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 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 + #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 + #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 +@@ -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 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