Update to version 5.1.

Many minor enhancements and bugfixes. Manual updated.

5 files changed, 20 insertions, 50 deletions

diff --git a/biology/puzzle/Makefile b/biology/puzzle/Makefile
index e04296d81a3..449316a2d1f 100644
--- a/biology/puzzle/Makefile
+++ b/biology/puzzle/Makefile
@@ -1,7 +1,7 @@
-# $NetBSD: Makefile,v 1.3 2001/07/08 13:36:33 jtb Exp $
+# $NetBSD: Makefile,v 1.4 2003/05/10 23:46:15 jtb Exp $
 
-DISTNAME=	tree-puzzle-5.0
-PKGNAME=	puzzle-5.0
+DISTNAME=	tree-puzzle-5.1
+PKGNAME=	puzzle-5.1
 CATEGORIES=	biology
 MASTER_SITES=	http://members.tripod.de/korbi/puzzle/ \
 		ftp://ftp.ebi.ac.uk/pub/software/unix/puzzle/ \
@@ -19,10 +19,13 @@ GNU_CONFIGURE=	yes
 
 post-install:
 	${INSTALL_DATA_DIR} ${PREFIX}/share/doc/puzzle
-	cd ${WRKSRC}/doc; ${INSTALL_DATA} manual.html *.gif 		\
+	cd ${WRKSRC}/doc && ${INSTALL_DATA} tree-puzzle.pdf	\
 		${PREFIX}/share/doc/puzzle
+	${INSTALL_DATA_DIR} ${PREFIX}/share/doc/html/puzzle
+	cd ${WRKSRC}/doc && ${INSTALL_DATA} tree-puzzle.html	\
+		*.gif ${PREFIX}/share/doc/html/puzzle
 	${INSTALL_DATA_DIR} ${PREFIX}/share/examples/puzzle
-	cd ${WRKSRC}/data; ${INSTALL_DATA} atp6.a globin.a		\
-		marswolf.n primates.b ${PREFIX}/share/examples/puzzle
+	cd ${WRKSRC}/data && ${INSTALL_DATA} EF.* *.a *.n *.b	\
+		${PREFIX}/share/examples/puzzle
 
 .include "../../mk/bsd.pkg.mk"
diff --git a/biology/puzzle/PLIST b/biology/puzzle/PLIST
index d11c95b0e34..ff59d506049 100644
--- a/biology/puzzle/PLIST
+++ b/biology/puzzle/PLIST
@@ -1,12 +1,16 @@
-@comment $NetBSD: PLIST,v 1.1 2001/10/31 21:28:12 zuntum Exp $
+@comment $NetBSD: PLIST,v 1.2 2003/05/10 23:46:15 jtb Exp $
 bin/ppuzzle
 bin/puzzle
-share/doc/puzzle/manual.html
-share/doc/puzzle/ppuzzle.gif
-share/doc/puzzle/puzzle.gif
+share/doc/html/puzzle/ppuzzle.gif
+share/doc/html/puzzle/puzzle.gif
+share/doc/html/puzzle/tree-puzzle.html
+share/doc/puzzle/tree-puzzle.pdf
+share/examples/puzzle/EF.3trees
+share/examples/puzzle/EF.phy
 share/examples/puzzle/atp6.a
 share/examples/puzzle/globin.a
 share/examples/puzzle/marswolf.n
 share/examples/puzzle/primates.b
 @dirrm share/doc/puzzle
+@dirrm share/doc/html/puzzle
 @dirrm share/examples/puzzle
diff --git a/biology/puzzle/distinfo b/biology/puzzle/distinfo
index cf329710c3b..383522b0a7c 100644
--- a/biology/puzzle/distinfo
+++ b/biology/puzzle/distinfo
@@ -1,6 +1,4 @@
-$NetBSD: distinfo,v 1.3 2001/07/08 13:36:33 jtb Exp $
+$NetBSD: distinfo,v 1.4 2003/05/10 23:46:15 jtb Exp $
 
-SHA1 (tree-puzzle-5.0.tar.gz) = 8c73c003a874c4c701b21b9fbdf0bbed496eda1a
-Size (tree-puzzle-5.0.tar.gz) = 190137 bytes
-SHA1 (patch-aa) = 4391e9ba6d8b01b59240f80dee09bf33b04e12ff
-SHA1 (patch-ab) = cf32c3bf87b3fba7b3e3476ae2ceb489610d2463
+SHA1 (tree-puzzle-5.1.tar.gz) = f55464587cd04c9afb0eb83231318d91b8614798
+Size (tree-puzzle-5.1.tar.gz) = 612216 bytes
diff --git a/biology/puzzle/patches/patch-aa b/biology/puzzle/patches/patch-aa
deleted file mode 100644
index 22c98752f2d..00000000000
--- a/biology/puzzle/patches/patch-aa
+++ /dev/null
@@ -1,13 +0,0 @@
-$NetBSD: patch-aa,v 1.2 2001/07/08 13:36:33 jtb Exp $
-
---- src/ml.h.orig	Thu May 24 05:12:06 2001
-+++ src/ml.h
-@@ -173,7 +173,7 @@
- /* function prototypes of all ml function */
- 
- void convfreq(dvector);
--void radixsort(cmatrix, ivector, int, int, int *);
-+void my_radixsort(cmatrix, ivector, int, int, int *);
- void condenceseq(cmatrix, ivector, cmatrix, ivector, int, int, int);
- void countconstantsites(cmatrix, ivector, int, int, int *, int*);
- void evaluateseqs(void);
diff --git a/biology/puzzle/patches/patch-ab b/biology/puzzle/patches/patch-ab
deleted file mode 100644
index 4781fa4c25c..00000000000
--- a/biology/puzzle/patches/patch-ab
+++ /dev/null
@@ -1,22 +0,0 @@
-$NetBSD: patch-ab,v 1.2 2001/07/08 13:36:33 jtb Exp $
-
---- src/ml1.c.orig	Thu May 24 05:12:15 2001
-+++ src/ml1.c
-@@ -78,7 +78,7 @@
- }
- 
- /* sort site patters of original input data */
--void radixsort(cmatrix seqchar, ivector ali, int maxspc, int maxsite,
-+void my_radixsort(cmatrix seqchar, ivector ali, int maxspc, int maxsite,
- 	int *numptrn)
- {
- 	int i, j, k, l, n, pass;
-@@ -196,7 +196,7 @@
- 
- 	convfreq(Freqtpm); /* make all frequencies slightly different */
- 	ali = new_ivector(Maxsite);
--	radixsort(Seqchar, ali, Maxspc, Maxsite, &Numptrn);
-+	my_radixsort(Seqchar, ali, Maxspc, Maxsite, &Numptrn);
- 	Seqpat = new_cmatrix(Maxspc, Numptrn);
- 	constpat = new_ivector(Numptrn);
- 	Weight = new_ivector(Numptrn);