[med-svn] r3133 - in trunk/packages/emboss/trunk/debian: . patches
plessy at alioth.debian.org
plessy at alioth.debian.org
Sun Feb 22 00:22:51 UTC 2009
Author: plessy
Date: 2009-02-22 00:22:51 +0000 (Sun, 22 Feb 2009)
New Revision: 3133
Modified:
trunk/packages/emboss/trunk/debian/changelog
trunk/packages/emboss/trunk/debian/patches/upstream.patch
Log:
New upstream patch.
Modified: trunk/packages/emboss/trunk/debian/changelog
===================================================================
--- trunk/packages/emboss/trunk/debian/changelog 2009-02-21 07:14:30 UTC (rev 3132)
+++ trunk/packages/emboss/trunk/debian/changelog 2009-02-22 00:22:51 UTC (rev 3133)
@@ -1,11 +1,9 @@
emboss (6.0.1-4) UNRELEASED; urgency=low
- TODO: Let's wait the end of the freeze to upload to unstable. After this, it
- would be much safer to rebuild the embassy packages and update their
- orig.tar.gz, that did not change name upstream but was modified.
-
- * New upstream patch (patch-1-4), removing unnecessary whitespaces in
- edialign.acd.
+ * New upstream patch (patch-1-5):
+ - removes unnecessary whitespaces in edialign.acd.
+ - saves Citations and comments in EMBL/GenBank formats for each new
+ entry processed.
* debian/control uses the official homepage URL as confirmed by Upstream.
* debian/rules:
- Pass --bindir=/usr/lib/emboss directly instead of moving files.
Modified: trunk/packages/emboss/trunk/debian/patches/upstream.patch
===================================================================
--- trunk/packages/emboss/trunk/debian/patches/upstream.patch 2009-02-21 07:14:30 UTC (rev 3132)
+++ trunk/packages/emboss/trunk/debian/patches/upstream.patch 2009-02-22 00:22:51 UTC (rev 3133)
@@ -3,11 +3,146 @@
This is an upstream patch, it does not need to be forwarded.
Description: Official upstream patch.
This patch was downloaded from:
- ftp://emboss.open-bio.org/pub/EMBOSS/fixes/patches/patch-1-4.gz
+ ftp://emboss.open-bio.org/pub/EMBOSS/fixes/patches/patch-1-5.gz
+diff -c -N --recursive EMBOSS-6.0.1old/ajax/ajseq.c EMBOSS-6.0.1/ajax/ajseq.c
+*** EMBOSS-6.0.1old/ajax/ajseq.c 2008-07-14 15:54:44.000000000 +0100
+--- EMBOSS-6.0.1/ajax/ajseq.c 2009-02-21 09:21:14.000000000 +0000
+***************
+*** 287,292 ****
+--- 287,293 ----
+ pthis->Sv = ajStrNew();
+ pthis->Gi = ajStrNew();
+ pthis->Tax = ajStrNew();
++ pthis->Organelle = ajStrNew();
+ pthis->Type = ajStrNew();
+ pthis->Db = ajStrNew();
+ pthis->Full = ajStrNew();
+***************
+*** 317,322 ****
+--- 318,326 ----
+ pthis->Acclist = ajListstrNew();
+ pthis->Keylist = ajListstrNew();
+ pthis->Taxlist = ajListstrNew();
++ pthis->Cmtlist = ajListstrNew();
++ pthis->Xreflist = ajListstrNew();
++ pthis->Reflist = ajListstrNew();
+
+ return pthis;
+ }
+***************
+*** 344,349 ****
+--- 348,354 ----
+ pthis->Sv = ajStrNew();
+ pthis->Gi = ajStrNew();
+ pthis->Tax = ajStrNew();
++ pthis->Organelle = ajStrNew();
+ pthis->Type = ajStrNew();
+ pthis->Db = ajStrNew();
+ pthis->Full = ajStrNew();
+***************
+*** 374,379 ****
+--- 379,387 ----
+ pthis->Acclist = ajListstrNew();
+ pthis->Keylist = ajListstrNew();
+ pthis->Taxlist = ajListstrNew();
++ pthis->Cmtlist = ajListstrNew();
++ pthis->Xreflist = ajListstrNew();
++ pthis->Reflist = ajListstrNew();
+
+ return pthis;
+ }
+***************
+*** 435,440 ****
+--- 443,449 ----
+ pthis->Sv = ajStrNew();
+ pthis->Gi = ajStrNew();
+ pthis->Tax = ajStrNew();
++ pthis->Organelle = ajStrNew();
+ pthis->Type = ajStrNew();
+ pthis->Db = ajStrNew();
+ pthis->Full = ajStrNew();
+***************
+*** 473,478 ****
+--- 482,490 ----
+ pthis->Acclist = ajListstrNew();
+ pthis->Keylist = ajListstrNew();
+ pthis->Taxlist = ajListstrNew();
++ pthis->Cmtlist = ajListstrNew();
++ pthis->Xreflist = ajListstrNew();
++ pthis->Reflist = ajListstrNew();
+
+ ajDebug("ajSeqNewRangeC rev:%B offset:%d/%d offend:%d/%d\n",
+ rev, offset, pthis->Offset, offend, pthis->Offend);
+***************
+*** 552,557 ****
+--- 564,570 ----
+ pthis->Sv = ajStrNew();
+ pthis->Gi = ajStrNew();
+ pthis->Tax = ajStrNew();
++ pthis->Organelle = ajStrNew();
+ pthis->Type = ajStrNew();
+ pthis->Db = ajStrNew();
+ pthis->Full = ajStrNew();
+***************
+*** 623,628 ****
+--- 636,642 ----
+ ajStrAssignS(&pthis->Sv, seq->Sv);
+ ajStrAssignS(&pthis->Gi, seq->Gi);
+ ajStrAssignS(&pthis->Tax, seq->Tax);
++ ajStrAssignS(&pthis->Organelle, seq->Organelle);
+ ajStrAssignS(&pthis->Type, seq->Type);
+
+ pthis->EType = seq->EType;
+***************
+*** 662,667 ****
+--- 676,688 ----
+
+ pthis->Taxlist = ajListstrNewList(seq->Taxlist);
+
++ pthis->Cmtlist = ajListstrNewList(seq->Cmtlist);
++
++ pthis->Xreflist = ajListstrNewList(seq->Xreflist);
++
++ pthis->Reflist = ajListstrNew();
++ ajSeqreflistClone(seq->Reflist, pthis->Reflist);
++
+ ajStrAssignS(&pthis->Seq, seq->Seq);
+ if (seq->Fttable)
+ pthis->Fttable = ajFeattableCopy(seq->Fttable);
+***************
+*** 730,735 ****
+--- 751,757 ----
+ ajStrDel(&seq->Sv);
+ ajStrDel(&seq->Gi);
+ ajStrDel(&seq->Tax);
++ ajStrDel(&seq->Organelle);
+ ajStrDel(&seq->Type);
+ ajStrDel(&seq->Molecule);
+ ajStrDel(&seq->Class);
+***************
+*** 1591,1596 ****
+--- 1613,1619 ----
+ ajStrSetClear(&seq->Sv);
+ ajStrSetClear(&seq->Gi);
+ ajStrSetClear(&seq->Tax);
++ ajStrSetClear(&seq->Organelle);
+ ajStrSetClear(&seq->Type);
+ ajStrSetClear(&seq->Molecule);
+ ajStrSetClear(&seq->Class);
diff -c -N --recursive EMBOSS-6.0.1old/ajax/ajseqwrite.c EMBOSS-6.0.1/ajax/ajseqwrite.c
*** EMBOSS-6.0.1old/ajax/ajseqwrite.c 2008-07-14 15:58:07.000000000 +0100
---- EMBOSS-6.0.1/ajax/ajseqwrite.c 2009-02-04 12:58:15.000000000 +0000
+--- EMBOSS-6.0.1/ajax/ajseqwrite.c 2009-02-21 09:21:21.000000000 +0000
***************
+*** 451,456 ****
+--- 451,457 ----
+ pthis->Sv = ajStrNew();
+ pthis->Gi = ajStrNew();
+ pthis->Tax = ajStrNew();
++ pthis->Organelle = ajStrNew();
+ pthis->Desc = ajStrNew();
+ pthis->Type = ajStrNew();
+ pthis->EType = 0;
+***************
*** 3743,3749 ****
ajFmtPrintF(outseq->File, "DE %S\n", outseq->Desc);
@@ -16,7 +151,7 @@
if(ajListGetLength(outseq->Taxlist) > 1)
{
---- 3743,3749 ----
+--- 3744,3750 ----
ajFmtPrintF(outseq->File, "DE %S\n", outseq->Desc);
if(ajStrGetLen(outseq->Tax))
@@ -24,9 +159,37 @@
if(ajListGetLength(outseq->Taxlist) > 1)
{
+***************
+*** 6175,6180 ****
+--- 6176,6182 ----
+ static void seqDeclone(AjPSeqout outseq)
+ {
+ AjPStr ptr = NULL;
++ AjPSeqRef tmpref = NULL;
+
+ ajStrSetClear(&outseq->Db);
+ ajStrSetClear(&outseq->Setdb);
+***************
+*** 6200,6205 ****
+--- 6202,6216 ----
+ while(ajListstrPop(outseq->Taxlist,&ptr))
+ ajStrDel(&ptr);
+
++ while(ajListstrPop(outseq->Cmtlist,&ptr))
++ ajStrDel(&ptr);
++
++ while(ajListstrPop(outseq->Xreflist,&ptr))
++ ajStrDel(&ptr);
++
++ while(ajListPop(outseq->Reflist,(void **)&tmpref))
++ ajSeqrefDel(&tmpref);
++
+ ajStrSetClear(&outseq->Seq);
+ AJFREE(outseq->Accuracy);
+
diff -c -N --recursive EMBOSS-6.0.1old/emboss/acd/edialign.acd EMBOSS-6.0.1/emboss/acd/edialign.acd
*** EMBOSS-6.0.1old/emboss/acd/edialign.acd 2008-04-04 16:54:03.000000000 +0100
---- EMBOSS-6.0.1/emboss/acd/edialign.acd 2009-02-04 13:03:14.000000000 +0000
+--- EMBOSS-6.0.1/emboss/acd/edialign.acd 2009-02-21 09:20:54.000000000 +0000
***************
*** 26,32 ****
information: "Nucleic acid sequence alignment mode"
@@ -73,7 +236,7 @@
endsection: output
diff -c -N --recursive EMBOSS-6.0.1old/emboss/acd/Makefile.am EMBOSS-6.0.1/emboss/acd/Makefile.am
*** EMBOSS-6.0.1old/emboss/acd/Makefile.am 2008-07-14 16:46:31.000000000 +0100
---- EMBOSS-6.0.1/emboss/acd/Makefile.am 2009-02-04 12:58:15.000000000 +0000
+--- EMBOSS-6.0.1/emboss/acd/Makefile.am 2009-02-21 09:20:54.000000000 +0000
***************
*** 21,27 ****
fuzznuc.acd fuzzpro.acd fuzztran.acd \
@@ -113,7 +276,7 @@
diff -c -N --recursive EMBOSS-6.0.1old/emboss/acd/Makefile.in EMBOSS-6.0.1/emboss/acd/Makefile.in
*** EMBOSS-6.0.1old/emboss/acd/Makefile.in 2008-07-16 19:33:19.000000000 +0100
---- EMBOSS-6.0.1/emboss/acd/Makefile.in 2009-02-04 12:58:15.000000000 +0000
+--- EMBOSS-6.0.1/emboss/acd/Makefile.in 2009-02-21 09:20:54.000000000 +0000
***************
*** 209,215 ****
fuzznuc.acd fuzzpro.acd fuzztran.acd \
@@ -153,7 +316,7 @@
diff -c -N --recursive EMBOSS-6.0.1old/emboss/data/Makefile.am EMBOSS-6.0.1/emboss/data/Makefile.am
*** EMBOSS-6.0.1old/emboss/data/Makefile.am 2008-07-14 16:09:23.000000000 +0100
---- EMBOSS-6.0.1/emboss/data/Makefile.am 2009-02-04 12:58:15.000000000 +0000
+--- EMBOSS-6.0.1/emboss/data/Makefile.am 2009-02-21 09:20:54.000000000 +0000
***************
*** 30,36 ****
Epprofile Eprior1.plib Eprior30.plib Erna.melt Eresidues.iub \
@@ -173,7 +336,7 @@
embossre.equ Emwfilter.dat Emass.dat Emassmod.dat \
diff -c -N --recursive EMBOSS-6.0.1old/emboss/data/Makefile.in EMBOSS-6.0.1/emboss/data/Makefile.in
*** EMBOSS-6.0.1old/emboss/data/Makefile.in 2008-07-16 19:33:20.000000000 +0100
---- EMBOSS-6.0.1/emboss/data/Makefile.in 2009-02-04 12:58:15.000000000 +0000
+--- EMBOSS-6.0.1/emboss/data/Makefile.in 2009-02-21 09:20:54.000000000 +0000
***************
*** 228,234 ****
Epprofile Eprior1.plib Eprior30.plib Erna.melt Eresidues.iub \
@@ -193,7 +356,7 @@
embossre.equ Emwfilter.dat Emass.dat Emassmod.dat \
diff -c -N --recursive EMBOSS-6.0.1old/emboss/jaspscan.c EMBOSS-6.0.1/emboss/jaspscan.c
*** EMBOSS-6.0.1old/emboss/jaspscan.c 2008-06-26 09:39:09.000000000 +0100
---- EMBOSS-6.0.1/emboss/jaspscan.c 2009-02-04 12:58:15.000000000 +0000
+--- EMBOSS-6.0.1/emboss/jaspscan.c 2009-02-21 09:20:54.000000000 +0000
***************
*** 293,299 ****
@@ -226,7 +389,7 @@
ajStrDel(&excl);
diff -c -N --recursive EMBOSS-6.0.1old/emboss/vectorstrip.c EMBOSS-6.0.1/emboss/vectorstrip.c
*** EMBOSS-6.0.1old/emboss/vectorstrip.c 2008-06-26 09:39:09.000000000 +0100
---- EMBOSS-6.0.1/emboss/vectorstrip.c 2009-02-04 12:58:15.000000000 +0000
+--- EMBOSS-6.0.1/emboss/vectorstrip.c 2009-02-21 09:20:54.000000000 +0000
***************
*** 174,180 ****
vectorlist = ajListNew();
@@ -246,7 +409,7 @@
{
diff -c -N --recursive EMBOSS-6.0.1old/nucleus/embprop.c EMBOSS-6.0.1/nucleus/embprop.c
*** EMBOSS-6.0.1old/nucleus/embprop.c 2008-07-14 23:13:33.000000000 +0100
---- EMBOSS-6.0.1/nucleus/embprop.c 2009-02-04 12:58:15.000000000 +0000
+--- EMBOSS-6.0.1/nucleus/embprop.c 2009-02-21 09:20:54.000000000 +0000
***************
*** 880,885 ****
--- 880,886 ----
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