[med-svn] r4406 - in trunk/packages/readseq/trunk/debian: . patches
Andreas Tille
tille at alioth.debian.org
Thu Nov 26 11:33:48 UTC 2009
Author: tille
Date: 2009-11-26 11:33:48 +0000 (Thu, 26 Nov 2009)
New Revision: 4406
Added:
trunk/packages/readseq/trunk/debian/compat
trunk/packages/readseq/trunk/debian/patches/20-Formats.patch
trunk/packages/readseq/trunk/debian/patches/20-Makefile.patch
trunk/packages/readseq/trunk/debian/patches/30-arb-code-patches.patch
trunk/packages/readseq/trunk/debian/patches/552830.patch
trunk/packages/readseq/trunk/debian/patches/series
Removed:
trunk/packages/readseq/trunk/debian/patches/00list
trunk/packages/readseq/trunk/debian/patches/20-Formats.dpatch
trunk/packages/readseq/trunk/debian/patches/20-Makefile.dpatch
trunk/packages/readseq/trunk/debian/patches/30-arb-code-patches.dpatch
Modified:
trunk/packages/readseq/trunk/debian/changelog
trunk/packages/readseq/trunk/debian/control
trunk/packages/readseq/trunk/debian/rules
Log:
Switch from dpatch to quilt, patch to fix #552830
Modified: trunk/packages/readseq/trunk/debian/changelog
===================================================================
--- trunk/packages/readseq/trunk/debian/changelog 2009-11-26 09:49:09 UTC (rev 4405)
+++ trunk/packages/readseq/trunk/debian/changelog 2009-11-26 11:33:48 UTC (rev 4406)
@@ -1,16 +1,19 @@
readseq (1-8) UNRELEASED; urgency=low
+ [ Charles Plessy ]
+ * DM-Upload-Allowed: Yes
+
[ Andreas Tille ]
* Added Vcs-Browser, Vcs-Svn
+ * Standards-Version: 3.8.3 (no changes needed)
+ * Debhelper 7
+ * Switch to quilt
+ * debian/patches/552830.patch: Patch from Ruben Molina <rmolina at udea.edu.co>
+ to fix build problem (thanks to Ruben)
+ Closes: #552830
- [ Charles Plessy ]
- * XS-DM-Upload-Allowed: Yes
+ -- Andreas Tille <tille at debian.org> Thu, 26 Nov 2009 12:31:49 +0100
- [ David Paleino ]
- * Updated to Standards-Version 3.7.3 (no changes needed)
-
- -- David Paleino <d.paleino at gmail.com> Wed, 06 Feb 2008 13:11:57 +0100
-
readseq (1-7) unstable; urgency=low
* Group maintainance by Debian-Med packaging group
Added: trunk/packages/readseq/trunk/debian/compat
===================================================================
--- trunk/packages/readseq/trunk/debian/compat (rev 0)
+++ trunk/packages/readseq/trunk/debian/compat 2009-11-26 11:33:48 UTC (rev 4406)
@@ -0,0 +1 @@
+7
Modified: trunk/packages/readseq/trunk/debian/control
===================================================================
--- trunk/packages/readseq/trunk/debian/control 2009-11-26 09:49:09 UTC (rev 4405)
+++ trunk/packages/readseq/trunk/debian/control 2009-11-26 11:33:48 UTC (rev 4406)
@@ -3,9 +3,9 @@
Priority: optional
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
DM-Upload-Allowed: yes
-Uploaders: Michael Schmitz <schmitz at debian.org>, Andreas Tille <tille at debian.org>
-Build-Depends: debhelper (>= 5.0), cdbs, dpatch, ncbi-tools-dev
-Standards-Version: 3.7.3
+Uploaders: Andreas Tille <tille at debian.org>
+Build-Depends: debhelper (>= 7.0), cdbs, quilt, ncbi-tools-dev
+Standards-Version: 3.8.3
Homepage: http://iubio.bio.indiana.edu/soft/molbio/readseq/
Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/readseq/trunk/?rev=0&sc=0
Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/readseq/trunk/
Deleted: trunk/packages/readseq/trunk/debian/patches/00list
===================================================================
--- trunk/packages/readseq/trunk/debian/patches/00list 2009-11-26 09:49:09 UTC (rev 4405)
+++ trunk/packages/readseq/trunk/debian/patches/00list 2009-11-26 11:33:48 UTC (rev 4406)
@@ -1,3 +0,0 @@
-20-Formats.dpatch
-20-Makefile.dpatch
-30-arb-code-patches.dpatch
Deleted: trunk/packages/readseq/trunk/debian/patches/20-Formats.dpatch
===================================================================
--- trunk/packages/readseq/trunk/debian/patches/20-Formats.dpatch 2009-11-26 09:49:09 UTC (rev 4405)
+++ trunk/packages/readseq/trunk/debian/patches/20-Formats.dpatch 2009-11-26 11:33:48 UTC (rev 4406)
@@ -1,30 +0,0 @@
-#! /bin/sh /usr/share/dpatch/dpatch-run
-## 20_Format.dpatch by <tille at debian.org>
-##
-## All lines beginning with `## DP:' are a description of the patch.
-## DP: Add new Formats for ARB
-
- at DPATCH@
-
---- readseq-1/Formats.orig 1992-12-30 01:00:00.000000000 +0100
-+++ readseq-1/Formats 2007-11-14 12:14:36.000000000 +0100
-@@ -978,3 +978,19 @@
- hist Seq-hist OPTIONAL } -- sequence history
-
- ------------------------------------------------
-+
-+||||||||||| LinAll sequence file format
-+----------------------------------------
-+
-+1234 seq1-id (1234 is sequence length, right justified)
-+abcdefghijklmnopqrstuvwxyzabcdefghijklmnopqrstuvwxyzabcdefghijklmnopqrstuvwxyzab
-+cdefghijklmnopqrstuvwxyzabcdefghijklmnopqrstuvwxyz
-+(80 characters per line, one sequence per file)
-+
-+||||||||||| Vienna RNA sequence file format
-+--------------------------------------------
-+
-+> seq1-id
-+jsdhkasjlhsdlkjcbsd ... (one single line)
-+> seq2-id
-+odjgoirhggonavdskgj ... (one single line)
Added: trunk/packages/readseq/trunk/debian/patches/20-Formats.patch
===================================================================
--- trunk/packages/readseq/trunk/debian/patches/20-Formats.patch (rev 0)
+++ trunk/packages/readseq/trunk/debian/patches/20-Formats.patch 2009-11-26 11:33:48 UTC (rev 4406)
@@ -0,0 +1,25 @@
+Author: Andreas Tille <tille at debian.org>
+Description: Add new Formats for ARB
+
+--- readseq-1/Formats.orig 1992-12-30 01:00:00.000000000 +0100
++++ readseq-1/Formats 2007-11-14 12:14:36.000000000 +0100
+@@ -978,3 +978,19 @@
+ hist Seq-hist OPTIONAL } -- sequence history
+
+ ------------------------------------------------
++
++||||||||||| LinAll sequence file format
++----------------------------------------
++
++1234 seq1-id (1234 is sequence length, right justified)
++abcdefghijklmnopqrstuvwxyzabcdefghijklmnopqrstuvwxyzabcdefghijklmnopqrstuvwxyzab
++cdefghijklmnopqrstuvwxyzabcdefghijklmnopqrstuvwxyz
++(80 characters per line, one sequence per file)
++
++||||||||||| Vienna RNA sequence file format
++--------------------------------------------
++
++> seq1-id
++jsdhkasjlhsdlkjcbsd ... (one single line)
++> seq2-id
++odjgoirhggonavdskgj ... (one single line)
Deleted: trunk/packages/readseq/trunk/debian/patches/20-Makefile.dpatch
===================================================================
--- trunk/packages/readseq/trunk/debian/patches/20-Makefile.dpatch 2009-11-26 09:49:09 UTC (rev 4405)
+++ trunk/packages/readseq/trunk/debian/patches/20-Makefile.dpatch 2009-11-26 11:33:48 UTC (rev 4406)
@@ -1,147 +0,0 @@
-#! /bin/sh /usr/share/dpatch/dpatch-run
-## 20_Makefile.dpatch by <tille at debian.org>
-##
-## All lines beginning with `## DP:' are a description of the patch.
-## DP: Enhanced Makefile
-
- at DPATCH@
-
---- readseq-1/Makefile.orig 1992-12-30 01:00:00.000000000 +0100
-+++ readseq-1/Makefile 2007-11-17 21:31:39.000000000 +0100
-@@ -10,7 +10,7 @@
- #CC=cc # SGI Irix
- #CC=vcc # some DEC Ultrix
-
--CFLAGS=
-+CFLAGS= -g -O2
- #CFLAGS= -DSMALLCHECKSUM # if you prefer to use a GCG-standard 13 bit checksum
- # instead of a full 32 bit checksum. This may enhance compatibility w/ GCG software
-
-@@ -29,63 +29,66 @@
- LIB2=-lncbiobj
- LIB3=-lncbicdr
- LIB4=-lvibrant
--INCPATH=$(NCBI)/include
--LIBPATH=$(NCBI)/lib
-+LIB5=-lncbimmdb -lncbiid1 -lnetcli
-+LIB6=-lncbiacc
-+LIB7=-lncbitool
-+INCPATH=/usr/include/ncbi
-+#LIBPATH=$(NCBI)/lib
- NCFLAGS=$(CFLAGS) -DNCBI -I$(INCPATH)
--NLDFLAGS=-I$(INCPATH) -L$(LIBPATH)
--NLIBS=$(LIB1) $(LIB2) $(OTHERLIBS)
-+NLDFLAGS=-I$(INCPATH)
-+NLIBS=$(LIB1) $(LIB2) $(LIB3) $(LIB6) $(LIB7) $(LIB5) $(OTHERLIBS)
-+ARBFLAGS=-DARB
-
-+all: build
-
--all: build test
--
--build: $(SOURCES)
-- @echo "Compiling readseq..."
-- $(CC) $(CFLAGS) -o readseq readseq.c ureadseq.c
-+#build: $(SOURCES)
-+# @echo "Compiling readseq..."
-+# $(CC) $(CFLAGS) -o readseq readseq.c ureadseq.c
-
- # if using NCBI, uncomment these lines in place of build: above
--#build: $(SOURCES)
--# @echo "Compiling readseq with NCBI toolkit support...";
--# $(CC) -o readseq $(NLDFLAGS) $(NCFLAGS) readseq.c ureadseq.c ureadasn.c $(NLIBS)
-+build: $(SOURCES)
-+ @echo "Compiling readseq with NCBI toolkit support and ARB patches";
-+ $(CC) -o readseq $(NLDFLAGS) $(NCFLAGS) $(ARBFLAGS) readseq.c ureadseq.c ureadasn.c $(NLIBS)
-
--test: $(SOURCES) readseq
-+test:
- @echo ""
- @echo "Test for general read/write of all chars:"
-- ./readseq -p alphabet.std -otest.alpha
-+ readseq -p alphabet.std -otest.alpha
- -diff test.alpha alphabet.std
-
- @echo ""
- @echo "Test for valid format conversions:"
-- ./readseq -v -p -f=ig nucleic.std -otest.ig
-- ./readseq -v -p -f=gb test.ig -otest.gb
-- ./readseq -v -p -f=nbrf test.gb -otest.nbrf
-- ./readseq -v -p -f=embl test.nbrf -otest.embl
-- ./readseq -v -p -f=gcg test.embl -otest.gcg
-- ./readseq -v -p -f=strider test.gcg -otest.strider
-- ./readseq -v -p -f=fitch test.strider -otest.fitch
-- ./readseq -v -p -f=fasta test.fitch -otest.fasta
-- ./readseq -v -p -f=pir test.fasta -otest.pir
-- ./readseq -v -p -f=ig test.pir -otest.ig-b
-+ readseq -v -p -f=ig nucleic.std -otest.ig
-+ readseq -v -p -f=gb test.ig -otest.gb
-+ readseq -v -p -f=nbrf test.gb -otest.nbrf
-+ readseq -v -p -f=embl test.nbrf -otest.embl
-+ readseq -v -p -f=gcg test.embl -otest.gcg
-+ readseq -v -p -f=strider test.gcg -otest.strider
-+ readseq -v -p -f=fitch test.strider -otest.fitch
-+ readseq -v -p -f=fasta test.fitch -otest.fasta
-+ readseq -v -p -f=pir test.fasta -otest.pir
-+ readseq -v -p -f=ig test.pir -otest.ig-b
- -diff test.ig test.ig-b
-
- @echo ""
- @echo "Test for multiple-sequence format conversions:"
-- ./readseq -p -f=ig multi.std -otest.m-ig
-- ./readseq -p -f=gb test.m-ig -otest.m-gb
-- ./readseq -p -f=nbrf test.m-gb -otest.m-nbrf
-- ./readseq -p -f=embl test.m-nbrf -otest.m-embl
-- ./readseq -p -f=fasta test.m-embl -otest.m-fasta
-- ./readseq -p -f=pir test.m-fasta -otest.m-pir
-- ./readseq -p -f=msf test.m-pir -otest.m-msf
-- ./readseq -p -f=paup test.m-msf -otest.m-paup
-- ./readseq -p -f=ig test.m-paup -otest.m-ig-b
-+ readseq -p -f=ig multi.std -otest.m-ig
-+ readseq -p -f=gb test.m-ig -otest.m-gb
-+ readseq -p -f=nbrf test.m-gb -otest.m-nbrf
-+ readseq -p -f=embl test.m-nbrf -otest.m-embl
-+ readseq -p -f=fasta test.m-embl -otest.m-fasta
-+ readseq -p -f=pir test.m-fasta -otest.m-pir
-+ readseq -p -f=msf test.m-pir -otest.m-msf
-+ readseq -p -f=paup test.m-msf -otest.m-paup
-+ readseq -p -f=ig test.m-paup -otest.m-ig-b
- -diff test.m-ig test.m-ig-b
- #
- # if using NCBI, uncomment these lines
--# @echo ""
--# @echo "Test of NCBI ASN.1 conversions:"
--# ./readseq -p -f=asn test.m-ig -otest.m-asn
--# ./readseq -p -f=ig test.m-asn -otest.m-ig-c
--# -diff test.m-ig test.m-ig-c
-+ @echo ""
-+ @echo "Test of NCBI ASN.1 conversions:"
-+ readseq -p -f=asn test.m-ig -otest.m-asn
-+ readseq -p -f=ig test.m-asn -otest.m-ig-c
-+ -diff test.m-ig test.m-ig-c
- #
- @echo ""
- @echo "Expect differences in the header lines due to"
-@@ -97,8 +100,13 @@
- @echo " make clean"
-
-
-+install:
-+ install readseq $(DESTDIR)/usr/bin
-+ install *.std $(DESTDIR)/usr/share/doc/readseq/tests
-+ install Makefile $(DESTDIR)/usr/share/doc/readseq/tests
-+
- clean:
-- rm -f *.o core test.*
-+ rm -f *.o core test.* readseq
-
- shar:
- @echo "shell archiving files..."
-@@ -109,3 +117,7 @@
- shar -v readseqd > readseq.shar
- rm -rf readseqd
-
-+
-+
-+
-+
Added: trunk/packages/readseq/trunk/debian/patches/20-Makefile.patch
===================================================================
--- trunk/packages/readseq/trunk/debian/patches/20-Makefile.patch (rev 0)
+++ trunk/packages/readseq/trunk/debian/patches/20-Makefile.patch 2009-11-26 11:33:48 UTC (rev 4406)
@@ -0,0 +1,142 @@
+Author: Andreas Tille <tille at debian.org>
+Description: Enhanced Makefile
+
+--- readseq-1/Makefile.orig 1992-12-30 01:00:00.000000000 +0100
++++ readseq-1/Makefile 2007-11-17 21:31:39.000000000 +0100
+@@ -10,7 +10,7 @@
+ #CC=cc # SGI Irix
+ #CC=vcc # some DEC Ultrix
+
+-CFLAGS=
++CFLAGS= -g -O2
+ #CFLAGS= -DSMALLCHECKSUM # if you prefer to use a GCG-standard 13 bit checksum
+ # instead of a full 32 bit checksum. This may enhance compatibility w/ GCG software
+
+@@ -29,63 +29,66 @@
+ LIB2=-lncbiobj
+ LIB3=-lncbicdr
+ LIB4=-lvibrant
+-INCPATH=$(NCBI)/include
+-LIBPATH=$(NCBI)/lib
++LIB5=-lncbimmdb -lncbiid1 -lnetcli
++LIB6=-lncbiacc
++LIB7=-lncbitool
++INCPATH=/usr/include/ncbi
++#LIBPATH=$(NCBI)/lib
+ NCFLAGS=$(CFLAGS) -DNCBI -I$(INCPATH)
+-NLDFLAGS=-I$(INCPATH) -L$(LIBPATH)
+-NLIBS=$(LIB1) $(LIB2) $(OTHERLIBS)
++NLDFLAGS=-I$(INCPATH)
++NLIBS=$(LIB1) $(LIB2) $(LIB3) $(LIB6) $(LIB7) $(LIB5) $(OTHERLIBS)
++ARBFLAGS=-DARB
+
++all: build
+
+-all: build test
+-
+-build: $(SOURCES)
+- @echo "Compiling readseq..."
+- $(CC) $(CFLAGS) -o readseq readseq.c ureadseq.c
++#build: $(SOURCES)
++# @echo "Compiling readseq..."
++# $(CC) $(CFLAGS) -o readseq readseq.c ureadseq.c
+
+ # if using NCBI, uncomment these lines in place of build: above
+-#build: $(SOURCES)
+-# @echo "Compiling readseq with NCBI toolkit support...";
+-# $(CC) -o readseq $(NLDFLAGS) $(NCFLAGS) readseq.c ureadseq.c ureadasn.c $(NLIBS)
++build: $(SOURCES)
++ @echo "Compiling readseq with NCBI toolkit support and ARB patches";
++ $(CC) -o readseq $(NLDFLAGS) $(NCFLAGS) $(ARBFLAGS) readseq.c ureadseq.c ureadasn.c $(NLIBS)
+
+-test: $(SOURCES) readseq
++test:
+ @echo ""
+ @echo "Test for general read/write of all chars:"
+- ./readseq -p alphabet.std -otest.alpha
++ readseq -p alphabet.std -otest.alpha
+ -diff test.alpha alphabet.std
+
+ @echo ""
+ @echo "Test for valid format conversions:"
+- ./readseq -v -p -f=ig nucleic.std -otest.ig
+- ./readseq -v -p -f=gb test.ig -otest.gb
+- ./readseq -v -p -f=nbrf test.gb -otest.nbrf
+- ./readseq -v -p -f=embl test.nbrf -otest.embl
+- ./readseq -v -p -f=gcg test.embl -otest.gcg
+- ./readseq -v -p -f=strider test.gcg -otest.strider
+- ./readseq -v -p -f=fitch test.strider -otest.fitch
+- ./readseq -v -p -f=fasta test.fitch -otest.fasta
+- ./readseq -v -p -f=pir test.fasta -otest.pir
+- ./readseq -v -p -f=ig test.pir -otest.ig-b
++ readseq -v -p -f=ig nucleic.std -otest.ig
++ readseq -v -p -f=gb test.ig -otest.gb
++ readseq -v -p -f=nbrf test.gb -otest.nbrf
++ readseq -v -p -f=embl test.nbrf -otest.embl
++ readseq -v -p -f=gcg test.embl -otest.gcg
++ readseq -v -p -f=strider test.gcg -otest.strider
++ readseq -v -p -f=fitch test.strider -otest.fitch
++ readseq -v -p -f=fasta test.fitch -otest.fasta
++ readseq -v -p -f=pir test.fasta -otest.pir
++ readseq -v -p -f=ig test.pir -otest.ig-b
+ -diff test.ig test.ig-b
+
+ @echo ""
+ @echo "Test for multiple-sequence format conversions:"
+- ./readseq -p -f=ig multi.std -otest.m-ig
+- ./readseq -p -f=gb test.m-ig -otest.m-gb
+- ./readseq -p -f=nbrf test.m-gb -otest.m-nbrf
+- ./readseq -p -f=embl test.m-nbrf -otest.m-embl
+- ./readseq -p -f=fasta test.m-embl -otest.m-fasta
+- ./readseq -p -f=pir test.m-fasta -otest.m-pir
+- ./readseq -p -f=msf test.m-pir -otest.m-msf
+- ./readseq -p -f=paup test.m-msf -otest.m-paup
+- ./readseq -p -f=ig test.m-paup -otest.m-ig-b
++ readseq -p -f=ig multi.std -otest.m-ig
++ readseq -p -f=gb test.m-ig -otest.m-gb
++ readseq -p -f=nbrf test.m-gb -otest.m-nbrf
++ readseq -p -f=embl test.m-nbrf -otest.m-embl
++ readseq -p -f=fasta test.m-embl -otest.m-fasta
++ readseq -p -f=pir test.m-fasta -otest.m-pir
++ readseq -p -f=msf test.m-pir -otest.m-msf
++ readseq -p -f=paup test.m-msf -otest.m-paup
++ readseq -p -f=ig test.m-paup -otest.m-ig-b
+ -diff test.m-ig test.m-ig-b
+ #
+ # if using NCBI, uncomment these lines
+-# @echo ""
+-# @echo "Test of NCBI ASN.1 conversions:"
+-# ./readseq -p -f=asn test.m-ig -otest.m-asn
+-# ./readseq -p -f=ig test.m-asn -otest.m-ig-c
+-# -diff test.m-ig test.m-ig-c
++ @echo ""
++ @echo "Test of NCBI ASN.1 conversions:"
++ readseq -p -f=asn test.m-ig -otest.m-asn
++ readseq -p -f=ig test.m-asn -otest.m-ig-c
++ -diff test.m-ig test.m-ig-c
+ #
+ @echo ""
+ @echo "Expect differences in the header lines due to"
+@@ -97,8 +100,13 @@
+ @echo " make clean"
+
+
++install:
++ install readseq $(DESTDIR)/usr/bin
++ install *.std $(DESTDIR)/usr/share/doc/readseq/tests
++ install Makefile $(DESTDIR)/usr/share/doc/readseq/tests
++
+ clean:
+- rm -f *.o core test.*
++ rm -f *.o core test.* readseq
+
+ shar:
+ @echo "shell archiving files..."
+@@ -109,3 +117,7 @@
+ shar -v readseqd > readseq.shar
+ rm -rf readseqd
+
++
++
++
++
Deleted: trunk/packages/readseq/trunk/debian/patches/30-arb-code-patches.dpatch
===================================================================
--- trunk/packages/readseq/trunk/debian/patches/30-arb-code-patches.dpatch 2009-11-26 09:49:09 UTC (rev 4405)
+++ trunk/packages/readseq/trunk/debian/patches/30-arb-code-patches.dpatch 2009-11-26 11:33:48 UTC (rev 4406)
@@ -1,558 +0,0 @@
-#! /bin/sh /usr/share/dpatch/dpatch-run
-## 30_arb_changes.dpatch by <tille at debian.org>
-##
-## All lines beginning with `## DP:' are a description of the patch.
-## DP: Several patches for arb that enable new formats and contain other
-## DP: needed fixes
-
- at DPATCH@
-
-diff -ubrN readseq-1.orig/readseq.c readseq-1/readseq.c
---- readseq-1.orig/readseq.c 1993-02-01 01:00:00.000000000 +0100
-+++ readseq-1/readseq.c 2007-11-14 12:14:36.000000000 +0100
-@@ -93,6 +93,10 @@
- = fix bug for possible memory overrun when truncating seqs for
- Phylip or Paup formats (thanks Anthony Persechini)
-
-+ 13 Sep 96 GSt + RL (Steger at biophys.uni-duesseldorf.de)
-+ * real time in MSF format (Main); #include <time.h>
-+ + added VIE multi sequence file format
-+ + added LinAll sequence file format
- */
-
-
-@@ -169,8 +173,11 @@
-
-
- #include <stdio.h>
-+#include <stdlib.h> /* MSch */
- #include <string.h>
- #include <ctype.h>
-+#include <time.h> /* RL */
-+#include <ncbi.h>
-
- #include "ureadseq.h"
-
-@@ -199,9 +206,11 @@
- "16. ASN.1",
- "17. PAUP/NEXUS",
- "18. Pretty (out-only)",
-+ "19. LinAll",
-+ "20. Vienna",
- "" };
-
--#define kFormCount 30
-+#define kFormCount 32
- #define kMaxFormName 15
-
- const struct formatTable {
-@@ -238,6 +247,8 @@
- {"paup", kPAUP},
- {"nexus", kPAUP},
- {"pretty", kPretty},
-+ {"linall", kLINALL},
-+ {"vie", kVIE},
- };
-
- const char *kASN1headline = "Bioseq-set ::= {\nseq-set {\n";
-@@ -415,7 +426,7 @@
- fprintf( stderr, " %-20s %-20s\n",
- formats[i], formats[midi+i]);
- fprintf(stderr,"\nChoose an output format (name or #): \n");
-- gets(sform);
-+ fgets(sform, 127, stdin);
- outform = parseformat(sform);
- if (outform == kNoformat) outform = kPearson;
- return outform;
-@@ -708,8 +719,12 @@
- #else
- #define Exit(a) exit(a)
-
-+#ifdef NCBI
-+Nlm_Int2 Nlm_Main(void)
-+#else
- main( int argc, char *argv[])
- #endif
-+#endif
- {
- boolean closein = false;
- short ifile, nseq, atseq, format, err = 0, seqtype = kDNA,
-@@ -721,6 +736,14 @@
- char stempstore[256], *stemp = stempstore;
- FILE *ftmp, *fin, *fout;
- long outindexmax= 0, noutindex= 0, *outindex = NULL;
-+time_t time_val; /* GSt + RL */
-+size_t size_timestr = 50;/* GSt + RL */
-+char timestr[50]; /* GSt + RL */
-+
-+#ifdef NCBI
-+int argc;
-+char** argv;
-+#endif
-
- #define exit_main(err) { \
- if (closeout) fclose(fout); \
-@@ -739,6 +762,10 @@
-
-
- resetGlobals();
-+#if NCBI
-+ argc = Nlm_GetArgc();
-+ argv = Nlm_GetArgv();
-+#endif
- foo = stdout;
- progname = argv[0];
- *oname = 0;
-@@ -764,7 +791,7 @@
-
- quietly = (dopipe || (gotinputfile && (listonly || whichSeq != 0)));
-
-- if (verbose || (!quietly && !gotinputfile)) fprintf( stderr, title);
-+ //if (verbose || (!quietly && !gotinputfile)) fprintf( stderr, "%s\n", title);
- ifile = 1;
-
- /* UI: Choose output */
-@@ -1003,6 +1030,13 @@
- else if (dolower)
- for (i = 0; i<seqlen; i++) seq[i] = to_lower(seq[i]);
-
-+/* This is an undocumented patch from ARB which hopefully does no harm A. Tille */
-+#ifdef ARB
-+ if (outform==kPhylip){
-+ for (i = 0; i<seqlen; i++) if (seq[i] == '.') seq[i] = '?';
-+ }
-+#endif
-+
- if (doreverse) {
- long j, k;
- char ctemp;
-@@ -1014,8 +1048,15 @@
- }
-
- if ((gPretty.isactive || outform==kPAUP) && gPretty.domatch && firstseq != NULL) {
-+#ifdef ARB
-+ for (i=0; i<seqlen; i++){
-+ if (seq[i] == gPretty.matchchar) seq[i] = 'o';
-+ if (seq[i]==firstseq[i]) seq[i]= gPretty.matchchar;
-+ }
-+#else
- for (i=0; i<seqlen; i++)
- if (seq[i]==firstseq[i]) seq[i]= gPretty.matchchar;
-+#endif
- }
-
-
-@@ -1070,9 +1111,15 @@
- }
-
- if (outform == kMSF) {
-+ time(&time_val); /* GSt + RL */
-+ strftime(timestr, size_timestr, "%B %e, %Y %H:%M", localtime(&time_val)); /* GSt + RL */
- if (*oname) cp= oname; else cp= inputfile;
-+ fprintf(foo,"\n %s MSF: %d Type: N %s Check: %d ..\n\n", /* GSt + RL */
-+ cp, seqlen, timestr, checkall);
-+/*
- fprintf(foo,"\n %s MSF: %d Type: N January 01, 1776 12:00 Check: %d ..\n\n",
- cp, seqlen, checkall);
-+*/
- }
-
- if (outform == kPAUP) {
-diff -ubrN readseq-1.orig/ureadseq.c readseq-1/ureadseq.c
---- readseq-1.orig/ureadseq.c 1998-09-03 02:00:00.000000000 +0200
-+++ readseq-1/ureadseq.c 2007-11-14 12:14:36.000000000 +0100
-@@ -18,11 +18,14 @@
-
-
- #include <stdio.h>
-+#define __NO_CTYPE
-+#include <stdlib.h> /* MSch */
- #include <ctype.h>
- #include <string.h>
-
- #define UREADSEQ_G
- #include "ureadseq.h"
-+/* changed according to original which is the same with the changed header (at) */
-
- #pragma segment ureadseq
-
-@@ -66,7 +69,7 @@
- # define Local static /* local functions */
- #endif
-
--#define kStartLength 500
-+#define kStartLength 500000 /* 20Apr93 temp. bug fix */
-
- const char *aminos = "ABCDEFGHIKLMNPQRSTVWXYZ*";
- const char *primenuc = "ACGTU";
-@@ -101,6 +104,9 @@
- long linestart;
- char s[256], *sp;
-
-+#ifdef ARB
-+ int (*isseqcharfirst8)(); /* Patch by o. strunk (ARB) to allow numbers in genbank sequences*/
-+#endif
- int (*isseqchar)();
- /* int (*isseqchar)(int c); << sgi cc hates (int c) */
- };
-@@ -150,9 +156,23 @@
- Local void addseq(char *s, struct ReadSeqVars *V)
- {
- char *ptr;
-+#ifdef ARB
-+ /* Patch by o. strunk (ARB) to allow numbers in genbank sequences */
-+ int count = 0;
-+#endif
-
-+#ifdef ARB
-+ if (V->addit){
-+ for (;*s != 0;s++,count++) {
-+ if (count < 9 && V->isseqcharfirst8) {
-+ if (!(V->isseqcharfirst8) (*s)) continue;
-+ }else{
-+ if (!(V->isseqchar) (*s)) continue;
-+ }
-+#else
- if (V->addit) while (*s != 0) {
- if ((V->isseqchar)(*s)) {
-+#endif
- if (V->seqlen >= V->maxseq) {
- V->maxseq += kStartLength;
- ptr = (char*) realloc(V->seq, V->maxseq+1);
-@@ -164,7 +184,9 @@
- }
- V->seq[(V->seqlen)++] = *s;
- }
-+#ifndef ARB
- s++;
-+#endif
- }
- }
-
-@@ -324,6 +346,11 @@
- Local void readGenBank(struct ReadSeqVars *V)
- { /*GenBank -- many seqs/file */
-
-+#ifdef ARB
-+ /* Patch by o. strunk (ARB) to allow numbers in genbank sequences */
-+ V->isseqchar = isSeqNumChar;
-+ V->isseqcharfirst8 = isSeqChar;
-+#endif
- while (!V->allDone) {
- strcpy(V->seqid, (V->s)+12);
- while (! (feof(V->f) || strstr(V->s,"ORIGIN") == V->s))
-@@ -337,9 +364,44 @@
- }
- if (feof(V->f)) V->allDone = true;
- }
-+#ifdef ARB
-+ V->isseqchar = isSeqChar;
-+ V->isseqcharfirst8 = 0;
-+#endif
- }
-
-
-+Local boolean endVIE( boolean *addend, boolean *ungetend, struct ReadSeqVars *V) /* GSt + RL */
-+{
-+ if (*V->s == '>') { /* start of next seq */
-+ *addend = false;
-+ *ungetend= true;
-+ return(true);
-+ }
-+ else
-+ return(false);
-+}
-+
-+
-+Local void readVIE(struct ReadSeqVars *V) /* GSt + RL */
-+{
-+ while (!V->allDone) {
-+ strcpy(V->seqid, (V->s)+2);
-+ readLoop(0, false, endVIE, V);
-+ if (feof(V->f)) V->allDone = true;
-+ }
-+/*
-+ printf("readVIE: V->nseq = %d\n",V->nseq);
-+ printf("readVIE: V->choice = %d\n",V->choice);
-+ printf("readVIE: V->addit = %d\n",V->addit);
-+ printf("readVIE: V->seqlen = %ld\n",V->seqlen);
-+ printf("readVIE: V->seqid = %s\n",V->seqid);
-+ printf("readVIE: V->s = %s\n",V->s);
-+ printf("readVIE: V->seqid = %s\n",V->seqid);
-+ printf("readVIE: V->s = %s\n<<<last action\n",V->s);
-+*/
-+}
-+
- Local boolean endNBRF( boolean *addend, boolean *ungetend, struct ReadSeqVars *V)
- {
- char *a;
-@@ -449,6 +511,46 @@
- }
- }
-
-+Local void readLINALL(struct ReadSeqVars *V) /* GSt */
-+{
-+ /* SeqLen[I4] Label[Char*60]
-+ Seq[Char*70 per line]
-+ */
-+ int laenge;
-+ int i;
-+
-+ V->nseq++; /* but there is only a single sequence ? */
-+ // dprintf(("readLINALL: V->nseq = %d\n",V->nseq));
-+ /* V->addit = (V->choice > 0); */ /* what's that for ???? */
-+ // dprintf(("readLINALL: V->choice = %d\n",V->choice));
-+ // dprintf(("readLINALL: V->addit = %d\n",V->addit));
-+ // dprintf(("readLINALL: V->seqid = %s\n",V->seqid));
-+ // dprintf(("readLINALL: V->s = %s\n",V->s));
-+ /* if (V->addit) V->seqlen = 0; */ /* what's that for ???? */
-+ sscanf(V->s, "%4d", &laenge); /* seqlen is in 1st 4 chars of 1st line */
-+ // dprintf(("readLINALL: laenge = %d\n",laenge));
-+ // fflush(stdout);
-+ strcpy(V->seqid, (V->s)+5); /* label starts after 5th char of 1st line */
-+ // dprintf(("readLINALL: V->seqid = %s\n",V->seqid));
-+ // fflush(stdout);
-+ do {
-+ V->done = feof(V->f);
-+ getline(V);
-+ if (!V->done) addseq((V->s), V);
-+ } while ( !(V->done) && (V->seqlen)<=laenge );
-+ V->seqlen = laenge; /* only laenge chars are relevant for V->seq */
-+ // dprintf(("readLINALL: V->s = %s\n",V->s));
-+ /* if (V->choice == kListSequences) addinfo(V->seqid, V); */ /* what's that for ???? */
-+ // dprintf(("readLINALL: V->seqid = %s\n",V->seqid));
-+ // dprintf(("readLINALL: V->seqlen = %ld\n",V->seqlen));
-+ // dprintf(("readLINALL: V->seq =>"));
-+ // for ( i=0; i<V->seqlen; i++ ) dprintf(("%c",V->seq[i]));
-+ // dprintf(("<\n"));
-+ // dprintf(("readLINALL: V->s = %s\n<<<last action\n",V->s));
-+ V->allDone = true;
-+
-+}
-+
-
-
- Local boolean endFitch( boolean *addend, boolean *ungetend, struct ReadSeqVars *V)
-@@ -956,6 +1058,8 @@
- case kZuker : readZuker(V); break;
- case kOlsen : readOlsen(V); break;
- case kMSF : readMSF(V); break;
-+ case kLINALL: readLINALL(V); break;
-+ case kVIE : readVIE(V); break;
-
- case kPAUP : {
- boolean done= false;
-@@ -1049,6 +1153,9 @@
- V.err = 0;
- V.nseq = 0;
- V.isseqchar = isSeqChar;
-+#ifdef ARB
-+ V.isseqcharfirst8 = 0;
-+#endif
- if (V.choice == kListSequences) ; /* leave as is */
- else if (V.choice <= 0) V.choice = 1; /* default ?? */
- V.addit = (V.choice > 0);
-@@ -1092,6 +1199,9 @@
- V.err = 0;
- V.nseq = 0;
- V.isseqchar = isSeqChar;
-+#ifdef ARB
-+ V.isseqcharfirst8 = 0;
-+#endif
- if (V.choice == kListSequences) ; /* leave as is */
- else if (V.choice <= 0) V.choice = 1; /* default ?? */
- V.addit = (V.choice > 0);
-@@ -1152,6 +1262,7 @@
- boolean foundDNA= false, foundIG= false, foundStrider= false,
- foundGB= false, foundPIR= false, foundEMBL= false, foundNBRF= false,
- foundPearson= false, foundFitch= false, foundPhylip= false, foundZuker= false,
-+ foundLINALL= false, foundVIE= false,
- gotolsen= false, gotpaup = false, gotasn1 = false, gotuw= false, gotMSF= false,
- isfitch= false, isphylip= false, done= false;
- short format= kUnknown;
-@@ -1159,6 +1270,8 @@
- char sp[256];
- long linestart=0;
- int maxlines2check=500;
-+ int linallSeqLen;
-+ char linallHeader[60];
-
- #define ReadOneLine(sp) \
- { done |= (feof(fseq)); \
-@@ -1225,8 +1338,9 @@
- foundPIR= true;
-
- else if (*sp == '>') {
-- if (sp[3] == ';') foundNBRF= true;
-- else foundPearson= true;
-+ if (sp[3] == ';') foundNBRF= true; /* {foundNBRF= true; printf("foundNBRF\n");} */
-+ else if (sp[1] == ' ') foundVIE= true; /* {foundVIE= true; printf("foundVIE\n");} */
-+ else foundPearson= true; /* {foundPearson= true; printf("foundPearson\n");} */
- }
-
- else if (strstr(sp,"ID ") == sp)
-@@ -1239,9 +1353,16 @@
-
- else {
- if (nlines - *skiplines == 1) {
-- int ispp= 0, ilen= 0;
-- sscanf( sp, "%d%d", &ispp, &ilen);
-- if (ispp > 0 && ilen > 0) isphylip= true;
-+ int ispp= 0, ilen= 0, icnt=0;
-+ char junkstr[120];
-+ memset(junkstr,0,120);
-+ icnt= sscanf( sp, "%d%d%c", &ispp, &ilen, junkstr);
-+ if (icnt == 2 && ispp > 0 && ilen > 0) {
-+ isphylip= true;
-+ }
-+ else if (icnt==3 && ispp > 0 && ilen > 0 && *junkstr == ' ') {
-+ isphylip= true;
-+ }
- }
- else if (isphylip && nlines - *skiplines == 2) {
- int tseq;
-@@ -1257,6 +1378,65 @@
- }
- if (isfitch & (splen > 20)) foundFitch= true;
-
-+#ifdef DEBUG_LINALL
-+ dprintf(("Check for LINALL\n"));
-+ dprintf(("\tstrtol(sp,NULL,0) = %d\n",strtol(sp,NULL,0)));
-+ dprintf(("\tnlines = %d\n",nlines));
-+ dprintf(("\tisphylip = %d\n",isphylip));
-+ dprintf(("\tfoundPhylip = %d\n",foundPhylip));
-+ dprintf(("\tisfitch = %d\n",isfitch));
-+ dprintf(("\tfoundFitch = %d\n",foundFitch));
-+#endif
-+
-+ /*
-+ * This format detection was highly bogus ...
-+ * Lesson 1: always initialize variables (in case the conversion fails...)
-+ * Lesson 2: strings are passed to sscanf _without_ & (string variable is a pointer already)
-+ * Lesson 3: forget to check return codes from syscalls: you lose.
-+ */
-+
-+ if (nlines==1) {
-+ int rv;
-+#ifdef DEBUG_LINALL
-+ int i, sane=1;
-+ char *spp;
-+
-+ /*
-+ * possible sanity check, for losers (see above)
-+ */
-+ for (spp=sp, i=0; i<4; i++, spp++)
-+ if (!(isspace(*spp) || isdigit(*spp))) {
-+ dprintf(("bogus linall format header: %s\n", sp));
-+ sane=0;
-+ break;
-+ }
-+#endif
-+
-+ linallSeqLen = 0;
-+ *linallHeader = '\0';
-+ rv = sscanf( sp, "%d %s", &linallSeqLen, linallHeader);
-+
-+#ifdef DEBUG_LINALL
-+ dprintf(("\tsscanf rval = %d\n",rv));
-+ dprintf(("\tlinallSeqLen = %d\n",linallSeqLen));
-+ dprintf(("\tlinallHeader = %s\n",linallHeader));
-+ dprintf(("\tlinallHeader = %d\n",strlen(linallHeader)));
-+#endif
-+
-+ if (rv > 0 && linallSeqLen>0 &&
-+ strlen(linallHeader)>0 &&
-+ !(isphylip || foundPhylip)) {
-+ /* !(isphylip || foundPhylip || isfitch || foundFitch)) { */
-+ foundLINALL= true; /* The 1st line contains the seqlength (4 digits), a blank, and a label (up to 60 char). */
-+ /* The following lines contain the sequence with 70 chars per line. */
-+#ifdef DEBUG_LINALL
-+ dprintf(("debug: foundLINALL: %ld<\n",strtol(sp,NULL,0)));
-+ dprintf(("debug: sp:%s<\n\n",sp));
-+#endif
-+ }
-+
-+ }
-+
- /* kRNA && kDNA are fairly certain...*/
- switch (getseqtype( sp, splen)) {
- case kOtherSeq: otherlines++; break;
-@@ -1302,6 +1482,16 @@
- done= true;
- }
-
-+ else if (foundLINALL) {
-+ format= kLINALL;
-+ done= true;
-+ }
-+
-+ else if (foundVIE) {
-+ format= kVIE;
-+ done= true;
-+ }
-+
- else if ((dnalines > 1) || done || (nlines > maxlines2check)) {
- /* decide on most likely format */
- /* multichar idents: */
-@@ -1785,6 +1975,27 @@
- linesout += 2;
- break;
-
-+ case kLINALL: /* GSt */
-+ fprintf(outf,"%4d %-60s\n",seqlen,seqname);
-+ strcpy(endstr,"\n");
-+ linesout++;
-+ width = 70;
-+ tab = 0;
-+ spacer = 0;
-+ nameleft = false;
-+ nameright = false;
-+ numleft = false;
-+ numright = false;
-+ break;
-+
-+ case kVIE: /* GSt + RL */
-+ if ( strchr(seqname,' ') != NULL ) seqname[strchr(seqname,' ')-seqname] = '\0'; /* no blanks in label line */
-+ fprintf(outf,"> %-s\n", seqname);
-+ linesout++;
-+ fprintf(outf,"%s\n\n",seq); /* complete sequence in one line; additional blank line before next sequence */
-+ return linesout; /* thus, do nothing else */
-+ break;
-+
- default :
- case kZuker: /* don't attempt Zuker's ftn format */
- case kPearson:
-@@ -1841,7 +2052,8 @@
- s[l++] = ' ';
- if (!baseonlynum) ibase++;
- else if (0==strchr(nocountsymbols,seq[i])) ibase++;
-- s[l++] = seq[i++];
-+ if (outform==kLINALL) { s[l++] = to_upper(seq[i]); i++; } /* GSt */
-+ else s[l++] = seq[i++] ;
- }
-
- if (l1 == width || i == seqlen) {
-diff -ubrN readseq-1.orig/ureadseq.h readseq-1/ureadseq.h
---- readseq-1.orig/ureadseq.h 1992-12-30 01:00:00.000000000 +0100
-+++ readseq-1/ureadseq.h 2007-11-14 12:14:36.000000000 +0100
-@@ -66,8 +66,10 @@
- #define kASN1 16
- #define kPAUP 17
- #define kPretty 18
-+#define kLINALL 19
-+#define kVIE 20
-
--#define kMaxFormat 18
-+#define kMaxFormat 20
- #define kMinFormat 1
- #define kNoformat -1 /* format not tested */
- #define kUnknown 0 /* format not determinable */
-@@ -100,7 +102,7 @@
- p.noleaves= p.domatch= p.degap= false;\
- p.matchchar='.';\
- p.gapchar='-';\
-- p.namewidth=8;\
-+ p.namewidth=10;\
- p.numwidth=5;\
- p.interline=1;\
- p.spacer=10;\
Added: trunk/packages/readseq/trunk/debian/patches/30-arb-code-patches.patch
===================================================================
--- trunk/packages/readseq/trunk/debian/patches/30-arb-code-patches.patch (rev 0)
+++ trunk/packages/readseq/trunk/debian/patches/30-arb-code-patches.patch 2009-11-26 11:33:48 UTC (rev 4406)
@@ -0,0 +1,553 @@
+Author: Andreas Tille <tille at debian.org>
+Description: Several patches for arb that enable new formats and contain other
+ needed fixes
+
+diff -ubrN readseq-1.orig/readseq.c readseq-1/readseq.c
+--- readseq-1.orig/readseq.c 1993-02-01 01:00:00.000000000 +0100
++++ readseq-1/readseq.c 2007-11-14 12:14:36.000000000 +0100
+@@ -93,6 +93,10 @@
+ = fix bug for possible memory overrun when truncating seqs for
+ Phylip or Paup formats (thanks Anthony Persechini)
+
++ 13 Sep 96 GSt + RL (Steger at biophys.uni-duesseldorf.de)
++ * real time in MSF format (Main); #include <time.h>
++ + added VIE multi sequence file format
++ + added LinAll sequence file format
+ */
+
+
+@@ -169,8 +173,11 @@
+
+
+ #include <stdio.h>
++#include <stdlib.h> /* MSch */
+ #include <string.h>
+ #include <ctype.h>
++#include <time.h> /* RL */
++#include <ncbi.h>
+
+ #include "ureadseq.h"
+
+@@ -199,9 +206,11 @@
+ "16. ASN.1",
+ "17. PAUP/NEXUS",
+ "18. Pretty (out-only)",
++ "19. LinAll",
++ "20. Vienna",
+ "" };
+
+-#define kFormCount 30
++#define kFormCount 32
+ #define kMaxFormName 15
+
+ const struct formatTable {
+@@ -238,6 +247,8 @@
+ {"paup", kPAUP},
+ {"nexus", kPAUP},
+ {"pretty", kPretty},
++ {"linall", kLINALL},
++ {"vie", kVIE},
+ };
+
+ const char *kASN1headline = "Bioseq-set ::= {\nseq-set {\n";
+@@ -415,7 +426,7 @@
+ fprintf( stderr, " %-20s %-20s\n",
+ formats[i], formats[midi+i]);
+ fprintf(stderr,"\nChoose an output format (name or #): \n");
+- gets(sform);
++ fgets(sform, 127, stdin);
+ outform = parseformat(sform);
+ if (outform == kNoformat) outform = kPearson;
+ return outform;
+@@ -708,8 +719,12 @@
+ #else
+ #define Exit(a) exit(a)
+
++#ifdef NCBI
++Nlm_Int2 Nlm_Main(void)
++#else
+ main( int argc, char *argv[])
+ #endif
++#endif
+ {
+ boolean closein = false;
+ short ifile, nseq, atseq, format, err = 0, seqtype = kDNA,
+@@ -721,6 +736,14 @@
+ char stempstore[256], *stemp = stempstore;
+ FILE *ftmp, *fin, *fout;
+ long outindexmax= 0, noutindex= 0, *outindex = NULL;
++time_t time_val; /* GSt + RL */
++size_t size_timestr = 50;/* GSt + RL */
++char timestr[50]; /* GSt + RL */
++
++#ifdef NCBI
++int argc;
++char** argv;
++#endif
+
+ #define exit_main(err) { \
+ if (closeout) fclose(fout); \
+@@ -739,6 +762,10 @@
+
+
+ resetGlobals();
++#if NCBI
++ argc = Nlm_GetArgc();
++ argv = Nlm_GetArgv();
++#endif
+ foo = stdout;
+ progname = argv[0];
+ *oname = 0;
+@@ -764,7 +791,7 @@
+
+ quietly = (dopipe || (gotinputfile && (listonly || whichSeq != 0)));
+
+- if (verbose || (!quietly && !gotinputfile)) fprintf( stderr, title);
++ //if (verbose || (!quietly && !gotinputfile)) fprintf( stderr, "%s\n", title);
+ ifile = 1;
+
+ /* UI: Choose output */
+@@ -1003,6 +1030,13 @@
+ else if (dolower)
+ for (i = 0; i<seqlen; i++) seq[i] = to_lower(seq[i]);
+
++/* This is an undocumented patch from ARB which hopefully does no harm A. Tille */
++#ifdef ARB
++ if (outform==kPhylip){
++ for (i = 0; i<seqlen; i++) if (seq[i] == '.') seq[i] = '?';
++ }
++#endif
++
+ if (doreverse) {
+ long j, k;
+ char ctemp;
+@@ -1014,8 +1048,15 @@
+ }
+
+ if ((gPretty.isactive || outform==kPAUP) && gPretty.domatch && firstseq != NULL) {
++#ifdef ARB
++ for (i=0; i<seqlen; i++){
++ if (seq[i] == gPretty.matchchar) seq[i] = 'o';
++ if (seq[i]==firstseq[i]) seq[i]= gPretty.matchchar;
++ }
++#else
+ for (i=0; i<seqlen; i++)
+ if (seq[i]==firstseq[i]) seq[i]= gPretty.matchchar;
++#endif
+ }
+
+
+@@ -1070,9 +1111,15 @@
+ }
+
+ if (outform == kMSF) {
++ time(&time_val); /* GSt + RL */
++ strftime(timestr, size_timestr, "%B %e, %Y %H:%M", localtime(&time_val)); /* GSt + RL */
+ if (*oname) cp= oname; else cp= inputfile;
++ fprintf(foo,"\n %s MSF: %d Type: N %s Check: %d ..\n\n", /* GSt + RL */
++ cp, seqlen, timestr, checkall);
++/*
+ fprintf(foo,"\n %s MSF: %d Type: N January 01, 1776 12:00 Check: %d ..\n\n",
+ cp, seqlen, checkall);
++*/
+ }
+
+ if (outform == kPAUP) {
+diff -ubrN readseq-1.orig/ureadseq.c readseq-1/ureadseq.c
+--- readseq-1.orig/ureadseq.c 1998-09-03 02:00:00.000000000 +0200
++++ readseq-1/ureadseq.c 2007-11-14 12:14:36.000000000 +0100
+@@ -18,11 +18,14 @@
+
+
+ #include <stdio.h>
++#define __NO_CTYPE
++#include <stdlib.h> /* MSch */
+ #include <ctype.h>
+ #include <string.h>
+
+ #define UREADSEQ_G
+ #include "ureadseq.h"
++/* changed according to original which is the same with the changed header (at) */
+
+ #pragma segment ureadseq
+
+@@ -66,7 +69,7 @@
+ # define Local static /* local functions */
+ #endif
+
+-#define kStartLength 500
++#define kStartLength 500000 /* 20Apr93 temp. bug fix */
+
+ const char *aminos = "ABCDEFGHIKLMNPQRSTVWXYZ*";
+ const char *primenuc = "ACGTU";
+@@ -101,6 +104,9 @@
+ long linestart;
+ char s[256], *sp;
+
++#ifdef ARB
++ int (*isseqcharfirst8)(); /* Patch by o. strunk (ARB) to allow numbers in genbank sequences*/
++#endif
+ int (*isseqchar)();
+ /* int (*isseqchar)(int c); << sgi cc hates (int c) */
+ };
+@@ -150,9 +156,23 @@
+ Local void addseq(char *s, struct ReadSeqVars *V)
+ {
+ char *ptr;
++#ifdef ARB
++ /* Patch by o. strunk (ARB) to allow numbers in genbank sequences */
++ int count = 0;
++#endif
+
++#ifdef ARB
++ if (V->addit){
++ for (;*s != 0;s++,count++) {
++ if (count < 9 && V->isseqcharfirst8) {
++ if (!(V->isseqcharfirst8) (*s)) continue;
++ }else{
++ if (!(V->isseqchar) (*s)) continue;
++ }
++#else
+ if (V->addit) while (*s != 0) {
+ if ((V->isseqchar)(*s)) {
++#endif
+ if (V->seqlen >= V->maxseq) {
+ V->maxseq += kStartLength;
+ ptr = (char*) realloc(V->seq, V->maxseq+1);
+@@ -164,7 +184,9 @@
+ }
+ V->seq[(V->seqlen)++] = *s;
+ }
++#ifndef ARB
+ s++;
++#endif
+ }
+ }
+
+@@ -324,6 +346,11 @@
+ Local void readGenBank(struct ReadSeqVars *V)
+ { /*GenBank -- many seqs/file */
+
++#ifdef ARB
++ /* Patch by o. strunk (ARB) to allow numbers in genbank sequences */
++ V->isseqchar = isSeqNumChar;
++ V->isseqcharfirst8 = isSeqChar;
++#endif
+ while (!V->allDone) {
+ strcpy(V->seqid, (V->s)+12);
+ while (! (feof(V->f) || strstr(V->s,"ORIGIN") == V->s))
+@@ -337,9 +364,44 @@
+ }
+ if (feof(V->f)) V->allDone = true;
+ }
++#ifdef ARB
++ V->isseqchar = isSeqChar;
++ V->isseqcharfirst8 = 0;
++#endif
+ }
+
+
++Local boolean endVIE( boolean *addend, boolean *ungetend, struct ReadSeqVars *V) /* GSt + RL */
++{
++ if (*V->s == '>') { /* start of next seq */
++ *addend = false;
++ *ungetend= true;
++ return(true);
++ }
++ else
++ return(false);
++}
++
++
++Local void readVIE(struct ReadSeqVars *V) /* GSt + RL */
++{
++ while (!V->allDone) {
++ strcpy(V->seqid, (V->s)+2);
++ readLoop(0, false, endVIE, V);
++ if (feof(V->f)) V->allDone = true;
++ }
++/*
++ printf("readVIE: V->nseq = %d\n",V->nseq);
++ printf("readVIE: V->choice = %d\n",V->choice);
++ printf("readVIE: V->addit = %d\n",V->addit);
++ printf("readVIE: V->seqlen = %ld\n",V->seqlen);
++ printf("readVIE: V->seqid = %s\n",V->seqid);
++ printf("readVIE: V->s = %s\n",V->s);
++ printf("readVIE: V->seqid = %s\n",V->seqid);
++ printf("readVIE: V->s = %s\n<<<last action\n",V->s);
++*/
++}
++
+ Local boolean endNBRF( boolean *addend, boolean *ungetend, struct ReadSeqVars *V)
+ {
+ char *a;
+@@ -449,6 +511,46 @@
+ }
+ }
+
++Local void readLINALL(struct ReadSeqVars *V) /* GSt */
++{
++ /* SeqLen[I4] Label[Char*60]
++ Seq[Char*70 per line]
++ */
++ int laenge;
++ int i;
++
++ V->nseq++; /* but there is only a single sequence ? */
++ // dprintf(("readLINALL: V->nseq = %d\n",V->nseq));
++ /* V->addit = (V->choice > 0); */ /* what's that for ???? */
++ // dprintf(("readLINALL: V->choice = %d\n",V->choice));
++ // dprintf(("readLINALL: V->addit = %d\n",V->addit));
++ // dprintf(("readLINALL: V->seqid = %s\n",V->seqid));
++ // dprintf(("readLINALL: V->s = %s\n",V->s));
++ /* if (V->addit) V->seqlen = 0; */ /* what's that for ???? */
++ sscanf(V->s, "%4d", &laenge); /* seqlen is in 1st 4 chars of 1st line */
++ // dprintf(("readLINALL: laenge = %d\n",laenge));
++ // fflush(stdout);
++ strcpy(V->seqid, (V->s)+5); /* label starts after 5th char of 1st line */
++ // dprintf(("readLINALL: V->seqid = %s\n",V->seqid));
++ // fflush(stdout);
++ do {
++ V->done = feof(V->f);
++ getline(V);
++ if (!V->done) addseq((V->s), V);
++ } while ( !(V->done) && (V->seqlen)<=laenge );
++ V->seqlen = laenge; /* only laenge chars are relevant for V->seq */
++ // dprintf(("readLINALL: V->s = %s\n",V->s));
++ /* if (V->choice == kListSequences) addinfo(V->seqid, V); */ /* what's that for ???? */
++ // dprintf(("readLINALL: V->seqid = %s\n",V->seqid));
++ // dprintf(("readLINALL: V->seqlen = %ld\n",V->seqlen));
++ // dprintf(("readLINALL: V->seq =>"));
++ // for ( i=0; i<V->seqlen; i++ ) dprintf(("%c",V->seq[i]));
++ // dprintf(("<\n"));
++ // dprintf(("readLINALL: V->s = %s\n<<<last action\n",V->s));
++ V->allDone = true;
++
++}
++
+
+
+ Local boolean endFitch( boolean *addend, boolean *ungetend, struct ReadSeqVars *V)
+@@ -956,6 +1058,8 @@
+ case kZuker : readZuker(V); break;
+ case kOlsen : readOlsen(V); break;
+ case kMSF : readMSF(V); break;
++ case kLINALL: readLINALL(V); break;
++ case kVIE : readVIE(V); break;
+
+ case kPAUP : {
+ boolean done= false;
+@@ -1049,6 +1153,9 @@
+ V.err = 0;
+ V.nseq = 0;
+ V.isseqchar = isSeqChar;
++#ifdef ARB
++ V.isseqcharfirst8 = 0;
++#endif
+ if (V.choice == kListSequences) ; /* leave as is */
+ else if (V.choice <= 0) V.choice = 1; /* default ?? */
+ V.addit = (V.choice > 0);
+@@ -1092,6 +1199,9 @@
+ V.err = 0;
+ V.nseq = 0;
+ V.isseqchar = isSeqChar;
++#ifdef ARB
++ V.isseqcharfirst8 = 0;
++#endif
+ if (V.choice == kListSequences) ; /* leave as is */
+ else if (V.choice <= 0) V.choice = 1; /* default ?? */
+ V.addit = (V.choice > 0);
+@@ -1152,6 +1262,7 @@
+ boolean foundDNA= false, foundIG= false, foundStrider= false,
+ foundGB= false, foundPIR= false, foundEMBL= false, foundNBRF= false,
+ foundPearson= false, foundFitch= false, foundPhylip= false, foundZuker= false,
++ foundLINALL= false, foundVIE= false,
+ gotolsen= false, gotpaup = false, gotasn1 = false, gotuw= false, gotMSF= false,
+ isfitch= false, isphylip= false, done= false;
+ short format= kUnknown;
+@@ -1159,6 +1270,8 @@
+ char sp[256];
+ long linestart=0;
+ int maxlines2check=500;
++ int linallSeqLen;
++ char linallHeader[60];
+
+ #define ReadOneLine(sp) \
+ { done |= (feof(fseq)); \
+@@ -1225,8 +1338,9 @@
+ foundPIR= true;
+
+ else if (*sp == '>') {
+- if (sp[3] == ';') foundNBRF= true;
+- else foundPearson= true;
++ if (sp[3] == ';') foundNBRF= true; /* {foundNBRF= true; printf("foundNBRF\n");} */
++ else if (sp[1] == ' ') foundVIE= true; /* {foundVIE= true; printf("foundVIE\n");} */
++ else foundPearson= true; /* {foundPearson= true; printf("foundPearson\n");} */
+ }
+
+ else if (strstr(sp,"ID ") == sp)
+@@ -1239,9 +1353,16 @@
+
+ else {
+ if (nlines - *skiplines == 1) {
+- int ispp= 0, ilen= 0;
+- sscanf( sp, "%d%d", &ispp, &ilen);
+- if (ispp > 0 && ilen > 0) isphylip= true;
++ int ispp= 0, ilen= 0, icnt=0;
++ char junkstr[120];
++ memset(junkstr,0,120);
++ icnt= sscanf( sp, "%d%d%c", &ispp, &ilen, junkstr);
++ if (icnt == 2 && ispp > 0 && ilen > 0) {
++ isphylip= true;
++ }
++ else if (icnt==3 && ispp > 0 && ilen > 0 && *junkstr == ' ') {
++ isphylip= true;
++ }
+ }
+ else if (isphylip && nlines - *skiplines == 2) {
+ int tseq;
+@@ -1257,6 +1378,65 @@
+ }
+ if (isfitch & (splen > 20)) foundFitch= true;
+
++#ifdef DEBUG_LINALL
++ dprintf(("Check for LINALL\n"));
++ dprintf(("\tstrtol(sp,NULL,0) = %d\n",strtol(sp,NULL,0)));
++ dprintf(("\tnlines = %d\n",nlines));
++ dprintf(("\tisphylip = %d\n",isphylip));
++ dprintf(("\tfoundPhylip = %d\n",foundPhylip));
++ dprintf(("\tisfitch = %d\n",isfitch));
++ dprintf(("\tfoundFitch = %d\n",foundFitch));
++#endif
++
++ /*
++ * This format detection was highly bogus ...
++ * Lesson 1: always initialize variables (in case the conversion fails...)
++ * Lesson 2: strings are passed to sscanf _without_ & (string variable is a pointer already)
++ * Lesson 3: forget to check return codes from syscalls: you lose.
++ */
++
++ if (nlines==1) {
++ int rv;
++#ifdef DEBUG_LINALL
++ int i, sane=1;
++ char *spp;
++
++ /*
++ * possible sanity check, for losers (see above)
++ */
++ for (spp=sp, i=0; i<4; i++, spp++)
++ if (!(isspace(*spp) || isdigit(*spp))) {
++ dprintf(("bogus linall format header: %s\n", sp));
++ sane=0;
++ break;
++ }
++#endif
++
++ linallSeqLen = 0;
++ *linallHeader = '\0';
++ rv = sscanf( sp, "%d %s", &linallSeqLen, linallHeader);
++
++#ifdef DEBUG_LINALL
++ dprintf(("\tsscanf rval = %d\n",rv));
++ dprintf(("\tlinallSeqLen = %d\n",linallSeqLen));
++ dprintf(("\tlinallHeader = %s\n",linallHeader));
++ dprintf(("\tlinallHeader = %d\n",strlen(linallHeader)));
++#endif
++
++ if (rv > 0 && linallSeqLen>0 &&
++ strlen(linallHeader)>0 &&
++ !(isphylip || foundPhylip)) {
++ /* !(isphylip || foundPhylip || isfitch || foundFitch)) { */
++ foundLINALL= true; /* The 1st line contains the seqlength (4 digits), a blank, and a label (up to 60 char). */
++ /* The following lines contain the sequence with 70 chars per line. */
++#ifdef DEBUG_LINALL
++ dprintf(("debug: foundLINALL: %ld<\n",strtol(sp,NULL,0)));
++ dprintf(("debug: sp:%s<\n\n",sp));
++#endif
++ }
++
++ }
++
+ /* kRNA && kDNA are fairly certain...*/
+ switch (getseqtype( sp, splen)) {
+ case kOtherSeq: otherlines++; break;
+@@ -1302,6 +1482,16 @@
+ done= true;
+ }
+
++ else if (foundLINALL) {
++ format= kLINALL;
++ done= true;
++ }
++
++ else if (foundVIE) {
++ format= kVIE;
++ done= true;
++ }
++
+ else if ((dnalines > 1) || done || (nlines > maxlines2check)) {
+ /* decide on most likely format */
+ /* multichar idents: */
+@@ -1785,6 +1975,27 @@
+ linesout += 2;
+ break;
+
++ case kLINALL: /* GSt */
++ fprintf(outf,"%4d %-60s\n",seqlen,seqname);
++ strcpy(endstr,"\n");
++ linesout++;
++ width = 70;
++ tab = 0;
++ spacer = 0;
++ nameleft = false;
++ nameright = false;
++ numleft = false;
++ numright = false;
++ break;
++
++ case kVIE: /* GSt + RL */
++ if ( strchr(seqname,' ') != NULL ) seqname[strchr(seqname,' ')-seqname] = '\0'; /* no blanks in label line */
++ fprintf(outf,"> %-s\n", seqname);
++ linesout++;
++ fprintf(outf,"%s\n\n",seq); /* complete sequence in one line; additional blank line before next sequence */
++ return linesout; /* thus, do nothing else */
++ break;
++
+ default :
+ case kZuker: /* don't attempt Zuker's ftn format */
+ case kPearson:
+@@ -1841,7 +2052,8 @@
+ s[l++] = ' ';
+ if (!baseonlynum) ibase++;
+ else if (0==strchr(nocountsymbols,seq[i])) ibase++;
+- s[l++] = seq[i++];
++ if (outform==kLINALL) { s[l++] = to_upper(seq[i]); i++; } /* GSt */
++ else s[l++] = seq[i++] ;
+ }
+
+ if (l1 == width || i == seqlen) {
+diff -ubrN readseq-1.orig/ureadseq.h readseq-1/ureadseq.h
+--- readseq-1.orig/ureadseq.h 1992-12-30 01:00:00.000000000 +0100
++++ readseq-1/ureadseq.h 2007-11-14 12:14:36.000000000 +0100
+@@ -66,8 +66,10 @@
+ #define kASN1 16
+ #define kPAUP 17
+ #define kPretty 18
++#define kLINALL 19
++#define kVIE 20
+
+-#define kMaxFormat 18
++#define kMaxFormat 20
+ #define kMinFormat 1
+ #define kNoformat -1 /* format not tested */
+ #define kUnknown 0 /* format not determinable */
+@@ -100,7 +102,7 @@
+ p.noleaves= p.domatch= p.degap= false;\
+ p.matchchar='.';\
+ p.gapchar='-';\
+- p.namewidth=8;\
++ p.namewidth=10;\
+ p.numwidth=5;\
+ p.interline=1;\
+ p.spacer=10;\
Added: trunk/packages/readseq/trunk/debian/patches/552830.patch
===================================================================
--- trunk/packages/readseq/trunk/debian/patches/552830.patch (rev 0)
+++ trunk/packages/readseq/trunk/debian/patches/552830.patch 2009-11-26 11:33:48 UTC (rev 4406)
@@ -0,0 +1,252 @@
+Author: Ruben Molina <rmolina at udea.edu.co>
+Description: Fixes error: conflicting types for 'getline' problem (#552830)
+
+--- readseq-1.orig/ureadseq.c
++++ readseq-1/ureadseq.c
+@@ -142,7 +142,7 @@
+ }
+ }
+
+-Local void getline(struct ReadSeqVars *V)
++Local void mygetline(struct ReadSeqVars *V)
+ {
+ readline(V->f, V->s, &V->linestart);
+ }
+@@ -237,7 +237,7 @@
+
+ if (addfirst) addseq(V->s, V);
+ do {
+- getline(V);
++ mygetline(V);
+ V->done = feof(V->f);
+ V->done |= (*endTest)( &addend, &ungetend, V);
+ if (V->addit && (addend || !V->done) && (strlen(V->s) > margin)) {
+@@ -268,7 +268,7 @@
+
+ while (!V->allDone) {
+ do {
+- getline(V);
++ mygetline(V);
+ for (si= V->s; *si != 0 && *si < ' '; si++) *si= ' '; /* drop controls */
+ if (*si == 0) *V->s= 0; /* chop line to empty */
+ } while (! (feof(V->f) || ((*V->s != 0) && (*V->s != ';') ) ));
+@@ -294,13 +294,13 @@
+ { /* ? only 1 seq/file ? */
+
+ while (!V->allDone) {
+- getline(V);
++ mygetline(V);
+ if (strstr(V->s,"; DNA sequence ") == V->s)
+ strcpy(V->seqid, (V->s)+16);
+ else
+ strcpy(V->seqid, (V->s)+1);
+ while ((!feof(V->f)) && (*V->s == ';')) {
+- getline(V);
++ mygetline(V);
+ }
+ if (feof(V->f)) V->allDone = true;
+ else readLoop(0, true, endStrider, V);
+@@ -320,16 +320,16 @@
+
+ while (!V->allDone) {
+ while (! (feof(V->f) || strstr(V->s,"ENTRY") || strstr(V->s,"SEQUENCE")) )
+- getline(V);
++ mygetline(V);
+ strcpy(V->seqid, (V->s)+16);
+ while (! (feof(V->f) || strstr(V->s,"SEQUENCE") == V->s))
+- getline(V);
++ mygetline(V);
+ readLoop(0, false, endPIR, V);
+
+ if (!V->allDone) {
+ while (! (feof(V->f) || ((*V->s != 0)
+ && (strstr( V->s,"ENTRY") == V->s))))
+- getline(V);
++ mygetline(V);
+ }
+ if (feof(V->f)) V->allDone = true;
+ }
+@@ -354,13 +354,13 @@
+ while (!V->allDone) {
+ strcpy(V->seqid, (V->s)+12);
+ while (! (feof(V->f) || strstr(V->s,"ORIGIN") == V->s))
+- getline(V);
++ mygetline(V);
+ readLoop(0, false, endGB, V);
+
+ if (!V->allDone) {
+ while (! (feof(V->f) || ((*V->s != 0)
+ && (strstr( V->s,"LOCUS") == V->s))))
+- getline(V);
++ mygetline(V);
+ }
+ if (feof(V->f)) V->allDone = true;
+ }
+@@ -426,11 +426,11 @@
+ {
+ while (!V->allDone) {
+ strcpy(V->seqid, (V->s)+4);
+- getline(V); /*skip title-junk line*/
++ mygetline(V); /*skip title-junk line*/
+ readLoop(0, false, endNBRF, V);
+ if (!V->allDone) {
+ while (!(feof(V->f) || (*V->s != 0 && *V->s == '>')))
+- getline(V);
++ mygetline(V);
+ }
+ if (feof(V->f)) V->allDone = true;
+ }
+@@ -452,7 +452,7 @@
+ readLoop(0, false, endPearson, V);
+ if (!V->allDone) {
+ while (!(feof(V->f) || ((*V->s != 0) && (*V->s == '>'))))
+- getline(V);
++ mygetline(V);
+ }
+ if (feof(V->f)) V->allDone = true;
+ }
+@@ -472,14 +472,14 @@
+ while (!V->allDone) {
+ strcpy(V->seqid, (V->s)+5);
+ do {
+- getline(V);
++ mygetline(V);
+ } while (!(feof(V->f) | (strstr(V->s,"SQ ") == V->s)));
+
+ readLoop(0, false, endEMBL, V);
+ if (!V->allDone) {
+ while (!(feof(V->f) |
+ ((*V->s != '\0') & (strstr(V->s,"ID ") == V->s))))
+- getline(V);
++ mygetline(V);
+ }
+ if (feof(V->f)) V->allDone = true;
+ }
+@@ -499,13 +499,13 @@
+ /*! 1st string is Zuker's Fortran format */
+
+ while (!V->allDone) {
+- getline(V); /*s == "seqLen seqid string..."*/
++ mygetline(V); /*s == "seqLen seqid string..."*/
+ strcpy(V->seqid, (V->s)+6);
+ readLoop(0, false, endZuker, V);
+ if (!V->allDone) {
+ while (!(feof(V->f) |
+ ((*V->s != '\0') & (*V->s == '('))))
+- getline(V);
++ mygetline(V);
+ }
+ if (feof(V->f)) V->allDone = true;
+ }
+@@ -588,7 +588,7 @@
+ do {
+ addseq(V->s, V);
+ V->done = feof(V->f);
+- getline(V);
++ mygetline(V);
+ } while (!V->done);
+ if (V->choice == kListSequences) addinfo(V->seqid, V);
+ V->allDone = true;
+@@ -614,7 +614,7 @@
+ else if (si = strstr(V->seqid,"..")) *si = 0;
+ do {
+ V->done = feof(V->f);
+- getline(V);
++ mygetline(V);
+ if (!V->done) addseq((V->s), V);
+ } while (!V->done);
+ if (V->choice == kListSequences) addinfo(V->seqid, V);
+@@ -633,7 +633,7 @@
+ if (V->addit) V->seqlen = 0;
+ rewind(V->f); V->nseq= 0;
+ do {
+- getline(V);
++ mygetline(V);
+ V->done = feof(V->f);
+
+ if (V->done && !(*V->s)) break;
+@@ -716,7 +716,7 @@
+ if (V->addit) V->seqlen = 0;
+ rewind(V->f); V->nseq= 0;
+ do {
+- getline(V);
++ mygetline(V);
+ V->done = feof(V->f);
+
+ if (V->done && !(*V->s)) break;
+@@ -787,7 +787,7 @@
+ domatch= (V->matchchar > 0);
+
+ do {
+- getline(V);
++ mygetline(V);
+ V->done = feof(V->f);
+
+ if (V->done && !(*V->s)) break;
+@@ -868,7 +868,7 @@
+ /* rewind(V->f); V->nseq= 0; << do in caller !*/
+ indata= true; /* call here after we find "matrix" */
+ do {
+- getline(V);
++ mygetline(V);
+ V->done = feof(V->f);
+
+ if (V->done && !(*V->s)) break;
+@@ -953,7 +953,7 @@
+ /* fprintf(stderr,"Phylip-ileaf: topnseq=%d topseqlen=%d\n",V->topnseq, V->topseqlen); */
+
+ do {
+- getline(V);
++ mygetline(V);
+ V->done = feof(V->f);
+
+ if (V->done && !(*V->s)) break;
+@@ -1006,7 +1006,7 @@
+ while (isdigit(*si)) si++;
+ skipwhitespace(si);
+ V->topseqlen= atol(si);
+- getline(V);
++ mygetline(V);
+ while (!V->allDone) {
+ V->seqlencount= 0;
+ strncpy(V->seqid, (V->s), 10);
+@@ -1037,10 +1037,10 @@
+ V->err = eFileNotFound;
+ else {
+
+- for (l = skiplines_; l > 0; l--) getline( V);
++ for (l = skiplines_; l > 0; l--) mygetline( V);
+
+ do {
+- getline( V);
++ mygetline( V);
+ for (l= strlen(V->s); (l > 0) && (V->s[l] == ' '); l--) ;
+ } while ((l == 0) && !feof(V->f));
+
+@@ -1067,7 +1067,7 @@
+ char *cp;
+ /* rewind(V->f); V->nseq= 0; ?? assume it is at top ?? skiplines ... */
+ while (!done) {
+- getline( V);
++ mygetline( V);
+ tolowerstr( V->s);
+ if (strstr( V->s, "matrix")) done= true;
+ if (strstr( V->s, "interleav")) interleaved= true;
+@@ -1099,7 +1099,7 @@
+ break;
+
+ case kFitch :
+- strcpy(V->seqid, V->s); getline(V);
++ strcpy(V->seqid, V->s); mygetline(V);
+ readFitch(V);
+ break;
+
+@@ -1107,7 +1107,7 @@
+ do {
+ gotuw = (strstr(V->s,"..") != NULL);
+ if (gotuw) readUWGCG(V);
+- getline(V);
++ mygetline(V);
+ } while (!(feof(V->f) || V->allDone));
+ break;
+ }
Added: trunk/packages/readseq/trunk/debian/patches/series
===================================================================
--- trunk/packages/readseq/trunk/debian/patches/series (rev 0)
+++ trunk/packages/readseq/trunk/debian/patches/series 2009-11-26 11:33:48 UTC (rev 4406)
@@ -0,0 +1,4 @@
+20-Formats.patch
+20-Makefile.patch
+30-arb-code-patches.patch
+552830.patch
Modified: trunk/packages/readseq/trunk/debian/rules
===================================================================
--- trunk/packages/readseq/trunk/debian/rules 2009-11-26 09:49:09 UTC (rev 4405)
+++ trunk/packages/readseq/trunk/debian/rules 2009-11-26 11:33:48 UTC (rev 4406)
@@ -2,7 +2,7 @@
# debian/rules for readseq using cdbs
# Andreas Tille <tille at debian.org>, GPL
-include /usr/share/cdbs/1/rules/dpatch.mk
+include /usr/share/cdbs/1/rules/patchsys-quilt.mk
include /usr/share/cdbs/1/rules/debhelper.mk
include /usr/share/cdbs/1/class/makefile.mk
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