From owner-freebsd-ports Tue Aug 21 3:30:24 2001 Delivered-To: freebsd-ports@hub.freebsd.org Received: from freefall.freebsd.org (freefall.freebsd.org [216.136.204.21]) by hub.freebsd.org (Postfix) with ESMTP id 1968737B40C for ; Tue, 21 Aug 2001 03:30:07 -0700 (PDT) (envelope-from gnats@FreeBSD.org) Received: (from gnats@localhost) by freefall.freebsd.org (8.11.4/8.11.4) id f7LAU6308936; Tue, 21 Aug 2001 03:30:06 -0700 (PDT) (envelope-from gnats) Received: from mss.rdc2.nsw.optushome.com.au (ha1.rdc2.nsw.optushome.com.au [203.164.2.50]) by hub.freebsd.org (Postfix) with ESMTP id 1F5DB37B416 for ; Tue, 21 Aug 2001 03:26:00 -0700 (PDT) (envelope-from tonym@biolateral.com.au) Received: from dt.home ([203.164.148.68]) by mss.rdc2.nsw.optushome.com.au (InterMail vM.4.01.03.20 201-229-121-120-20010223) with ESMTP id <20010821102558.GQLI4715.mss.rdc2.nsw.optushome.com.au@dt.home> for ; Tue, 21 Aug 2001 20:25:58 +1000 Received: (from tonym@localhost) by dt.home (8.11.5/8.11.5) id f7LAORb59595; Tue, 21 Aug 2001 20:24:27 +1000 (EST) (envelope-from tonym) Message-Id: <200108211024.f7LAORb59595@dt.home> Date: Tue, 21 Aug 2001 20:24:27 +1000 (EST) From: Tony Maher Reply-To: Tony Maher To: FreeBSD-gnats-submit@freebsd.org X-Send-Pr-Version: 3.113 Subject: ports/29922: New port: biology/seqio - a set of C functions to read/write bilogical sequences Sender: owner-freebsd-ports@FreeBSD.ORG Precedence: bulk List-ID: List-Archive: (Web Archive) List-Help: (List Instructions) List-Subscribe: List-Unsubscribe: X-Loop: FreeBSD.org >Number: 29922 >Category: ports >Synopsis: New port: biology/seqio - a set of C functions to read/write bilogical sequences >Confidential: no >Severity: non-critical >Priority: low >Responsible: freebsd-ports >State: open >Quarter: >Keywords: >Date-Required: >Class: change-request >Submitter-Id: current-users >Arrival-Date: Tue Aug 21 03:30:06 PDT 2001 >Closed-Date: >Last-Modified: >Originator: Tony Maher >Release: FreeBSD 4.4-RC i386 >Organization: Biolateral >Environment: System: FreeBSD dt.home 4.4-RC FreeBSD 4.4-RC #6: Fri Aug 17 14:21:47 EST 2001 root@dt.home:/usr/src/sys/compile/DT i386 >Description: "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 It also has 4 useful executables that utilize seqio. >How-To-Repeat: >Fix: # This is a shell archive. Save it in a file, remove anything before # this line, and then unpack it by entering "sh file". Note, it may # create directories; files and directories will be owned by you and # have default permissions. # # This archive contains: # # seqio # seqio/files # seqio/files/patch-grepseq # seqio/files/patch-fmtseq # seqio/files/patch-seqio # seqio/files/patch-Makefile # seqio/pkg-plist # seqio/pkg-descr # seqio/pkg-comment # seqio/distinfo # seqio/Makefile # echo c - seqio mkdir -p seqio > /dev/null 2>&1 echo c - seqio/files mkdir -p seqio/files > /dev/null 2>&1 echo x - seqio/files/patch-grepseq sed 's/^X//' >seqio/files/patch-grepseq << 'END-of-seqio/files/patch-grepseq' X--- grepseq.c.orig Sat Aug 18 16:19:15 2001 X+++ grepseq.c Sat Aug 18 16:37:58 2001 X@@ -18,7 +18,6 @@ X #include X #include "seqio.h" X X-extern char *sys_errlist[]; X X #define ASCII 4 X X@@ -475,7 +474,7 @@ X ascii_alpha_mask[num] |= mask; X } X else X- ascii_alpha_mask[*s] |= mask; X+ ascii_alpha_mask[(int) *s] |= mask; X break; X X case '.': X@@ -518,7 +517,7 @@ X ascii_alpha_mask[num] |= mask; X } X else X- ascii_alpha_mask[*s] |= mask; X+ ascii_alpha_mask[(int) *s] |= mask; X } X else { X if (dna_flag) { X@@ -526,17 +525,17 @@ X dna_flag = 0; X else X for ( ; *t; t++) X- dna_alpha_mask[*t] |= mask; X+ dna_alpha_mask[(int) *t] |= mask; X } X if (prt_flag) { X if ((t = prt_expand(*s)) == NULL) X prt_flag = 0; X else X for ( ; *t; t++) X- prt_alpha_mask[*t] |= mask; X+ prt_alpha_mask[(int) *t] |= mask; X } X X- ascii_alpha_mask[*s] |= mask; X+ ascii_alpha_mask[(int) *s] |= mask; X } X } X X@@ -557,17 +556,17 @@ X dna_flag = 0; X else X for ( ; *t; t++) X- dna_alpha_mask[*t] |= mask; X+ dna_alpha_mask[(int) *t] |= mask; X } X if (prt_flag) { X if ((t = prt_expand(*s)) == NULL) X prt_flag = 0; X else X for ( ; *t; t++) X- prt_alpha_mask[*t] |= mask; X+ prt_alpha_mask[(int) *t] |= mask; X } X X- ascii_alpha_mask[*s] |= mask; X+ ascii_alpha_mask[(int) *s] |= mask; X } X X /* X@@ -677,16 +676,16 @@ X */ X if (num_errors == 0) { X score = 0; X- while ((ch = *s) && table[ch] && X- !((masklist0 = ((masklist0 << 1) & alpha_mask[*s]) + 1) & X+ while ((ch = *s) && table[(int) ch] && X+ !((masklist0 = ((masklist0 << 1) & alpha_mask[(int) *s]) + 1) & X accept_mask)) X s++; X } X else if (num_errors == 1) { X score = -1; X if (misonly_flag) { X- while ((ch = *s) && table[ch]) { X- chmask = alpha_mask[ch]; X+ while ((ch = *s) && table[(int) ch]) { X+ chmask = alpha_mask[(int) ch]; X last_mask = masklist0; X masklist0 = ((masklist0 << 1) & chmask) + 1; X masklist1 = ((masklist1 << 1) & chmask) | (last_mask << 1); X@@ -703,8 +702,8 @@ X } X } X else { X- while ((ch = *s) && table[ch]) { X- chmask = alpha_mask[ch]; X+ while ((ch = *s) && table[(int) ch]) { X+ chmask = alpha_mask[(int) ch]; X last_mask = masklist0; X masklist0 = ((masklist0 << 1) & chmask) + 1; X masklist1 = ((masklist1 << 1) & chmask) | /* match */ X@@ -727,8 +726,8 @@ X else if (num_errors == 2) { X score = -1; X if (misonly_flag) { X- while ((ch = *s) && table[ch]) { X- chmask = alpha_mask[ch]; X+ while ((ch = *s) && table[(int) ch]) { X+ chmask = alpha_mask[(int) ch]; X last_mask = masklist0; X masklist0 = ((masklist0 << 1) & chmask) + 1; X newmask = ((masklist1 << 1) & chmask) | (last_mask << 1); X@@ -752,8 +751,8 @@ X } X } X else { X- while ((ch = *s) && table[ch]) { X- chmask = alpha_mask[ch]; X+ while ((ch = *s) && table[(int) ch]) { X+ chmask = alpha_mask[(int) ch]; X last_mask = masklist0; X masklist0 = ((masklist0 << 1) & chmask) + 1; X newmask = ((masklist1 << 1) & chmask) | /* match */ X@@ -785,8 +784,8 @@ X } X else if (misonly_flag) { X score = -1; X- while ((ch = *s) && table[ch]) { X- chmask = alpha_mask[ch]; X+ while ((ch = *s) && table[(int) ch]) { X+ chmask = alpha_mask[(int) ch]; X X last_mask = masklist[0]; X masklist[0] = ((masklist[0] << 1) & chmask) + 1; X@@ -808,8 +807,8 @@ X } X else { X score = -1; X- while ((ch = *s) && table[ch]) { X- chmask = alpha_mask[ch]; X+ while ((ch = *s) && table[(int) ch]) { X+ chmask = alpha_mask[(int) ch]; X X last_mask = masklist[0]; X masklist[0] = ((masklist[0] << 1) & chmask) + 1; X@@ -835,7 +834,7 @@ X X if (!ch) X break; X- else if (!table[ch]) { X+ else if (!table[(int) ch]) { X fprintf(stderr, "%s, entry %d: Sequence contains invalid characters.\n", X seqffilename(sfp, 0), seqfentryno(sfp)); X return NULL; END-of-seqio/files/patch-grepseq echo x - seqio/files/patch-fmtseq sed 's/^X//' >seqio/files/patch-fmtseq << 'END-of-seqio/files/patch-fmtseq' X--- fmtseq.c.orig Wed Jul 10 12:58:39 1996 X+++ fmtseq.c Tue Aug 21 13:17:23 2001 X@@ -37,7 +37,6 @@ X #include X #include "seqio.h" X X-extern char *sys_errlist[]; X X X #ifdef WIN32 X@@ -70,6 +69,7 @@ X #define ASK 2 X #define ITEMLIST 3 X X+#define MAXLINE 128 X X int pretty_flag, pretty_count; X FILE *fpout; X@@ -81,7 +81,7 @@ X } pretty; X X X-char dna_complement[128], rna_complement[128]; X+char dna_complement[MAXLINE], rna_complement[MAXLINE]; X X X /* X@@ -222,7 +222,7 @@ X void print_options(int flag) X { X int i, j; X- char line[128]; X+ char line[MAXLINE]; X X printf("Program Options (text in [...] is optional):\n"); X printf(" -al[l] select all sequences\n"); X@@ -249,7 +249,7 @@ X X if (flag) { X printf("More? "); X- gets(line); X+ fgets(line,MAXLINE-1,stdin); X if (line[0] == 'q' || line[0] == 'Q') X return; X } X@@ -264,7 +264,7 @@ X X if (flag) { X printf("More? "); X- gets(line); X+ fgets(line,MAXLINE-1,stdin); X if (line[0] == 'q' || line[0] == 'Q') X return; X } X@@ -1646,7 +1646,7 @@ X s = line; X while (*s == '\0') { X printf("Enter: "); X- gets(line); X+ fgets(line,MAXLINE-1,stdin); X for (s=line; *s && isspace(*s); s++) ; X } X printf("----------------------\n\n"); X@@ -1701,7 +1701,7 @@ X { X static char defch = 'y'; X int init_print, count; X- char *s, *entry, *eptr, line[128]; X+ char *s, *entry, *eptr, line[MAXLINE]; X X putchar('\n'); X if (seqcount == 1) { X@@ -1717,7 +1717,7 @@ X eptr = entry = NULL; X while (1) { X printf("Select? [%c] ", defch); X- gets(line); X+ fgets(line,MAXLINE-1,stdin); X X if (line[0] == '\0') X line[0] = defch; X@@ -1771,7 +1771,7 @@ X SEQINFO *info, int mode) X { X int len; X- char *temp, tempbuffer[128]; X+ char *temp, tempbuffer[MAXLINE]; X X if (buf != NULL) X temp = buf; X@@ -1803,7 +1803,7 @@ X X int pretty_store(char *seq, int seqlen, SEQINFO *info) X { X- char buffer[128]; X+ char buffer[MAXLINE]; X X if (pretty_count == psize) { X if (psize == 0) { X@@ -2582,7 +2582,7 @@ X X void blastout_store(SEQFILE *sfp, char *seq, int seqlen, SEQINFO *info) X { X- static otherstrand = 0; X+ static int otherstrand = 0; X int pos, al_start, ingap, len; X char *s, *t1, *entry, *end, *line1, *line2; X ALIGN newalign; X@@ -3017,7 +3017,7 @@ X { X int i; X X- for (i=0; i < 128; i++) X+ for (i=0; i < MAXLINE; i++) X dna_complement[i] = dna_complement[i] = i; X X dna_complement['a'] = 't'; dna_complement['A'] = 'T'; END-of-seqio/files/patch-fmtseq echo x - seqio/files/patch-seqio sed 's/^X//' >seqio/files/patch-seqio << 'END-of-seqio/files/patch-seqio' X--- seqio.c.orig Sat Aug 18 16:20:53 2001 X+++ seqio.c Sat Aug 18 16:21:23 2001 X@@ -147,7 +147,6 @@ X * files, and replacement functions for system calls that don't exist on X * one or more machines. X */ X-extern char *sys_errlist[]; X X #if defined(__sun) && !defined(FILENAME_MAX) X #include X@@ -158,7 +157,6 @@ X static int ctype_initflag = 0; X static char tubuf[384], *tuary; X X-#define toupper(chr) tuary[(int) (chr)] X X static void init_ctype(void) X { END-of-seqio/files/patch-seqio echo x - seqio/files/patch-Makefile sed 's/^X//' >seqio/files/patch-Makefile << 'END-of-seqio/files/patch-Makefile' X--- Makefile.orig Tue Aug 21 12:50:44 2001 X+++ Makefile Tue Aug 21 12:51:13 2001 X@@ -12,7 +12,7 @@ X CFLAGS= -g -O2 -Wall -Wshadow X X X-all: grepseq fmtseq idxseq typeseq wcseq examples X+all: grepseq fmtseq idxseq typeseq wcseq X X grepseq: grepseq.o seqio.o X $(CC) $(CFLAGS) -o grepseq grepseq.o seqio.o END-of-seqio/files/patch-Makefile echo x - seqio/pkg-plist sed 's/^X//' >seqio/pkg-plist << 'END-of-seqio/pkg-plist' Xbin/fmtseq Xbin/grepseq Xbin/idxseq Xbin/typeseq Xbin/wcseq Xshare/doc/seqio/html/bigaln_example.html Xshare/doc/seqio/html/examples_doc.html Xshare/doc/seqio/html/fmtseq_doc.html Xshare/doc/seqio/html/idxseq_doc.html Xshare/doc/seqio/html/seqio.html Xshare/doc/seqio/html/seqio_bioseq.html Xshare/doc/seqio/html/seqio_changes.html Xshare/doc/seqio/html/seqio_doc.html Xshare/doc/seqio/html/seqio_format.html Xshare/doc/seqio/html/seqio_progr.html Xshare/doc/seqio/html/seqio_qref.html Xshare/doc/seqio/html/seqio_readme.html Xshare/doc/seqio/html/seqio_toc.html Xshare/doc/seqio/html/seqio_todo.html Xshare/doc/seqio/html/seqio_user.html Xshare/doc/seqio/bioseq.txt Xshare/doc/seqio/examples.doc Xshare/doc/seqio/fmtseq.doc Xshare/doc/seqio/format.doc Xshare/doc/seqio/idxseq.doc Xshare/doc/seqio/programr.doc Xshare/doc/seqio/quickref.doc Xshare/doc/seqio/seqio.doc Xshare/doc/seqio/user.doc Xshare/examples/seqio/example1.c Xshare/examples/seqio/example2.c Xshare/examples/seqio/example3.c Xshare/examples/seqio/example4.c Xshare/examples/seqio/seqio.c Xshare/examples/seqio/seqio.h Xshare/examples/seqio/Makefile X@dirrm share/doc/seqio/html X@dirrm share/doc/seqio X@dirrm share/examples/seqio END-of-seqio/pkg-plist echo x - seqio/pkg-descr sed 's/^X//' >seqio/pkg-descr << 'END-of-seqio/pkg-descr' X"The SEQIO package is a set of C functions which can read and write Xbiological sequence files formatted using various file formats and which Xcan be used to perform database searches on biological databases." X- from the README file X XWWW: http://www.cs.ucdavis.edu/~gusfield/seqio.html X X-- XTony Maher END-of-seqio/pkg-descr echo x - seqio/pkg-comment sed 's/^X//' >seqio/pkg-comment << 'END-of-seqio/pkg-comment' XA set of C functions which can read/write biological sequence files END-of-seqio/pkg-comment echo x - seqio/distinfo sed 's/^X//' >seqio/distinfo << 'END-of-seqio/distinfo' XMD5 (seqio.tar.gz) = c8e5d44485c8202082d4cfa516f9e0db END-of-seqio/distinfo echo x - seqio/Makefile sed 's/^X//' >seqio/Makefile << 'END-of-seqio/Makefile' X# New ports collection makefile for: seqio X# Date created: 17 August 2001 X# Whom: Tony Maher X# X# $FreeBSD$ X# X XPORTNAME= seqio XPORTVERSION= 1.2.2 XCATEGORIES= biology XMASTER_SITES= http://www.cs.ucdavis.edu/~gusfield/ XDISTNAME= ${PORTNAME} X XMAINTAINER= tonym@biolateral.com.au X XWRKSRC= ${WRKDIR}/${PORTNAME}-${PORTVERSION} X XEXAMPLESDIR= ${PREFIX}/share/examples/${PORTNAME} XEXAMPLES= example1.c example2.c example3.c example4.c seqio.c seqio.h Makefile XPROGRAMS= fmtseq grepseq idxseq typeseq wcseq X Xdo-install: X ${MKDIR} ${DOCSDIR} X ${MKDIR} ${DOCSDIR}/html X ${MKDIR} ${EXAMPLESDIR} X cd ${WRKSRC}; \ X for file in ${PROGRAMS}; do \ X ${INSTALL_PROGRAM} $$file ${PREFIX}/bin; \ X done X cd ${WRKSRC}; \ X for file in ${EXAMPLES}; do \ X ${INSTALL_DATA} $$file ${EXAMPLESDIR}; \ X done X ${INSTALL_DATA} ${WRKSRC}/bioseq.txt ${DOCSDIR} X cd ${WRKSRC}/doc; \ X for file in *.doc; do \ X ${INSTALL_DATA} $$file ${DOCSDIR}; \ X done X cd ${WRKSRC}/html; \ X for file in *.html; do \ X ${INSTALL_DATA} $$file ${DOCSDIR}/html; \ X done X X.include END-of-seqio/Makefile exit >Release-Note: >Audit-Trail: >Unformatted: To Unsubscribe: send mail to majordomo@FreeBSD.org with "unsubscribe freebsd-ports" in the body of the message