8 files changed, 72 insertions, 30 deletions

diff --git a/biology/seaview/Makefile b/biology/seaview/Makefile
index a4e06a6157fc..21df6296c076 100644
--- a/biology/seaview/Makefile
+++ b/biology/seaview/Makefile
@@ -6,26 +6,26 @@
 #
 
 PORTNAME=	seaview
-PORTVERSION=	1.0
+PORTVERSION=	2002.10.18
 CATEGORIES=	biology
 MASTER_SITES=	ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/seaview/
 DISTNAME=	${PORTNAME}
 EXTRACT_SUFX=	.tar
 
-MAINTAINER=	frankch@waru.life.nthu.edu.tw
+MAINTAINER=	ports@FreeBSD.org
 
-BROKEN=		"Checksum is incorrect"
-
-LIB_DEPENDS=	forms.1:${PORTSDIR}/x11-toolkits/xforms
+LIB_DEPENDS=	fltk.1:${PORTSDIR}/x11-toolkits/fltk
 
 USE_X_PREFIX=	YES
 NO_WRKSUBDIR=	YES
 EXTRACT_CMD=		${TAR}
 EXTRACT_BEFORE_ARGS=	-xf
 EXTRACT_AFTER_ARGS=	# empty
+MAKEFILE=	makefile
 
 do-install:
 	@ ${INSTALL_PROGRAM} ${WRKSRC}/${DISTNAME} ${PREFIX}/bin
+	@ ${INSTALL_SCRIPT} ${WRKSRC}/seaview_align.sh ${PREFIX}/bin
 	@ (${MKDIR} ${PREFIX}/lib/X11/seaview)
 	@ ${INSTALL_DATA} ${WRKSRC}/seaview.help ${PREFIX}/lib/X11/seaview
 
diff --git a/biology/seaview/distinfo b/biology/seaview/distinfo
index 28018709d128..866bdaf801e9 100644
--- a/biology/seaview/distinfo
+++ b/biology/seaview/distinfo
@@ -1 +1 @@
-MD5 (seaview.tar) = 2e0b15423aae80a91709b253fc7c5cab
+MD5 (seaview.tar) = 1f9b5157966b98f2724428d3fb1f6b17
diff --git a/biology/seaview/files/patch-aa b/biology/seaview/files/patch-aa
index b326a5a807a0..fdca7da38e5f 100644
--- a/biology/seaview/files/patch-aa
+++ b/biology/seaview/files/patch-aa
@@ -1,20 +1,23 @@
---- Makefile.orig	Mon Aug 30 20:54:56 1999
-+++ Makefile	Mon Aug 30 20:55:48 1999
-@@ -0,0 +1,17 @@
-+#matpt.h
-+#seaview.h
-+CC	?= gcc
-+CFLAGS+= -I${X11BASE}/include
-+LIBS	= -L${X11BASE}/lib -lxforms -lX11 -lm
-+SRCS	= align.c comlines.c load_seq.c regions.c seaview.c use_mase_files.c xfmatpt.c
-+OBJS	= align.o comlines.o load_seq.o regions.o seaview.o use_mase_files.o xfmatpt.o
+--- makefile.orig	Wed Sep 25 23:58:15 2002
++++ makefile	Mon Nov 18 11:26:42 2002
+@@ -1,13 +1,15 @@
+-FLTK = ../fltk-1.1.0
++OPT = -O2
+ 
+-OBJECTS = seaview.o use_mase_files.o regions.o load_seq.o align.o xfmatpt.o comlines.o chooser_plus.o resource.o nexus.o old_file_chooser.o
++OBJECTS = seaview.o use_mase_files.o regions.o load_seq.o align.o xfmatpt.o comlines.o chooser_plus.o resource.o nexus.o
+ 
+-CFLAGS  = -c $(OPT) -I$(FLTK)
++CFLAGS  = -c $(OPT) -I$(PREFIX)/include
+ 
+-CXX = CC
++CXX = g++
 +
 +all: seaview
-+
-+seaview: $(OBJS)
-+	$(CC) -o seaview $(OBJS) $(LIBS)
-+
-+c.o.: $(SRCS)
-+	$(CC) $(CFLAGS) -c $(SRCS)
-+
-+
+ 
+ seaview : $(OBJECTS) 
+-	$(CXX) -o $@ $(OBJECTS) -L$(FLTK)/lib -lfltk -lX11 -lm
++	$(CXX) -o $@ $(OBJECTS) -L$(PREFIX)/lib -lfltk -lX11 -lMesaGL -lXext -lm
+ 
+ 
+ .SUFFIXES:	.cxx .h .o
diff --git a/biology/seaview/files/patch-align.cxx b/biology/seaview/files/patch-align.cxx
new file mode 100644
index 000000000000..9947269dd135
--- /dev/null
+++ b/biology/seaview/files/patch-align.cxx
@@ -0,0 +1,18 @@
+--- align.cxx.orig	Tue Oct  8 19:43:40 2002
++++ align.cxx	Mon Nov 18 11:40:08 2002
+@@ -1,5 +1,6 @@
+ #include "seaview.h"
+ #include <stdlib.h>
++#include <unistd.h>
+ #include <ctype.h>
+ #ifndef WIN32
+ #include <FL/x.H>
+@@ -155,7 +156,7 @@
+ #endif
+ debut = view->active_region->list->debut;
+ fin = view->active_region->list->fin;
+-tmpnam(base_fname);
++mkstemp(base_fname);
+ /* 
+ convertir en minuscules car clustalw n'accepte pas les majuscules ds filenames
+ */
diff --git a/biology/seaview/files/patch-chooser_plus.cxx b/biology/seaview/files/patch-chooser_plus.cxx
new file mode 100644
index 000000000000..fe62a4edf2d6
--- /dev/null
+++ b/biology/seaview/files/patch-chooser_plus.cxx
@@ -0,0 +1,20 @@
+--- chooser_plus.cxx.orig	Mon Nov 18 11:14:10 2002
++++ chooser_plus.cxx	Mon Nov 18 11:17:52 2002
+@@ -442,7 +442,7 @@
+ 					   strcmp(pat,f->browser.pattern))) {
+     // if pattern is different, remove name but leave old directory:
+     const char* p = f->input.value();
+-    const char* q = fl_filename_name(p);
++    const char* q = filename_name(p);
+     f->input.value(p, q-p);
+   }
+   f->browser.pattern = pat;
+@@ -500,7 +500,7 @@
+ 					   strcmp(pat,f->browser.pattern))) {
+     // if pattern is different, remove name but leave old directory:
+     const char* p = f->input.value();
+-    const char* q = fl_filename_name(p);
++    const char* q = filename_name(p);
+     f->input.value(p, q-p);
+   }
+   f->browser.pattern = pat;
diff --git a/biology/seaview/pkg-comment b/biology/seaview/pkg-comment
index 624e358fd953..7cee832df80f 100644
--- a/biology/seaview/pkg-comment
+++ b/biology/seaview/pkg-comment
@@ -1 +1 @@
-Multiple DNA sequence alignment editor
+Multiple DNA/protein sequence alignment editor
diff --git a/biology/seaview/pkg-descr b/biology/seaview/pkg-descr
index 351ecddde5b1..19847132b9ae 100644
--- a/biology/seaview/pkg-descr
+++ b/biology/seaview/pkg-descr
@@ -1,15 +1,15 @@
-Seaview is a multiple DNA sequence alignment editor.
-You can align DNA sequences from several organisms, and find out their
+Seaview is a multiple sequence alignment editor.
+You can align DNA/protein sequences from several organisms, and find out their
 relative postions in phylogenic tree.
 
-File test.mase can be used as an example file.
 Open the on-line help window through button 'Help' to learn seaview usage.
+Example mase files could be found at:
 
-WWW: http://pbil.univ-lyon1.fr/software/seaview.html
+	ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/seaview/
 
 *****************************************************************************
 *   The help file (seaview.help) is located in /usr/X11R6/lib/X11/seaview/ .
-*   Add an entry in your Xresources or Xdefaults file with:
+*   Add an entry in your .Xresources or .Xdefaults file with:
 *
 *   seaview*helpfile:	/usr/X11R6/lib/X11/seaview/seaview.help
 *****************************************************************************
diff --git a/biology/seaview/pkg-plist b/biology/seaview/pkg-plist
index b4a419f0bd9f..6f5cd13faa7e 100644
--- a/biology/seaview/pkg-plist
+++ b/biology/seaview/pkg-plist
@@ -1,3 +1,4 @@
 bin/seaview
+bin/seaview_align.sh
 lib/X11/seaview/seaview.help
 @dirrm lib/X11/seaview