[Debian-med-packaging] [SCM] The European Molecular Biology Open Software Suite. branch, master, updated. upstream/6.2.0-23-g7b66dee
Charles Plessy
plessy at debian.org
Tue Jun 22 08:26:42 UTC 2010
The following commit has been merged in the master branch:
commit 74532119e054c9b1f400c60299323d583de93732
Author: Charles Plessy <plessy at debian.org>
Date: Mon Jun 21 22:39:20 2010 +0900
Updated to patch 1-19.
diff --git a/debian/patches/official-upstream-patch.patch b/debian/patches/official-upstream-patch.patch
index 669a673..6d11a0d 100644
--- a/debian/patches/official-upstream-patch.patch
+++ b/debian/patches/official-upstream-patch.patch
@@ -155,12 +155,20 @@ Description: Official upstream patch.
Fix 18. EMBOSS-6.2.0/ajax/core/ajsys.c
.
02-Mar-2010: Add .exe extension when searching for CYGWIN executables
-Origin: ftp://emboss.open-bio.org/pub/EMBOSS/fixes/patches/patch-1-18.gz
+ .
+ .
+ Fix 19.EMBOSS-6.2.0/nucleus/embaln.h
+ EMBOSS-6.2.0/nucleus/embaln.c
+ EMBOSS-6.2.0/emboss/needle.c
+ EMBOSS-6.2.0/emboss/needleall.c
+ .
+ 15-June-2010: Fix needle traceback problem
+Origin: ftp://emboss.open-bio.org/pub/EMBOSS/fixes/patches/patch-1-19.gz
Forwarded: not-needed
diff -c -N --recursive -a EMBOSS-6.2.0old/ajax/core/ajfeat.c EMBOSS-6.2.0/ajax/core/ajfeat.c
*** EMBOSS-6.2.0old/ajax/core/ajfeat.c 2010-01-12 20:18:26.000000000 +0000
---- EMBOSS-6.2.0/ajax/core/ajfeat.c 2010-03-02 09:34:07.000000000 +0000
+--- EMBOSS-6.2.0/ajax/core/ajfeat.c 2010-06-15 09:56:47.000000000 +0100
***************
*** 487,493 ****
** Input feature formats
@@ -1091,7 +1099,7 @@ diff -c -N --recursive -a EMBOSS-6.2.0old/ajax/core/ajfeat.c EMBOSS-6.2.0/ajax/c
** @return [void]
diff -c -N --recursive -a EMBOSS-6.2.0old/ajax/core/ajlist.c EMBOSS-6.2.0/ajax/core/ajlist.c
*** EMBOSS-6.2.0old/ajax/core/ajlist.c 2009-07-09 10:21:44.000000000 +0100
---- EMBOSS-6.2.0/ajax/core/ajlist.c 2010-03-02 09:34:07.000000000 +0000
+--- EMBOSS-6.2.0/ajax/core/ajlist.c 2010-06-15 09:56:47.000000000 +0100
***************
*** 498,504 ****
** @nam3rule Sort Apply function to each node
@@ -1242,7 +1250,7 @@ diff -c -N --recursive -a EMBOSS-6.2.0old/ajax/core/ajlist.c EMBOSS-6.2.0/ajax/c
** @nam4rule PeekNumber Pointer to numbered value
diff -c -N --recursive -a EMBOSS-6.2.0old/ajax/core/ajlist.h EMBOSS-6.2.0/ajax/core/ajlist.h
*** EMBOSS-6.2.0old/ajax/core/ajlist.h 2009-08-24 14:59:06.000000000 +0100
---- EMBOSS-6.2.0/ajax/core/ajlist.h 2010-03-02 09:34:07.000000000 +0000
+--- EMBOSS-6.2.0/ajax/core/ajlist.h 2010-06-15 09:56:47.000000000 +0100
***************
*** 150,155 ****
--- 150,157 ----
@@ -1256,7 +1264,7 @@ diff -c -N --recursive -a EMBOSS-6.2.0old/ajax/core/ajlist.h EMBOSS-6.2.0/ajax/c
AjBool ajListMapfind (const AjPList listhead,
diff -c -N --recursive -a EMBOSS-6.2.0old/ajax/core/ajpat.c EMBOSS-6.2.0/ajax/core/ajpat.c
*** EMBOSS-6.2.0old/ajax/core/ajpat.c 2009-12-01 14:34:10.000000000 +0000
---- EMBOSS-6.2.0/ajax/core/ajpat.c 2010-03-02 09:34:07.000000000 +0000
+--- EMBOSS-6.2.0/ajax/core/ajpat.c 2010-06-15 09:56:47.000000000 +0100
***************
*** 1228,1236 ****
--- 1228,1240 ----
@@ -1359,7 +1367,7 @@ diff -c -N --recursive -a EMBOSS-6.2.0old/ajax/core/ajpat.c EMBOSS-6.2.0/ajax/co
ajPatternSeqGetPattern(pat));
diff -c -N --recursive -a EMBOSS-6.2.0old/ajax/core/ajseqread.c EMBOSS-6.2.0/ajax/core/ajseqread.c
*** EMBOSS-6.2.0old/ajax/core/ajseqread.c 2010-01-12 12:32:40.000000000 +0000
---- EMBOSS-6.2.0/ajax/core/ajseqread.c 2010-03-02 09:34:07.000000000 +0000
+--- EMBOSS-6.2.0/ajax/core/ajseqread.c 2010-06-15 09:56:47.000000000 +0100
***************
*** 582,588 ****
static const AjPStr seqAppendWarn(AjPStr* seq, const AjPStr line);
@@ -2072,7 +2080,7 @@ diff -c -N --recursive -a EMBOSS-6.2.0old/ajax/core/ajseqread.c EMBOSS-6.2.0/aja
{
diff -c -N --recursive -a EMBOSS-6.2.0old/ajax/core/ajseqwrite.c EMBOSS-6.2.0/ajax/core/ajseqwrite.c
*** EMBOSS-6.2.0old/ajax/core/ajseqwrite.c 2009-12-29 16:42:41.000000000 +0000
---- EMBOSS-6.2.0/ajax/core/ajseqwrite.c 2010-03-02 09:34:07.000000000 +0000
+--- EMBOSS-6.2.0/ajax/core/ajseqwrite.c 2010-06-15 09:56:47.000000000 +0100
***************
*** 341,347 ****
AJFALSE, AJFALSE, AJFALSE, AJTRUE, AJFALSE,
@@ -2661,7 +2669,7 @@ diff -c -N --recursive -a EMBOSS-6.2.0old/ajax/core/ajseqwrite.c EMBOSS-6.2.0/aj
** @param [r] format [const AjPStr] Output format required.
diff -c -N --recursive -a EMBOSS-6.2.0old/ajax/core/ajsys.c EMBOSS-6.2.0/ajax/core/ajsys.c
*** EMBOSS-6.2.0old/ajax/core/ajsys.c 2009-12-11 15:49:35.000000000 +0000
---- EMBOSS-6.2.0/ajax/core/ajsys.c 2010-03-02 09:34:07.000000000 +0000
+--- EMBOSS-6.2.0/ajax/core/ajsys.c 2010-06-15 09:56:47.000000000 +0100
***************
*** 259,265 ****
** Needed for very fussy compilers i.e. Digital C
@@ -2704,7 +2712,7 @@ diff -c -N --recursive -a EMBOSS-6.2.0old/ajax/core/ajsys.c EMBOSS-6.2.0/ajax/co
ajStrAssignS(Pfilename,sysFname);
diff -c -N --recursive -a EMBOSS-6.2.0old/ajax/graphics/ajgraph.c EMBOSS-6.2.0/ajax/graphics/ajgraph.c
*** EMBOSS-6.2.0old/ajax/graphics/ajgraph.c 2010-01-08 12:41:06.000000000 +0000
---- EMBOSS-6.2.0/ajax/graphics/ajgraph.c 2010-03-02 09:34:07.000000000 +0000
+--- EMBOSS-6.2.0/ajax/graphics/ajgraph.c 2010-06-15 09:56:47.000000000 +0100
***************
*** 302,308 ****
#endif
@@ -3458,7 +3466,7 @@ diff -c -N --recursive -a EMBOSS-6.2.0old/ajax/graphics/ajgraph.c EMBOSS-6.2.0/a
** will be written (in deg).
diff -c -N --recursive -a EMBOSS-6.2.0old/doc/programs/html/density.2.density.gif EMBOSS-6.2.0/doc/programs/html/density.2.density.gif
*** EMBOSS-6.2.0old/doc/programs/html/density.2.density.gif 1970-01-01 01:00:00.000000000 +0100
---- EMBOSS-6.2.0/doc/programs/html/density.2.density.gif 2010-03-02 09:34:07.000000000 +0000
+--- EMBOSS-6.2.0/doc/programs/html/density.2.density.gif 2010-06-15 09:56:47.000000000 +0100
***************
*** 0 ****
--- 1,75 ----
@@ -3540,7 +3548,7 @@ diff -c -N --recursive -a EMBOSS-6.2.0old/doc/programs/html/density.2.density.gi
\ No newline at end of file
diff -c -N --recursive -a EMBOSS-6.2.0old/doc/programs/html/density.3.density.gif EMBOSS-6.2.0/doc/programs/html/density.3.density.gif
*** EMBOSS-6.2.0old/doc/programs/html/density.3.density.gif 1970-01-01 01:00:00.000000000 +0100
---- EMBOSS-6.2.0/doc/programs/html/density.3.density.gif 2010-03-02 09:34:07.000000000 +0000
+--- EMBOSS-6.2.0/doc/programs/html/density.3.density.gif 2010-06-15 09:56:47.000000000 +0100
***************
*** 0 ****
--- 1,38 ----
@@ -3585,7 +3593,7 @@ diff -c -N --recursive -a EMBOSS-6.2.0old/doc/programs/html/density.3.density.gi
\ No newline at end of file
diff -c -N --recursive -a EMBOSS-6.2.0old/doc/programs/html/extractfeat.html EMBOSS-6.2.0/doc/programs/html/extractfeat.html
*** EMBOSS-6.2.0old/doc/programs/html/extractfeat.html 2010-01-08 12:51:28.000000000 +0000
---- EMBOSS-6.2.0/doc/programs/html/extractfeat.html 2010-03-02 09:34:07.000000000 +0000
+--- EMBOSS-6.2.0/doc/programs/html/extractfeat.html 2010-06-15 09:56:47.000000000 +0100
***************
*** 205,213 ****
-type string [*] By default every feature in the feature
@@ -3688,7 +3696,7 @@ diff -c -N --recursive -a EMBOSS-6.2.0old/doc/programs/html/extractfeat.html EMB
History
diff -c -N --recursive -a EMBOSS-6.2.0old/doc/programs/html/Makefile EMBOSS-6.2.0/doc/programs/html/Makefile
*** EMBOSS-6.2.0old/doc/programs/html/Makefile 2010-01-15 10:54:49.000000000 +0000
---- EMBOSS-6.2.0/doc/programs/html/Makefile 2010-03-02 09:34:07.000000000 +0000
+--- EMBOSS-6.2.0/doc/programs/html/Makefile 2010-06-15 09:56:47.000000000 +0100
***************
*** 224,230 ****
pkgdata_DATA = abiview.1.abiview.gif \
@@ -3709,7 +3717,7 @@ diff -c -N --recursive -a EMBOSS-6.2.0old/doc/programs/html/Makefile EMBOSS-6.2.
findkm.1.findkm.gif \
diff -c -N --recursive -a EMBOSS-6.2.0old/doc/programs/html/Makefile.am EMBOSS-6.2.0/doc/programs/html/Makefile.am
*** EMBOSS-6.2.0old/doc/programs/html/Makefile.am 2010-01-12 17:32:32.000000000 +0000
---- EMBOSS-6.2.0/doc/programs/html/Makefile.am 2010-03-02 09:34:07.000000000 +0000
+--- EMBOSS-6.2.0/doc/programs/html/Makefile.am 2010-06-15 09:56:47.000000000 +0100
***************
*** 1,7 ****
pkgdata_DATA = abiview.1.abiview.gif \
@@ -3730,7 +3738,7 @@ diff -c -N --recursive -a EMBOSS-6.2.0old/doc/programs/html/Makefile.am EMBOSS-6
findkm.1.findkm.gif \
diff -c -N --recursive -a EMBOSS-6.2.0old/doc/programs/html/Makefile.in EMBOSS-6.2.0/doc/programs/html/Makefile.in
*** EMBOSS-6.2.0old/doc/programs/html/Makefile.in 2010-01-15 10:54:40.000000000 +0000
---- EMBOSS-6.2.0/doc/programs/html/Makefile.in 2010-03-02 09:34:07.000000000 +0000
+--- EMBOSS-6.2.0/doc/programs/html/Makefile.in 2010-06-15 09:56:47.000000000 +0100
***************
*** 224,230 ****
pkgdata_DATA = abiview.1.abiview.gif \
@@ -3751,7 +3759,7 @@ diff -c -N --recursive -a EMBOSS-6.2.0old/doc/programs/html/Makefile.in EMBOSS-6
findkm.1.findkm.gif \
diff -c -N --recursive -a EMBOSS-6.2.0old/doc/programs/html/maskfeat.html EMBOSS-6.2.0/doc/programs/html/maskfeat.html
*** EMBOSS-6.2.0old/doc/programs/html/maskfeat.html 2010-01-08 12:51:29.000000000 +0000
---- EMBOSS-6.2.0/doc/programs/html/maskfeat.html 2010-03-02 09:34:07.000000000 +0000
+--- EMBOSS-6.2.0/doc/programs/html/maskfeat.html 2010-06-15 09:56:47.000000000 +0100
***************
*** 104,114 ****
feature table with a type starting 'repeat'
@@ -3823,7 +3831,7 @@ diff -c -N --recursive -a EMBOSS-6.2.0old/doc/programs/html/maskfeat.html EMBOSS
<H2>
diff -c -N --recursive -a EMBOSS-6.2.0old/doc/programs/html/showfeat.html EMBOSS-6.2.0/doc/programs/html/showfeat.html
*** EMBOSS-6.2.0old/doc/programs/html/showfeat.html 2010-01-08 12:51:29.000000000 +0000
---- EMBOSS-6.2.0/doc/programs/html/showfeat.html 2010-03-02 09:34:07.000000000 +0000
+--- EMBOSS-6.2.0/doc/programs/html/showfeat.html 2010-06-15 09:56:47.000000000 +0100
***************
*** 126,136 ****
-typematch string [*] By default any feature type in the
@@ -4026,7 +4034,7 @@ diff -c -N --recursive -a EMBOSS-6.2.0old/doc/programs/html/showfeat.html EMBOSS
diff -c -N --recursive -a EMBOSS-6.2.0old/doc/programs/html/showpep.html EMBOSS-6.2.0/doc/programs/html/showpep.html
*** EMBOSS-6.2.0old/doc/programs/html/showpep.html 2010-01-08 12:51:29.000000000 +0000
---- EMBOSS-6.2.0/doc/programs/html/showpep.html 2010-03-02 09:34:07.000000000 +0000
+--- EMBOSS-6.2.0/doc/programs/html/showpep.html 2010-06-15 09:56:47.000000000 +0100
***************
*** 285,295 ****
-typematch string [*] By default any feature type in the
@@ -4132,7 +4140,7 @@ diff -c -N --recursive -a EMBOSS-6.2.0old/doc/programs/html/showpep.html EMBOSS-
<H2>
diff -c -N --recursive -a EMBOSS-6.2.0old/doc/programs/html/showseq.html EMBOSS-6.2.0/doc/programs/html/showseq.html
*** EMBOSS-6.2.0old/doc/programs/html/showseq.html 2010-01-08 12:51:29.000000000 +0000
---- EMBOSS-6.2.0/doc/programs/html/showseq.html 2010-03-02 09:34:07.000000000 +0000
+--- EMBOSS-6.2.0/doc/programs/html/showseq.html 2010-06-15 09:56:47.000000000 +0100
***************
*** 382,392 ****
-typematch string [*] By default any feature type in the
@@ -4343,7 +4351,7 @@ diff -c -N --recursive -a EMBOSS-6.2.0old/doc/programs/html/showseq.html EMBOSS-
<H2>
diff -c -N --recursive -a EMBOSS-6.2.0old/doc/programs/html/twofeat.html EMBOSS-6.2.0/doc/programs/html/twofeat.html
*** EMBOSS-6.2.0old/doc/programs/html/twofeat.html 2010-01-08 12:51:30.000000000 +0000
---- EMBOSS-6.2.0/doc/programs/html/twofeat.html 2010-03-02 09:34:07.000000000 +0000
+--- EMBOSS-6.2.0/doc/programs/html/twofeat.html 2010-06-15 09:56:47.000000000 +0100
***************
*** 127,137 ****
-atype string [*] By default every feature in the feature
@@ -4522,7 +4530,7 @@ diff -c -N --recursive -a EMBOSS-6.2.0old/doc/programs/html/twofeat.html EMBOSS-
History
diff -c -N --recursive -a EMBOSS-6.2.0old/doc/programs/text/extractfeat.txt EMBOSS-6.2.0/doc/programs/text/extractfeat.txt
*** EMBOSS-6.2.0old/doc/programs/text/extractfeat.txt 2010-01-08 12:51:31.000000000 +0000
---- EMBOSS-6.2.0/doc/programs/text/extractfeat.txt 2010-03-02 09:34:07.000000000 +0000
+--- EMBOSS-6.2.0/doc/programs/text/extractfeat.txt 2010-06-15 09:56:47.000000000 +0100
***************
*** 154,162 ****
-type string [*] By default every feature in the feature
@@ -4590,7 +4598,7 @@ diff -c -N --recursive -a EMBOSS-6.2.0old/doc/programs/text/extractfeat.txt EMBO
Written (Dec 12 2001) - Gary Williams
diff -c -N --recursive -a EMBOSS-6.2.0old/doc/programs/text/maskfeat.txt EMBOSS-6.2.0/doc/programs/text/maskfeat.txt
*** EMBOSS-6.2.0old/doc/programs/text/maskfeat.txt 2010-01-08 12:51:31.000000000 +0000
---- EMBOSS-6.2.0/doc/programs/text/maskfeat.txt 2010-03-02 09:34:07.000000000 +0000
+--- EMBOSS-6.2.0/doc/programs/text/maskfeat.txt 2010-06-15 09:56:47.000000000 +0100
***************
*** 68,78 ****
feature table with a type starting 'repeat'
@@ -4644,7 +4652,7 @@ diff -c -N --recursive -a EMBOSS-6.2.0old/doc/programs/text/maskfeat.txt EMBOSS-
Written (2000) - Gary Williams
diff -c -N --recursive -a EMBOSS-6.2.0old/doc/programs/text/showfeat.txt EMBOSS-6.2.0/doc/programs/text/showfeat.txt
*** EMBOSS-6.2.0old/doc/programs/text/showfeat.txt 2010-01-08 12:51:31.000000000 +0000
---- EMBOSS-6.2.0/doc/programs/text/showfeat.txt 2010-03-02 09:34:07.000000000 +0000
+--- EMBOSS-6.2.0/doc/programs/text/showfeat.txt 2010-06-15 09:56:47.000000000 +0100
***************
*** 87,97 ****
-typematch string [*] By default any feature type in the
@@ -4823,7 +4831,7 @@ diff -c -N --recursive -a EMBOSS-6.2.0old/doc/programs/text/showfeat.txt EMBOSS-
Written 1999 - Gary Williams
diff -c -N --recursive -a EMBOSS-6.2.0old/doc/programs/text/showpep.txt EMBOSS-6.2.0/doc/programs/text/showpep.txt
*** EMBOSS-6.2.0old/doc/programs/text/showpep.txt 2010-01-08 12:51:31.000000000 +0000
---- EMBOSS-6.2.0/doc/programs/text/showpep.txt 2010-03-02 09:34:07.000000000 +0000
+--- EMBOSS-6.2.0/doc/programs/text/showpep.txt 2010-06-15 09:56:47.000000000 +0100
***************
*** 232,242 ****
-typematch string [*] By default any feature type in the
@@ -4894,7 +4902,7 @@ diff -c -N --recursive -a EMBOSS-6.2.0old/doc/programs/text/showpep.txt EMBOSS-6
Target users
diff -c -N --recursive -a EMBOSS-6.2.0old/doc/programs/text/showseq.txt EMBOSS-6.2.0/doc/programs/text/showseq.txt
*** EMBOSS-6.2.0old/doc/programs/text/showseq.txt 2010-01-08 12:51:31.000000000 +0000
---- EMBOSS-6.2.0/doc/programs/text/showseq.txt 2010-03-02 09:34:07.000000000 +0000
+--- EMBOSS-6.2.0/doc/programs/text/showseq.txt 2010-06-15 09:56:47.000000000 +0100
***************
*** 327,337 ****
-typematch string [*] By default any feature type in the
@@ -5019,7 +5027,7 @@ diff -c -N --recursive -a EMBOSS-6.2.0old/doc/programs/text/showseq.txt EMBOSS-6
Written 1999 - GWW
diff -c -N --recursive -a EMBOSS-6.2.0old/doc/programs/text/twofeat.txt EMBOSS-6.2.0/doc/programs/text/twofeat.txt
*** EMBOSS-6.2.0old/doc/programs/text/twofeat.txt 2010-01-08 12:51:31.000000000 +0000
---- EMBOSS-6.2.0/doc/programs/text/twofeat.txt 2010-03-02 09:34:07.000000000 +0000
+--- EMBOSS-6.2.0/doc/programs/text/twofeat.txt 2010-06-15 09:56:47.000000000 +0100
***************
*** 107,117 ****
-atype string [*] By default every feature in the feature
@@ -5146,7 +5154,7 @@ diff -c -N --recursive -a EMBOSS-6.2.0old/doc/programs/text/twofeat.txt EMBOSS-6
Written (2002) - Gary Williams
diff -c -N --recursive -a EMBOSS-6.2.0old/emboss/acd/cirdna.acd EMBOSS-6.2.0/emboss/acd/cirdna.acd
*** EMBOSS-6.2.0old/emboss/acd/cirdna.acd 2010-01-11 19:54:14.000000000 +0000
---- EMBOSS-6.2.0/emboss/acd/cirdna.acd 2010-03-02 09:34:07.000000000 +0000
+--- EMBOSS-6.2.0/emboss/acd/cirdna.acd 2010-06-15 09:56:47.000000000 +0100
***************
*** 13,19 ****
parameter: "Y"
@@ -5166,7 +5174,7 @@ diff -c -N --recursive -a EMBOSS-6.2.0old/emboss/acd/cirdna.acd EMBOSS-6.2.0/emb
diff -c -N --recursive -a EMBOSS-6.2.0old/emboss/acd/extractfeat.acd EMBOSS-6.2.0/emboss/acd/extractfeat.acd
*** EMBOSS-6.2.0old/emboss/acd/extractfeat.acd 2010-01-14 21:51:23.000000000 +0000
---- EMBOSS-6.2.0/emboss/acd/extractfeat.acd 2010-03-02 09:34:07.000000000 +0000
+--- EMBOSS-6.2.0/emboss/acd/extractfeat.acd 2010-06-15 09:56:47.000000000 +0100
***************
*** 83,89 ****
information: "Type of feature to extract"
@@ -5186,7 +5194,7 @@ diff -c -N --recursive -a EMBOSS-6.2.0old/emboss/acd/extractfeat.acd EMBOSS-6.2.
for a list of the Uniprot feature types. \
diff -c -N --recursive -a EMBOSS-6.2.0old/emboss/acd/jaspextract.acd EMBOSS-6.2.0/emboss/acd/jaspextract.acd
*** EMBOSS-6.2.0old/emboss/acd/jaspextract.acd 2009-09-15 11:25:52.000000000 +0100
---- EMBOSS-6.2.0/emboss/acd/jaspextract.acd 2010-03-02 09:34:07.000000000 +0000
+--- EMBOSS-6.2.0/emboss/acd/jaspextract.acd 2010-06-15 09:56:47.000000000 +0100
***************
*** 15,23 ****
directory: directory [
@@ -5209,7 +5217,7 @@ diff -c -N --recursive -a EMBOSS-6.2.0old/emboss/acd/jaspextract.acd EMBOSS-6.2.
]
diff -c -N --recursive -a EMBOSS-6.2.0old/emboss/acd/jaspscan.acd EMBOSS-6.2.0/emboss/acd/jaspscan.acd
*** EMBOSS-6.2.0old/emboss/acd/jaspscan.acd 2009-09-15 11:25:52.000000000 +0100
---- EMBOSS-6.2.0/emboss/acd/jaspscan.acd 2010-03-02 09:34:07.000000000 +0000
+--- EMBOSS-6.2.0/emboss/acd/jaspscan.acd 2010-06-15 09:56:47.000000000 +0100
***************
*** 21,27 ****
default: "C"
@@ -5293,7 +5301,7 @@ diff -c -N --recursive -a EMBOSS-6.2.0old/emboss/acd/jaspscan.acd EMBOSS-6.2.0/e
]
diff -c -N --recursive -a EMBOSS-6.2.0old/emboss/acd/knowntypes.standard EMBOSS-6.2.0/emboss/acd/knowntypes.standard
*** EMBOSS-6.2.0old/emboss/acd/knowntypes.standard 2009-12-18 13:59:32.000000000 +0000
---- EMBOSS-6.2.0/emboss/acd/knowntypes.standard 2010-03-02 09:34:07.000000000 +0000
+--- EMBOSS-6.2.0/emboss/acd/knowntypes.standard 2010-06-15 09:56:47.000000000 +0100
***************
*** 20,25 ****
--- 20,26 ----
@@ -5306,7 +5314,7 @@ diff -c -N --recursive -a EMBOSS-6.2.0old/emboss/acd/knowntypes.standard EMBOSS-
codon_list | string | "EDAM: Codon string" | Codon triplet(s)
diff -c -N --recursive -a EMBOSS-6.2.0old/emboss/acd/maskfeat.acd EMBOSS-6.2.0/emboss/acd/maskfeat.acd
*** EMBOSS-6.2.0old/emboss/acd/maskfeat.acd 2009-09-15 11:25:52.000000000 +0100
---- EMBOSS-6.2.0/emboss/acd/maskfeat.acd 2010-03-02 09:34:07.000000000 +0000
+--- EMBOSS-6.2.0/emboss/acd/maskfeat.acd 2010-06-15 09:56:47.000000000 +0100
***************
*** 31,39 ****
help: "By default any feature in the feature table with a type
@@ -5330,7 +5338,7 @@ diff -c -N --recursive -a EMBOSS-6.2.0old/emboss/acd/maskfeat.acd EMBOSS-6.2.0/e
If you wish to mask more than one type, separate their names with
diff -c -N --recursive -a EMBOSS-6.2.0old/emboss/acd/remap.acd EMBOSS-6.2.0/emboss/acd/remap.acd
*** EMBOSS-6.2.0old/emboss/acd/remap.acd 2010-01-14 21:51:23.000000000 +0000
---- EMBOSS-6.2.0/emboss/acd/remap.acd 2010-03-02 09:34:07.000000000 +0000
+--- EMBOSS-6.2.0/emboss/acd/remap.acd 2010-06-15 09:56:47.000000000 +0100
***************
*** 91,97 ****
integer: maxcuts [
@@ -5343,7 +5351,7 @@ diff -c -N --recursive -a EMBOSS-6.2.0old/emboss/acd/remap.acd EMBOSS-6.2.0/embo
--- 91,96 ----
diff -c -N --recursive -a EMBOSS-6.2.0old/emboss/acd/restover.acd EMBOSS-6.2.0/emboss/acd/restover.acd
*** EMBOSS-6.2.0old/emboss/acd/restover.acd 2009-10-12 15:42:43.000000000 +0100
---- EMBOSS-6.2.0/emboss/acd/restover.acd 2010-03-02 09:34:07.000000000 +0000
+--- EMBOSS-6.2.0/emboss/acd/restover.acd 2010-06-15 09:56:47.000000000 +0100
***************
*** 61,67 ****
@@ -5356,7 +5364,7 @@ diff -c -N --recursive -a EMBOSS-6.2.0old/emboss/acd/restover.acd EMBOSS-6.2.0/e
--- 61,66 ----
diff -c -N --recursive -a EMBOSS-6.2.0old/emboss/acd/restrict.acd EMBOSS-6.2.0/emboss/acd/restrict.acd
*** EMBOSS-6.2.0old/emboss/acd/restrict.acd 2010-01-14 21:51:23.000000000 +0000
---- EMBOSS-6.2.0/emboss/acd/restrict.acd 2010-03-02 09:34:07.000000000 +0000
+--- EMBOSS-6.2.0/emboss/acd/restrict.acd 2010-06-15 09:56:47.000000000 +0100
***************
*** 97,103 ****
@@ -5369,7 +5377,7 @@ diff -c -N --recursive -a EMBOSS-6.2.0old/emboss/acd/restrict.acd EMBOSS-6.2.0/e
--- 97,102 ----
diff -c -N --recursive -a EMBOSS-6.2.0old/emboss/acd/showfeat.acd EMBOSS-6.2.0/emboss/acd/showfeat.acd
*** EMBOSS-6.2.0old/emboss/acd/showfeat.acd 2010-01-14 21:51:23.000000000 +0000
---- EMBOSS-6.2.0/emboss/acd/showfeat.acd 2010-03-02 09:34:07.000000000 +0000
+--- EMBOSS-6.2.0/emboss/acd/showfeat.acd 2010-06-15 09:56:47.000000000 +0100
***************
*** 47,55 ****
information: "Type of feature to display"
@@ -5393,7 +5401,7 @@ diff -c -N --recursive -a EMBOSS-6.2.0old/emboss/acd/showfeat.acd EMBOSS-6.2.0/e
If you wish to show more than one type, separate their names with
diff -c -N --recursive -a EMBOSS-6.2.0old/emboss/acd/showpep.acd EMBOSS-6.2.0/emboss/acd/showpep.acd
*** EMBOSS-6.2.0old/emboss/acd/showpep.acd 2010-01-14 21:51:23.000000000 +0000
---- EMBOSS-6.2.0/emboss/acd/showpep.acd 2010-03-02 09:34:07.000000000 +0000
+--- EMBOSS-6.2.0/emboss/acd/showpep.acd 2010-06-15 09:56:47.000000000 +0100
***************
*** 152,161 ****
help: "By default any feature type in the feature table is
@@ -5419,7 +5427,7 @@ diff -c -N --recursive -a EMBOSS-6.2.0old/emboss/acd/showpep.acd EMBOSS-6.2.0/em
with the character '|', eg: \
diff -c -N --recursive -a EMBOSS-6.2.0old/emboss/acd/showseq.acd EMBOSS-6.2.0/emboss/acd/showseq.acd
*** EMBOSS-6.2.0old/emboss/acd/showseq.acd 2010-01-14 21:51:23.000000000 +0000
---- EMBOSS-6.2.0/emboss/acd/showseq.acd 2010-03-02 09:34:07.000000000 +0000
+--- EMBOSS-6.2.0/emboss/acd/showseq.acd 2010-06-15 09:56:47.000000000 +0100
***************
*** 249,258 ****
help: "By default any feature type in the feature table is
@@ -5466,7 +5474,7 @@ diff -c -N --recursive -a EMBOSS-6.2.0old/emboss/acd/showseq.acd EMBOSS-6.2.0/em
--- 389,394 ----
diff -c -N --recursive -a EMBOSS-6.2.0old/emboss/acd/trimseq.acd EMBOSS-6.2.0/emboss/acd/trimseq.acd
*** EMBOSS-6.2.0old/emboss/acd/trimseq.acd 2009-09-15 11:25:52.000000000 +0100
---- EMBOSS-6.2.0/emboss/acd/trimseq.acd 2010-03-02 09:34:07.000000000 +0000
+--- EMBOSS-6.2.0/emboss/acd/trimseq.acd 2010-06-15 09:56:47.000000000 +0100
***************
*** 26,31 ****
--- 26,32 ----
@@ -5479,7 +5487,7 @@ diff -c -N --recursive -a EMBOSS-6.2.0old/emboss/acd/trimseq.acd EMBOSS-6.2.0/em
when deciding whether the percentage of ambiguity is greater than
diff -c -N --recursive -a EMBOSS-6.2.0old/emboss/acd/twofeat.acd EMBOSS-6.2.0/emboss/acd/twofeat.acd
*** EMBOSS-6.2.0old/emboss/acd/twofeat.acd 2009-09-15 11:25:52.000000000 +0100
---- EMBOSS-6.2.0/emboss/acd/twofeat.acd 2010-03-02 09:34:07.000000000 +0000
+--- EMBOSS-6.2.0/emboss/acd/twofeat.acd 2010-06-15 09:56:47.000000000 +0100
***************
*** 45,54 ****
information: "Type of first feature"
@@ -5549,7 +5557,7 @@ diff -c -N --recursive -a EMBOSS-6.2.0old/emboss/acd/twofeat.acd EMBOSS-6.2.0/em
knowntype: "feature key"
diff -c -N --recursive -a EMBOSS-6.2.0old/emboss/coderet.c EMBOSS-6.2.0/emboss/coderet.c
*** EMBOSS-6.2.0old/emboss/coderet.c 2009-12-01 14:39:23.000000000 +0000
---- EMBOSS-6.2.0/emboss/coderet.c 2010-03-02 09:34:07.000000000 +0000
+--- EMBOSS-6.2.0/emboss/coderet.c 2010-06-15 09:56:47.000000000 +0100
***************
*** 121,188 ****
imrna = 0;
@@ -5696,7 +5704,7 @@ diff -c -N --recursive -a EMBOSS-6.2.0old/emboss/coderet.c EMBOSS-6.2.0/emboss/c
ajFmtPrintF(logf, "%6d", icds);
diff -c -N --recursive -a EMBOSS-6.2.0old/emboss/emma.c EMBOSS-6.2.0/emboss/emma.c
*** EMBOSS-6.2.0old/emboss/emma.c 2009-12-11 15:37:59.000000000 +0000
---- EMBOSS-6.2.0/emboss/emma.c 2010-03-02 09:34:07.000000000 +0000
+--- EMBOSS-6.2.0/emboss/emma.c 2010-06-15 09:56:47.000000000 +0100
***************
*** 390,406 ****
@@ -5732,7 +5740,7 @@ diff -c -N --recursive -a EMBOSS-6.2.0old/emboss/emma.c EMBOSS-6.2.0/emboss/emma
{
diff -c -N --recursive -a EMBOSS-6.2.0old/emboss/jaspextract.c EMBOSS-6.2.0/emboss/jaspextract.c
*** EMBOSS-6.2.0old/emboss/jaspextract.c 2008-11-14 17:22:57.000000000 +0000
---- EMBOSS-6.2.0/emboss/jaspextract.c 2010-03-02 09:34:07.000000000 +0000
+--- EMBOSS-6.2.0/emboss/jaspextract.c 2010-06-15 09:56:47.000000000 +0100
***************
*** 22,70 ****
@@ -6466,7 +6474,7 @@ diff -c -N --recursive -a EMBOSS-6.2.0old/emboss/jaspextract.c EMBOSS-6.2.0/embo
}
diff -c -N --recursive -a EMBOSS-6.2.0old/emboss/jaspscan.c EMBOSS-6.2.0/emboss/jaspscan.c
*** EMBOSS-6.2.0old/emboss/jaspscan.c 2009-10-09 12:26:35.000000000 +0100
---- EMBOSS-6.2.0/emboss/jaspscan.c 2010-03-02 09:34:07.000000000 +0000
+--- EMBOSS-6.2.0/emboss/jaspscan.c 2010-06-15 09:56:47.000000000 +0100
***************
*** 36,53 ****
#define JASPTAB_GUESS 1000
@@ -6919,7 +6927,7 @@ diff -c -N --recursive -a EMBOSS-6.2.0old/emboss/jaspscan.c EMBOSS-6.2.0/emboss/
ajStrDel(&skey);
diff -c -N --recursive -a EMBOSS-6.2.0old/emboss/jembossctl.c EMBOSS-6.2.0/emboss/jembossctl.c
*** EMBOSS-6.2.0old/emboss/jembossctl.c 2008-06-26 09:39:09.000000000 +0100
---- EMBOSS-6.2.0/emboss/jembossctl.c 2010-03-02 09:34:07.000000000 +0000
+--- EMBOSS-6.2.0/emboss/jembossctl.c 2010-06-15 09:56:47.000000000 +0100
***************
*** 1278,1284 ****
return ajFalse;
@@ -7150,7 +7158,7 @@ diff -c -N --recursive -a EMBOSS-6.2.0old/emboss/jembossctl.c EMBOSS-6.2.0/embos
}
diff -c -N --recursive -a EMBOSS-6.2.0old/emboss/matcher.c EMBOSS-6.2.0/emboss/matcher.c
*** EMBOSS-6.2.0old/emboss/matcher.c 2010-01-08 12:43:41.000000000 +0000
---- EMBOSS-6.2.0/emboss/matcher.c 2010-03-02 09:34:07.000000000 +0000
+--- EMBOSS-6.2.0/emboss/matcher.c 2010-06-15 09:56:47.000000000 +0100
***************
*** 27,33 ****
@@ -7272,9 +7280,236 @@ diff -c -N --recursive -a EMBOSS-6.2.0old/emboss/matcher.c EMBOSS-6.2.0/emboss/m
*sp1 = '\0';
*nident = nid;
--- 1568,1573 ----
+diff -c -N --recursive -a EMBOSS-6.2.0old/emboss/needleall.c EMBOSS-6.2.0/emboss/needleall.c
+*** EMBOSS-6.2.0old/emboss/needleall.c 2010-01-08 12:43:41.000000000 +0000
+--- EMBOSS-6.2.0/emboss/needleall.c 2010-06-15 09:58:18.000000000 +0100
+***************
+*** 46,53 ****
+ AjPStr ss;
+ AjPFile errorf;
+
+! ajuint lena;
+! ajuint lenb;
+ ajuint k;
+
+ const char *p;
+--- 46,53 ----
+ AjPStr ss;
+ AjPFile errorf;
+
+! ajint lena;
+! ajint lenb;
+ ajuint k;
+
+ const char *p;
+***************
+*** 56,62 ****
+ ajint start1 = 0;
+ ajint start2 = 0;
+
+- float *path;
+ ajint *compass;
+ float* ix;
+ float* iy;
+--- 56,61 ----
+***************
+*** 107,113 ****
+ gapopen = ajRoundFloat(gapopen, 8);
+ gapextend = ajRoundFloat(gapextend, 8);
+
+- AJCNEW(path, maxarr);
+ AJCNEW(compass, maxarr);
+ AJCNEW(m, maxarr);
+ AJCNEW(ix, maxarr);
+--- 106,111 ----
+***************
+*** 131,137 ****
+ lena = ajSeqGetLen(seqa);
+
+
+! if(lenb > (ULONG_MAX/(ajulong)(lena+1)))
+ ajFatal("Sequences too big.");
+
+ len = lena*lenb;
+--- 129,135 ----
+ lena = ajSeqGetLen(seqa);
+
+
+! if(lenb > (LONG_MAX/(ajlong)(lena+1)))
+ ajFatal("Sequences too big.");
+
+ len = lena*lenb;
+***************
+*** 139,150 ****
+ if(len>maxarr)
+ {
+ stlen = (size_t) len;
+- AJCRESIZETRY(path,stlen);
+ AJCRESIZETRY(compass,stlen);
+ AJCRESIZETRY(m,stlen);
+ AJCRESIZETRY(ix,stlen);
+ AJCRESIZETRY(iy,stlen);
+! if(!path || !compass || !m || !ix || !iy)
+ ajDie("Sequences too big.");
+ maxarr=len;
+ }
+--- 137,147 ----
+ if(len>maxarr)
+ {
+ stlen = (size_t) len;
+ AJCRESIZETRY(compass,stlen);
+ AJCRESIZETRY(m,stlen);
+ AJCRESIZETRY(ix,stlen);
+ AJCRESIZETRY(iy,stlen);
+! if(!compass || !m || !ix || !iy)
+ ajDie("Sequences too big.");
+ maxarr=len;
+ }
+***************
+*** 158,164 ****
+
+ score = embAlignPathCalcWithEndGapPenalties(p, q, lena, lenb,
+ gapopen, gapextend, endgapopen, endgapextend,
+! &start1, &start2, path, sub, cvt, m, ix, iy,
+ compass, ajFalse, endweight);
+
+ embAlignWalkNWMatrixUsingCompass(p, q, &alga, &algb,
+--- 155,161 ----
+
+ score = embAlignPathCalcWithEndGapPenalties(p, q, lena, lenb,
+ gapopen, gapextend, endgapopen, endgapextend,
+! &start1, &start2, sub, cvt, m, ix, iy,
+ compass, ajFalse, endweight);
+
+ embAlignWalkNWMatrixUsingCompass(p, q, &alga, &algb,
+***************
+*** 223,229 ****
+ ajSeqDel(&seqb);
+
+ AJFREE(compass);
+- AJFREE(path);
+ AJFREE(ix);
+ AJFREE(iy);
+ AJFREE(m);
+--- 220,225 ----
+diff -c -N --recursive -a EMBOSS-6.2.0old/emboss/needle.c EMBOSS-6.2.0/emboss/needle.c
+*** EMBOSS-6.2.0old/emboss/needle.c 2010-01-08 12:43:41.000000000 +0000
+--- EMBOSS-6.2.0/emboss/needle.c 2010-06-15 09:58:12.000000000 +0100
+***************
+*** 40,47 ****
+ AjPStr algb;
+ AjPStr ss;
+
+! ajuint lena;
+! ajuint lenb;
+
+ const char *p;
+ const char *q;
+--- 40,47 ----
+ AjPStr algb;
+ AjPStr ss;
+
+! ajint lena;
+! ajint lenb;
+
+ const char *p;
+ const char *q;
+***************
+*** 49,55 ****
+ ajint start1 = 0;
+ ajint start2 = 0;
+
+- float *path;
+ ajint *compass;
+ float* ix;
+ float* iy;
+--- 49,54 ----
+***************
+*** 64,70 ****
+ float endgapopen;
+ float endgapextend;
+ ajulong maxarr = 1000; /* arbitrary. realloc'd if needed */
+! ajulong len;
+
+ float score;
+
+--- 63,69 ----
+ float endgapopen;
+ float endgapextend;
+ ajulong maxarr = 1000; /* arbitrary. realloc'd if needed */
+! ajulong len;
+
+ float score;
+
+***************
+*** 98,104 ****
+ gapopen = ajRoundFloat(gapopen, 8);
+ gapextend = ajRoundFloat(gapextend, 8);
+
+- AJCNEW(path, maxarr);
+ AJCNEW(compass, maxarr);
+ AJCNEW(m, maxarr);
+ AJCNEW(ix, maxarr);
+--- 97,102 ----
+***************
+*** 118,124 ****
+ ajSeqTrim(b);
+ lenb = ajSeqGetLen(b);
+
+! if(lenb > (ULONG_MAX/(ajulong)(lena+1)))
+ ajFatal("Sequences too big. Try 'stretcher' or 'supermatcher'");
+
+ len = lena*lenb;
+--- 116,122 ----
+ ajSeqTrim(b);
+ lenb = ajSeqGetLen(b);
+
+! if(lenb > (LONG_MAX/(ajlong)(lena+1)))
+ ajFatal("Sequences too big. Try 'stretcher' or 'supermatcher'");
+
+ len = lena*lenb;
+***************
+*** 126,134 ****
+ if(len>maxarr)
+ {
+ stlen = (size_t) len;
+- AJCRESIZETRY(path,stlen);
+- if(!path)
+- ajDie("Sequences too big. Try 'stretcher'");
+ AJCRESIZETRY(compass,stlen);
+ if(!compass)
+ ajDie("Sequences too big. Try 'stretcher'");
+--- 124,129 ----
+***************
+*** 153,159 ****
+
+ score = embAlignPathCalcWithEndGapPenalties(p, q, lena, lenb,
+ gapopen, gapextend, endgapopen, endgapextend,
+! &start1, &start2, path, sub, cvt,
+ m, ix, iy, compass, ajTrue, endweight);
+
+
+--- 148,154 ----
+
+ score = embAlignPathCalcWithEndGapPenalties(p, q, lena, lenb,
+ gapopen, gapextend, endgapopen, endgapextend,
+! &start1, &start2, sub, cvt,
+ m, ix, iy, compass, ajTrue, endweight);
+
+
+***************
+*** 195,201 ****
+ ajSeqDel(&b);
+
+ AJFREE(compass);
+- AJFREE(path);
+ AJFREE(ix);
+ AJFREE(iy);
+ AJFREE(m);
+--- 190,195 ----
diff -c -N --recursive -a EMBOSS-6.2.0old/emboss/prettyplot.c EMBOSS-6.2.0/emboss/prettyplot.c
*** EMBOSS-6.2.0old/emboss/prettyplot.c 2010-01-08 12:43:41.000000000 +0000
---- EMBOSS-6.2.0/emboss/prettyplot.c 2010-03-02 09:34:07.000000000 +0000
+--- EMBOSS-6.2.0/emboss/prettyplot.c 2010-06-15 09:56:47.000000000 +0100
***************
*** 434,457 ****
@@ -7374,7 +7609,7 @@ diff -c -N --recursive -a EMBOSS-6.2.0old/emboss/prettyplot.c EMBOSS-6.2.0/embos
}
diff -c -N --recursive -a EMBOSS-6.2.0old/emboss/recoder.c EMBOSS-6.2.0/emboss/recoder.c
*** EMBOSS-6.2.0old/emboss/recoder.c 2009-08-24 15:33:44.000000000 +0100
---- EMBOSS-6.2.0/emboss/recoder.c 2010-03-02 09:34:07.000000000 +0000
+--- EMBOSS-6.2.0/emboss/recoder.c 2010-06-15 09:56:47.000000000 +0100
***************
*** 33,44 ****
@@ -7742,7 +7977,7 @@ diff -c -N --recursive -a EMBOSS-6.2.0old/emboss/recoder.c EMBOSS-6.2.0/emboss/r
ajStrDel(&(*mut)->site);
diff -c -N --recursive -a EMBOSS-6.2.0old/emboss/remap.c EMBOSS-6.2.0/emboss/remap.c
*** EMBOSS-6.2.0old/emboss/remap.c 2009-12-01 14:30:08.000000000 +0000
---- EMBOSS-6.2.0/emboss/remap.c 2010-03-02 09:34:07.000000000 +0000
+--- EMBOSS-6.2.0/emboss/remap.c 2010-06-15 09:56:47.000000000 +0100
***************
*** 777,784 ****
/* push all enzyme names without the required criteria onto nocutlist */
@@ -7767,7 +8002,7 @@ diff -c -N --recursive -a EMBOSS-6.2.0old/emboss/remap.c EMBOSS-6.2.0/emboss/rem
** this is one of that explicit list
diff -c -N --recursive -a EMBOSS-6.2.0old/emboss/restrict.c EMBOSS-6.2.0/emboss/restrict.c
*** EMBOSS-6.2.0old/emboss/restrict.c 2009-08-24 15:33:44.000000000 +0100
---- EMBOSS-6.2.0/emboss/restrict.c 2010-03-02 09:34:07.000000000 +0000
+--- EMBOSS-6.2.0/emboss/restrict.c 2010-06-15 09:56:47.000000000 +0100
***************
*** 951,958 ****
@@ -7792,7 +8027,7 @@ diff -c -N --recursive -a EMBOSS-6.2.0old/emboss/restrict.c EMBOSS-6.2.0/emboss/
ajStrFmtUpper(&key);
diff -c -N --recursive -a EMBOSS-6.2.0old/emboss/showfeat.c EMBOSS-6.2.0/emboss/showfeat.c
*** EMBOSS-6.2.0old/emboss/showfeat.c 2009-08-24 15:33:44.000000000 +0100
---- EMBOSS-6.2.0/emboss/showfeat.c 2010-03-02 09:34:07.000000000 +0000
+--- EMBOSS-6.2.0/emboss/showfeat.c 2010-06-15 09:56:47.000000000 +0100
***************
*** 266,272 ****
{
@@ -7973,7 +8208,7 @@ diff -c -N --recursive -a EMBOSS-6.2.0old/emboss/showfeat.c EMBOSS-6.2.0/emboss/
}
diff -c -N --recursive -a EMBOSS-6.2.0old/emboss/showpep.c EMBOSS-6.2.0/emboss/showpep.c
*** EMBOSS-6.2.0old/emboss/showpep.c 2009-08-24 15:33:44.000000000 +0100
---- EMBOSS-6.2.0/emboss/showpep.c 2010-03-02 09:34:07.000000000 +0000
+--- EMBOSS-6.2.0/emboss/showpep.c 2010-06-15 09:56:47.000000000 +0100
***************
*** 238,244 ****
ajFmtPrintF(outfile, "\n");
@@ -7993,7 +8228,7 @@ diff -c -N --recursive -a EMBOSS-6.2.0old/emboss/showpep.c EMBOSS-6.2.0/emboss/s
diff -c -N --recursive -a EMBOSS-6.2.0old/emboss/showseq.c EMBOSS-6.2.0/emboss/showseq.c
*** EMBOSS-6.2.0old/emboss/showseq.c 2009-08-24 15:33:44.000000000 +0100
---- EMBOSS-6.2.0/emboss/showseq.c 2010-03-02 09:34:07.000000000 +0000
+--- EMBOSS-6.2.0/emboss/showseq.c 2010-06-15 09:56:47.000000000 +0100
***************
*** 380,386 ****
ajFmtPrintF(outfile, "\n");
@@ -8013,7 +8248,7 @@ diff -c -N --recursive -a EMBOSS-6.2.0old/emboss/showseq.c EMBOSS-6.2.0/emboss/s
diff -c -N --recursive -a EMBOSS-6.2.0old/emboss/silent.c EMBOSS-6.2.0/emboss/silent.c
*** EMBOSS-6.2.0old/emboss/silent.c 2009-08-24 15:33:44.000000000 +0100
---- EMBOSS-6.2.0/emboss/silent.c 2010-03-02 09:34:07.000000000 +0000
+--- EMBOSS-6.2.0/emboss/silent.c 2010-06-15 09:56:47.000000000 +0100
***************
*** 27,38 ****
@@ -8334,7 +8569,7 @@ diff -c -N --recursive -a EMBOSS-6.2.0old/emboss/silent.c EMBOSS-6.2.0/emboss/si
}
diff -c -N --recursive -a EMBOSS-6.2.0old/emboss/splitter.c EMBOSS-6.2.0/emboss/splitter.c
*** EMBOSS-6.2.0old/emboss/splitter.c 2009-08-24 15:33:44.000000000 +0100
---- EMBOSS-6.2.0/emboss/splitter.c 2010-03-02 09:34:07.000000000 +0000
+--- EMBOSS-6.2.0/emboss/splitter.c 2010-06-15 09:56:47.000000000 +0100
***************
*** 102,111 ****
pos += size;
@@ -8605,7 +8840,7 @@ diff -c -N --recursive -a EMBOSS-6.2.0old/emboss/splitter.c EMBOSS-6.2.0/emboss/
}
diff -c -N --recursive -a EMBOSS-6.2.0old/jemboss/lib/jemboss.jar EMBOSS-6.2.0/jemboss/lib/jemboss.jar
*** EMBOSS-6.2.0old/jemboss/lib/jemboss.jar 2010-01-15 10:55:02.000000000 +0000
---- EMBOSS-6.2.0/jemboss/lib/jemboss.jar 2010-03-02 09:34:07.000000000 +0000
+--- EMBOSS-6.2.0/jemboss/lib/jemboss.jar 2010-06-15 09:56:47.000000000 +0100
***************
*** 1,41 ****
PK
@@ -14668,7 +14903,7 @@ diff -c -N --recursive -a EMBOSS-6.2.0old/jemboss/lib/jemboss.jar EMBOSS-6.2.0/j
\ No newline at end of file
diff -c -N --recursive -a EMBOSS-6.2.0old/jemboss/org/emboss/jemboss/gui/filetree/DragTree.java EMBOSS-6.2.0/jemboss/org/emboss/jemboss/gui/filetree/DragTree.java
*** EMBOSS-6.2.0old/jemboss/org/emboss/jemboss/gui/filetree/DragTree.java 2010-01-06 15:24:58.000000000 +0000
---- EMBOSS-6.2.0/jemboss/org/emboss/jemboss/gui/filetree/DragTree.java 2010-03-02 09:34:07.000000000 +0000
+--- EMBOSS-6.2.0/jemboss/org/emboss/jemboss/gui/filetree/DragTree.java 2010-06-15 09:56:47.000000000 +0100
***************
*** 688,694 ****
public static void showFilePane(String filename, JembossParams mysettings)
@@ -14695,7 +14930,7 @@ diff -c -N --recursive -a EMBOSS-6.2.0old/jemboss/org/emboss/jemboss/gui/filetre
}
diff -c -N --recursive -a EMBOSS-6.2.0old/jemboss/org/emboss/jemboss/gui/filetree/RemoteDragTree.java EMBOSS-6.2.0/jemboss/org/emboss/jemboss/gui/filetree/RemoteDragTree.java
*** EMBOSS-6.2.0old/jemboss/org/emboss/jemboss/gui/filetree/RemoteDragTree.java 2008-07-04 14:33:08.000000000 +0100
---- EMBOSS-6.2.0/jemboss/org/emboss/jemboss/gui/filetree/RemoteDragTree.java 2010-03-02 09:34:07.000000000 +0000
+--- EMBOSS-6.2.0/jemboss/org/emboss/jemboss/gui/filetree/RemoteDragTree.java 2010-06-15 09:56:47.000000000 +0100
***************
*** 743,748 ****
--- 743,754 ----
@@ -14713,7 +14948,7 @@ diff -c -N --recursive -a EMBOSS-6.2.0old/jemboss/org/emboss/jemboss/gui/filetre
else
diff -c -N --recursive -a EMBOSS-6.2.0old/jemboss/org/emboss/jemboss/gui/form/BuildJembossForm.java EMBOSS-6.2.0/jemboss/org/emboss/jemboss/gui/form/BuildJembossForm.java
*** EMBOSS-6.2.0old/jemboss/org/emboss/jemboss/gui/form/BuildJembossForm.java 2010-01-14 17:51:49.000000000 +0000
---- EMBOSS-6.2.0/jemboss/org/emboss/jemboss/gui/form/BuildJembossForm.java 2010-03-02 09:34:07.000000000 +0000
+--- EMBOSS-6.2.0/jemboss/org/emboss/jemboss/gui/form/BuildJembossForm.java 2010-06-15 09:56:47.000000000 +0100
***************
*** 469,475 ****
{
@@ -15058,7 +15293,7 @@ diff -c -N --recursive -a EMBOSS-6.2.0old/jemboss/org/emboss/jemboss/gui/form/Bu
}
diff -c -N --recursive -a EMBOSS-6.2.0old/jemboss/org/emboss/jemboss/gui/ShowResultSet.java EMBOSS-6.2.0/jemboss/org/emboss/jemboss/gui/ShowResultSet.java
*** EMBOSS-6.2.0old/jemboss/org/emboss/jemboss/gui/ShowResultSet.java 2009-10-26 13:31:54.000000000 +0000
---- EMBOSS-6.2.0/jemboss/org/emboss/jemboss/gui/ShowResultSet.java 2010-03-02 09:34:07.000000000 +0000
+--- EMBOSS-6.2.0/jemboss/org/emboss/jemboss/gui/ShowResultSet.java 2010-06-15 09:56:47.000000000 +0100
***************
*** 189,194 ****
--- 189,196 ----
@@ -15072,7 +15307,7 @@ diff -c -N --recursive -a EMBOSS-6.2.0old/jemboss/org/emboss/jemboss/gui/ShowRes
remove(toolbar);
diff -c -N --recursive -a EMBOSS-6.2.0old/jemboss/org/emboss/jemboss/JembossParams.java EMBOSS-6.2.0/jemboss/org/emboss/jemboss/JembossParams.java
*** EMBOSS-6.2.0old/jemboss/org/emboss/jemboss/JembossParams.java 2008-07-03 15:54:02.000000000 +0100
---- EMBOSS-6.2.0/jemboss/org/emboss/jemboss/JembossParams.java 2010-03-02 09:34:07.000000000 +0000
+--- EMBOSS-6.2.0/jemboss/org/emboss/jemboss/JembossParams.java 2010-06-15 09:56:47.000000000 +0100
***************
*** 22,27 ****
--- 22,28 ----
@@ -15104,7 +15339,7 @@ diff -c -N --recursive -a EMBOSS-6.2.0old/jemboss/org/emboss/jemboss/JembossPara
{
diff -c -N --recursive -a EMBOSS-6.2.0old/jemboss/org/emboss/jemboss/programs/RunEmbossApplication2.java EMBOSS-6.2.0/jemboss/org/emboss/jemboss/programs/RunEmbossApplication2.java
*** EMBOSS-6.2.0old/jemboss/org/emboss/jemboss/programs/RunEmbossApplication2.java 2009-07-06 14:49:20.000000000 +0100
---- EMBOSS-6.2.0/jemboss/org/emboss/jemboss/programs/RunEmbossApplication2.java 2010-03-02 09:34:07.000000000 +0000
+--- EMBOSS-6.2.0/jemboss/org/emboss/jemboss/programs/RunEmbossApplication2.java 2010-06-15 09:56:47.000000000 +0100
***************
*** 141,150 ****
while((nc = stderrRead.read(c,0,100)) != -1)
@@ -15131,7 +15366,7 @@ diff -c -N --recursive -a EMBOSS-6.2.0old/jemboss/org/emboss/jemboss/programs/Ru
{
diff -c -N --recursive -a EMBOSS-6.2.0old/jemboss/org/emboss/jemboss/server/JembossAuthServer.java EMBOSS-6.2.0/jemboss/org/emboss/jemboss/server/JembossAuthServer.java
*** EMBOSS-6.2.0old/jemboss/org/emboss/jemboss/server/JembossAuthServer.java 2010-01-06 11:55:24.000000000 +0000
---- EMBOSS-6.2.0/jemboss/org/emboss/jemboss/server/JembossAuthServer.java 2010-03-02 09:34:07.000000000 +0000
+--- EMBOSS-6.2.0/jemboss/org/emboss/jemboss/server/JembossAuthServer.java 2010-06-15 09:56:47.000000000 +0100
***************
*** 45,53 ****
/** Jemboss error log file */
@@ -15206,7 +15441,7 @@ diff -c -N --recursive -a EMBOSS-6.2.0old/jemboss/org/emboss/jemboss/server/Jemb
*
diff -c -N --recursive -a EMBOSS-6.2.0old/jemboss/org/emboss/jemboss/server/JembossServer.java EMBOSS-6.2.0/jemboss/org/emboss/jemboss/server/JembossServer.java
*** EMBOSS-6.2.0old/jemboss/org/emboss/jemboss/server/JembossServer.java 2010-01-06 15:11:44.000000000 +0000
---- EMBOSS-6.2.0/jemboss/org/emboss/jemboss/server/JembossServer.java 2010-03-02 09:34:07.000000000 +0000
+--- EMBOSS-6.2.0/jemboss/org/emboss/jemboss/server/JembossServer.java 2010-06-15 09:56:47.000000000 +0100
***************
*** 73,79 ****
/** user name */
@@ -15711,7 +15946,7 @@ diff -c -N --recursive -a EMBOSS-6.2.0old/jemboss/org/emboss/jemboss/server/Jemb
--- 1154,1158 ----
diff -c -N --recursive -a EMBOSS-6.2.0old/jemboss/org/emboss/jemboss/server/JembossThread.java EMBOSS-6.2.0/jemboss/org/emboss/jemboss/server/JembossThread.java
*** EMBOSS-6.2.0old/jemboss/org/emboss/jemboss/server/JembossThread.java 2004-02-29 20:47:22.000000000 +0000
---- EMBOSS-6.2.0/jemboss/org/emboss/jemboss/server/JembossThread.java 2010-03-02 09:34:07.000000000 +0000
+--- EMBOSS-6.2.0/jemboss/org/emboss/jemboss/server/JembossThread.java 2010-06-15 09:56:47.000000000 +0100
***************
*** 55,62 ****
{
@@ -15781,7 +16016,7 @@ diff -c -N --recursive -a EMBOSS-6.2.0old/jemboss/org/emboss/jemboss/server/Jemb
{
diff -c -N --recursive -a EMBOSS-6.2.0old/jemboss/org/emboss/jemboss/soap/AuthPopup.java EMBOSS-6.2.0/jemboss/org/emboss/jemboss/soap/AuthPopup.java
*** EMBOSS-6.2.0old/jemboss/org/emboss/jemboss/soap/AuthPopup.java 2010-01-11 13:43:55.000000000 +0000
---- EMBOSS-6.2.0/jemboss/org/emboss/jemboss/soap/AuthPopup.java 2010-03-02 09:34:07.000000000 +0000
+--- EMBOSS-6.2.0/jemboss/org/emboss/jemboss/soap/AuthPopup.java 2010-06-15 09:56:47.000000000 +0100
***************
*** 176,182 ****
@@ -15834,7 +16069,7 @@ diff -c -N --recursive -a EMBOSS-6.2.0old/jemboss/org/emboss/jemboss/soap/AuthPo
--- 334,339 ----
diff -c -N --recursive -a EMBOSS-6.2.0old/jemboss/org/emboss/jemboss/soap/JembossRun.java EMBOSS-6.2.0/jemboss/org/emboss/jemboss/soap/JembossRun.java
*** EMBOSS-6.2.0old/jemboss/org/emboss/jemboss/soap/JembossRun.java 2009-07-01 10:20:30.000000000 +0100
---- EMBOSS-6.2.0/jemboss/org/emboss/jemboss/soap/JembossRun.java 2010-03-02 09:34:07.000000000 +0000
+--- EMBOSS-6.2.0/jemboss/org/emboss/jemboss/soap/JembossRun.java 2010-06-15 09:56:47.000000000 +0100
***************
*** 44,85 ****
private Hashtable proganswer;
@@ -15958,7 +16193,7 @@ diff -c -N --recursive -a EMBOSS-6.2.0old/jemboss/org/emboss/jemboss/soap/Jembos
status = proganswer.get("status").toString();
diff -c -N --recursive -a EMBOSS-6.2.0old/jemboss/org/emboss/jemboss/soap/PrivateRequest.java EMBOSS-6.2.0/jemboss/org/emboss/jemboss/soap/PrivateRequest.java
*** EMBOSS-6.2.0old/jemboss/org/emboss/jemboss/soap/PrivateRequest.java 2008-05-21 12:14:41.000000000 +0100
---- EMBOSS-6.2.0/jemboss/org/emboss/jemboss/soap/PrivateRequest.java 2010-03-02 09:34:07.000000000 +0000
+--- EMBOSS-6.2.0/jemboss/org/emboss/jemboss/soap/PrivateRequest.java 2010-06-15 09:56:47.000000000 +0100
***************
*** 85,91 ****
org.apache.axis.client.Service serv =
@@ -16025,7 +16260,7 @@ diff -c -N --recursive -a EMBOSS-6.2.0old/jemboss/org/emboss/jemboss/soap/Privat
}
diff -c -N --recursive -a EMBOSS-6.2.0old/jemboss/utils/install-jemboss-server.sh EMBOSS-6.2.0/jemboss/utils/install-jemboss-server.sh
*** EMBOSS-6.2.0old/jemboss/utils/install-jemboss-server.sh 2010-01-11 12:24:48.000000000 +0000
---- EMBOSS-6.2.0/jemboss/utils/install-jemboss-server.sh 2010-03-02 09:34:07.000000000 +0000
+--- EMBOSS-6.2.0/jemboss/utils/install-jemboss-server.sh 2010-06-15 09:56:47.000000000 +0100
***************
*** 173,179 ****
./configure --with-thread=$PLATFORM \
@@ -16090,9 +16325,709 @@ diff -c -N --recursive -a EMBOSS-6.2.0old/jemboss/utils/install-jemboss-server.s
#
# create resources.jar archive of the scoring matrix
--- 1241,1246 ----
+diff -c -N --recursive -a EMBOSS-6.2.0old/nucleus/embaln.c EMBOSS-6.2.0/nucleus/embaln.c
+*** EMBOSS-6.2.0old/nucleus/embaln.c 2009-12-01 14:28:19.000000000 +0000
+--- EMBOSS-6.2.0/nucleus/embaln.c 2010-06-15 09:57:53.000000000 +0100
+***************
+*** 33,50 ****
+ #define LEFT 1
+ #define DOWN 2
+
+
+
+
+ static void printPathMatrix(const float* path, const ajint* compass,
+ ajuint lena, ajuint lenb);
+
+! static float embAlignGetScoreNWMatrix(const float *path, ajint lena,
+ ajint lenb, ajint *xpos, ajint *ypos, AjBool endweight);
+
+
+
+-
+ /* @func embAlignPathCalc *****************************************************
+ **
+ ** Create path matrix for Needleman-Wunsch
+--- 33,52 ----
+ #define LEFT 1
+ #define DOWN 2
+
++ #define U_FEPS 1.192e-6F /* 1.0F + E_FEPS != 1.0F */
++ #define E_FPEQ(a,b,e) (((b - e) < a) && (a < (b + e)))
+
+
+
+ static void printPathMatrix(const float* path, const ajint* compass,
+ ajuint lena, ajuint lenb);
+
+! static float embAlignGetScoreNWMatrix(
+! const float *ix, const float *iy, const float *m, ajint lena,
+ ajint lenb, ajint *xpos, ajint *ypos, AjBool endweight);
+
+
+
+ /* @func embAlignPathCalc *****************************************************
+ **
+ ** Create path matrix for Needleman-Wunsch
+***************
+*** 237,244 ****
+ **
+ ** @param [r] a [const char *] first sequence
+ ** @param [r] b [const char *] second sequence
+! ** @param [r] lena [ajuint] length of first sequence
+! ** @param [r] lenb [ajuint] length of second sequence
+ ** @param [r] gapopen [float] gap opening penalty
+ ** @param [r] gapextend [float] gap extension penalty
+ ** @param [r] endgapopen [float] end gap opening penalty
+--- 239,246 ----
+ **
+ ** @param [r] a [const char *] first sequence
+ ** @param [r] b [const char *] second sequence
+! ** @param [r] lena [ajint] length of first sequence
+! ** @param [r] lenb [ajint] length of second sequence
+ ** @param [r] gapopen [float] gap opening penalty
+ ** @param [r] gapextend [float] gap extension penalty
+ ** @param [r] endgapopen [float] end gap opening penalty
+***************
+*** 261,471 ****
+ ******************************************************************************/
+
+ float embAlignPathCalcWithEndGapPenalties(const char *a, const char *b,
+! ajuint lena, ajuint lenb,
+ float gapopen, float gapextend,
+ float endgapopen, float endgapextend,
+ ajint *start1, ajint *start2,
+! float *path, float * const *sub, const AjPSeqCvt cvt,
+ float *m, float *ix, float *iy,
+ ajint *compass, AjBool show,
+ AjBool endweight)
+ {
+! ajuint xpos;
+! ajuint ypos;
+! ajuint i;
+! ajuint j;
+ ajint bconvcode;
+-
+ float match;
+ float ixp;
+ float iyp;
+ float mp;
+ ajint cursor;
+ ajint cursorp;
+!
+ float testog;
+ float testeg;
+- float testdg;
+ float score;
+
+ ajDebug("embAlignPathCalcWithEndGapPenalties\n");
+
+ match = sub[ajSeqcvtGetCodeK(cvt, a[0])][ajSeqcvtGetCodeK(cvt, b[0])];
+- compass[0] = 0;
+- path[0] = (float) match;
+
+! if(endweight && -endgapopen > match)
+! path[0] = endgapopen;
+
+! ix[0] = INT_MIN;
+! iy[0] = INT_MIN;
+! m[0] = path[0];
+
+! /* First initialise the first column and row */
+! for (i = 1; i < lena; ++i)
+ {
+! match = sub[ajSeqcvtGetCodeK(cvt, a[i])][ajSeqcvtGetCodeK(cvt, b[0])];
+
+! if(!endweight)
+! {
+! path[i * lenb] = (float) match;
+! compass[i * lenb] = 0;
+! m[i*lenb] = (float)match;
+! ix[i*lenb] = INT_MIN;
+! iy[i*lenb] = INT_MIN;
+! }
+! else
+! {
+! ypos=i;
+! cursor = ypos * lenb;
+! cursorp = (ypos-1) * lenb;
+! testog = m[cursorp] - endgapopen;
+! testeg = iy[cursorp] - endgapextend;
+
+! if(testog >= testeg)
+! iy[cursor] = testog;
+! else
+! iy[cursor] = testeg;
+!
+! m[cursor] = match - (endgapopen + (i - 1) * endgapextend);
+! ix[cursor] = INT_MIN;
+
+! if(m[cursor]>iy[cursor])
+! {
+! path[cursor] = m[cursor];
+! compass[cursor] = 0;
+! }
+! else
+! {
+! path[cursor] = iy[cursor];
+! compass[cursor] = 2;
+! }
+! }
+ }
+
+! for (j = 1; j < lenb; ++j)
+! {
+! match = sub[ajSeqcvtGetCodeK(cvt, a[0])][ajSeqcvtGetCodeK(cvt, b[j])];
+
+! if(!endweight)
+! {
+! path[j] = (float) match;
+! compass[j] = 0;
+! ix[j] = INT_MIN;
+! iy[j] = INT_MIN;
+! m[j] = (float) match;
+! }
+! else
+! {
+! xpos=j;
+! cursor = xpos;
+! cursorp = xpos -1;
+! testog = m[cursorp] - endgapopen;
+! testeg = iy[cursorp] - endgapextend;
+
+! if(testog >= testeg)
+! ix[cursor] = testog;
+! else
+! ix[cursor] = testeg;
+
+! m[cursor] = match - (endgapopen + (j - 1) * endgapextend);
+! iy[cursor] = INT_MIN;
+
+! if(m[cursor]>ix[cursor])
+! {
+! path[cursor] = m[cursor];
+! compass[cursor] = 0;
+! }
+! else
+! {
+! path[cursor] = ix[cursor];
+! compass[cursor] = 1;
+! }
+! }
+ }
+
+! /* xpos and ypos are the diagonal steps so start at 1 */
+ xpos = 1;
+
+ while (xpos != lenb)
+ {
+ ypos = 1;
+ bconvcode = ajSeqcvtGetCodeK(cvt, *++b);
+
+ while (ypos < lena)
+ {
+ /* get match for current xpos/ypos */
+! match = sub[ajSeqcvtGetCodeK(cvt, a[ypos])][bconvcode];
+
+! /* coordinates of the cells being processed */
+! cursorp = (ypos-1) * lenb + xpos-1;
+! cursor = ypos * lenb + xpos;
+!
+ mp = m[cursorp];
+ ixp = ix[cursorp];
+ iyp = iy[cursorp];
+
+! if(mp >= ixp && mp >= iyp)
+ m[cursor] = mp+match;
+ else if(ixp > iyp)
+ m[cursor] = ixp+match;
+ else
+ m[cursor] = iyp+match;
+
+! testog = m[++cursorp] - gapopen;
+! testeg = iy[cursorp] - gapextend;
+! testdg = ix[cursorp] - gapopen;
+
+! if(testog >= testeg && testog >= testdg)
+ iy[cursor] = testog;
+- else if(testeg >testdg)
+- iy[cursor] = testeg;
+ else
+! iy[cursor] = testdg;
+
+ cursorp += lenb;
+-
+- testog = m[--cursorp] - gapopen;
+- testeg = ix[cursorp] - gapextend;
+- testdg = iy[cursorp] - gapopen;
+-
+- if(testog >= testeg && testog >= testdg)
+- ix[cursor] = testog;
+- else if(testeg >testdg)
+- ix[cursor] = testeg;
+- else
+- ix[cursor] = testdg;
+
+!
+! mp = m[cursor];
+!
+! if(mp >= ix[cursor] && mp>=iy[cursor])
+! {
+! path[cursor] = mp;
+! compass[cursor] = 0;
+! }
+! else if(ix[cursor]>=iy[cursor])
+ {
+! path[cursor] = ix[cursor];
+! compass[cursor] = 1;
+ }
+ else
+ {
+! path[cursor] = iy[cursor];
+! compass[cursor] = 2;
+ }
+
+- ++ypos;
+ }
+
+! ++xpos;
+ }
+
+ if(show)
+! printPathMatrix(path, compass, lena, lenb);
+
+- score = embAlignGetScoreNWMatrix(path, lena, lenb,
+- start1, start2, endweight);
+
+ return score;
+ }
+--- 263,513 ----
+ ******************************************************************************/
+
+ float embAlignPathCalcWithEndGapPenalties(const char *a, const char *b,
+! ajint lena, ajint lenb,
+ float gapopen, float gapextend,
+ float endgapopen, float endgapextend,
+ ajint *start1, ajint *start2,
+! float * const *sub, const AjPSeqCvt cvt,
+ float *m, float *ix, float *iy,
+ ajint *compass, AjBool show,
+ AjBool endweight)
+ {
+! ajint xpos;
+! ajint ypos;
+ ajint bconvcode;
+ float match;
+ float ixp;
+ float iyp;
+ float mp;
+ ajint cursor;
+ ajint cursorp;
+!
+ float testog;
+ float testeg;
+ float score;
++
+
+ ajDebug("embAlignPathCalcWithEndGapPenalties\n");
+
++ if (!endweight)
++ {
++ endgapopen=0;
++ endgapextend=0;
++ endweight=ajTrue;
++ }
++
+ match = sub[ajSeqcvtGetCodeK(cvt, a[0])][ajSeqcvtGetCodeK(cvt, b[0])];
+
+! ix[0] = -endgapopen-gapopen;
+! iy[0] = -endgapopen-gapopen;
+! m[0] = match;
+
+! cursor =0;
+
+! /* First initialise the first column */
+! for (ypos = 1; ypos < lena; ++ypos)
+ {
+! match = sub[ajSeqcvtGetCodeK(cvt,a[ypos])][ajSeqcvtGetCodeK(cvt,b[0])];
+! cursor = ypos * lenb;
+! cursorp = (ypos-1) * lenb;
+
+! testog = m[cursorp] - gapopen;
+! testeg = iy[cursorp] - gapextend;
+
+! if(testog >= testeg)
+! iy[cursor] = testog;
+! else
+! iy[cursor] = testeg;
+
+! m[cursor] = match - (endgapopen + (ypos - 1) * endgapextend);
+! ix[cursor] = -endgapopen - ypos * endgapextend - gapopen;
+ }
+
+! ix[cursor] -= endgapopen;
+! ix[cursor] += gapopen;
+
+! cursor=0;
+
+! /* Now initialise the first row */
+! for (xpos = 1; xpos < lenb; ++xpos)
+! {
+! match = sub[ajSeqcvtGetCodeK(cvt,a[0])][ajSeqcvtGetCodeK(cvt,b[xpos])];
+! cursor = xpos;
+! cursorp = xpos -1;
+
+! testog = m[cursorp] - gapopen;
+! testeg = ix[cursorp] - gapextend;
+
+! if(testog >= testeg)
+! ix[cursor] = testog;
+! else
+! ix[cursor] = testeg;
+!
+! m[cursor] = match - (endgapopen + (xpos - 1) * endgapextend);
+! iy[cursor] = -endgapopen - xpos * endgapextend -gapopen;
+ }
+
+! iy[cursor] -= endgapopen;
+! iy[cursor] += gapopen;
+!
+ xpos = 1;
+
++ /* Now construct match, ix, and iy matrices */
+ while (xpos != lenb)
+ {
+ ypos = 1;
+ bconvcode = ajSeqcvtGetCodeK(cvt, *++b);
+
++ /* coordinates of the cells being processed */
++ cursorp = xpos-1;
++ cursor = xpos++;
++
+ while (ypos < lena)
+ {
+ /* get match for current xpos/ypos */
+! match = sub[ajSeqcvtGetCodeK(cvt, a[ypos++])][bconvcode];
+
+! cursor += lenb;
+!
+! /* match matrix calculations */
+ mp = m[cursorp];
+ ixp = ix[cursorp];
+ iyp = iy[cursorp];
+
+! if(mp > ixp && mp > iyp)
+ m[cursor] = mp+match;
+ else if(ixp > iyp)
+ m[cursor] = ixp+match;
+ else
+ m[cursor] = iyp+match;
+
+! /* iy matrix calculations */
+! if(xpos==lenb)
+! {
+! testog = m[++cursorp] - endgapopen;
+! testeg = iy[cursorp] - endgapextend;
+! }
+! else
+! {
+! testog = m[++cursorp];
+!
+! if (testog<ix[cursorp])
+! testog = ix[cursorp];
+!
+! testog -= gapopen;
+! testeg = iy[cursorp] - gapextend;
+! }
+
+! if(testog > testeg)
+ iy[cursor] = testog;
+ else
+! iy[cursor] = testeg;
+
+ cursorp += lenb;
+
+! /* ix matrix calculations */
+! if(ypos==lena)
+ {
+! testog = m[--cursorp] - endgapopen;
+! testeg = ix[cursorp] - endgapextend;
+ }
+ else
+ {
+! testog = m[--cursorp];
+!
+! if (testog<iy[cursorp])
+! testog = iy[cursorp];
+!
+! testog -= gapopen;
+! testeg = ix[cursorp] - gapextend;
+ }
++
++ if(testog > testeg )
++ ix[cursor] = testog;
++ else
++ ix[cursor] = testeg;
+
+ }
++ }
++
++ score = embAlignGetScoreNWMatrix(ix, iy, m, lena, lenb,
++ start1, start2, endweight);
++
++ xpos = *start2;
++ ypos = *start1;
++
++ /* In the following loop the three matrices (m, ix, iy) are traced back
++ * and path/alignment decision/selection is made.
++ * 0 means match: go up and left in the matrix
++ * 1 means: go left in the matrix, i.e. gap in the first sequence(seq a)
++ * 2 means: go up in the matrix, i.e. gap in the second sequence(seq b)
++ */
++ cursorp=0;
++ cursor=1;
++
++ while (xpos>=0 && ypos>=0)
++ {
++ cursor = ypos*lenb+xpos;
++ mp = m[cursor];
++
++ if(cursorp == LEFT && E_FPEQ((ypos==0||(ypos==lena-1)?
++ endgapextend:gapextend), (ix[cursor]-ix[cursor+1]),U_FEPS))
++ {
++ compass[cursor] = LEFT;
++ xpos--;
++ }
++ else if(cursorp== DOWN && E_FPEQ((xpos==0||(xpos==lenb-1)?
++ endgapextend:gapextend), (iy[cursor]-iy[cursor+lenb]),U_FEPS))
++ {
++ compass[cursor] = DOWN;
++ ypos--;
++ }
++ else if(mp >= ix[cursor] && mp>= iy[cursor])
++ {
++
++ if(cursorp == LEFT && E_FPEQ(mp,ix[cursor],U_FEPS))
++ {
++ compass[cursor] = LEFT;
++ xpos--;
++ }
++ else if(cursorp == DOWN && E_FPEQ(mp,iy[cursor],U_FEPS))
++ {
++ compass[cursor] = DOWN;
++ ypos--;
++ }
++ else
++ {
++ compass[cursor] = 0;
++ ypos--;
++ xpos--;
++ }
+
+! }
+! else if(ix[cursor]>=iy[cursor] && xpos>-1)
+! {
+! compass[cursor] = LEFT;
+! xpos--;
+! }
+! else if(ypos>-1)
+! {
+! compass[cursor] = DOWN;
+! ypos--;
+! }
+! else
+! {
+! ajErr("something is seriously wrong in the traceback algorithm");
+! ajExitAbort();
+! }
+! cursorp = compass[cursor];
+ }
+
+ if(show)
+! {
+! printPathMatrix(m, compass, lena, lenb);
+! printPathMatrix(ix, compass, lena, lenb);
+! printPathMatrix(iy, compass, lena, lenb);
+! }
+
+
+ return score;
+ }
+***************
+*** 2844,2852 ****
+ ** Returns score of the optimal global or overlap alignment for
+ ** the specified path matrix for Needleman Wunsch
+ **
+! ** @param [r] path [const float*] path matrix
+! ** @param [r] lena [ajint] length of first sequence
+! ** @param [r] lenb [ajint] length of second sequence
+ ** @param [w] start1 [ajint *] start of alignment in first sequence
+ ** @param [w] start2 [ajint *] start of alignment in second sequence
+ ** @param [r] endweight [AjBool] whether the matrix was built for
+--- 2886,2902 ----
+ ** Returns score of the optimal global or overlap alignment for
+ ** the specified path matrix for Needleman Wunsch
+ **
+! ** @param [r] ix [const float*] Gap scores array, ix(i,j) is the best score
+! ** given that a(i) is aligned to a gap
+! ** (in an insertion with respect to b)
+! ** @param [r] iy [const float*] Gap scores array, iy(i,j) is the best score
+! ** given that b(i) is in an insertion
+! ** with respect to a
+! **
+! ** @param [r] m [const float*] Match scores array, m(i,j) is the best score
+! ** up to (i,j) given that a(i) is aligned to b(j)
+! ** @param [r] lena [ajint] length of the first sequence
+! ** @param [r] lenb [ajint] length of the second sequence
+ ** @param [w] start1 [ajint *] start of alignment in first sequence
+ ** @param [w] start2 [ajint *] start of alignment in second sequence
+ ** @param [r] endweight [AjBool] whether the matrix was built for
+***************
+*** 2855,2867 ****
+ ** @return [float] optimal score
+ ******************************************************************************/
+
+! static float embAlignGetScoreNWMatrix(const float *path,
+ ajint lena, ajint lenb,
+ ajint *start1, ajint *start2,
+ AjBool endweight)
+ {
+! ajint i,j;
+! float score = FLT_MIN;
+ *start1 = lena-1;
+ *start2 = lenb-1;
+
+--- 2905,2918 ----
+ ** @return [float] optimal score
+ ******************************************************************************/
+
+! static float embAlignGetScoreNWMatrix(
+! const float *ix, const float *iy, const float *m,
+ ajint lena, ajint lenb,
+ ajint *start1, ajint *start2,
+ AjBool endweight)
+ {
+! ajint i,j, cursor;
+! float score = INT_MIN;
+ *start1 = lena-1;
+ *start2 = lenb-1;
+
+***************
+*** 2869,2892 ****
+ {
+ /* when using end gap penalties the score of the optimal global
+ * alignment is stored in the final cell of the path matrix */
+! score = path[lena * lenb - 1];
+ }
+ else {
+
+ for (i = 0; i < lenb; ++i)
+! if(path[(lena - 1) * lenb + i] > score)
+ {
+! *start2 = i;
+! score = path[(lena - 1) * lenb + i];
+ }
+
+ for (j = 0; j < lena; ++j)
+! if(path[j * lenb + lenb - 1] > score)
+ {
+! *start1 = j;
+! *start2 = lenb-1;
+! score = path[j * lenb + lenb - 1];
+ }
+ }
+ return score;
+ }
+--- 2920,2977 ----
+ {
+ /* when using end gap penalties the score of the optimal global
+ * alignment is stored in the final cell of the path matrix */
+! cursor = lena * lenb - 1;
+! if(m[cursor]>ix[cursor]&&m[cursor]>iy[cursor])
+! score = m[cursor];
+! else if(ix[cursor]>iy[cursor])
+! score = ix[cursor];
+! else
+! score = iy[cursor];
+ }
+ else {
+
+ for (i = 0; i < lenb; ++i)
+! {
+! cursor = (lena - 1) * lenb + i;
+! if(m[cursor]>score)
+! {
+! *start2 = i;
+! score = m[cursor];
+! }
+! if(ix[cursor]>score)
+! {
+! score = ix[cursor];
+! *start2 = i;
+! }
+! if(iy[cursor]>score)
+ {
+! score = iy[cursor];
+! *start2 = i;
+ }
++ }
+
+ for (j = 0; j < lena; ++j)
+! {
+! cursor = j * lenb + lenb - 1;
+! if(m[cursor]>score)
+! {
+! *start1 = j;
+! *start2 = lenb-1;
+! score = m[cursor];
+! }
+! if(ix[cursor]>score)
+ {
+! score = ix[cursor];
+! *start1 = j;
+! *start2 = lenb-1;
+ }
++ if(iy[cursor]>score)
++ {
++ score = iy[cursor];
++ *start1 = j;
++ *start2 = lenb-1;
++ }
++ }
+ }
+ return score;
+ }
+diff -c -N --recursive -a EMBOSS-6.2.0old/nucleus/embaln.h EMBOSS-6.2.0/nucleus/embaln.h
+*** EMBOSS-6.2.0old/nucleus/embaln.h 2009-11-25 14:02:23.000000000 +0000
+--- EMBOSS-6.2.0/nucleus/embaln.h 2010-06-15 09:57:58.000000000 +0100
+***************
+*** 28,38 ****
+ ajint *compass, AjBool show);
+
+ float embAlignPathCalcWithEndGapPenalties(const char *a, const char *b,
+! ajuint lena, ajuint lenb,
+ float gapopen, float gapextend,
+ float endgapopen, float endgapextend,
+ ajint *start1, ajint *start2,
+! float *path, float * const *sub, const AjPSeqCvt cvt,
+ float *m, float *ix, float *iy,
+ ajint *compass, AjBool show,
+ AjBool endweight);
+--- 28,38 ----
+ ajint *compass, AjBool show);
+
+ float embAlignPathCalcWithEndGapPenalties(const char *a, const char *b,
+! ajint lena, ajint lenb,
+ float gapopen, float gapextend,
+ float endgapopen, float endgapextend,
+ ajint *start1, ajint *start2,
+! float * const *sub, const AjPSeqCvt cvt,
+ float *m, float *ix, float *iy,
+ ajint *compass, AjBool show,
+ AjBool endweight);
diff -c -N --recursive -a EMBOSS-6.2.0old/nucleus/embpat.c EMBOSS-6.2.0/nucleus/embpat.c
*** EMBOSS-6.2.0old/nucleus/embpat.c 2009-10-02 12:27:00.000000000 +0100
---- EMBOSS-6.2.0/nucleus/embpat.c 2010-03-02 09:34:07.000000000 +0000
+--- EMBOSS-6.2.0/nucleus/embpat.c 2010-06-15 09:56:47.000000000 +0100
***************
*** 800,807 ****
--
The European Molecular Biology Open Software Suite.
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