboss/parser
-@dirrm %%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/startup
-@dirrm %%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/sequenceChooser
-@dirrm %%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/form
 @dirrm %%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/filetree
+@dirrm %%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/form
+@dirrm %%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/sequenceChooser
+@dirrm %%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/startup
 @dirrm %%DATADIR%%/jemboss/api/org/emboss/jemboss/gui
+@dirrm %%DATADIR%%/jemboss/api/org/emboss/jemboss/parser/acd
+@dirrm %%DATADIR%%/jemboss/api/org/emboss/jemboss/parser
+@dirrm %%DATADIR%%/jemboss/api/org/emboss/jemboss/programs
+@dirrm %%DATADIR%%/jemboss/api/org/emboss/jemboss/soap
 @dirrm %%DATADIR%%/jemboss/api/org/emboss/jemboss
 @dirrm %%DATADIR%%/jemboss/api/org/emboss
 @dirrm %%DATADIR%%/jemboss/api/org
 @dirrm %%DATADIR%%/jemboss/api
+@dirrm %%DATADIR%%/jemboss/images
+@dirrm %%DATADIR%%/jemboss/lib/axis
+@dirrm %%DATADIR%%/jemboss/lib
+@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/editor
+@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/draw
+@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/graphics
+@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/gui/filetree
+@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/gui/form
+@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/gui/sequenceChooser
+@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/gui/startup
+@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/gui
+@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/parser/acd
+@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/parser
+@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/programs
+@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/server
+@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/soap
+@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss
+@dirrm %%DATADIR%%/jemboss/org/emboss
+@dirrm %%DATADIR%%/jemboss/org
+@dirrm %%DATADIR%%/jemboss/resources
+@dirrm %%DATADIR%%/jemboss/utils
 @dirrm %%DATADIR%%/jemboss
-@dirrm %%DATADIR%%/data/REBASE
-@dirrm %%DATADIR%%/data/PROSITE
-@dirrm %%DATADIR%%/data/PRINTS
-@dirrm %%DATADIR%%/data/CODONS
-@dirrm %%DATADIR%%/data/AAINDEX
-@dirrm %%DATADIR%%/data
-@dirrm %%DATADIR%%/acd
-@dirrm %%DATADIR%%
+@dirrmtry %%DATADIR%%
+@dirrmtry bin
+@dirrmtry include
+@dirrmtry lib
+@dirrmtry share/doc
+@dirrmtry share