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authorPetar Petrov <ppetrov@paju.oulu.fi>2011-10-19 19:39:37 -0200
committerNiels Horn <niels.horn@slackbuilds.org>2011-10-21 15:59:16 -0200
commitfd8480905d0892cfcb2fb02f548442a80cd41627 (patch)
tree674f78da1761c9d9335861c22616263f56c01d4d
parent8d5c20db4abffdde22060be57b4f9b2fd78c1819 (diff)
academic/EMBOSS: Updated with newest patches.
Signed-off-by: Niels Horn <niels.horn@slackbuilds.org>
Diffstat
-rw-r--r--academic/EMBOSS/EMBOSS.SlackBuild6
-rw-r--r--academic/EMBOSS/patch-1-24 (renamed from academic/EMBOSS/patch-1-21)152
2 files changed, 126 insertions, 32 deletions
diff --git a/academic/EMBOSS/EMBOSS.SlackBuild b/academic/EMBOSS/EMBOSS.SlackBuild
index 900b1fd602fa..0321ba1146b2 100644
--- a/academic/EMBOSS/EMBOSS.SlackBuild
+++ b/academic/EMBOSS/EMBOSS.SlackBuild
@@ -10,7 +10,7 @@
PRGNAM=EMBOSS
VERSION=${VERSION:-6.4.0}
-BUILD=${BUILD:-2}
+BUILD=${BUILD:-3}
TAG=${TAG:-_SBo}
if [ -z "$ARCH" ]; then
@@ -49,8 +49,8 @@ rm -rf $PRGNAM-$VERSION
tar xvf $CWD/$PRGNAM-$VERSION.tar.gz
cd $PRGNAM-$VERSION
-# Apply EMBOSS bug-fix set 1-21. Thanks to ajb@ebi.ac.uk!
-patch -p1 < $CWD/patch-1-21
+# Apply EMBOSS bug-fix set 1-24. Thanks to Alan at ajb@ebi.ac.uk!
+patch -p1 < $CWD/patch-1-24
chown -R root:root .
find . \
diff --git a/academic/EMBOSS/patch-1-21 b/academic/EMBOSS/patch-1-24
index cb182c65c877..04fe05ba2b38 100644
--- a/academic/EMBOSS/patch-1-21
+++ b/academic/EMBOSS/patch-1-24
@@ -1,6 +1,6 @@
diff -c -N --recursive -a EMBOSS-6.4.0old/ajax/ajaxdb/ajtextdb.c EMBOSS-6.4.0/ajax/ajaxdb/ajtextdb.c
*** EMBOSS-6.4.0old/ajax/ajaxdb/ajtextdb.c 2011-07-06 17:09:36.000000000 +0100
---- EMBOSS-6.4.0/ajax/ajaxdb/ajtextdb.c 2011-09-05 12:23:43.000000000 +0100
+--- EMBOSS-6.4.0/ajax/ajaxdb/ajtextdb.c 2011-10-05 14:56:07.000000000 +0100
***************
*** 2580,2588 ****
{
@@ -41,7 +41,7 @@ diff -c -N --recursive -a EMBOSS-6.4.0old/ajax/ajaxdb/ajtextdb.c EMBOSS-6.4.0/aj
{
diff -c -N --recursive -a EMBOSS-6.4.0old/ajax/core/ajarch.h EMBOSS-6.4.0/ajax/core/ajarch.h
*** EMBOSS-6.4.0old/ajax/core/ajarch.h 2011-06-08 11:35:28.000000000 +0100
---- EMBOSS-6.4.0/ajax/core/ajarch.h 2011-09-05 12:23:43.000000000 +0100
+--- EMBOSS-6.4.0/ajax/core/ajarch.h 2011-10-05 14:56:07.000000000 +0100
***************
*** 137,143 ****
@@ -68,7 +68,7 @@ diff -c -N --recursive -a EMBOSS-6.4.0old/ajax/core/ajarch.h EMBOSS-6.4.0/ajax/c
--- 159,161 ----
diff -c -N --recursive -a EMBOSS-6.4.0old/ajax/core/ajfeatread.c EMBOSS-6.4.0/ajax/core/ajfeatread.c
*** EMBOSS-6.4.0old/ajax/core/ajfeatread.c 2011-07-07 17:37:21.000000000 +0100
---- EMBOSS-6.4.0/ajax/core/ajfeatread.c 2011-09-05 12:23:43.000000000 +0100
+--- EMBOSS-6.4.0/ajax/core/ajfeatread.c 2011-10-05 14:56:07.000000000 +0100
***************
*** 3035,3041 ****
AjPStr TvString = NULL;
@@ -141,7 +141,7 @@ diff -c -N --recursive -a EMBOSS-6.4.0old/ajax/core/ajfeatread.c EMBOSS-6.4.0/aj
diff -c -N --recursive -a EMBOSS-6.4.0old/ajax/core/ajfeatwrite.c EMBOSS-6.4.0/ajax/core/ajfeatwrite.c
*** EMBOSS-6.4.0old/ajax/core/ajfeatwrite.c 2011-06-23 11:56:06.000000000 +0100
---- EMBOSS-6.4.0/ajax/core/ajfeatwrite.c 2011-09-05 12:23:43.000000000 +0100
+--- EMBOSS-6.4.0/ajax/core/ajfeatwrite.c 2011-10-05 14:56:07.000000000 +0100
***************
*** 4134,4140 ****
tmpid = owner->Seqid;
@@ -169,9 +169,52 @@ diff -c -N --recursive -a EMBOSS-6.4.0old/ajax/core/ajfeatwrite.c EMBOSS-6.4.0/a
outtag = tv->Tag;
if(!outtag)
+diff -c -N --recursive -a EMBOSS-6.4.0old/ajax/core/ajfileio.c EMBOSS-6.4.0/ajax/core/ajfileio.c
+*** EMBOSS-6.4.0old/ajax/core/ajfileio.c 2011-05-24 13:51:54.000000000 +0100
+--- EMBOSS-6.4.0/ajax/core/ajfileio.c 2011-10-05 14:56:07.000000000 +0100
+***************
+*** 2006,2025 ****
+ {
+ AjBool ret;
+ ajlong fpos = 0;
+- AjPStr dest;
+
+ ret = ajBuffreadLinePos(buff, Pdest, &fpos);
+
+ /* trim any trailing newline */
+
+- dest = *Pdest;
+-
+ /*ajDebug("Remove carriage-return characters from PC-style files\n");*/
+! if(ajStrGetCharLast(dest) == '\n')
+ ajStrCutEnd(Pdest, 1);
+
+ /* PC files have \r\n Macintosh files have just \r : this fixes both */
+! if(ajStrGetCharLast(dest) == '\r')
+ ajStrCutEnd(Pdest, 1);
+
+ return ret;
+--- 2006,2022 ----
+ {
+ AjBool ret;
+ ajlong fpos = 0;
+
+ ret = ajBuffreadLinePos(buff, Pdest, &fpos);
+
+ /* trim any trailing newline */
+
+ /*ajDebug("Remove carriage-return characters from PC-style files\n");*/
+! if(ajStrGetCharLast(*Pdest) == '\n')
+ ajStrCutEnd(Pdest, 1);
+
+ /* PC files have \r\n Macintosh files have just \r : this fixes both */
+! if(ajStrGetCharLast(*Pdest) == '\r')
+ ajStrCutEnd(Pdest, 1);
+
+ return ret;
diff -c -N --recursive -a EMBOSS-6.4.0old/ajax/core/ajfmt.c EMBOSS-6.4.0/ajax/core/ajfmt.c
*** EMBOSS-6.4.0old/ajax/core/ajfmt.c 2011-05-16 11:31:26.000000000 +0100
---- EMBOSS-6.4.0/ajax/core/ajfmt.c 2011-09-05 12:24:01.000000000 +0100
+--- EMBOSS-6.4.0/ajax/core/ajfmt.c 2011-10-05 18:22:48.000000000 +0100
***************
*** 50,55 ****
--- 50,65 ----
@@ -741,9 +784,25 @@ diff -c -N --recursive -a EMBOSS-6.4.0old/ajax/core/ajfmt.c EMBOSS-6.4.0/ajax/co
/* @funcstatic fmtVscan *******************************************************
**
** Scan a string according to fmt and load the va_list variable pointers
+diff -c -N --recursive -a EMBOSS-6.4.0old/ajax/core/ajindex.c EMBOSS-6.4.0/ajax/core/ajindex.c
+*** EMBOSS-6.4.0old/ajax/core/ajindex.c 2011-07-13 11:59:06.000000000 +0100
+--- EMBOSS-6.4.0/ajax/core/ajindex.c 2011-10-05 14:56:07.000000000 +0100
+***************
+*** 650,655 ****
+--- 650,659 ----
+ ajTablePut(btreeFieldsTable,
+ field->Name,
+ (void*) field);
++ field = btreeFieldNewField(&btreeFields[i]);
++ ajTablePut(btreeFieldsTable,
++ field->Extension,
++ (void*) field);
+ }
+
+ return;
diff -c -N --recursive -a EMBOSS-6.4.0old/ajax/core/ajnam.c EMBOSS-6.4.0/ajax/core/ajnam.c
*** EMBOSS-6.4.0old/ajax/core/ajnam.c 2011-07-15 08:15:37.000000000 +0100
---- EMBOSS-6.4.0/ajax/core/ajnam.c 2011-09-05 12:23:43.000000000 +0100
+--- EMBOSS-6.4.0/ajax/core/ajnam.c 2011-10-05 14:56:07.000000000 +0100
***************
*** 8172,8177 ****
--- 8172,8181 ----
@@ -831,7 +890,7 @@ diff -c -N --recursive -a EMBOSS-6.4.0old/ajax/core/ajnam.c EMBOSS-6.4.0/ajax/co
}
diff -c -N --recursive -a EMBOSS-6.4.0old/ajax/core/ajnexus.c EMBOSS-6.4.0/ajax/core/ajnexus.c
*** EMBOSS-6.4.0old/ajax/core/ajnexus.c 2011-03-16 17:14:10.000000000 +0000
---- EMBOSS-6.4.0/ajax/core/ajnexus.c 2011-09-05 12:23:43.000000000 +0100
+--- EMBOSS-6.4.0/ajax/core/ajnexus.c 2011-10-05 14:56:07.000000000 +0100
***************
*** 2,24 ****
** @source AJAX nexus file parsing functions
@@ -2028,7 +2087,7 @@ diff -c -N --recursive -a EMBOSS-6.4.0old/ajax/core/ajnexus.c EMBOSS-6.4.0/ajax/
diff -c -N --recursive -a EMBOSS-6.4.0old/ajax/core/ajpat.c EMBOSS-6.4.0/ajax/core/ajpat.c
*** EMBOSS-6.4.0old/ajax/core/ajpat.c 2010-04-14 09:04:16.000000000 +0100
---- EMBOSS-6.4.0/ajax/core/ajpat.c 2011-09-05 12:23:43.000000000 +0100
+--- EMBOSS-6.4.0/ajax/core/ajpat.c 2011-10-05 14:56:07.000000000 +0100
***************
*** 752,757 ****
--- 752,759 ----
@@ -2059,7 +2118,7 @@ diff -c -N --recursive -a EMBOSS-6.4.0old/ajax/core/ajpat.c EMBOSS-6.4.0/ajax/co
ajStrCutStart(&line,1);
diff -c -N --recursive -a EMBOSS-6.4.0old/ajax/core/ajquery.c EMBOSS-6.4.0/ajax/core/ajquery.c
*** EMBOSS-6.4.0old/ajax/core/ajquery.c 2011-07-03 12:39:13.000000000 +0100
---- EMBOSS-6.4.0/ajax/core/ajquery.c 2011-09-05 12:23:43.000000000 +0100
+--- EMBOSS-6.4.0/ajax/core/ajquery.c 2011-10-05 14:56:07.000000000 +0100
***************
*** 1609,1615 ****
--- 1609,1622 ----
@@ -2118,7 +2177,7 @@ diff -c -N --recursive -a EMBOSS-6.4.0old/ajax/core/ajquery.c EMBOSS-6.4.0/ajax/
ajStrTrimWhite(&lastoper);
diff -c -N --recursive -a EMBOSS-6.4.0old/ajax/core/ajrange.c EMBOSS-6.4.0/ajax/core/ajrange.c
*** EMBOSS-6.4.0old/ajax/core/ajrange.c 2010-05-21 11:54:40.000000000 +0100
---- EMBOSS-6.4.0/ajax/core/ajrange.c 2011-09-05 12:23:43.000000000 +0100
+--- EMBOSS-6.4.0/ajax/core/ajrange.c 2011-10-05 14:56:07.000000000 +0100
***************
*** 179,185 ****
ajuint minsize, ajuint size)
@@ -2217,9 +2276,23 @@ diff -c -N --recursive -a EMBOSS-6.4.0old/ajax/core/ajrange.c EMBOSS-6.4.0/ajax/
}
+diff -c -N --recursive -a EMBOSS-6.4.0old/ajax/core/ajreport.c EMBOSS-6.4.0/ajax/core/ajreport.c
+*** EMBOSS-6.4.0old/ajax/core/ajreport.c 2011-07-08 15:54:59.000000000 +0100
+--- EMBOSS-6.4.0/ajax/core/ajreport.c 2011-10-05 14:56:07.000000000 +0100
+***************
+*** 677,682 ****
+--- 677,684 ----
+ istart = feature->Start;
+ iend = feature->End;
+ ilen = iend - istart + 1;
++ if(ilen == 2 && (feature->Flags & FEATFLAG_BETWEEN_SEQ))
++ ilen = 0;
+ ajStrAssignSubS(&subseq, seqalias, istart-1, iend-1);
+ /* ajStrFmtUpper(&subseq); */
+ i++;
diff -c -N --recursive -a EMBOSS-6.4.0old/ajax/core/ajseqabi.c EMBOSS-6.4.0/ajax/core/ajseqabi.c
*** EMBOSS-6.4.0old/ajax/core/ajseqabi.c 2011-05-19 11:28:09.000000000 +0100
---- EMBOSS-6.4.0/ajax/core/ajseqabi.c 2011-09-05 12:23:43.000000000 +0100
+--- EMBOSS-6.4.0/ajax/core/ajseqabi.c 2011-10-05 14:56:07.000000000 +0100
***************
*** 181,186 ****
--- 181,187 ----
@@ -2242,7 +2315,7 @@ diff -c -N --recursive -a EMBOSS-6.4.0old/ajax/core/ajseqabi.c EMBOSS-6.4.0/ajax
return ajTrue;
diff -c -N --recursive -a EMBOSS-6.4.0old/ajax/core/ajseqread.c EMBOSS-6.4.0/ajax/core/ajseqread.c
*** EMBOSS-6.4.0old/ajax/core/ajseqread.c 2011-06-27 08:38:44.000000000 +0100
---- EMBOSS-6.4.0/ajax/core/ajseqread.c 2011-09-05 12:23:43.000000000 +0100
+--- EMBOSS-6.4.0/ajax/core/ajseqread.c 2011-10-05 14:56:07.000000000 +0100
***************
*** 5497,5502 ****
--- 5497,5503 ----
@@ -2612,7 +2685,7 @@ diff -c -N --recursive -a EMBOSS-6.4.0old/ajax/core/ajseqread.c EMBOSS-6.4.0/aja
ajFeattableDel(&thys->Fttable);
diff -c -N --recursive -a EMBOSS-6.4.0old/ajax/ensembl/ensdatabaseadaptor.c EMBOSS-6.4.0/ajax/ensembl/ensdatabaseadaptor.c
*** EMBOSS-6.4.0old/ajax/ensembl/ensdatabaseadaptor.c 2011-07-06 22:50:28.000000000 +0100
---- EMBOSS-6.4.0/ajax/ensembl/ensdatabaseadaptor.c 2011-09-05 12:23:43.000000000 +0100
+--- EMBOSS-6.4.0/ajax/ensembl/ensdatabaseadaptor.c 2011-10-05 14:56:07.000000000 +0100
***************
*** 156,163 ****
** @argrule Ini dbc [EnsPDatabaseconnection] Ensembl Database Connection
@@ -2835,7 +2908,7 @@ diff -c -N --recursive -a EMBOSS-6.4.0old/ajax/ensembl/ensdatabaseadaptor.c EMBO
** @argrule Species species [AjPStr] Species
diff -c -N --recursive -a EMBOSS-6.4.0old/ajax/ensembl/ensdatabaseadaptor.h EMBOSS-6.4.0/ajax/ensembl/ensdatabaseadaptor.h
*** EMBOSS-6.4.0old/ajax/ensembl/ensdatabaseadaptor.h 2011-07-06 22:50:28.000000000 +0100
---- EMBOSS-6.4.0/ajax/ensembl/ensdatabaseadaptor.h 2011-09-05 12:23:43.000000000 +0100
+--- EMBOSS-6.4.0/ajax/ensembl/ensdatabaseadaptor.h 2011-10-05 14:56:07.000000000 +0100
***************
*** 121,127 ****
@@ -2855,7 +2928,7 @@ diff -c -N --recursive -a EMBOSS-6.4.0old/ajax/ensembl/ensdatabaseadaptor.h EMBO
diff -c -N --recursive -a EMBOSS-6.4.0old/ajax/ensembl/ensregistry.c EMBOSS-6.4.0/ajax/ensembl/ensregistry.c
*** EMBOSS-6.4.0old/ajax/ensembl/ensregistry.c 2011-07-08 12:43:41.000000000 +0100
---- EMBOSS-6.4.0/ajax/ensembl/ensregistry.c 2011-09-05 12:23:43.000000000 +0100
+--- EMBOSS-6.4.0/ajax/ensembl/ensregistry.c 2011-10-05 14:56:07.000000000 +0100
***************
*** 569,576 ****
const RegistryPQualityCheck rqc,
@@ -3327,7 +3400,7 @@ diff -c -N --recursive -a EMBOSS-6.4.0old/ajax/ensembl/ensregistry.c EMBOSS-6.4.
alias, species);
diff -c -N --recursive -a EMBOSS-6.4.0old/ajax/ensembl/ensregistry.h EMBOSS-6.4.0/ajax/ensembl/ensregistry.h
*** EMBOSS-6.4.0old/ajax/ensembl/ensregistry.h 2011-05-25 20:55:04.000000000 +0100
---- EMBOSS-6.4.0/ajax/ensembl/ensregistry.h 2011-09-05 12:23:43.000000000 +0100
+--- EMBOSS-6.4.0/ajax/ensembl/ensregistry.h 2011-10-05 14:56:07.000000000 +0100
***************
*** 116,122 ****
AjBool ensRegistryRemoveDatabaseadaptor(EnsPDatabaseadaptor* Pdba);
@@ -3347,7 +3420,7 @@ diff -c -N --recursive -a EMBOSS-6.4.0old/ajax/ensembl/ensregistry.h EMBOSS-6.4.
AjPStr ensRegistryGetStableidentifierprefix(EnsPDatabaseadaptor dba);
diff -c -N --recursive -a EMBOSS-6.4.0old/emboss/cacheensembl.c EMBOSS-6.4.0/emboss/cacheensembl.c
*** EMBOSS-6.4.0old/emboss/cacheensembl.c 2011-07-08 17:29:51.000000000 +0100
---- EMBOSS-6.4.0/emboss/cacheensembl.c 2011-09-05 12:23:43.000000000 +0100
+--- EMBOSS-6.4.0/emboss/cacheensembl.c 2011-10-05 14:56:07.000000000 +0100
***************
*** 181,186 ****
--- 181,191 ----
@@ -3364,7 +3437,7 @@ diff -c -N --recursive -a EMBOSS-6.4.0old/emboss/cacheensembl.c EMBOSS-6.4.0/emb
ajFmtPrintF(cachef, " url: \"%S\"\n", dbcurl);
diff -c -N --recursive -a EMBOSS-6.4.0old/emboss/cirdna.c EMBOSS-6.4.0/emboss/cirdna.c
*** EMBOSS-6.4.0old/emboss/cirdna.c 2011-05-16 11:17:10.000000000 +0100
---- EMBOSS-6.4.0/emboss/cirdna.c 2011-09-05 12:23:43.000000000 +0100
+--- EMBOSS-6.4.0/emboss/cirdna.c 2011-10-05 14:56:07.000000000 +0100
***************
*** 970,976 ****
{
@@ -3432,7 +3505,7 @@ diff -c -N --recursive -a EMBOSS-6.4.0old/emboss/cirdna.c EMBOSS-6.4.0/emboss/ci
cirdna_HorTextPile(xDraw, yDraw,
diff -c -N --recursive -a EMBOSS-6.4.0old/emboss/data/Efeatures.gff3protein EMBOSS-6.4.0/emboss/data/Efeatures.gff3protein
*** EMBOSS-6.4.0old/emboss/data/Efeatures.gff3protein 2009-03-06 12:37:43.000000000 +0000
---- EMBOSS-6.4.0/emboss/data/Efeatures.gff3protein 2011-09-05 12:23:43.000000000 +0100
+--- EMBOSS-6.4.0/emboss/data/Efeatures.gff3protein 2011-10-05 14:56:08.000000000 +0100
***************
*** 193,199 ****
@@ -3507,7 +3580,7 @@ diff -c -N --recursive -a EMBOSS-6.4.0old/emboss/data/Efeatures.gff3protein EMBO
/ftid
diff -c -N --recursive -a EMBOSS-6.4.0old/emboss/data/Etcode.dat EMBOSS-6.4.0/emboss/data/Etcode.dat
*** EMBOSS-6.4.0old/emboss/data/Etcode.dat 2003-03-07 09:45:22.000000000 +0000
---- EMBOSS-6.4.0/emboss/data/Etcode.dat 2011-09-05 12:23:43.000000000 +0100
+--- EMBOSS-6.4.0/emboss/data/Etcode.dat 2011-10-05 14:56:08.000000000 +0100
***************
*** 22,27 ****
--- 22,28 ----
@@ -3520,7 +3593,7 @@ diff -c -N --recursive -a EMBOSS-6.4.0old/emboss/data/Etcode.dat EMBOSS-6.4.0/em
#
diff -c -N --recursive -a EMBOSS-6.4.0old/emboss/dbiflat.c EMBOSS-6.4.0/emboss/dbiflat.c
*** EMBOSS-6.4.0old/emboss/dbiflat.c 2011-06-23 19:18:45.000000000 +0100
---- EMBOSS-6.4.0/emboss/dbiflat.c 2011-09-05 12:23:43.000000000 +0100
+--- EMBOSS-6.4.0/emboss/dbiflat.c 2011-10-05 14:56:08.000000000 +0100
***************
*** 91,96 ****
--- 91,100 ----
@@ -3941,7 +4014,7 @@ diff -c -N --recursive -a EMBOSS-6.4.0old/emboss/dbiflat.c EMBOSS-6.4.0/emboss/d
** Parse the ID, accession from an EMBL entry.
diff -c -N --recursive -a EMBOSS-6.4.0old/emboss/dbxflat.c EMBOSS-6.4.0/emboss/dbxflat.c
*** EMBOSS-6.4.0old/emboss/dbxflat.c 2011-06-23 19:18:45.000000000 +0100
---- EMBOSS-6.4.0/emboss/dbxflat.c 2011-09-05 12:23:43.000000000 +0100
+--- EMBOSS-6.4.0/emboss/dbxflat.c 2011-10-05 14:56:08.000000000 +0100
***************
*** 32,37 ****
--- 32,38 ----
@@ -4075,7 +4148,7 @@ diff -c -N --recursive -a EMBOSS-6.4.0old/emboss/dbxflat.c EMBOSS-6.4.0/emboss/d
** Parse the next entry from a flatfile
diff -c -N --recursive -a EMBOSS-6.4.0old/emboss/dbxresource.c EMBOSS-6.4.0/emboss/dbxresource.c
*** EMBOSS-6.4.0old/emboss/dbxresource.c 2011-06-23 19:18:45.000000000 +0100
---- EMBOSS-6.4.0/emboss/dbxresource.c 2011-09-05 12:23:43.000000000 +0100
+--- EMBOSS-6.4.0/emboss/dbxresource.c 2011-10-05 14:56:08.000000000 +0100
***************
*** 535,540 ****
--- 535,553 ----
@@ -4098,9 +4171,30 @@ diff -c -N --recursive -a EMBOSS-6.4.0old/emboss/dbxresource.c EMBOSS-6.4.0/embo
else if(ajStrSuffixC(name, "Cat"))
{
if(catfield && !ajStrMatchC(rest, "None"))
+diff -c -N --recursive -a EMBOSS-6.4.0old/emboss/diffseq.c EMBOSS-6.4.0/emboss/diffseq.c
+*** EMBOSS-6.4.0old/emboss/diffseq.c 2010-04-14 09:19:27.000000000 +0100
+--- EMBOSS-6.4.0/emboss/diffseq.c 2011-10-05 14:56:08.000000000 +0100
+***************
+*** 338,344 ****
+ }
+ else
+ {
+! gf = ajFeatNewII(ftab, diff->End1, diff->End1-1);
+ ajStrAssignC(&tmp, "");
+ }
+ diffseq_Features("first_feature", gf,
+--- 338,345 ----
+ }
+ else
+ {
+! gf = ajFeatNewII(ftab, diff->Start1-1, diff->Start1);
+! gf->Flags |= FEATFLAG_BETWEEN_SEQ;
+ ajStrAssignC(&tmp, "");
+ }
+ diffseq_Features("first_feature", gf,
diff -c -N --recursive -a EMBOSS-6.4.0old/emboss/drfinddata.c EMBOSS-6.4.0/emboss/drfinddata.c
*** EMBOSS-6.4.0old/emboss/drfinddata.c 2011-05-25 10:10:32.000000000 +0100
---- EMBOSS-6.4.0/emboss/drfinddata.c 2011-09-05 12:23:43.000000000 +0100
+--- EMBOSS-6.4.0/emboss/drfinddata.c 2011-10-05 14:56:08.000000000 +0100
***************
*** 155,162 ****
{
@@ -4123,7 +4217,7 @@ diff -c -N --recursive -a EMBOSS-6.4.0old/emboss/drfinddata.c EMBOSS-6.4.0/embos
(void *) 1);
diff -c -N --recursive -a EMBOSS-6.4.0old/emboss/drfindformat.c EMBOSS-6.4.0/emboss/drfindformat.c
*** EMBOSS-6.4.0old/emboss/drfindformat.c 2011-05-25 13:41:47.000000000 +0100
---- EMBOSS-6.4.0/emboss/drfindformat.c 2011-09-05 12:23:43.000000000 +0100
+--- EMBOSS-6.4.0/emboss/drfindformat.c 2011-10-05 14:56:08.000000000 +0100
***************
*** 152,159 ****
{
@@ -4146,7 +4240,7 @@ diff -c -N --recursive -a EMBOSS-6.4.0old/emboss/drfindformat.c EMBOSS-6.4.0/emb
(void *) 1);
diff -c -N --recursive -a EMBOSS-6.4.0old/emboss/drfindid.c EMBOSS-6.4.0/emboss/drfindid.c
*** EMBOSS-6.4.0old/emboss/drfindid.c 2011-05-25 13:41:47.000000000 +0100
---- EMBOSS-6.4.0/emboss/drfindid.c 2011-09-05 12:23:43.000000000 +0100
+--- EMBOSS-6.4.0/emboss/drfindid.c 2011-10-05 14:56:08.000000000 +0100
***************
*** 152,159 ****
{
@@ -4169,7 +4263,7 @@ diff -c -N --recursive -a EMBOSS-6.4.0old/emboss/drfindid.c EMBOSS-6.4.0/emboss/
(void *) 1);
diff -c -N --recursive -a EMBOSS-6.4.0old/emboss/drfindresource.c EMBOSS-6.4.0/emboss/drfindresource.c
*** EMBOSS-6.4.0old/emboss/drfindresource.c 2011-04-12 17:30:58.000000000 +0100
---- EMBOSS-6.4.0/emboss/drfindresource.c 2011-09-05 12:23:43.000000000 +0100
+--- EMBOSS-6.4.0/emboss/drfindresource.c 2011-10-05 14:56:08.000000000 +0100
***************
*** 162,170 ****
{
@@ -4194,7 +4288,7 @@ diff -c -N --recursive -a EMBOSS-6.4.0old/emboss/drfindresource.c EMBOSS-6.4.0/e
}
diff -c -N --recursive -a EMBOSS-6.4.0old/emboss/server.ensemblgenomes EMBOSS-6.4.0/emboss/server.ensemblgenomes
*** EMBOSS-6.4.0old/emboss/server.ensemblgenomes 2011-07-06 23:14:17.000000000 +0100
---- EMBOSS-6.4.0/emboss/server.ensemblgenomes 2011-09-05 12:23:43.000000000 +0100
+--- EMBOSS-6.4.0/emboss/server.ensemblgenomes 2011-10-05 14:56:08.000000000 +0100
***************
*** 1,4 ****
! # server.ensemblgenomes 2011-07-05 00:00:00
@@ -7212,7 +7306,7 @@ diff -c -N --recursive -a EMBOSS-6.4.0old/emboss/server.ensemblgenomes EMBOSS-6.
url: "mysql://anonymous@mysql.ebi.ac.uk:4157/wolbachia_collection_core_9_62_1a"
diff -c -N --recursive -a EMBOSS-6.4.0old/nucleus/embgroup.c EMBOSS-6.4.0/nucleus/embgroup.c
*** EMBOSS-6.4.0old/nucleus/embgroup.c 2011-05-16 11:14:30.000000000 +0100
---- EMBOSS-6.4.0/nucleus/embgroup.c 2011-09-05 12:23:43.000000000 +0100
+--- EMBOSS-6.4.0/nucleus/embgroup.c 2011-10-05 14:56:08.000000000 +0100
***************
*** 1173,1179 ****
AjPStr tail;
generated by cgit v1.2.3 (git 2.26.2) at 2024-11-27 16:31:59 +0000