Add seqio 1.2.2, a set of C functions which can read/write

biological sequence files.

PR:		29922
Submitted by:	Tony Maher <tonym@biolateral.com.au>

10 files changed, 400 insertions, 0 deletions

diff --git a/biology/Makefile b/biology/Makefile
index 2b424f67029d..a672c9011d82 100644
--- a/biology/Makefile
+++ b/biology/Makefile
@@ -37,6 +37,7 @@
     SUBDIR += rasmol
     SUBDIR += recombine
     SUBDIR += seaview
+    SUBDIR += seqio
     SUBDIR += sim4
     SUBDIR += tinker
     SUBDIR += treeviewx
diff --git a/biology/seqio/Makefile b/biology/seqio/Makefile
new file mode 100644
index 000000000000..cef43ebbeef1
--- /dev/null
+++ b/biology/seqio/Makefile
@@ -0,0 +1,48 @@
+# New ports collection makefile for:	seqio
+# Date created:				17 August 2001
+# Whom:					Tony Maher
+#
+# $FreeBSD$
+#
+
+PORTNAME=	seqio
+PORTVERSION=	1.2.2
+CATEGORIES=	biology
+MASTER_SITES=	http://www.cs.ucdavis.edu/~gusfield/
+DISTNAME=	${PORTNAME}
+
+MAINTAINER=	tonym@biolateral.com.au
+
+WRKSRC=		${WRKDIR}/${PORTNAME}-${PORTVERSION}
+
+EXAMPLESDIR=	${PREFIX}/share/examples/${PORTNAME}
+EXAMPLES=	example1.c example2.c example3.c example4.c seqio.c \
+		seqio.h Makefile
+PROGRAMS=	fmtseq grepseq idxseq typeseq wcseq
+
+do-install:
+	${MKDIR} ${DOCSDIR}
+	${MKDIR} ${DOCSDIR}/html
+	${MKDIR} ${EXAMPLESDIR}
+	cd ${WRKSRC}; \
+	for file in ${PROGRAMS}; do \
+		${INSTALL_PROGRAM} $$file ${PREFIX}/bin; \
+	done
+post-install:
+.if !defined(NOPORTDOCS)
+	cd ${WRKSRC}; \
+	for file in ${EXAMPLES}; do \
+		${INSTALL_DATA} $$file ${EXAMPLESDIR}; \
+	done
+	${INSTALL_DATA} ${WRKSRC}/bioseq.txt ${DOCSDIR}
+	cd ${WRKSRC}/doc; \
+	for file in *.doc; do \
+		${INSTALL_DATA} $$file ${DOCSDIR}; \
+	done
+	cd ${WRKSRC}/html; \
+	for file in *.html; do \
+		${INSTALL_DATA} $$file ${DOCSDIR}/html; \
+	done
+.endif
+
+.include <bsd.port.mk>
diff --git a/biology/seqio/distinfo b/biology/seqio/distinfo
new file mode 100644
index 000000000000..de46c4ef2c6e
--- /dev/null
+++ b/biology/seqio/distinfo
@@ -0,0 +1 @@
+MD5 (seqio.tar.gz) = c8e5d44485c8202082d4cfa516f9e0db
diff --git a/biology/seqio/files/patch-Makefile b/biology/seqio/files/patch-Makefile
new file mode 100644
index 000000000000..0efbc6f3f255
--- /dev/null
+++ b/biology/seqio/files/patch-Makefile
@@ -0,0 +1,11 @@
+--- Makefile.orig	Tue Aug 21 12:50:44 2001
++++ Makefile	Tue Aug 21 12:51:13 2001
+@@ -12,7 +12,7 @@
+ CFLAGS= -g -O2 -Wall -Wshadow
+ 
+ 
+-all: grepseq fmtseq idxseq typeseq wcseq examples
++all: grepseq fmtseq idxseq typeseq wcseq
+ 
+ grepseq: grepseq.o seqio.o
+ 	$(CC) $(CFLAGS) -o grepseq grepseq.o seqio.o
diff --git a/biology/seqio/files/patch-fmtseq b/biology/seqio/files/patch-fmtseq
new file mode 100644
index 000000000000..a11d0218d513
--- /dev/null
+++ b/biology/seqio/files/patch-fmtseq
@@ -0,0 +1,117 @@
+--- fmtseq.c.orig	Wed Jul 10 12:58:39 1996
++++ fmtseq.c	Tue Aug 21 13:17:23 2001
+@@ -37,7 +37,6 @@
+ #include <sys/stat.h>
+ #include "seqio.h"
+ 
+-extern char *sys_errlist[];
+ 
+ 
+ #ifdef WIN32
+@@ -70,6 +69,7 @@
+ #define ASK 2
+ #define ITEMLIST 3
+ 
++#define	MAXLINE	128
+ 
+ int pretty_flag, pretty_count;
+ FILE *fpout;
+@@ -81,7 +81,7 @@
+ } pretty;
+ 
+ 
+-char dna_complement[128], rna_complement[128];
++char dna_complement[MAXLINE], rna_complement[MAXLINE];
+ 
+ 
+ /*
+@@ -222,7 +222,7 @@
+ void print_options(int flag)
+ {
+   int i, j;
+-  char line[128];
++  char line[MAXLINE];
+ 
+   printf("Program Options (text in [...] is optional):\n");
+   printf("  -al[l]            select all sequences\n");
+@@ -249,7 +249,7 @@
+ 
+   if (flag) {
+     printf("More? ");
+-    gets(line);
++    fgets(line,MAXLINE-1,stdin);
+     if (line[0] == 'q' || line[0] == 'Q')
+       return;
+   }
+@@ -264,7 +264,7 @@
+ 
+   if (flag) {
+     printf("More? ");
+-    gets(line);
++    fgets(line,MAXLINE-1,stdin);
+     if (line[0] == 'q' || line[0] == 'Q')
+       return;
+   }
+@@ -1646,7 +1646,7 @@
+     s = line;
+     while (*s == '\0') {
+       printf("Enter: ");
+-      gets(line);
++      fgets(line,MAXLINE-1,stdin);
+       for (s=line; *s && isspace(*s); s++) ;
+     }
+     printf("----------------------\n\n");
+@@ -1701,7 +1701,7 @@
+ {
+   static char defch = 'y';
+   int init_print, count;
+-  char *s, *entry, *eptr, line[128];
++  char *s, *entry, *eptr, line[MAXLINE];
+ 
+   putchar('\n');
+   if (seqcount == 1) {
+@@ -1717,7 +1717,7 @@
+   eptr = entry = NULL;
+   while (1) {
+     printf("Select? [%c] ", defch);
+-    gets(line);
++    fgets(line,MAXLINE-1,stdin);
+ 
+     if (line[0] == '\0')
+       line[0] = defch;
+@@ -1771,7 +1771,7 @@
+                    SEQINFO *info, int mode)
+ {
+   int len;
+-  char *temp, tempbuffer[128];
++  char *temp, tempbuffer[MAXLINE];
+ 
+   if (buf != NULL)
+     temp = buf;
+@@ -1803,7 +1803,7 @@
+ 
+ int pretty_store(char *seq, int seqlen, SEQINFO *info)
+ {
+-  char buffer[128];
++  char buffer[MAXLINE];
+ 
+   if (pretty_count == psize) {
+     if (psize == 0) {
+@@ -2582,7 +2582,7 @@
+ 
+ void blastout_store(SEQFILE *sfp, char *seq, int seqlen, SEQINFO *info)
+ {
+-  static otherstrand = 0;
++  static int otherstrand = 0;
+   int pos, al_start, ingap, len;
+   char *s, *t1, *entry, *end, *line1, *line2;
+   ALIGN newalign;
+@@ -3017,7 +3017,7 @@
+ {
+   int i;
+ 
+-  for (i=0; i < 128; i++)
++  for (i=0; i < MAXLINE; i++)
+     dna_complement[i] = dna_complement[i] = i;
+ 
+   dna_complement['a'] = 't';  dna_complement['A'] = 'T';
diff --git a/biology/seqio/files/patch-grepseq b/biology/seqio/files/patch-grepseq
new file mode 100644
index 000000000000..a501901e0b47
--- /dev/null
+++ b/biology/seqio/files/patch-grepseq
@@ -0,0 +1,155 @@
+--- grepseq.c.orig	Sat Aug 18 16:19:15 2001
++++ grepseq.c	Sat Aug 18 16:37:58 2001
+@@ -18,7 +18,6 @@
+ #include <string.h>
+ #include "seqio.h"
+ 
+-extern char *sys_errlist[];
+ 
+ #define ASCII 4
+ 
+@@ -475,7 +474,7 @@
+         ascii_alpha_mask[num] |= mask;
+       }
+       else
+-        ascii_alpha_mask[*s] |= mask;
++        ascii_alpha_mask[(int) *s] |= mask;
+       break;
+       
+     case '.':
+@@ -518,7 +517,7 @@
+             ascii_alpha_mask[num] |= mask;
+           }
+           else
+-            ascii_alpha_mask[*s] |= mask;
++            ascii_alpha_mask[(int) *s] |= mask;
+         }
+         else {
+           if (dna_flag) {
+@@ -526,17 +525,17 @@
+               dna_flag = 0;
+             else
+               for ( ; *t; t++)
+-                dna_alpha_mask[*t] |= mask;
++                dna_alpha_mask[(int) *t] |= mask;
+           }
+           if (prt_flag) {
+             if ((t = prt_expand(*s)) == NULL)
+               prt_flag = 0;
+             else
+               for ( ; *t; t++)
+-                prt_alpha_mask[*t] |= mask;
++                prt_alpha_mask[(int) *t] |= mask;
+           }
+               
+-          ascii_alpha_mask[*s] |= mask;
++          ascii_alpha_mask[(int) *s] |= mask;
+         }
+       }
+         
+@@ -557,17 +556,17 @@
+           dna_flag = 0;
+         else
+           for ( ; *t; t++)
+-            dna_alpha_mask[*t] |= mask;
++            dna_alpha_mask[(int) *t] |= mask;
+       }
+       if (prt_flag) {
+         if ((t = prt_expand(*s)) == NULL)
+           prt_flag = 0;
+         else
+           for ( ; *t; t++)
+-            prt_alpha_mask[*t] |= mask;
++            prt_alpha_mask[(int) *t] |= mask;
+       }
+               
+-      ascii_alpha_mask[*s] |= mask;
++      ascii_alpha_mask[(int) *s] |= mask;
+     }
+ 
+     /*
+@@ -677,16 +676,16 @@
+      */
+     if (num_errors == 0) {
+       score = 0;
+-      while ((ch = *s) && table[ch] &&
+-             !((masklist0 = ((masklist0 << 1) & alpha_mask[*s]) + 1) &
++      while ((ch = *s) && table[(int) ch] &&
++             !((masklist0 = ((masklist0 << 1) & alpha_mask[(int) *s]) + 1) &
+                accept_mask))
+         s++;
+     }
+     else if (num_errors == 1) {
+       score = -1;
+       if (misonly_flag) {
+-        while ((ch = *s) && table[ch]) {
+-          chmask = alpha_mask[ch];
++        while ((ch = *s) && table[(int) ch]) {
++          chmask = alpha_mask[(int) ch];
+           last_mask = masklist0;
+           masklist0 = ((masklist0 << 1) & chmask) + 1;
+           masklist1 = ((masklist1 << 1) & chmask) | (last_mask << 1);
+@@ -703,8 +702,8 @@
+         }
+       }
+       else {
+-        while ((ch = *s) && table[ch]) {
+-          chmask = alpha_mask[ch];
++        while ((ch = *s) && table[(int) ch]) {
++          chmask = alpha_mask[(int) ch];
+           last_mask = masklist0;
+           masklist0 = ((masklist0 << 1) & chmask) + 1;
+           masklist1 = ((masklist1 << 1) & chmask) |  /* match */
+@@ -727,8 +726,8 @@
+     else if (num_errors == 2) {
+       score = -1;
+       if (misonly_flag) {
+-        while ((ch = *s) && table[ch]) {
+-          chmask = alpha_mask[ch];
++        while ((ch = *s) && table[(int) ch]) {
++          chmask = alpha_mask[(int) ch];
+           last_mask = masklist0;
+           masklist0 = ((masklist0 << 1) & chmask) + 1;
+           newmask = ((masklist1 << 1) & chmask) | (last_mask << 1);
+@@ -752,8 +751,8 @@
+         }
+       }
+       else {
+-        while ((ch = *s) && table[ch]) {
+-          chmask = alpha_mask[ch];
++        while ((ch = *s) && table[(int) ch]) {
++          chmask = alpha_mask[(int) ch];
+           last_mask = masklist0;
+           masklist0 = ((masklist0 << 1) & chmask) + 1;
+           newmask = ((masklist1 << 1) & chmask) |  /* match */
+@@ -785,8 +784,8 @@
+     }
+     else if (misonly_flag) {
+       score = -1;
+-      while ((ch = *s) && table[ch]) {
+-        chmask = alpha_mask[ch];
++      while ((ch = *s) && table[(int) ch]) {
++        chmask = alpha_mask[(int) ch];
+ 
+         last_mask = masklist[0];
+         masklist[0] = ((masklist[0] << 1) & chmask) + 1;
+@@ -808,8 +807,8 @@
+     }
+     else {
+       score = -1;
+-      while ((ch = *s) && table[ch]) {
+-        chmask = alpha_mask[ch];
++      while ((ch = *s) && table[(int) ch]) {
++        chmask = alpha_mask[(int) ch];
+ 
+         last_mask = masklist[0];
+         masklist[0] = ((masklist[0] << 1) & chmask) + 1;
+@@ -835,7 +834,7 @@
+       
+     if (!ch)
+       break;
+-    else if (!table[ch]) {
++    else if (!table[(int) ch]) {
+       fprintf(stderr, "%s, entry %d:  Sequence contains invalid characters.\n",
+               seqffilename(sfp, 0), seqfentryno(sfp));
+       return NULL;
diff --git a/biology/seqio/files/patch-seqio b/biology/seqio/files/patch-seqio
new file mode 100644
index 000000000000..3e637ebacbc5
--- /dev/null
+++ b/biology/seqio/files/patch-seqio
@@ -0,0 +1,18 @@
+--- seqio.c.orig	Sat Aug 18 16:20:53 2001
++++ seqio.c	Sat Aug 18 16:21:23 2001
+@@ -147,7 +147,6 @@
+  * files, and replacement functions for system calls that don't exist on
+  * one or more machines.
+  */
+-extern char *sys_errlist[];
+ 
+ #if defined(__sun) && !defined(FILENAME_MAX)
+ #include <sys/param.h>
+@@ -158,7 +157,6 @@
+ static int ctype_initflag = 0;
+ static char tubuf[384], *tuary;
+ 
+-#define toupper(chr) tuary[(int) (chr)]
+ 
+ static void init_ctype(void)
+ {
diff --git a/biology/seqio/pkg-comment b/biology/seqio/pkg-comment
new file mode 100644
index 000000000000..28a8996b157a
--- /dev/null
+++ b/biology/seqio/pkg-comment
@@ -0,0 +1 @@
+A set of C functions which can read/write biological sequence files 
diff --git a/biology/seqio/pkg-descr b/biology/seqio/pkg-descr
new file mode 100644
index 000000000000..d1fd69575d0c
--- /dev/null
+++ b/biology/seqio/pkg-descr
@@ -0,0 +1,9 @@
+"The SEQIO package is a set of C functions which can read and write
+biological sequence files formatted using various file formats and which
+can be used to perform database searches on biological databases."
+- from the README file
+
+WWW: http://www.cs.ucdavis.edu/~gusfield/seqio.html
+
+--
+Tony Maher <tonym@biolateral.com.au>
diff --git a/biology/seqio/pkg-plist b/biology/seqio/pkg-plist
new file mode 100644
index 000000000000..4e929f3152e4
--- /dev/null
+++ b/biology/seqio/pkg-plist
@@ -0,0 +1,39 @@
+bin/fmtseq
+bin/grepseq
+bin/idxseq
+bin/typeseq
+bin/wcseq
+%%PORTDOCS%%share/doc/seqio/html/bigaln_example.html
+%%PORTDOCS%%share/doc/seqio/html/examples_doc.html
+%%PORTDOCS%%share/doc/seqio/html/fmtseq_doc.html
+%%PORTDOCS%%share/doc/seqio/html/idxseq_doc.html
+%%PORTDOCS%%share/doc/seqio/html/seqio.html
+%%PORTDOCS%%share/doc/seqio/html/seqio_bioseq.html
+%%PORTDOCS%%share/doc/seqio/html/seqio_changes.html
+%%PORTDOCS%%share/doc/seqio/html/seqio_doc.html
+%%PORTDOCS%%share/doc/seqio/html/seqio_format.html
+%%PORTDOCS%%share/doc/seqio/html/seqio_progr.html
+%%PORTDOCS%%share/doc/seqio/html/seqio_qref.html
+%%PORTDOCS%%share/doc/seqio/html/seqio_readme.html
+%%PORTDOCS%%share/doc/seqio/html/seqio_toc.html
+%%PORTDOCS%%share/doc/seqio/html/seqio_todo.html
+%%PORTDOCS%%share/doc/seqio/html/seqio_user.html
+%%PORTDOCS%%share/doc/seqio/bioseq.txt
+%%PORTDOCS%%share/doc/seqio/examples.doc
+%%PORTDOCS%%share/doc/seqio/fmtseq.doc
+%%PORTDOCS%%share/doc/seqio/format.doc
+%%PORTDOCS%%share/doc/seqio/idxseq.doc
+%%PORTDOCS%%share/doc/seqio/programr.doc
+%%PORTDOCS%%share/doc/seqio/quickref.doc
+%%PORTDOCS%%share/doc/seqio/seqio.doc
+%%PORTDOCS%%share/doc/seqio/user.doc
+%%PORTDOCS%%share/examples/seqio/example1.c
+%%PORTDOCS%%share/examples/seqio/example2.c
+%%PORTDOCS%%share/examples/seqio/example3.c
+%%PORTDOCS%%share/examples/seqio/example4.c
+%%PORTDOCS%%share/examples/seqio/seqio.c
+%%PORTDOCS%%share/examples/seqio/seqio.h
+%%PORTDOCS%%share/examples/seqio/Makefile
+%%PORTDOCS%%@dirrm share/doc/seqio/html
+%%PORTDOCS%%@dirrm share/doc/seqio
+%%PORTDOCS%%@dirrm share/examples/seqio