5 files changed, 56 insertions, 76 deletions

diff --git a/biology/seaview/Makefile b/biology/seaview/Makefile
index 98273d96ba31..6f085072b01f 100644
--- a/biology/seaview/Makefile
+++ b/biology/seaview/Makefile
@@ -2,31 +2,69 @@
 # $FreeBSD$
 
 PORTNAME=	seaview
-PORTVERSION=	2006.02.13
-PORTREVISION=	9
+PORTVERSION=	4.4.0
+PORTEPOCH=	1
 CATEGORIES=	biology
-MASTER_SITES=	ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/seaview/archive/
-DISTNAME=	${PORTNAME}${PORTVERSION:S/.//g}
-EXTRACT_SUFX=	.tar
+MASTER_SITES=	http://pbil.univ-lyon1.fr/software/seaview_data/archive/
+DISTNAME=	${PORTNAME}_${PORTVERSION}
 
 MAINTAINER=	ports@FreeBSD.org
 COMMENT=	Multiple DNA/protein sequence alignment editor
 
-LIB_DEPENDS=	fltk.1:${PORTSDIR}/x11-toolkits/fltk \
-		pdf.6:${PORTSDIR}/print/pdflib
+LIB_DEPENDS=	pthread-stubs:${PORTSDIR}/devel/libpthread-stubs \
+		jpeg:${PORTSDIR}/graphics/jpeg \
+		png15:${PORTSDIR}/graphics/png \
+		freetype:${PORTSDIR}/print/freetype2 \
+		expat:${PORTSDIR}/textproc/expat2 \
+		fontconfig:${PORTSDIR}/x11-fonts/fontconfig \
+		fltk:${PORTSDIR}/x11-toolkits/fltk \
+		xcb:${PORTSDIR}/x11/libxcb
 
-NO_WRKSUBDIR=	yes
-EXTRACT_CMD=	${CAT}
-EXTRACT_BEFORE_ARGS=	#
+OPTIONS_DEFINE=	PDFLIB
+OPTIONS_DEFAULT=PDFLIB
+PDFLIB_DESC=	PDFlib support
+
+WRKSRC=		${WRKDIR}/${PORTNAME}
+
+USE_XORG=	x11 xau xdmcp xext xft xinerama xrender
+USE_GMAKE=	yes
+MAKE_ENV=	HELPFILE='-DDEFAULT_HELPFILE=\"${DATADIR}/seaview.html\"' \
+		PHYMLNAME='-DPHYMLNAME=\"phyml\"' \
+		IFLTK='-I${LOCALBASE}/include' \
+		LFLTK='-L${LOCALBASE}/lib' \
+		USE_XFT='-DUSE_XFT' \
+		OPT="${CFLAGS}"
 ALL_TARGET=	${PORTNAME}
+MAKE_JOBS_SAFE=	yes
+
+DESKTOP_ENTRIES="${PORTNAME}" "${COMMENT}" "" "${PORTNAME}" \
+		"Application;Science;Biology;" "true"
+
+PLIST_FILES=	bin/seaview %%DATADIR%%/seaview.html
+PLIST_DIRS=	%%DATADIR%%
+
+.include <bsd.port.options.mk>
+
+.if ${PORT_OPTIONS:MPDFLIB}
+LIB_DEPENDS+=	pdf:${PORTSDIR}/print/pdflib
+MAKE_ENV+=	LPDF='-L${LOCALBASE}/lib -lpdf'
+.else
+MAKE_ENV+=	PDF_PS_FLAGS='-DNO_PDF'
+.endif
 
-CFLAGS+=	-D HAVE_DIRENT_H \
-		-D DEFAULT_HELPFILE=${PREFIX}/lib/X11/${PORTNAME}/seaview.help
+post-patch:
+	@${REINPLACE_CMD} -e \
+		's|^PDF_PS_FLAGS |#PDF_PS_FLAGS | ; \
+		 s|^FLTK |#FLTK | ; \
+		 s|^USE_XFT |#USE_XFT | ; \
+		 s|^CC |#CC | ; \
+		 s|^CXX |#CXX | ; \
+		 s|^OPT |#OPT | ; \
+		 s|-lpthread|${PTHREAD_LIBS}|' ${WRKSRC}/Makefile
 
 do-install:
-	${INSTALL_PROGRAM} ${WRKDIR}/${PORTNAME} ${PREFIX}/bin
-	${INSTALL_SCRIPT} ${WRKDIR}/seaview_align.sh ${PREFIX}/bin
-	@${MKDIR} ${PREFIX}/lib/X11/${PORTNAME}
-	${INSTALL_DATA} ${WRKDIR}/seaview.help ${PREFIX}/lib/X11/${PORTNAME}
+	${INSTALL_PROGRAM} ${WRKSRC}/${PORTNAME} ${PREFIX}/bin
+	@${MKDIR} ${DATADIR}
+	${INSTALL_DATA} ${WRKSRC}/seaview.html ${DATADIR}
 
 .include <bsd.port.mk>
diff --git a/biology/seaview/distinfo b/biology/seaview/distinfo
index 352e1943d89a..8854d3fdb49c 100644
--- a/biology/seaview/distinfo
+++ b/biology/seaview/distinfo
@@ -1,2 +1,2 @@
-SHA256 (seaview20060213.tar) = 3b6cd132a8c9c2d29881e3bcb14a85b9a52524a5974317a9df09d9e15ffc7776
-SIZE (seaview20060213.tar) = 573952
+SHA256 (seaview_4.4.0.tar.gz) = e1dcaef67cb93da63bfa6fa102042340297c18055928645f03defb6547e9ede3
+SIZE (seaview_4.4.0.tar.gz) = 309611
diff --git a/biology/seaview/files/patch-Makefile b/biology/seaview/files/patch-Makefile
deleted file mode 100644
index 230b42d736bf..000000000000
--- a/biology/seaview/files/patch-Makefile
+++ /dev/null
@@ -1,25 +0,0 @@
---- Makefile.orig	2010-01-08 13:42:25.000000000 +0100
-+++ Makefile	2010-01-08 13:42:24.000000000 +0100
-@@ -1,18 +1,15 @@
--FLTK = ../fltk
--PDF = ../PDFlib-Lite-6.0.1/libs/pdflib
--X11 = /usr/X11R6
- CXX = g++
- 
--CFLAGS  = -Dunix  -U__APPLE__  -c $(OPT) -I$(FLTK) -I$(PDF) -I$(X11)/include 
-+CFLAGS+= -Dunix -U__APPLE__ -c $(OPT) `fltk-config --cflags`
- 
- 
- OBJECTS = seaview.o pdf.o custom.o use_mase_files.o regions.o load_seq.o align.o xfmatpt.o comlines.o chooser_plus.o resource.o nexus.o
- 
- 
- seaview : $(OBJECTS) 
--	$(CXX) -o $@ $(OBJECTS) -L$(FLTK)/lib -lfltk \
--             -Xlinker -Bstatic -L$(PDF)/.libs -lpdf -Xlinker -Bdynamic \
--             -L$(X11)/lib -lX11 -lm 
-+	$(CXX) -o $@ $(OBJECTS) `fltk-config --ldflags` \
-+             -Xlinker -Bstatic -lpdf -Xlinker -Bdynamic \
-+             -L$(LOCALBASE)/lib -lX11 -lm 
- 	strip $@
- 
- 
diff --git a/biology/seaview/files/patch-use_mase_files.cxx b/biology/seaview/files/patch-use_mase_files.cxx
deleted file mode 100644
index 6f437c439880..000000000000
--- a/biology/seaview/files/patch-use_mase_files.cxx
+++ /dev/null
@@ -1,29 +0,0 @@
---- use_mase_files.cxx.orig	2011-11-17 14:20:13.000000000 +0100
-+++ use_mase_files.cxx	2011-11-17 14:20:01.000000000 +0100
-@@ -1457,8 +1457,6 @@
- 
- #else
- 
--extern "C" { int stat(char *, void *); }
--
- int check_path(char *fname)  
- /* to check for presence of file fname 
- searching for it through all path directories 
-@@ -1468,7 +1466,7 @@
- #define Mxdir 200
-     char dir[Mxdir+1], *path, *deb, *fin;
-     int lf, ltot;
--    static char stat_struct[250]; /* bigger than necessary */
-+	 struct stat sb;
-     path=getenv("PATH"); 	/* get the list of path directories, 
- 				    separated by :
- 				*/
-@@ -1488,7 +1486,7 @@
- 		    dir[ltot]='/';
- 		    strcpy(dir+ltot+1,fname); 
- 			/* now dir is appended with filename */
--		    if( stat(dir, stat_struct)  == 0) return 0;
-+		    if( stat(dir, &sb)  == 0) return 0;
- 		    }
- 	    deb=fin+1;
- 	    }
diff --git a/biology/seaview/pkg-plist b/biology/seaview/pkg-plist
deleted file mode 100644
index 6f5cd13faa7e..000000000000
--- a/biology/seaview/pkg-plist
+++ /dev/null
@@ -1,4 +0,0 @@
-bin/seaview
-bin/seaview_align.sh
-lib/X11/seaview/seaview.help
-@dirrm lib/X11/seaview