[Debian-med-packaging] [SCM] The European Molecular Biology Open Software Suite. branch, master, updated. upstream/6.2.0-19-g8e8b522
Charles Plessy
plessy at debian.org
Tue May 25 12:44:09 UTC 2010
The following commit has been merged in the master branch:
commit dbd8c62213654b9232b47bde6d8cbe7928ce193c
Author: Charles Plessy <plessy at debian.org>
Date: Tue May 25 18:29:47 2010 +0900
Official upstream patch.
Downloaded from ‘ftp://emboss.open-bio.org/pub/EMBOSS/fixes/patches/patch-1-18.gz’.
diff --git a/debian/patches/official-upstream-patch.patch b/debian/patches/official-upstream-patch.patch
new file mode 100644
index 0000000..669a673
--- /dev/null
+++ b/debian/patches/official-upstream-patch.patch
@@ -0,0 +1,16263 @@
+Description: Official upstream patch.
+ Fix 1. EMBOSS-6.2.0/emboss/jembossctl.c
+ EMBOSS-6.2.0/jemboss/lib/jemboss.jar
+ EMBOSS-6.2.0/jemboss/org/emboss/jemboss/gui/filetree/DragTree.java
+ EMBOSS-6.2.0/jemboss/org/emboss/jemboss/gui/filetree/RemoteDragTree.java
+ EMBOSS-6.2.0/jemboss/org/emboss/jemboss/gui/form/BuildJembossForm.java
+ EMBOSS-6.2.0/jemboss/org/emboss/jemboss/gui/ShowResultSet.java
+ EMBOSS-6.2.0/jemboss/org/emboss/jemboss/JembossParams.java
+ EMBOSS-6.2.0/jemboss/org/emboss/jemboss/programs/RunEmbossApplication2.java
+ EMBOSS-6.2.0/jemboss/org/emboss/jemboss/server/JembossAuthServer.java
+ EMBOSS-6.2.0/jemboss/org/emboss/jemboss/server/JembossServer.java
+ EMBOSS-6.2.0/jemboss/org/emboss/jemboss/server/JembossThread.java
+ EMBOSS-6.2.0/jemboss/org/emboss/jemboss/soap/AuthPopup.java
+ EMBOSS-6.2.0/jemboss/org/emboss/jemboss/soap/JembossRun.java
+ EMBOSS-6.2.0/jemboss/org/emboss/jemboss/soap/PrivateRequest.java
+ EMBOSS-6.2.0/jemboss/utils/install-jemboss-server.sh
+ .
+ 26 Feb 2010: Various Jemboss fixes including allowing multiple
+ parameters to "wossname" and reporting of stderr
+ output
+ .
+ .
+ Fix 2. EMBOSS-6.2.0/emboss/acd/jaspextract.acd
+ EMBOSS-6.2.0/emboss/acd/jaspscan.acd
+ EMBOSS-6.2.0/emboss/jaspextract.c
+ EMBOSS-6.2.0/emboss/jaspscan.c
+ .
+ 26 Feb 2010: jaspextract and jaspscan can use the latest-format data at
+ http://jaspar.genereg.net/html/DOWNLOAD/Archive.zip
+ jaspextract uses the data in the "all_data/FlatFileDir"
+ directory. It is advisable to clear delete any old data files
+ from your EMBOSS data file area e.g. from the
+ /usr/local/emboss/share/EMBOSS/data/JASPAR_* directories
+ .
+ .
+ Fix 3. EMBOSS-6.2.0/emboss/emma.c
+
+ 26 Feb 2010: Takes note once again of any EMBOSS_CLUSTALW environment variable
+ setting.
+ .
+ .
+ Fix 4. EMBOSS-6.2.0/emboss/acd/trimseq.acd
+
+ 26 Feb 2010: Place limit on the maximum window size
+ .
+ .
+ Fix 5. EMBOSS-6.2.0/ajax/core/ajpat.c
+ EMBOSS-6.2.0/nucleus/embpat.c
+ .
+ 26 Feb 2010: Fix crash when excessive mismatches requested in one of the
+ fuzzpro search algorithms.
+ .
+ .
+ Fix 6. EMBOSS-6.2.0/emboss/coderet.c
+ EMBOSS-6.2.0/emboss/splitter.c
+ .
+ 26 Feb 2010: Fix crash if no features in the source sequence
+ .
+ .
+ Fix 7. EMBOSS-6.2.0/emboss/matcher.c
+ .
+ 26 Feb 2010: Fix memory allocation problem
+ .
+ .
+ Fix 8. EMBOSS-6.2.0/ajax/core/ajseqread.c
+ EMBOSS-6.2.0/ajax/core/ajseqwrite.c
+ .
+ 01-Mar-2010: Fix sequence format 'refseqp' to be a valid protein
+ output format and to preserve more fields from refseqp input.
+ .
+ .
+ Fix 9. EMBOSS-6.2.0/ajax/core/ajlist.c
+ EMBOSS-6.2.0/ajax/core/ajlist.h
+ EMBOSS-6.2.0/emboss/showfeat.c
+ .
+ 01-Mar-2010: Fix showfeat sorted feature output to correctly sort exons
+ for 'join' feature locations.
+ .
+ .
+ Fix 10.EMBOSS-6.2.0/ajax/graphics/ajgraph.c
+ EMBOSS-6.2.0/emboss/prettyplot.c
+ .
+ 01-Mar-2010: Fix PNG graphics output format to remove large blank
+ margins added by the plplot driver. Improve prettyplot
+ output to better centre sequence characters within boxes.
+ .
+ .
+ Fix 11.EMBOSS-6.2.0/emboss/recoder.c
+ EMBOSS-6.2.0/emboss/remap.c
+ EMBOSS-6.2.0/emboss/restrict.c
+ EMBOSS-6.2.0/emboss/showseq.c
+ EMBOSS-6.2.0/emboss/silent.c
+ .
+ 01-Mar-2010: Skip bad enzyme file records
+ .
+ .
+ Fix 12.EMBOSS-6.2.0/emboss/showpep.c
+ EMBOSS-6.2.0/emboss/showseq.c
+ .
+ 01-Mar-2010: Correct HTML output closing tag.
+ .
+ .
+ Fix 13.EMBOSS-6.2.0/ajax/core/ajfeat.c
+ .
+ 01-Mar-2010: Remove warnings for accessions and repeat features in
+ ensembl format EMBL files.
+ .
+ .
+ Fix 14.EMBOSS-6.2.0/emboss/acd/cirdna.acd
+ EMBOSS-6.2.0/emboss/acd/knowntypes.standard
+ .
+ 01-Mar-2010: Fix description of cirdna input
+ .
+ .
+ Fix 15.EMBOSS-6.2.0/emboss/acd/extractfeat.acd
+ EMBOSS-6.2.0/emboss/acd/maskfeat.acd
+ EMBOSS-6.2.0/emboss/acd/showfeat.acd
+ EMBOSS-6.2.0/emboss/acd/showpep.acd
+ EMBOSS-6.2.0/emboss/acd/showseq.acd
+ EMBOSS-6.2.0/emboss/acd/twofeat.acd
+ EMBOSS-6.2.0/doc/programs/html/extractfeat.html
+ EMBOSS-6.2.0/doc/programs/html/maskfeat.html
+ EMBOSS-6.2.0/doc/programs/html/showfeat.html
+ EMBOSS-6.2.0/doc/programs/html/showpep.html
+ EMBOSS-6.2.0/doc/programs/html/showseq.html
+ EMBOSS-6.2.0/doc/programs/html/twofeat.html
+ EMBOSS-6.2.0/doc/programs/text/extractfeat.txt
+ EMBOSS-6.2.0/doc/programs/text/maskfeat.txt
+ EMBOSS-6.2.0/doc/programs/text/showfeat.txt
+ EMBOSS-6.2.0/doc/programs/text/showpep.txt
+ EMBOSS-6.2.0/doc/programs/text/showseq.txt
+ EMBOSS-6.2.0/doc/programs/text/twofeat.txt
+ .
+ 01-Mar-2010: Fix URLs for EMBL/GenBank and SwissProt feature table
+ descriptions in help and documentation.
+ .
+ .
+ Fix 16.EMBOSS-6.2.0/emboss/acd/remap.acd
+ EMBOSS-6.2.0/emboss/acd/restover.acd
+ EMBOSS-6.2.0/emboss/acd/restrict.acd
+ EMBOSS-6.2.0/emboss/acd/showseq.acd
+ .
+ 01-Mar-2010: Remove artificial upper limit on number of restriction cuts
+ .
+ .
+ Fix 17.EMBOSS-6.2.0/doc/programs/html/density.2.density.gif
+ EMBOSS-6.2.0/doc/programs/html/density.3.density.gif
+ EMBOSS-6.2.0/doc/programs/html/Makefile.am
+ EMBOSS-6.2.0/doc/programs/html/Makefile.in
+ EMBOSS-6.2.0/doc/programs/html/Makefile
+ .
+ 01-Mar-2010: Missing images for density usage examples
+ .
+ .
+ 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
+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
+***************
+*** 487,493 ****
+ ** Input feature formats
+ **
+ ** Includes the read function (featRead), and initialising (featInitReg)
+! ** and deletion (featDelReg) of parsing resular expression.
+ **
+ ******************************************************************************/
+
+--- 487,493 ----
+ ** Input feature formats
+ **
+ ** Includes the read function (featRead), and initialising (featInitReg)
+! ** and deletion (featDelReg) of parsing regular expression.
+ **
+ ******************************************************************************/
+
+***************
+*** 1839,1845 ****
+ /* @funcstatic featFeatNewProt ************************************************
+ **
+ ** Constructor for a new protein feature,
+! ** automatically added to the specififed table.
+ **
+ ** @param [u] thys [AjPFeattable] Pointer to the ajFeattable which
+ ** will own the feature
+--- 1839,1845 ----
+ /* @funcstatic featFeatNewProt ************************************************
+ **
+ ** Constructor for a new protein feature,
+! ** automatically added to the specified table.
+ **
+ ** @param [u] thys [AjPFeattable] Pointer to the ajFeattable which
+ ** will own the feature
+***************
+*** 2312,2318 ****
+
+ /* @funcstatic featTableInit **************************************************
+ **
+! ** Initialize the components of a previously allocated AjPFeattable object.
+ **
+ ** @param [u] thys [AjPFeattable] Target feature table object
+ ** @param [r] name [const AjPStr] Name of the table (e.g.
+--- 2312,2318 ----
+
+ /* @funcstatic featTableInit **************************************************
+ **
+! ** Initialise the components of a previously allocated AjPFeattable object.
+ **
+ ** @param [u] thys [AjPFeattable] Target feature table object
+ ** @param [r] name [const AjPStr] Name of the table (e.g.
+***************
+*** 2327,2333 ****
+ {
+ /*ajDebug("featTableInit Entering...\n");*/
+
+! /*ajDebug("featTableInit initializing seqid: '%S'\n", name);*/
+ ajStrAssignS(&thys->Seqid,name) ;
+ thys->DefFormat = 0;
+
+--- 2327,2333 ----
+ {
+ /*ajDebug("featTableInit Entering...\n");*/
+
+! /*ajDebug("featTableInit initialising seqid: '%S'\n", name);*/
+ ajStrAssignS(&thys->Seqid,name) ;
+ thys->DefFormat = 0;
+
+***************
+*** 3386,3392 ****
+ /*
+ * Version 2 or greater: parse groupfield for semicolon ';'
+ * delimited tag-value structures, taking special care about
+! * double quoted string context. rbskfirst version of code was
+ * adapted from GFF.pm (th/rbsk), itself inherited from AceParse.pm,
+ * courtesy of James Gilbert
+ */
+--- 3386,3392 ----
+ /*
+ * Version 2 or greater: parse groupfield for semicolon ';'
+ * delimited tag-value structures, taking special care about
+! * double quoted string context. rbsk first version of code was
+ * adapted from GFF.pm (th/rbsk), itself inherited from AceParse.pm,
+ * courtesy of James Gilbert
+ */
+***************
+*** 3736,3743 ****
+ {
+ ajRegSubI(SwRegexFtid, 1, ¬e);
+ ajRegSubI(SwRegexFtid, 2, &ftid);
+! /*ajDebug("Swiss ftid found\nftid: '%S'\n",
+! ftid);*/
+ ajStrAssignS(&tagstr, note);
+ ajStrTrimC(&tagstr, " .");
+ }
+--- 3736,3743 ----
+ {
+ ajRegSubI(SwRegexFtid, 1, ¬e);
+ ajRegSubI(SwRegexFtid, 2, &ftid);
+! /*ajDebug("Swiss ftid found\n");*/
+! /*ajDebug("ftid: '%S'\n",ftid);*/
+ ajStrAssignS(&tagstr, note);
+ ajStrTrimC(&tagstr, " .");
+ }
+***************
+*** 3781,3789 ****
+ **
+ ** Converts an input EMBL format line into a feature.
+ ** Starts a new feature by processing any existing feature data.
+! ** Creates or appends the type, location and tagvalue pairs.
+ ** With a NULL as the input line, simply processes the type, location
+! ** and tagvalues.
+ **
+ ** @param [u] thys [AjPFeattable] Feature table
+ ** @param [r] origline [const AjPStr] Input line (NULL to process last
+--- 3781,3789 ----
+ **
+ ** Converts an input EMBL format line into a feature.
+ ** Starts a new feature by processing any existing feature data.
+! ** Creates or appends the type, location and tag-value pairs.
+ ** With a NULL as the input line, simply processes the type, location
+! ** and tag-values.
+ **
+ ** @param [u] thys [AjPFeattable] Feature table
+ ** @param [r] origline [const AjPStr] Input line (NULL to process last
+***************
+*** 4671,4678 ****
+ **
+ ** Tests for a feature tag value next in the input string
+ **
+! ** @param [u] tags [AjPStr*] Feature tagvalues string, returned with
+! ** current tagvalue removed
+ ** @param [w] name [AjPStr*] Feature tag name
+ ** @param [w] value [AjPStr*] Feature tag value
+ ** @return [AjBool] ajTrue if a match was found
+--- 4671,4678 ----
+ **
+ ** Tests for a feature tag value next in the input string
+ **
+! ** @param [u] tags [AjPStr*] Feature tag-values string, returned with
+! ** current tag-value removed
+ ** @param [w] name [AjPStr*] Feature tag name
+ ** @param [w] value [AjPStr*] Feature tag value
+ ** @return [AjBool] ajTrue if a match was found
+***************
+*** 4858,4864 ****
+ **
+ ** Process bad tag-value text up to next qualifier
+ **
+! ** @param [u] tags [AjPStr*] Feature tagvalues string, returned with
+ ** skipped text removed
+ ** @param [w] skip [AjPStr*] Skipped text
+ ** @return [AjBool] ajTrue if a match was found
+--- 4858,4864 ----
+ **
+ ** Process bad tag-value text up to next qualifier
+ **
+! ** @param [u] tags [AjPStr*] Feature tag-values string, returned with
+ ** skipped text removed
+ ** @param [w] skip [AjPStr*] Skipped text
+ ** @return [AjBool] ajTrue if a match was found
+***************
+*** 5041,5047 ****
+
+ if(istag)
+ {
+! /* /tagname */
+ cp++;
+ cq = cp;
+ i = 0;
+--- 5041,5047 ----
+
+ if(istag)
+ {
+! /* /tag name */
+ cp++;
+ cq = cp;
+ i = 0;
+***************
+*** 5058,5064 ****
+ }
+ else
+ {
+! /* type internalid */
+ cq = cp;
+ i = 0;
+
+--- 5058,5064 ----
+ }
+ else
+ {
+! /* type internal id */
+ cq = cp;
+ i = 0;
+
+***************
+*** 5529,5537 ****
+ **
+ ** Converts an input RefSeq protein format line into a feature.
+ ** Starts a new feature by processing any existing feature data.
+! ** Creates or appends the type, location and tagvalue pairs.
+ ** With a NULL as the input line, simply processes the type, location
+! ** and tagvalues.
+ **
+ ** @param [u] thys [AjPFeattable] Feature table
+ ** @param [r] origline [const AjPStr] Input line (NULL to process last
+--- 5529,5537 ----
+ **
+ ** Converts an input RefSeq protein format line into a feature.
+ ** Starts a new feature by processing any existing feature data.
+! ** Creates or appends the type, location and tag-value pairs.
+ ** With a NULL as the input line, simply processes the type, location
+! ** and tag-values.
+ **
+ ** @param [u] thys [AjPFeattable] Feature table
+ ** @param [r] origline [const AjPStr] Input line (NULL to process last
+***************
+*** 5697,5703 ****
+ AjBool Order = ajFalse;
+ ajint Flags;
+ ajint ExonFlags;
+- char Strand = '+';
+ AjBool Mother = ajTrue;
+ ajint Frame = 0;
+ float Score = 0.0;
+--- 5697,5702 ----
+***************
+*** 5857,5866 ****
+ /* location has been read in, now store it */
+
+ Flags = ExonFlags = 0;
+- if(LocFwd)
+- Strand = '+';
+- else
+- Strand = '-';
+
+ if(Simple)
+ Flags |= FEATFLAG_POINT;
+--- 5856,5861 ----
+***************
+*** 6093,6099 ****
+
+ /* @funcstatic featRegInitEmbl ************************************************
+ **
+! ** Initialize regular expressions and data structures for
+ ** EMBL/GenBank/DDBJ format
+ **
+ ** @return [AjBool] ajTrue if successful
+--- 6088,6094 ----
+
+ /* @funcstatic featRegInitEmbl ************************************************
+ **
+! ** Initialise regular expressions and data structures for
+ ** EMBL/GenBank/DDBJ format
+ **
+ ** @return [AjBool] ajTrue if successful
+***************
+*** 6122,6128 ****
+
+ /* @funcstatic featRegInitRefseqp *********************************************
+ **
+! ** Initialize regular expressions and data structures for
+ ** RefSeq protein format
+ **
+ ** @return [AjBool] ajTrue if successful
+--- 6117,6123 ----
+
+ /* @funcstatic featRegInitRefseqp *********************************************
+ **
+! ** Initialise regular expressions and data structures for
+ ** RefSeq protein format
+ **
+ ** @return [AjBool] ajTrue if successful
+***************
+*** 6151,6157 ****
+
+ /* @funcstatic featRegInitSwiss ***********************************************
+ **
+! ** Initialize regular expressions and data structures for
+ ** SwissProt format
+ **
+ ** @return [AjBool] ajTrue if successful
+--- 6146,6152 ----
+
+ /* @funcstatic featRegInitSwiss ***********************************************
+ **
+! ** Initialise regular expressions and data structures for
+ ** SwissProt format
+ **
+ ** @return [AjBool] ajTrue if successful
+***************
+*** 6193,6200 ****
+
+ /* @funcstatic featRegInitPir *************************************************
+ **
+! ** Initialize regular expressions and data structures for ajFeat#
+! ** Pir format
+ **
+ ** @return [AjBool] ajTrue if successful
+ ** @@
+--- 6188,6195 ----
+
+ /* @funcstatic featRegInitPir *************************************************
+ **
+! ** Initialise regular expressions and data structures for ajFeat in
+! ** PIR format
+ **
+ ** @return [AjBool] ajTrue if successful
+ ** @@
+***************
+*** 6209,6215 ****
+
+ featVocabInitPir();
+
+! /*ajDebug("Tables pir Type: %x Tags: %x\n",
+ FeatTypeTablePir, FeatTagsTablePir);*/
+
+ /*ajDebug("featRegInitPir Compiling regexps\n");*/
+--- 6204,6210 ----
+
+ featVocabInitPir();
+
+! /*ajDebug("Tables PIR Type: %x Tags: %x\n",
+ FeatTypeTablePir, FeatTagsTablePir);*/
+
+ /*ajDebug("featRegInitPir Compiling regexps\n");*/
+***************
+*** 6235,6241 ****
+
+ /* @funcstatic featRegInitGff *************************************************
+ **
+! ** Initialize regular expressions and data structures for ajFeat GFF format
+ **
+ ** @return [AjBool] ajTrue if successful
+ ** @@
+--- 6230,6236 ----
+
+ /* @funcstatic featRegInitGff *************************************************
+ **
+! ** Initialise regular expressions and data structures for ajFeat GFF format
+ **
+ ** @return [AjBool] ajTrue if successful
+ ** @@
+***************
+*** 6278,6284 ****
+
+ /* @funcstatic featRegInitGff3 ************************************************
+ **
+! ** Initialize regular expressions and data structures for ajFeat GFF3 format
+ **
+ ** @return [AjBool] ajTrue if successful
+ ** @@
+--- 6273,6279 ----
+
+ /* @funcstatic featRegInitGff3 ************************************************
+ **
+! ** Initialise regular expressions and data structures for ajFeat GFF3 format
+ **
+ ** @return [AjBool] ajTrue if successful
+ ** @@
+***************
+*** 6322,6328 ****
+ **
+ ** Cleanup and exit routines. Free and destroy regular expressions
+ **
+! ** @return [AjBool] ajFalse if unsuccesful
+ ** @@
+ ******************************************************************************/
+
+--- 6317,6323 ----
+ **
+ ** Cleanup and exit routines. Free and destroy regular expressions
+ **
+! ** @return [AjBool] ajFalse if unsuccessful
+ ** @@
+ ******************************************************************************/
+
+***************
+*** 6346,6352 ****
+ **
+ ** Cleanup and exit routines. Free and destroy regular expressions
+ **
+! ** @return [AjBool] ajFalse if unsuccesful
+ ** @@
+ ******************************************************************************/
+
+--- 6341,6347 ----
+ **
+ ** Cleanup and exit routines. Free and destroy regular expressions
+ **
+! ** @return [AjBool] ajFalse if unsuccessful
+ ** @@
+ ******************************************************************************/
+
+***************
+*** 6375,6381 ****
+ **
+ ** Cleanup and exit routines. Free and destroy regular expressions
+ **
+! ** @return [AjBool] ajFalse if unsuccesful
+ ** @@
+ ******************************************************************************/
+
+--- 6370,6376 ----
+ **
+ ** Cleanup and exit routines. Free and destroy regular expressions
+ **
+! ** @return [AjBool] ajFalse if unsuccessful
+ ** @@
+ ******************************************************************************/
+
+***************
+*** 6399,6405 ****
+ **
+ ** Cleanup and exit routines. Free and destroy regular expressions
+ **
+! ** @return [AjBool] ajFalse if unsuccesful
+ ** @@
+ ******************************************************************************/
+
+--- 6394,6400 ----
+ **
+ ** Cleanup and exit routines. Free and destroy regular expressions
+ **
+! ** @return [AjBool] ajFalse if unsuccessful
+ ** @@
+ ******************************************************************************/
+
+***************
+*** 6428,6434 ****
+ **
+ ** Cleanup and exit routines. Free and destroy regular expressions
+ **
+! ** @return [AjBool] ajFalse if unsuccesful
+ ** @@
+ ******************************************************************************/
+
+--- 6423,6429 ----
+ **
+ ** Cleanup and exit routines. Free and destroy regular expressions
+ **
+! ** @return [AjBool] ajFalse if unsuccessful
+ ** @@
+ ******************************************************************************/
+
+***************
+*** 6466,6472 ****
+ **
+ ** Cleanup and exit routines. Free and destroy regular expressions
+ **
+! ** @return [AjBool] ajFalse if unsuccesful
+ ** @@
+ ******************************************************************************/
+
+--- 6461,6467 ----
+ **
+ ** Cleanup and exit routines. Free and destroy regular expressions
+ **
+! ** @return [AjBool] ajFalse if unsuccessful
+ ** @@
+ ******************************************************************************/
+
+***************
+*** 7848,7854 ****
+ ** but note that any feature will appear in a DASGFF viewer
+ ** unless there is some official dummy type available
+ **
+! ** Common practice is to ignore the DTD and wriet an empty SEGMENT
+ ** so this section should not be needed. DAS 1.6 will correct the spec
+ */
+
+--- 7843,7849 ----
+ ** but note that any feature will appear in a DASGFF viewer
+ ** unless there is some official dummy type available
+ **
+! ** Common practice is to ignore the DTD and write an empty SEGMENT
+ ** so this section should not be needed. DAS 1.6 will correct the spec
+ */
+
+***************
+*** 8181,8187 ****
+
+ /* @func ajFeattableIsNuc *****************************************************
+ **
+! ** Returns ajTrue if a feature table is knucleotide protein
+ **
+ ** @param [r] thys [const AjPFeattable] Feature table
+ ** @return [AjBool] ajTrue for a protein feature table
+--- 8176,8182 ----
+
+ /* @func ajFeattableIsNuc *****************************************************
+ **
+! ** Returns ajTrue if a feature table is nucleotide
+ **
+ ** @param [r] thys [const AjPFeattable] Feature table
+ ** @return [AjBool] ajTrue for a protein feature table
+***************
+*** 10471,10477 ****
+ ** @param [r] tag [const char*] Feature tag
+ ** @param [r] value [const AjPStr] Feature tag value
+ ** @return [AjBool] ajTrue is value was valid
+! ** ajFalse if it was "corrceted"
+ ** @@
+ ******************************************************************************/
+
+--- 10466,10472 ----
+ ** @param [r] tag [const char*] Feature tag
+ ** @param [r] value [const AjPStr] Feature tag value
+ ** @return [AjBool] ajTrue is value was valid
+! ** ajFalse if it was "corrected"
+ ** @@
+ ******************************************************************************/
+
+***************
+*** 10499,10505 ****
+ ** @param [r] tag [const AjPStr] Feature tag
+ ** @param [r] value [const AjPStr] Feature tag value
+ ** @return [AjBool] ajTrue is value was valid
+! ** ajFalse if it was "corrceted"
+ ** @@
+ ******************************************************************************/
+
+--- 10494,10500 ----
+ ** @param [r] tag [const AjPStr] Feature tag
+ ** @param [r] value [const AjPStr] Feature tag value
+ ** @return [AjBool] ajTrue is value was valid
+! ** ajFalse if it was "corrected"
+ ** @@
+ ******************************************************************************/
+
+***************
+*** 10766,10787 ****
+ ** @param [u] thys [AjPFeature] Feature
+ ** @param [r] tag [const AjPStr] Feature tag
+ ** @param [r] value [const AjPStr] feature tag value
+! ** @param [w] pdeftag [AjPStr*] Default tag
+! ** @param [w] pdefval [AjPStr*] Default tag value as "*tag: value"
+ ** @return [void]
+ ** @@
+ ******************************************************************************/
+
+ static void featTagSetDefault(AjPFeature thys,
+ const AjPStr tag, const AjPStr value,
+! AjPStr* pdeftag, AjPStr* pdefval)
+ {
+ featInit();
+
+ if(thys->Protein)
+! featTagSetDefaultDna(tag, value, pdeftag, pdefval);
+ else
+! featTagSetDefaultProt(tag, value, pdeftag, pdefval);
+
+ return;
+ }
+--- 10761,10782 ----
+ ** @param [u] thys [AjPFeature] Feature
+ ** @param [r] tag [const AjPStr] Feature tag
+ ** @param [r] value [const AjPStr] feature tag value
+! ** @param [w] Pdeftag [AjPStr*] Default tag
+! ** @param [w] Pdefval [AjPStr*] Default tag value as "*tag: value"
+ ** @return [void]
+ ** @@
+ ******************************************************************************/
+
+ static void featTagSetDefault(AjPFeature thys,
+ const AjPStr tag, const AjPStr value,
+! AjPStr* Pdeftag, AjPStr* Pdefval)
+ {
+ featInit();
+
+ if(thys->Protein)
+! featTagSetDefaultDna(tag, value, Pdeftag, Pdefval);
+ else
+! featTagSetDefaultProt(tag, value, Pdeftag, Pdefval);
+
+ return;
+ }
+***************
+*** 10795,10813 ****
+ **
+ ** @param [r] tag [const AjPStr] Feature tag
+ ** @param [r] value [const AjPStr] feature tag value
+! ** @param [w] pdeftag [AjPStr*] Default tag
+! ** @param [w] pdefval [AjPStr*] Default tag value as "*tag: value"
+ ** @return [void]
+ ** @@
+ ******************************************************************************/
+
+ static void featTagSetDefaultDna(const AjPStr tag, const AjPStr value,
+! AjPStr* pdeftag, AjPStr* pdefval)
+ {
+ featInit();
+
+! ajStrAssignS(pdeftag, (AjPStr) ajTableFetch(FeatTagsTableDna, ajStrNew()));
+! ajFmtPrintS(pdefval, "*%S: %S", tag, value);
+
+ return;
+ }
+--- 10790,10808 ----
+ **
+ ** @param [r] tag [const AjPStr] Feature tag
+ ** @param [r] value [const AjPStr] feature tag value
+! ** @param [w] Pdeftag [AjPStr*] Default tag
+! ** @param [w] Pdefval [AjPStr*] Default tag value as "*tag: value"
+ ** @return [void]
+ ** @@
+ ******************************************************************************/
+
+ static void featTagSetDefaultDna(const AjPStr tag, const AjPStr value,
+! AjPStr* Pdeftag, AjPStr* Pdefval)
+ {
+ featInit();
+
+! ajStrAssignS(Pdeftag, (AjPStr) ajTableFetch(FeatTagsTableDna, ajStrNew()));
+! ajFmtPrintS(Pdefval, "*%S: %S", tag, value);
+
+ return;
+ }
+***************
+*** 10821,10840 ****
+ **
+ ** @param [r] tag [const AjPStr] Feature tag
+ ** @param [r] value [const AjPStr] feature tag value
+! ** @param [w] pdeftag [AjPStr*] Default tag
+! ** @param [w] pdefval [AjPStr*] Default tag value as "*tag: value"
+ ** @return [void]
+ ** @@
+ ******************************************************************************/
+
+ static void featTagSetDefaultProt(const AjPStr tag, const AjPStr value,
+! AjPStr* pdeftag, AjPStr* pdefval)
+ {
+ featInit();
+
+! ajStrAssignS(pdeftag,
+ (AjPStr) ajTableFetch(FeatTagsTableProtein, ajStrNew()));
+! ajFmtPrintS(pdefval, "*%S: %S", tag, value);
+
+ return;
+ }
+--- 10816,10835 ----
+ **
+ ** @param [r] tag [const AjPStr] Feature tag
+ ** @param [r] value [const AjPStr] feature tag value
+! ** @param [w] Pdeftag [AjPStr*] Default tag
+! ** @param [w] Pdefval [AjPStr*] Default tag value as "*tag: value"
+ ** @return [void]
+ ** @@
+ ******************************************************************************/
+
+ static void featTagSetDefaultProt(const AjPStr tag, const AjPStr value,
+! AjPStr* Pdeftag, AjPStr* Pdefval)
+ {
+ featInit();
+
+! ajStrAssignS(Pdeftag,
+ (AjPStr) ajTableFetch(FeatTagsTableProtein, ajStrNew()));
+! ajFmtPrintS(Pdefval, "*%S: %S", tag, value);
+
+ return;
+ }
+***************
+*** 11891,11903 ****
+ ** Returns the tag-value pairs of a feature object
+ **
+ ** @param [u] iter [AjIList] List iterator from ajFeatTagIter
+! ** @param [w] tagnam [AjPStr*] Tag name
+! ** @param [w] tagval [AjPStr*] Tag val
+ ** @return [AjBool] ajTrue if another tag-value pair was returned
+ ** @@
+ ******************************************************************************/
+
+! AjBool ajFeatTagval(AjIList iter, AjPStr* tagnam, AjPStr* tagval)
+ {
+ FeatPTagval tv = NULL;
+
+--- 11886,11898 ----
+ ** Returns the tag-value pairs of a feature object
+ **
+ ** @param [u] iter [AjIList] List iterator from ajFeatTagIter
+! ** @param [w] Ptagnam [AjPStr*] Tag name
+! ** @param [w] Ptagval [AjPStr*] Tag val
+ ** @return [AjBool] ajTrue if another tag-value pair was returned
+ ** @@
+ ******************************************************************************/
+
+! AjBool ajFeatTagval(AjIList iter, AjPStr* Ptagnam, AjPStr* Ptagval)
+ {
+ FeatPTagval tv = NULL;
+
+***************
+*** 11906,11913 ****
+ if(!tv)
+ return ajFalse;
+
+! ajStrAssignS(tagnam, tv->Tag);
+! ajStrAssignS(tagval, tv->Value);
+
+ return ajTrue;
+ }
+--- 11901,11908 ----
+ if(!tv)
+ return ajFalse;
+
+! ajStrAssignS(Ptagnam, tv->Tag);
+! ajStrAssignS(Ptagval, tv->Value);
+
+ return ajTrue;
+ }
+***************
+*** 12609,12615 ****
+ **
+ ** Tests a string as a valid internal (EMBL) feature /anticodon tag
+ **
+! ** The format is (pos:<base_range>,aa:<amino_acid>)
+ **
+ ** @param [r] val [const AjPStr] parameter value
+ ** @return [AjBool] ajTrue for a valid value, possibly corrected
+--- 12604,12610 ----
+ **
+ ** Tests a string as a valid internal (EMBL) feature /anticodon tag
+ **
+! ** The format is (pos:base_range,aa:amino_acid)
+ **
+ ** @param [r] val [const AjPStr] parameter value
+ ** @return [AjBool] ajTrue for a valid value, possibly corrected
+***************
+*** 13397,13403 ****
+ ** FT 6.2 todo aa 3 letter codes, or Sec (U) or TERM or OTHER
+ **
+ ** FT 6.2 todo pos can be 1 or 2 bases for polyA-completed stops (TERM)
+! ** whcih should have a /note
+ **
+ ** @param [r] val [const AjPStr] parameter value
+ ** @return [AjBool] ajTrue for a valid value, possibly corrected
+--- 13392,13398 ----
+ ** FT 6.2 todo aa 3 letter codes, or Sec (U) or TERM or OTHER
+ **
+ ** FT 6.2 todo pos can be 1 or 2 bases for polyA-completed stops (TERM)
+! ** which should have a /note
+ **
+ ** @param [r] val [const AjPStr] parameter value
+ ** @return [AjBool] ajTrue for a valid value, possibly corrected
+***************
+*** 13586,13596 ****
+ i++;
+ }
+
+! if(!*cp && i > 5) /* ENSP then all numbers */
+! ret = ajTrue;
+
+- if(ret)
+- featWarn("ENSEMBL /protein_id value '%S'", val);
+ /*
+ if(saveit)
+ {
+--- 13581,13593 ----
+ i++;
+ }
+
+! /* ENSP then all numbers */
+! if(!*cp && i > 5)
+! ret = ajTrue;
+!
+! /* if(ret)
+! featWarn("ENSEMBL /protein_id value '%S'", val);*/
+
+ /*
+ if(saveit)
+ {
+***************
+*** 13682,13688 ****
+ /* and in misc_difference features */
+ if(!featRegTagReplace)
+ featRegTagReplace =
+! ajRegCompC("^([abcdghkmnrstuvwxyABCDGHKMNRSTUVWXY]*)$");
+
+ /* if(!featRegTagReplace)
+ featRegTagReplace = ajRegCompC("^\"([acgt]*)\"$");*/
+--- 13679,13685 ----
+ /* and in misc_difference features */
+ if(!featRegTagReplace)
+ featRegTagReplace =
+! ajRegCompC("^([abcdghkmnrstuvwxyABCDGHKMNRSTUVWXY/-]*)$");
+
+ /* if(!featRegTagReplace)
+ featRegTagReplace = ajRegCompC("^\"([acgt]*)\"$");*/
+***************
+*** 14107,14113 ****
+ ** Splits EMBL feature location at the last possible comma
+ ** and adds the appropriate prefix (e.g. the EMBL FT line type)
+ **
+! ** @param [u] ploc [AjPStr*] location as a string
+ ** @param [r] margin [ajuint] Right margin
+ ** @param [r] prefix [const char*] Left margin prefix string
+ ** @param [r] preftyp [const char*] Left margin prefix string for first line
+--- 14104,14110 ----
+ ** Splits EMBL feature location at the last possible comma
+ ** and adds the appropriate prefix (e.g. the EMBL FT line type)
+ **
+! ** @param [u] Ploc [AjPStr*] location as a string
+ ** @param [r] margin [ajuint] Right margin
+ ** @param [r] prefix [const char*] Left margin prefix string
+ ** @param [r] preftyp [const char*] Left margin prefix string for first line
+***************
+*** 14117,14123 ****
+ ** @@
+ ******************************************************************************/
+
+! static void featLocEmblWrapC(AjPStr *ploc, ajuint margin,
+ const char* prefix, const char* preftyp,
+ AjPStr* retstr)
+ {
+--- 14114,14120 ----
+ ** @@
+ ******************************************************************************/
+
+! static void featLocEmblWrapC(AjPStr *Ploc, ajuint margin,
+ const char* prefix, const char* preftyp,
+ AjPStr* retstr)
+ {
+***************
+*** 14132,14143 ****
+ left = strlen(prefix);
+ width = margin - left; /* available width for printing */
+
+! ajStrRemoveWhite(ploc); /* no white space in locations */
+! len = ajStrGetLen(*ploc);
+
+ k = width; /* for safety - will be set in time */
+
+! /* ajDebug("featLocEmblWrapC %d <%d> '%S'\n", len, width, *ploc); */
+ for(i=0; i < len; i+= k)
+ {
+ last = i + width - 1;
+--- 14129,14140 ----
+ left = strlen(prefix);
+ width = margin - left; /* available width for printing */
+
+! ajStrRemoveWhite(Ploc); /* no white space in locations */
+! len = ajStrGetLen(*Ploc);
+
+ k = width; /* for safety - will be set in time */
+
+! /* ajDebug("featLocEmblWrapC %d <%d> '%S'\n", len, width, *Ploc); */
+ for(i=0; i < len; i+= k)
+ {
+ last = i + width - 1;
+***************
+*** 14146,14158 ****
+
+ if((last+1) >= len) /* no need to split */
+ {
+! ajStrAssignSubS(&featTmpStr, *ploc, i, len-1);
+ /* ajDebug("last %d >= len %d\n", last, len); */
+ j = 0;
+ }
+ else
+ {
+! ajStrAssignSubS(&featTmpStr, *ploc, i, last); /* save max string */
+ j = ajStrFindlastC(featTmpStr, ","); /* last comma in featTmpStr */
+ /* ajDebug("comma at %d\n", j); */
+ }
+--- 14143,14155 ----
+
+ if((last+1) >= len) /* no need to split */
+ {
+! ajStrAssignSubS(&featTmpStr, *Ploc, i, len-1);
+ /* ajDebug("last %d >= len %d\n", last, len); */
+ j = 0;
+ }
+ else
+ {
+! ajStrAssignSubS(&featTmpStr, *Ploc, i, last); /* save max string */
+ j = ajStrFindlastC(featTmpStr, ","); /* last comma in featTmpStr */
+ /* ajDebug("comma at %d\n", j); */
+ }
+***************
+*** 17250,17256 ****
+
+ /* @func ajFeatPrintbookFormat ************************************************
+ **
+! ** Reports the input feature format internals in wikitext format
+ **
+ ** @param [u] outf [AjPFile] Output file
+ ** @return [void]
+--- 17247,17253 ----
+
+ /* @func ajFeatPrintbookFormat ************************************************
+ **
+! ** Reports the input feature format internals in wiki text format
+ **
+ ** @param [u] outf [AjPFile] Output file
+ ** @return [void]
+***************
+*** 17328,17334 ****
+
+ /* @func ajFeatPrintwikiFormat ************************************************
+ **
+! ** Reports the input feature format internals in wikitext format
+ **
+ ** @param [u] outf [AjPFile] Output file
+ ** @return [void]
+--- 17325,17331 ----
+
+ /* @func ajFeatPrintwikiFormat ************************************************
+ **
+! ** Reports the input feature format internals in wiki text format
+ **
+ ** @param [u] outf [AjPFile] Output file
+ ** @return [void]
+***************
+*** 17465,17471 ****
+
+ /* @func ajFeatoutPrintwikiFormat *********************************************
+ **
+! ** Reports the output feature format internals in wikitext format
+ **
+ ** @param [u] outf [AjPFile] Output file
+ ** @return [void]
+--- 17462,17468 ----
+
+ /* @func ajFeatoutPrintwikiFormat *********************************************
+ **
+! ** Reports the output feature format internals in wiki text format
+ **
+ ** @param [u] outf [AjPFile] Output file
+ ** @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
+***************
+*** 498,504 ****
+ ** @nam3rule Sort Apply function to each node
+ ** @nam4rule Two Apply second function to each equal node
+ ** @nam5rule Three Apply third function to each equal node
+! ** @suffix Unique Remove non-unique valukes from the list
+ **
+ ** @argrule * list [AjPList] List
+ ** @argrule Map apply [void function] Function to apply
+--- 498,504 ----
+ ** @nam3rule Sort Apply function to each node
+ ** @nam4rule Two Apply second function to each equal node
+ ** @nam5rule Three Apply third function to each equal node
+! ** @suffix Unique Remove non-unique values from the list
+ **
+ ** @argrule * list [AjPList] List
+ ** @argrule Map apply [void function] Function to apply
+***************
+*** 1175,1185 ****
+ ** @nam3rule Mapread Apply function to each node without modifying list or data
+ ** @nam3rule Mapfind Apply function to each node without modifying list
+ ** or data
+! ** @nam3rule Peek Pointer to nextvalue
+ ** @nam4rule PeekFirst Pointer to first value
+ ** @nam4rule PeekLast Pointer to last value
+ ** @nam4rule PeekNumber Pointer to numbered value
+ ** @nam3rule Toarray Build array of values
+ **
+ ** @argrule * list [const AjPList] List
+ ** @argrule Mapfind apply [AjBool function] Function to apply
+--- 1175,1186 ----
+ ** @nam3rule Mapread Apply function to each node without modifying list or data
+ ** @nam3rule Mapfind Apply function to each node without modifying list
+ ** or data
+! ** @nam3rule Peek Pointer to next value
+ ** @nam4rule PeekFirst Pointer to first value
+ ** @nam4rule PeekLast Pointer to last value
+ ** @nam4rule PeekNumber Pointer to numbered value
+ ** @nam3rule Toarray Build array of values
++ ** @nam3rule Toindex Sort index array by list node values
+ **
+ ** @argrule * list [const AjPList] List
+ ** @argrule Mapfind apply [AjBool function] Function to apply
+***************
+*** 1189,1200 ****
+--- 1190,1204 ----
+ ** @argrule PeekNumber ipos [ajuint] Position in list
+ ** @argrule Peek x [void**] Value
+ ** @argrule Toarray array [void***] Array of values, ending with NULL
++ ** @argrule Toindex lind [ajuint*] Populated ndex array to be sorted
++ ** @argrule Toindex sort1 [int* function] Function to compare two list items.
+ **
+ ** @valrule * [AjBool] True on success
+ ** @valrule *Length [ajuint] List length
+ ** @valrule *Mapfind [AjBool] True if function returns true
+ ** @valrule *Mapread [void]
+ ** @valrule *Toarray [ajuint] Array size, excluding final NULL
++ ** @valrule *Toindex [ajuint] Array size, excluding final NULL
+ **
+ ** @fcategory cast
+ **
+***************
+*** 1554,1559 ****
+--- 1558,1624 ----
+
+
+
++ /* @func ajListToindex ********************************************************
++ **
++ ** Create an array of the pointers to the data.
++ **
++ ** @param [r] list [const AjPList] List
++ ** @param [w] lind [ajuint*] Populated ndex array to be sorted
++ ** @param [f] sort1 [int* function] Function to compare two list items.
++ ** @return [ajuint] Size of index array.
++ ** @@
++ ******************************************************************************/
++
++ ajuint ajListToindex(const AjPList list, ajuint* lind,
++ int (*sort1) (const void*, const void*))
++ {
++ ajuint n;
++ ajuint s;
++ ajuint i;
++ ajint j;
++ ajuint t;
++
++ AjPListNode rest;
++ AjPListNode *nodes;
++ ajuint* idx = NULL;
++
++ n = list->Count;
++ rest = list->First;
++
++ if(!n)
++ return 0;
++
++ ajListToarray(list, (void***) &nodes);
++ AJCNEW0(idx, n);
++
++ for(i = 0; i < n; i++)
++ idx[i] = i;
++
++ for(s=n/2; s>0; s /= 2)
++ for(i=s; i<n; ++i)
++ {
++ for(j=i-s;
++ j>=0 && (sort1(&nodes[idx[j]],&nodes[idx[j+s]]) < 0);
++ j-=s)
++ {
++ t = lind[j];
++ lind[j] = lind[j+s];
++ lind[j+s] = t;
++ t = idx[j];
++ idx[j] = idx[j+s];
++ idx[j+s] = t;
++ }
++ }
++
++ AJFREE(nodes);
++ AJFREE(idx);
++
++ return n;
++ }
++
++
++
++
+ /* @section Trace functions ***************************************************
+ **
+ ** @fdata [AjPList]
+***************
+*** 3402,3408 ****
+ ** @nam3rule Mapfind Apply function to each node without modifying list
+ ** or data
+ ** @nam3rule Mapread Apply function to each node without modifying list or data
+! ** @nam3rule Peek Pointer to nextvalue
+ ** @nam4rule PeekFirst Pointer to first value
+ ** @nam4rule PeekLast Pointer to last value
+ ** @nam4rule PeekNumber Pointer to numbered value
+--- 3467,3473 ----
+ ** @nam3rule Mapfind Apply function to each node without modifying list
+ ** or data
+ ** @nam3rule Mapread Apply function to each node without modifying list or data
+! ** @nam3rule Peek Pointer to next value
+ ** @nam4rule PeekFirst Pointer to first value
+ ** @nam4rule PeekLast Pointer to last value
+ ** @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
+***************
+*** 150,155 ****
+--- 150,157 ----
+ void ajListstrTrace (const AjPList list);
+
+ ajuint ajListToarray (const AjPList list, void*** array);
++ ajuint ajListToindex(const AjPList list, ajuint* listindex,
++ int (*sort1) (const void*, const void*));
+ void ajListTrace (const AjPList list);
+
+ 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
+***************
+*** 1228,1236 ****
+--- 1228,1240 ----
+ AJFREE(thys->sotable);
+
+ if(thys->type==6)
++ {
+ for(i=0;i<thys->m;++i)
+ AJFREE(thys->skipm[i]);
+
++ AJFREE(thys->skipm);
++ }
++
+ AJFREE(*pthys);
+
+ return;
+***************
+*** 1330,1348 ****
+ ** Documents patterns to a formatted string
+ **
+ ** @param [u] plist [AjPPatlistRegex] Pattern list object
+! ** @param [w] pdoc [AjPStr*] Formatted string
+ ** @return [ajuint] Number of patterns
+ ** @@
+ ******************************************************************************/
+
+! ajuint ajPatlistRegexDoc (AjPPatlistRegex plist, AjPStr* pdoc)
+ {
+ AjPPatternRegex pat = NULL;
+
+! ajFmtPrintS(pdoc, "%-12S %S\n", "Pattern_name", "Pattern");
+
+ while (ajPatlistRegexGetNext(plist, &pat))
+! ajFmtPrintAppS(pdoc, "%-12S %S\n",
+ ajPatternRegexGetName(pat),
+ ajPatternRegexGetPattern(pat));
+
+--- 1334,1352 ----
+ ** Documents patterns to a formatted string
+ **
+ ** @param [u] plist [AjPPatlistRegex] Pattern list object
+! ** @param [w] Pdoc [AjPStr*] Formatted string
+ ** @return [ajuint] Number of patterns
+ ** @@
+ ******************************************************************************/
+
+! ajuint ajPatlistRegexDoc (AjPPatlistRegex plist, AjPStr* Pdoc)
+ {
+ AjPPatternRegex pat = NULL;
+
+! ajFmtPrintS(Pdoc, "%-12S %S\n", "Pattern_name", "Pattern");
+
+ while (ajPatlistRegexGetNext(plist, &pat))
+! ajFmtPrintAppS(Pdoc, "%-12S %S\n",
+ ajPatternRegexGetName(pat),
+ ajPatternRegexGetPattern(pat));
+
+***************
+*** 1357,1376 ****
+ ** Documents patterns to a formatted string
+ **
+ ** @param [u] plist [AjPPatlistSeq] Pattern list object
+! ** @param [w] pdoc [AjPStr*] Formatted string
+ ** @return [ajuint] Number of patterns
+ ** @@
+ ******************************************************************************/
+
+! ajuint ajPatlistSeqDoc (AjPPatlistSeq plist, AjPStr* pdoc)
+ {
+ AjPPatternSeq pat = NULL;
+
+! ajFmtPrintS(pdoc, "%-12s %8s %s\n",
+ "Pattern_name", "Mismatch", "Pattern");
+ while (ajPatlistSeqGetNext(plist, &pat))
+ {
+! ajFmtPrintAppS(pdoc, "%-12S %8d %S\n",
+ ajPatternSeqGetName(pat),
+ ajPatternSeqGetMismatch(pat),
+ ajPatternSeqGetPattern(pat));
+--- 1361,1380 ----
+ ** Documents patterns to a formatted string
+ **
+ ** @param [u] plist [AjPPatlistSeq] Pattern list object
+! ** @param [w] Pdoc [AjPStr*] Formatted string
+ ** @return [ajuint] Number of patterns
+ ** @@
+ ******************************************************************************/
+
+! ajuint ajPatlistSeqDoc (AjPPatlistSeq plist, AjPStr* Pdoc)
+ {
+ AjPPatternSeq pat = NULL;
+
+! ajFmtPrintS(Pdoc, "%-12s %8s %s\n",
+ "Pattern_name", "Mismatch", "Pattern");
+ while (ajPatlistSeqGetNext(plist, &pat))
+ {
+! ajFmtPrintAppS(Pdoc, "%-12S %8d %S\n",
+ ajPatternSeqGetName(pat),
+ ajPatternSeqGetMismatch(pat),
+ 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
+***************
+*** 582,588 ****
+ static const AjPStr seqAppendWarn(AjPStr* seq, const AjPStr line);
+ static ajuint seqAppendCommented(AjPStr* seq, AjBool* incomment,
+ const AjPStr line);
+! static AjBool seqClustalReadseq(const AjPStr seqReadLine,
+ const AjPTable msftable);
+ static AjBool seqDefine(AjPSeq thys, AjPSeqin seqin);
+ static AjBool seqFindInFormat(const AjPStr format, ajint *iformat);
+--- 582,588 ----
+ static const AjPStr seqAppendWarn(AjPStr* seq, const AjPStr line);
+ static ajuint seqAppendCommented(AjPStr* seq, AjBool* incomment,
+ const AjPStr line);
+! static AjBool seqClustalReadseq(const AjPStr rdLine,
+ const AjPTable msftable);
+ static AjBool seqDefine(AjPSeq thys, AjPSeqin seqin);
+ static AjBool seqFindInFormat(const AjPStr format, ajint *iformat);
+***************
+*** 594,602 ****
+ AjPStr* pline,
+ ajuint maxlines, ajuint *len);
+ static AjBool seqGcgMsfHeader(const AjPStr line, SeqPMsfItem* msfitem);
+! static AjBool seqGcgMsfReadseq(const AjPStr seqReadLine,
+ const AjPTable msftable);
+! static AjBool seqHennig86Readseq(const AjPStr seqReadLine,
+ const AjPTable msftable);
+ static AjBool seqinUfoLocal(const AjPSeqin thys);
+ static void seqListNoComment(AjPStr* text);
+--- 594,602 ----
+ AjPStr* pline,
+ ajuint maxlines, ajuint *len);
+ static AjBool seqGcgMsfHeader(const AjPStr line, SeqPMsfItem* msfitem);
+! static AjBool seqGcgMsfReadseq(const AjPStr rdline,
+ const AjPTable msftable);
+! static AjBool seqHennig86Readseq(const AjPStr rdline,
+ const AjPTable msftable);
+ static AjBool seqinUfoLocal(const AjPSeqin thys);
+ static void seqListNoComment(AjPStr* text);
+***************
+*** 607,613 ****
+ static void seqMsfItemDel(SeqPMsfItem* pthys);
+ static void seqMsfTabDel(void **key, void **value, void *cl);
+ static void seqMsfTabList(const void *key, void **value, void *cl);
+! static AjBool seqPhylipReadseq(const AjPStr seqReadLine,
+ const AjPTable phytable,
+ const AjPStr token,
+ ajuint len, ajuint* ilen, AjBool* done);
+--- 607,613 ----
+ static void seqMsfItemDel(SeqPMsfItem* pthys);
+ static void seqMsfTabDel(void **key, void **value, void *cl);
+ static void seqMsfTabList(const void *key, void **value, void *cl);
+! static AjBool seqPhylipReadseq(const AjPStr rdline,
+ const AjPTable phytable,
+ const AjPStr token,
+ ajuint len, ajuint* ilen, AjBool* done);
+***************
+*** 879,885 ****
+ AJFALSE, AJFALSE, AJTRUE, AJTRUE,
+ AJFALSE, AJTRUE, seqReadDbId, AJFALSE, AJFALSE}, /* odd fasta with id as
+ second token */
+! {"msf", "GCG MSF (mutiple sequence file) file format",
+ AJFALSE, AJTRUE, AJTRUE, AJTRUE,
+ AJFALSE, AJTRUE, seqReadMsf, AJFALSE, AJFALSE},
+ {"hennig86", "Hennig86 output format",
+--- 879,885 ----
+ AJFALSE, AJFALSE, AJTRUE, AJTRUE,
+ AJFALSE, AJTRUE, seqReadDbId, AJFALSE, AJFALSE}, /* odd fasta with id as
+ second token */
+! {"msf", "GCG MSF (multiple sequence file) file format",
+ AJFALSE, AJTRUE, AJTRUE, AJTRUE,
+ AJFALSE, AJTRUE, seqReadMsf, AJFALSE, AJFALSE},
+ {"hennig86", "Hennig86 output format",
+***************
+*** 1499,1505 ****
+ /* @func ajSeqinClearPos ******************************************************
+ **
+ ** Clears a Sequence input object position information as possibly read from
+! ** a USA that included the begni, end and direction
+ **
+ ** @param [u] thys [AjPSeqin] Sequence input
+ ** @return [void]
+--- 1499,1505 ----
+ /* @func ajSeqinClearPos ******************************************************
+ **
+ ** Clears a Sequence input object position information as possibly read from
+! ** a USA that included the begin, end and direction
+ **
+ ** @param [u] thys [AjPSeqin] Sequence input
+ ** @return [void]
+***************
+*** 1626,1632 ****
+
+ /* @section Sequence inputs **********************************************
+ **
+! ** These functions read the sequence provdied by the first argument
+ **
+ ******************************************************************************/
+
+--- 1626,1632 ----
+
+ /* @section Sequence inputs **********************************************
+ **
+! ** These functions read the sequence provided by the first argument
+ **
+ ******************************************************************************/
+
+***************
+*** 3198,3204 ****
+ if(i >= seqlen){
+ if(!badwarn)
+ ajWarn("Bad quality '%S' for base %d "
+! "in fastqint format\n",
+ qualstr, i);
+ badwarn = ajTrue;
+ }
+--- 3198,3204 ----
+ if(i >= seqlen){
+ if(!badwarn)
+ ajWarn("Bad quality '%S' for base %d "
+! "in fastq-int format\n",
+ qualstr, i);
+ badwarn = ajTrue;
+ }
+***************
+*** 3206,3212 ****
+ {
+ if(!badwarn)
+ ajWarn("Bad quality '%S' for base %d "
+! "in fastqint format\n",
+ qualstr, i);
+ badwarn = ajTrue;
+ i++;
+--- 3206,3212 ----
+ {
+ if(!badwarn)
+ ajWarn("Bad quality '%S' for base %d "
+! "in fastq-int format\n",
+ qualstr, i);
+ badwarn = ajTrue;
+ i++;
+***************
+*** 5978,5984 ****
+ ** using the SEQRES records.
+ **
+ ** This is the sequence observed in the structure. See seqReadPdbnucseq
+! ** for parsing the SEQRES records which give the soriginal sequence.
+ **
+ ** @param [w] thys [AjPSeq] Sequence object
+ ** @param [u] seqin [AjPSeqin] Sequence input object
+--- 5978,5984 ----
+ ** using the SEQRES records.
+ **
+ ** This is the sequence observed in the structure. See seqReadPdbnucseq
+! ** for parsing the SEQRES records which give the original sequence.
+ **
+ ** @param [w] thys [AjPSeq] Sequence object
+ ** @param [u] seqin [AjPSeqin] Sequence input object
+***************
+*** 9670,9676 ****
+ ** continue lines for OS
+ **
+ ** New line types:
+! ** OH organism host: list of taxids
+ **
+ ** CC line blocks -!- TOPIC:
+ ** can do this by parsing the stored comment block
+--- 9670,9676 ----
+ ** continue lines for OS
+ **
+ ** New line types:
+! ** OH organism host: list of tax ids
+ **
+ ** CC line blocks -!- TOPIC:
+ ** can do this by parsing the stored comment block
+***************
+*** 10979,10985 ****
+ ajStrAppendC(&cmtstr, "\n");
+ ajStrAppendS(&cmtstr, token);
+
+! /* trying to keep commments in one long string with embedded returns
+ ** probably fails for long comments - and also fails for contact details
+ ** which have very short comment lines
+ ** switch to just keeping original lines */
+--- 10979,10985 ----
+ ajStrAppendC(&cmtstr, "\n");
+ ajStrAppendS(&cmtstr, token);
+
+! /* trying to keep comments in one long string with embedded returns
+ ** probably fails for long comments - and also fails for contact details
+ ** which have very short comment lines
+ ** switch to just keeping original lines */
+***************
+*** 12648,12677 ****
+ {
+ switch(++i)
+ {
+! case 1:
+ break;
+! case 2:
+ seqSetName(thys, token);
+ break;
+! case 3:
+ ajStrToUint(token, &seqlen);
+ break;
+! case 4:
+ if(!ajStrMatchC(token, "aa"))
+ ajWarn("bad RefseqP LOCUS line '%S'", seqReadLine);
+ break;
+ case 5:
+- ajSeqmolSetGb(&thys->Molecule, token);
+- break;
+- case 6:
+- if(ajStrMatchC(token, "circular"))
+- thys->Circular = ajTrue;
+- break;
+- case 7:
+ ajSeqdivSetGb(&thys->Division, token);
+ ajSeqclsSetGb(&thys->Class, token);
+ break;
+! case 8:
+ if(!thys->Date)
+ thys->Date = ajSeqdateNew();
+ ajSeqdateSetModifyS(thys->Date, token);
+--- 12648,12670 ----
+ {
+ switch(++i)
+ {
+! case 1: /* 'LOCUS' */
+ break;
+! case 2: /* locus name */
+ seqSetName(thys, token);
+ break;
+! case 3: /* length */
+ ajStrToUint(token, &seqlen);
+ break;
+! case 4: /* 'aa' */
+ if(!ajStrMatchC(token, "aa"))
+ ajWarn("bad RefseqP LOCUS line '%S'", seqReadLine);
+ break;
+ case 5:
+ ajSeqdivSetGb(&thys->Division, token);
+ ajSeqclsSetGb(&thys->Class, token);
+ break;
+! case 6:
+ if(!thys->Date)
+ thys->Date = ajSeqdateNew();
+ ajSeqdateSetModifyS(thys->Date, token);
+***************
+*** 12806,12812 ****
+
+ while (ajStrTokenNextParse(&handle, &token))
+ {
+! if(ajStrMatchC(token, "(bases"))
+ continue;
+
+ if(ajStrMatchC(token, "to"))
+--- 12799,12805 ----
+
+ while (ajStrTokenNextParse(&handle, &token))
+ {
+! if(ajStrMatchC(token, "(residues"))
+ continue;
+
+ if(ajStrMatchC(token, "to"))
+***************
+*** 13684,13690 ****
+ ** Looks for the specified format(s) in the internal definitions and
+ ** returns the index.
+ **
+! ** Sets iformat as the recognized format, and returns ajTrue.
+ **
+ ** @param [r] format [const AjPStr] Format required.
+ ** @param [w] iformat [ajint*] Index
+--- 13677,13683 ----
+ ** Looks for the specified format(s) in the internal definitions and
+ ** returns the index.
+ **
+! ** Sets iformat as the recognised format, and returns ajTrue.
+ **
+ ** @param [r] format [const AjPStr] Format required.
+ ** @param [w] iformat [ajint*] Index
+***************
+*** 14008,14027 ****
+ ** Non sequence characters are reported in the return value
+ ** if EMBOSS_SEQWARN is set
+ **
+! ** @param [u] pqual [AjPStr*] Quality values as a string
+ ** @param [r] line [const AjPStr] Input line.
+ ** @return [void]
+ ** @@
+ ******************************************************************************/
+
+! static void seqqualAppendWarn(AjPStr* pqual, const AjPStr line)
+ {
+ AjPStr tmpstr = NULL;
+
+ ajStrAssignS(&tmpstr, line);
+
+ ajStrKeepSetAscii(&tmpstr, 33, 126);
+! ajStrAppendS(pqual, tmpstr);
+
+ ajStrDel(&tmpstr);
+
+--- 14001,14020 ----
+ ** Non sequence characters are reported in the return value
+ ** if EMBOSS_SEQWARN is set
+ **
+! ** @param [u] Pqual [AjPStr*] Quality values as a string
+ ** @param [r] line [const AjPStr] Input line.
+ ** @return [void]
+ ** @@
+ ******************************************************************************/
+
+! static void seqqualAppendWarn(AjPStr* Pqual, const AjPStr line)
+ {
+ AjPStr tmpstr = NULL;
+
+ ajStrAssignS(&tmpstr, line);
+
+ ajStrKeepSetAscii(&tmpstr, 33, 126);
+! ajStrAppendS(Pqual, tmpstr);
+
+ ajStrDel(&tmpstr);
+
+***************
+*** 14088,14094 ****
+ **
+ ** @param [u] thys [AjPSeq] Sequence.
+ ** @param [r] seqin [const AjPSeqin] Sequence input.
+! ** @param [u] pline [AjPStr*] Input buffer.
+ ** @param [r] maxlines [ajuint] Maximum number of lines to read
+ ** before giving up
+ ** @param [w] len [ajuint*] Length of sequence read.
+--- 14081,14087 ----
+ **
+ ** @param [u] thys [AjPSeq] Sequence.
+ ** @param [r] seqin [const AjPSeqin] Sequence input.
+! ** @param [u] Pline [AjPStr*] Input buffer.
+ ** @param [r] maxlines [ajuint] Maximum number of lines to read
+ ** before giving up
+ ** @param [w] len [ajuint*] Length of sequence read.
+***************
+*** 14097,14103 ****
+ ******************************************************************************/
+
+ static AjBool seqGcgDots(AjPSeq thys, const AjPSeqin seqin,
+! AjPStr* pline,
+ ajuint maxlines, ajuint* len)
+ {
+ AjPStr token = NULL;
+--- 14090,14096 ----
+ ******************************************************************************/
+
+ static AjBool seqGcgDots(AjPSeq thys, const AjPSeqin seqin,
+! AjPStr* Pline,
+ ajuint maxlines, ajuint* len)
+ {
+ AjPStr token = NULL;
+***************
+*** 14113,14134 ****
+ while(nlines < maxlines)
+ {
+ if(nlines++)
+! if(!ajBuffreadLineStore(buff, pline,
+ seqin->Text, &thys->TextPtr))
+ return ajFalse;
+
+ if(nlines > maxlines)
+ return ajFalse;
+
+! if(!ajRegExec(seqRegGcgDot, *pline))
+ continue;
+
+! ajDebug("seqGcgDots .. found\n'%S'\n", *pline);
+
+! if(!ajRegExec(seqRegGcgChk, *pline)) /* checksum required */
+ return ajFalse;
+
+! if(ajRegExec(seqRegGcgMsf, *pline)) /* oops - it's an MSF file */
+ return ajFalse;
+
+ ajRegSubI(seqRegGcgChk, 1, &token);
+--- 14106,14127 ----
+ while(nlines < maxlines)
+ {
+ if(nlines++)
+! if(!ajBuffreadLineStore(buff, Pline,
+ seqin->Text, &thys->TextPtr))
+ return ajFalse;
+
+ if(nlines > maxlines)
+ return ajFalse;
+
+! if(!ajRegExec(seqRegGcgDot, *Pline))
+ continue;
+
+! ajDebug("seqGcgDots .. found\n'%S'\n", *Pline);
+
+! if(!ajRegExec(seqRegGcgChk, *Pline)) /* checksum required */
+ return ajFalse;
+
+! if(ajRegExec(seqRegGcgMsf, *Pline)) /* oops - it's an MSF file */
+ return ajFalse;
+
+ ajRegSubI(seqRegGcgChk, 1, &token);
+***************
+*** 14136,14155 ****
+
+ ajDebug(" checksum %d\n", check);
+
+! if(ajRegExec(seqRegGcgLen, *pline))
+ {
+ ajRegSubI(seqRegGcgLen, 1, &token);
+ ajStrToUint(token, len);
+ ajDebug(" length %d\n", *len);
+ }
+
+! if(ajRegExec(seqRegGcgNam, *pline))
+ {
+ ajRegSubI(seqRegGcgNam, 0, &thys->Name);
+ ajDebug(" name '%S'\n", thys->Name);
+ }
+
+! if(ajRegExec(seqRegGcgTyp, *pline))
+ {
+ ajRegSubI(seqRegGcgTyp, 1, &thys->Type);
+ ajDebug(" type '%S'\n", thys->Type);
+--- 14129,14148 ----
+
+ ajDebug(" checksum %d\n", check);
+
+! if(ajRegExec(seqRegGcgLen, *Pline))
+ {
+ ajRegSubI(seqRegGcgLen, 1, &token);
+ ajStrToUint(token, len);
+ ajDebug(" length %d\n", *len);
+ }
+
+! if(ajRegExec(seqRegGcgNam, *Pline))
+ {
+ ajRegSubI(seqRegGcgNam, 0, &thys->Name);
+ ajDebug(" name '%S'\n", thys->Name);
+ }
+
+! if(ajRegExec(seqRegGcgTyp, *Pline))
+ {
+ ajRegSubI(seqRegGcgTyp, 1, &thys->Type);
+ ajDebug(" type '%S'\n", thys->Type);
+***************
+*** 14180,14186 ****
+ **
+ ** @param [u] thys [AjPSeq] Sequence.
+ ** @param [r] seqin [const AjPSeqin] Sequence input.
+! ** @param [u] pline [AjPStr*] Input buffer.
+ ** @param [r] maxlines [ajuint] Maximum number of lines to read
+ ** before giving up
+ ** @param [w] len [ajuint*] Length of sequence read.
+--- 14173,14179 ----
+ **
+ ** @param [u] thys [AjPSeq] Sequence.
+ ** @param [r] seqin [const AjPSeqin] Sequence input.
+! ** @param [u] Pline [AjPStr*] Input buffer.
+ ** @param [r] maxlines [ajuint] Maximum number of lines to read
+ ** before giving up
+ ** @param [w] len [ajuint*] Length of sequence read.
+***************
+*** 14188,14194 ****
+ ** @@
+ ******************************************************************************/
+
+! static AjBool seqGcgMsfDots(AjPSeq thys, const AjPSeqin seqin, AjPStr* pline,
+ ajuint maxlines, ajuint* len)
+ {
+ AjPStr token = NULL;
+--- 14181,14187 ----
+ ** @@
+ ******************************************************************************/
+
+! static AjBool seqGcgMsfDots(AjPSeq thys, const AjPSeqin seqin, AjPStr* Pline,
+ ajuint maxlines, ajuint* len)
+ {
+ AjPStr token = NULL;
+***************
+*** 14199,14229 ****
+
+ buff = seqin->Filebuff;
+
+! ajDebug("seqGcgMsfDots maxlines: %d\nline: '%S'\n", maxlines,*pline);
+
+ seqGcgRegInit();
+
+ while(nlines < maxlines)
+ {
+ if(nlines++)
+! if(!ajBuffreadLineStore(buff, pline,
+ seqin->Text, &thys->TextPtr))
+ return ajFalse;
+
+! ajDebug("testing line %d\n'%S'\n", nlines,*pline);
+
+ if(nlines > maxlines)
+ return ajFalse;
+
+! if(!ajRegExec(seqRegGcgDot, *pline))
+ continue;
+
+ /* dots found. This must be the line if this is MSF format */
+
+! if(!ajRegExec(seqRegGcgChk, *pline)) /* check: is required */
+ return ajFalse;
+
+! if(!ajRegExec(seqRegGcgMsf, *pline)) /* MSF: len required for GCG*/
+ return ajFalse;
+
+
+--- 14192,14222 ----
+
+ buff = seqin->Filebuff;
+
+! ajDebug("seqGcgMsfDots maxlines: %d\nline: '%S'\n", maxlines,*Pline);
+
+ seqGcgRegInit();
+
+ while(nlines < maxlines)
+ {
+ if(nlines++)
+! if(!ajBuffreadLineStore(buff, Pline,
+ seqin->Text, &thys->TextPtr))
+ return ajFalse;
+
+! ajDebug("testing line %d\n'%S'\n", nlines,*Pline);
+
+ if(nlines > maxlines)
+ return ajFalse;
+
+! if(!ajRegExec(seqRegGcgDot, *Pline))
+ continue;
+
+ /* dots found. This must be the line if this is MSF format */
+
+! if(!ajRegExec(seqRegGcgChk, *Pline)) /* check: is required */
+ return ajFalse;
+
+! if(!ajRegExec(seqRegGcgMsf, *Pline)) /* MSF: len required for GCG*/
+ return ajFalse;
+
+
+***************
+*** 14233,14242 ****
+ ajRegSubI(seqRegGcgChk, 1, &token);
+ ajStrToUint(token, &check);
+
+! if(ajRegExec(seqRegGcgNam, *pline))
+ ajRegSubI(seqRegGcgNam, 0, &thys->Name);
+
+! if(ajRegExec(seqRegGcgTyp, *pline))
+ ajRegSubI(seqRegGcgTyp, 1, &thys->Type);
+
+ ajStrDel(&token);
+--- 14226,14235 ----
+ ajRegSubI(seqRegGcgChk, 1, &token);
+ ajStrToUint(token, &check);
+
+! if(ajRegExec(seqRegGcgNam, *Pline))
+ ajRegSubI(seqRegGcgNam, 0, &thys->Name);
+
+! if(ajRegExec(seqRegGcgTyp, *Pline))
+ ajRegSubI(seqRegGcgTyp, 1, &thys->Type);
+
+ ajStrDel(&token);
+***************
+*** 14256,14272 ****
+ **
+ ** Parses data from a line of an MSF file header. The header stores
+ ** names and other data for all sequences in the file. Each file
+! ** is definied on a separate line. The results are stored
+ ** in the MSF internal table. The sequence data is read later in the
+ ** input file and added to the table.
+ **
+ ** @param [r] line [const AjPStr] Input line.
+! ** @param [u] pmsfitem [SeqPMsfItem*] MSF internal table item.
+ ** @return [AjBool] ajTrue on success.
+ ** @@
+ ******************************************************************************/
+
+! static AjBool seqGcgMsfHeader(const AjPStr line, SeqPMsfItem* pmsfitem)
+ {
+ AjPStr name = NULL; /* NOTE: not static. New each time for list */
+ AjPStr token = NULL;
+--- 14249,14265 ----
+ **
+ ** Parses data from a line of an MSF file header. The header stores
+ ** names and other data for all sequences in the file. Each file
+! ** is defined on a separate line. The results are stored
+ ** in the MSF internal table. The sequence data is read later in the
+ ** input file and added to the table.
+ **
+ ** @param [r] line [const AjPStr] Input line.
+! ** @param [u] Pmsfitem [SeqPMsfItem*] MSF internal table item.
+ ** @return [AjBool] ajTrue on success.
+ ** @@
+ ******************************************************************************/
+
+! static AjBool seqGcgMsfHeader(const AjPStr line, SeqPMsfItem* Pmsfitem)
+ {
+ AjPStr name = NULL; /* NOTE: not static. New each time for list */
+ AjPStr token = NULL;
+***************
+*** 14285,14291 ****
+
+ /*ajDebug("Check found\n");*/
+
+! *pmsfitem = AJNEW0(msfitem);
+ msfitem->Name = name;
+
+ ajRegSubI(seqRegGcgChk, 1, &token);
+--- 14278,14284 ----
+
+ /*ajDebug("Check found\n");*/
+
+! *Pmsfitem = AJNEW0(msfitem);
+ msfitem->Name = name;
+
+ ajRegSubI(seqRegGcgChk, 1, &token);
+***************
+*** 15072,15078 ****
+ {
+ ajStrTokenAssignC(&handle, seqReadLine, " \t\n\r");
+ ajStrTokenNextParse(&handle, &token);
+! /* ajDebug("Line '%S'\ntoken '%S'\n", seqReadLine, token); */
+
+ if(ajStrGetLen(token))
+ {
+--- 15065,15072 ----
+ {
+ ajStrTokenAssignC(&handle, seqReadLine, " \t\n\r");
+ ajStrTokenNextParse(&handle, &token);
+! /* ajDebug("Line '%S'\n");*/
+! /* ajDebug("token '%S'\n", seqReadLine, token); */
+
+ if(ajStrGetLen(token))
+ {
+***************
+*** 15323,15329 ****
+
+ /* @funcstatic seqnameSetName *************************************************
+ **
+! ** Sets the name usable by a seuqnece object by applying simple conversion
+ ** rules to the input which could be, for example, the name from a
+ ** FASTA format file.
+ **
+--- 15317,15323 ----
+
+ /* @funcstatic seqnameSetName *************************************************
+ **
+! ** Sets the name usable by a sequence object by applying simple conversion
+ ** rules to the input which could be, for example, the name from a
+ ** FASTA format file.
+ **
+***************
+*** 15568,15574 ****
+ **
+ ** All constructors return a new sequence query object by pointer. It
+ ** is the responsibility of the user to first destroy any previous
+! ** sequenceoutput object. The target pointer does not need to be
+ ** initialised to NULL, but it is good programming practice to do so
+ ** anyway.
+ **
+--- 15562,15568 ----
+ **
+ ** All constructors return a new sequence query object by pointer. It
+ ** is the responsibility of the user to first destroy any previous
+! ** sequence output object. The target pointer does not need to be
+ ** initialised to NULL, but it is good programming practice to do so
+ ** anyway.
+ **
+***************
+*** 16195,16201 ****
+
+ /* @funcstatic seqQryWildComp *************************************************
+ **
+! ** Compiles the reqular expressions for testing wild cards in queries.
+ ** These are held in static storage and built once only if needed.
+ **
+ ** @return [void]
+--- 16189,16195 ----
+
+ /* @funcstatic seqQryWildComp *************************************************
+ **
+! ** Compiles the regular expressions for testing wild cards in queries.
+ ** These are held in static storage and built once only if needed.
+ **
+ ** @return [void]
+***************
+*** 16622,16628 ****
+ }
+
+ /* works for NCBI formatdb reformatted blast databases
+! ** still checking for any misformatted databases elsewhere */
+
+ if(!strcmp(q,"bbs") || !strcmp(q,"lcl"))
+ {
+--- 16616,16622 ----
+ }
+
+ /* works for NCBI formatdb reformatted blast databases
+! ** still checking for any mis-formatted databases elsewhere */
+
+ if(!strcmp(q,"bbs") || !strcmp(q,"lcl"))
+ {
+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
+***************
+*** 341,347 ****
+ AJFALSE, AJFALSE, AJFALSE, AJTRUE, AJFALSE,
+ AJTRUE, AJTRUE, AJFALSE, seqWriteRefseq},
+ {"refseqp", "Refseqp entry format",
+! AJFALSE, AJFALSE, AJFALSE, AJTRUE, AJFALSE,
+ AJTRUE, AJTRUE, AJFALSE, seqWriteRefseqp},
+ {"gff2", "GFF2 feature file with sequence in the header",
+ AJFALSE, AJFALSE, AJFALSE, AJTRUE, AJTRUE,
+--- 341,347 ----
+ AJFALSE, AJFALSE, AJFALSE, AJTRUE, AJFALSE,
+ AJTRUE, AJTRUE, AJFALSE, seqWriteRefseq},
+ {"refseqp", "Refseqp entry format",
+! AJFALSE, AJFALSE, AJFALSE, AJFALSE, AJTRUE,
+ AJTRUE, AJTRUE, AJFALSE, seqWriteRefseqp},
+ {"gff2", "GFF2 feature file with sequence in the header",
+ AJFALSE, AJFALSE, AJFALSE, AJTRUE, AJTRUE,
+***************
+*** 382,388 ****
+ {"fitch", "Fitch program format",
+ AJFALSE, AJFALSE, AJFALSE, AJTRUE, AJTRUE,
+ AJFALSE, AJTRUE, AJFALSE, seqWriteFitch},
+! {"msf", "GCG MSF (mutiple sequence file) file format",
+ AJFALSE, AJFALSE, AJTRUE, AJTRUE, AJTRUE,
+ AJFALSE, AJTRUE, AJFALSE, seqWriteMsf},
+ {"clustal", "Clustalw multiple alignment format",
+--- 382,388 ----
+ {"fitch", "Fitch program format",
+ AJFALSE, AJFALSE, AJFALSE, AJTRUE, AJTRUE,
+ AJFALSE, AJTRUE, AJFALSE, seqWriteFitch},
+! {"msf", "GCG MSF (multiple sequence file) file format",
+ AJFALSE, AJFALSE, AJTRUE, AJTRUE, AJTRUE,
+ AJFALSE, AJTRUE, AJFALSE, seqWriteMsf},
+ {"clustal", "Clustalw multiple alignment format",
+***************
+*** 489,495 ****
+ **
+ ** All constructors return a new sequence output object by pointer. It
+ ** is the responsibility of the user to first destroy any previous
+! ** sequenceoutput object. The target pointer does not need to be
+ ** initialised to NULL, but it is good programming practice to do so
+ ** anyway.
+ **
+--- 489,495 ----
+ **
+ ** All constructors return a new sequence output object by pointer. It
+ ** is the responsibility of the user to first destroy any previous
+! ** sequence output object. The target pointer does not need to be
+ ** initialised to NULL, but it is good programming practice to do so
+ ** anyway.
+ **
+***************
+*** 592,598 ****
+
+ /* @func ajSeqoutNewFile ******************************************************
+ **
+! ** Creates a new sequence output object using a preopened file.
+ **
+ ** @param [u] file [AjPFile] Open file object
+ ** @return [AjPSeqout] New sequence output object.
+--- 592,598 ----
+
+ /* @func ajSeqoutNewFile ******************************************************
+ **
+! ** Creates a new sequence output object using a pre-opened file.
+ **
+ ** @param [u] file [AjPFile] Open file object
+ ** @return [AjPSeqout] New sequence output object.
+***************
+*** 2154,2160 ****
+ return;
+
+ itest = ajListToarray(outseq->Savelist, (void***) &seqs);
+! ajDebug("ajListToArray listed %d items\n", itest);
+ seqarr = (AjPSeq*) seqs;
+
+ for(i=0; i < isize; i++)
+--- 2154,2160 ----
+ return;
+
+ itest = ajListToarray(outseq->Savelist, (void***) &seqs);
+! ajDebug("ajListToarray listed %d items\n", itest);
+ seqarr = (AjPSeq*) seqs;
+
+ for(i=0; i < isize; i++)
+***************
+*** 2265,2271 ****
+ /* test for group description only when writing 2+ sequences (a set) */
+
+ itest = ajListToarray(outseq->Savelist, (void***) &seqs);
+! ajDebug("ajListToArray listed %u items\n", itest);
+ seqarr = (AjPSeq*) seqs;
+
+ seqfirst = seqarr[0];
+--- 2265,2271 ----
+ /* test for group description only when writing 2+ sequences (a set) */
+
+ itest = ajListToarray(outseq->Savelist, (void***) &seqs);
+! ajDebug("ajListToarray listed %u items\n", itest);
+ seqarr = (AjPSeq*) seqs;
+
+ seqfirst = seqarr[0];
+***************
+*** 2433,2439 ****
+ return;
+
+ itest = ajListToarray(outseq->Savelist, (void***) &seqs);
+! ajDebug("ajListToArray listed %d items\n", itest);
+ seqarr = (AjPSeq*) seqs;
+
+ seqfirst = seqarr[0];
+--- 2433,2439 ----
+ return;
+
+ itest = ajListToarray(outseq->Savelist, (void***) &seqs);
+! ajDebug("ajListToarray listed %d items\n", itest);
+ seqarr = (AjPSeq*) seqs;
+
+ seqfirst = seqarr[0];
+***************
+*** 2584,2590 ****
+ return;
+
+ itest = ajListToarray(outseq->Savelist, (void***) &seqs);
+! ajDebug("ajListToArray listed %d items\n", itest);
+ seqarr = (AjPSeq*) seqs;
+
+ for(i=0; i < isize; i++)
+--- 2584,2590 ----
+ return;
+
+ itest = ajListToarray(outseq->Savelist, (void***) &seqs);
+! ajDebug("ajListToarray listed %d items\n", itest);
+ seqarr = (AjPSeq*) seqs;
+
+ for(i=0; i < isize; i++)
+***************
+*** 2692,2698 ****
+ return;
+
+ itest = ajListToarray(outseq->Savelist, (void***) &seqs);
+! ajDebug("ajListToArray listed %d items\n", itest);
+ seqarr = (AjPSeq*) seqs;
+
+ for(i=0; i < isize; i++)
+--- 2692,2698 ----
+ return;
+
+ itest = ajListToarray(outseq->Savelist, (void***) &seqs);
+! ajDebug("ajListToarray listed %d items\n", itest);
+ seqarr = (AjPSeq*) seqs;
+
+ for(i=0; i < isize; i++)
+***************
+*** 2788,2794 ****
+ return;
+
+ itest = ajListToarray(outseq->Savelist, (void***) &seqs);
+! ajDebug("ajListToArray listed %d items\n", itest);
+ seqarr = (AjPSeq*) seqs;
+
+ for(i=0; i < isize; i++)
+--- 2788,2794 ----
+ return;
+
+ itest = ajListToarray(outseq->Savelist, (void***) &seqs);
+! ajDebug("ajListToarray listed %d items\n", itest);
+ seqarr = (AjPSeq*) seqs;
+
+ for(i=0; i < isize; i++)
+***************
+*** 2866,2872 ****
+ return;
+
+ itest = ajListToarray(outseq->Savelist, (void***) &seqs);
+! ajDebug("ajListToArray listed %d items\n", itest);
+ seqarr = (AjPSeq*) seqs;
+
+ for(i=0; i < isize; i++)
+--- 2866,2872 ----
+ return;
+
+ itest = ajListToarray(outseq->Savelist, (void***) &seqs);
+! ajDebug("ajListToarray listed %d items\n", itest);
+ seqarr = (AjPSeq*) seqs;
+
+ for(i=0; i < isize; i++)
+***************
+*** 2947,2953 ****
+ return;
+
+ itest = ajListToarray(outseq->Savelist, (void***) &seqs);
+! ajDebug("ajListToArray listed %d items\n", itest);
+ seqarr = (AjPSeq*) seqs;
+
+ for(i=0; i < isize; i++)
+--- 2947,2953 ----
+ return;
+
+ itest = ajListToarray(outseq->Savelist, (void***) &seqs);
+! ajDebug("ajListToarray listed %d items\n", itest);
+ seqarr = (AjPSeq*) seqs;
+
+ for(i=0; i < isize; i++)
+***************
+*** 3014,3020 ****
+ return;
+
+ itest = ajListToarray(outseq->Savelist, (void***) &seqs);
+! ajDebug("ajListToArray listed %d items\n", itest);
+ seqarr = (AjPSeq*) seqs;
+
+ for(i=0; i < isize; i++)
+--- 3014,3020 ----
+ return;
+
+ itest = ajListToarray(outseq->Savelist, (void***) &seqs);
+! ajDebug("ajListToarray listed %d items\n", itest);
+ seqarr = (AjPSeq*) seqs;
+
+ for(i=0; i < isize; i++)
+***************
+*** 3123,3129 ****
+ return;
+
+ test = ajListToarray(outseq->Savelist, (void***) &seqs);
+! ajDebug("ajListToArray listed %d items\n", test);
+
+
+
+--- 3123,3129 ----
+ return;
+
+ test = ajListToarray(outseq->Savelist, (void***) &seqs);
+! ajDebug("ajListToarray listed %d items\n", test);
+
+
+
+***************
+*** 3244,3250 ****
+ {
+ p = ajStrGetPtr(seqs[0]->Selexdata->rf);
+ if(i+50>=len)
+! ajFmtPrintF(outseq->File,"%S %s\n",rfstr,&p[i]);
+ else
+ ajFmtPrintF(outseq->File,"%S %-50.50s\n",rfstr,
+ &p[i]);
+--- 3244,3250 ----
+ {
+ p = ajStrGetPtr(seqs[0]->Selexdata->rf);
+ if(i+50>=len)
+! ajFmtPrintF(outseq->File,"%S %s\n",rfstr, &p[i]);
+ else
+ ajFmtPrintF(outseq->File,"%S %-50.50s\n",rfstr,
+ &p[i]);
+***************
+*** 3413,3419 ****
+
+ itest = ajListToarray(outseq->Savelist, (void***) &seqs);
+
+! ajDebug("ajListToArray listed %d items\n", itest);
+ seqarr = (AjPSeq*) seqs;
+ maxnamelen = 10;
+
+--- 3413,3419 ----
+
+ itest = ajListToarray(outseq->Savelist, (void***) &seqs);
+
+! ajDebug("ajListToarray listed %d items\n", itest);
+ seqarr = (AjPSeq*) seqs;
+ maxnamelen = 10;
+
+***************
+*** 6332,6338 ****
+
+ static SeqPSeqFormat sf = NULL;
+ /*ajuint b[5];*/ /* was used for BASE COUNT line */
+- AjPStr ftfmt = NULL;
+ AjPStr tmpstr = NULL;
+ AjPStr tmpstr2 = NULL;
+ const AjPStr tmpline = NULL;
+--- 6332,6337 ----
+***************
+*** 6341,6362 ****
+ AjPStr cur;
+ ajuint ilen;
+
+- if(!ftfmt)
+- ajStrAssignC(&ftfmt, "refseqp");
+-
+ ajSeqoutTrace(outseq);
+
+! ajFmtPrintF(outseq->File, "LOCUS %-17S %10u bp ",
+ outseq->Name, ajStrGetLen(outseq->Seq));
+
+- ajFmtPrintF(outseq->File, " %-7s",
+- ajSeqmolGetGb(outseq->Molecule));
+-
+- if(outseq->Circular)
+- ajFmtPrintF(outseq->File, " %-8s", "circular");
+- else
+- ajFmtPrintF(outseq->File, " %-8s", "linear");
+-
+ if(ajStrGetLen(outseq->Division))
+ ajFmtPrintF(outseq->File, " %-3s",ajSeqdivGetGb(outseq->Division));
+ else
+--- 6340,6350 ----
+ AjPStr cur;
+ ajuint ilen;
+
+ ajSeqoutTrace(outseq);
+
+! ajFmtPrintF(outseq->File, "LOCUS %-9S %7u aa ",
+ outseq->Name, ajStrGetLen(outseq->Seq));
+
+ if(ajStrGetLen(outseq->Division))
+ ajFmtPrintF(outseq->File, " %-3s",ajSeqdivGetGb(outseq->Division));
+ else
+***************
+*** 6365,6376 ****
+ if(outseq->Date)
+ {
+ if(outseq->Date->ModDate)
+! ajFmtPrintF(outseq->File, " %D", outseq->Date->ModDate);
+ else if(outseq->Date->CreDate)
+! ajFmtPrintF(outseq->File, " %D", outseq->Date->CreDate);
+ }
+ else
+! ajFmtPrintF(outseq->File, " %D", ajTimeRefTodayFmt("dtline"));
+
+ ajWritebinNewline(outseq->File);
+
+--- 6353,6364 ----
+ if(outseq->Date)
+ {
+ if(outseq->Date->ModDate)
+! ajFmtPrintF(outseq->File, " %D", outseq->Date->ModDate);
+ else if(outseq->Date->CreDate)
+! ajFmtPrintF(outseq->File, " %D", outseq->Date->CreDate);
+ }
+ else
+! ajFmtPrintF(outseq->File, " %D", ajTimeRefTodayFmt("dtline"));
+
+ ajWritebinNewline(outseq->File);
+
+***************
+*** 6517,6523 ****
+ {
+ ajStrAssignS(&tmpstr, seqref->Position);
+ ajStrExchangeCC(&tmpstr, "-", " to ");
+! ajFmtPrintF(outseq->File, " (bases %S)", tmpstr);
+ }
+
+ ajWritebinNewline(outseq->File);
+--- 6505,6511 ----
+ {
+ ajStrAssignS(&tmpstr, seqref->Position);
+ ajStrExchangeCC(&tmpstr, "-", " to ");
+! ajFmtPrintF(outseq->File, " (residues %S)", tmpstr);
+ }
+
+ ajWritebinNewline(outseq->File);
+***************
+*** 6594,6600 ****
+ if(seqoutUfoLocal(outseq))
+ {
+ ajFeattabOutDel(&outseq->Ftquery);
+! outseq->Ftquery = ajFeattabOutNewSSF(ftfmt, outseq->Name,
+ ajStrGetPtr(outseq->Type),
+ outseq->File);
+ if(!ajFeattableWrite(outseq->Ftquery, outseq->Fttable))
+--- 6582,6588 ----
+ if(seqoutUfoLocal(outseq))
+ {
+ ajFeattabOutDel(&outseq->Ftquery);
+! outseq->Ftquery = ajFeattabOutNewCSF("refseqp", outseq->Name,
+ ajStrGetPtr(outseq->Type),
+ outseq->File);
+ if(!ajFeattableWrite(outseq->Ftquery, outseq->Fttable))
+***************
+*** 6602,6620 ****
+ outseq->Ufo);
+ }
+
+! ajFmtPrintF(outseq->File, "ORIGIN\n");
+
+ seqSeqFormat(ajStrGetLen(outseq->Seq), &sf);
+ strcpy(sf->endstr, "\n//");
+! sf->tab = 1;
+ sf->spacer = 11;
+ sf->width = 60;
+ sf->numleft = ajTrue;
+! sf->numwidth = 8;
+!
+ seqWriteSeq(outseq, sf);
+ seqFormatDel(&sf);
+- ajStrDel(&ftfmt);
+ ajStrDel(&tmpstr);
+ ajStrDel(&tmpstr2);
+
+--- 6590,6607 ----
+ outseq->Ufo);
+ }
+
+! ajFmtPrintF(outseq->File, "ORIGIN \n");
+
+ seqSeqFormat(ajStrGetLen(outseq->Seq), &sf);
+ strcpy(sf->endstr, "\n//");
+! sf->tab = 0;
+ sf->spacer = 11;
+ sf->width = 60;
+ sf->numleft = ajTrue;
+! sf->numwidth = 9;
+!
+ seqWriteSeq(outseq, sf);
+ seqFormatDel(&sf);
+ ajStrDel(&tmpstr);
+ ajStrDel(&tmpstr2);
+
+***************
+*** 6948,6954 ****
+ return;
+
+ itest = ajListToarray(outseq->Savelist, (void***) &seqs);
+! ajDebug("ajListToArray listed %d items\n", itest);
+ seqarr = (AjPSeq*) seqs;
+
+ for(i=0; i < isize; i++)
+--- 6935,6941 ----
+ return;
+
+ itest = ajListToarray(outseq->Savelist, (void***) &seqs);
+! ajDebug("ajListToarray listed %d items\n", itest);
+ seqarr = (AjPSeq*) seqs;
+
+ for(i=0; i < isize; i++)
+***************
+*** 7044,7050 ****
+ return;
+
+ itest = ajListToarray(outseq->Savelist, (void***) &seqs);
+! ajDebug("ajListToArray listed %d items\n", itest);
+ seqarr = (AjPSeq*) seqs;
+
+ for(i=0; i < isize; i++)
+--- 7031,7037 ----
+ return;
+
+ itest = ajListToarray(outseq->Savelist, (void***) &seqs);
+! ajDebug("ajListToarray listed %d items\n", itest);
+ seqarr = (AjPSeq*) seqs;
+
+ for(i=0; i < isize; i++)
+***************
+*** 7809,7815 ****
+ fputc(' ',outf);
+ }
+
+! l1++; /* don't count spaces for width*/
+
+ if(sf->numline)
+ {
+--- 7796,7802 ----
+ fputc(' ',outf);
+ }
+
+! l1++; /* don't count spaces for width */
+
+ if(sf->numline)
+ {
+***************
+*** 8353,8359 ****
+ single = ajFalse;
+
+ if(single)
+! { /* ok, but nothing to open yet */
+ ajStrAssignEmptyS(&seqout->Extension, seqout->Formatstr);
+
+ return ajTrue;
+--- 8340,8346 ----
+ single = ajFalse;
+
+ if(single)
+! { /* OK, but nothing to open yet */
+ ajStrAssignEmptyS(&seqout->Extension, seqout->Formatstr);
+
+ return ajTrue;
+***************
+*** 9052,9063 ****
+ ** Initialises sequence output formatting parameters.
+ **
+ ** @param [r] seqlen [ajint] Sequence length
+! ** @param [u] psf [SeqPSeqFormat*] Sequence format object
+ ** @return [void]
+ ** @@
+ ******************************************************************************/
+
+! static void seqSeqFormat(ajint seqlen, SeqPSeqFormat* psf)
+ {
+ char numform[20];
+ SeqPSeqFormat sf;
+--- 9039,9050 ----
+ ** Initialises sequence output formatting parameters.
+ **
+ ** @param [r] seqlen [ajint] Sequence length
+! ** @param [u] Psf [SeqPSeqFormat*] Sequence format object
+ ** @return [void]
+ ** @@
+ ******************************************************************************/
+
+! static void seqSeqFormat(ajint seqlen, SeqPSeqFormat* Psf)
+ {
+ char numform[20];
+ SeqPSeqFormat sf;
+***************
+*** 9072,9080 ****
+ sprintf(numform, "%d", seqlen);
+ ajDebug("seqSeqFormat numwidth old: %d new: %d\n", strlen(numform)+1, j);
+
+! if(!*psf)
+ {
+! sf = AJNEW0(*psf);
+ sf->namewidth = 8;
+ sf->spacer = 0;
+ sf->width = 50;
+--- 9059,9067 ----
+ sprintf(numform, "%d", seqlen);
+ ajDebug("seqSeqFormat numwidth old: %d new: %d\n", strlen(numform)+1, j);
+
+! if(!*Psf)
+ {
+! sf = AJNEW0(*Psf);
+ sf->namewidth = 8;
+ sf->spacer = 0;
+ sf->width = 50;
+***************
+*** 9097,9103 ****
+ /*sf->interline = 1;*/
+ }
+ else
+! sf = *psf;
+
+ sf->numwidth = j; /* or 8 as a reasonable minimum */
+
+--- 9084,9090 ----
+ /*sf->interline = 1;*/
+ }
+ else
+! sf = *Psf;
+
+ sf->numwidth = j; /* or 8 as a reasonable minimum */
+
+***************
+*** 9124,9130 ****
+ ** @nam3rule Get Return an element or property
+ ** @nam4rule Basecount Counts of nucleotide bases
+ ** @nam4rule Checkgcg GCG checksum
+! ** @nam4rule Filename Ouptut filename
+ **
+ ** @argrule Get seqout [const AjPSeqout] Sequence output object
+ ** @argrule Basecount bases [ajuint*] Base counts
+--- 9111,9117 ----
+ ** @nam3rule Get Return an element or property
+ ** @nam4rule Basecount Counts of nucleotide bases
+ ** @nam4rule Checkgcg GCG checksum
+! ** @nam4rule Filename Output filename
+ **
+ ** @argrule Get seqout [const AjPSeqout] Sequence output object
+ ** @argrule Basecount bases [ajuint*] Base counts
+***************
+*** 10001,10007 ****
+ **
+ ** Checks whether an output format should go to single files, rather than
+ ** all sequences being written to one file. Some formats do not work when
+! ** more than one sequence is writte to a file. Obvious examples are plain
+ ** text and GCG formats.
+ **
+ ** @param [r] format [const AjPStr] Output format required.
+--- 9988,9994 ----
+ **
+ ** Checks whether an output format should go to single files, rather than
+ ** all sequences being written to one file. Some formats do not work when
+! ** more than one sequence is written to a file. Obvious examples are plain
+ ** text and GCG formats.
+ **
+ ** @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
+***************
+*** 259,265 ****
+ ** Needed for very fussy compilers i.e. Digital C
+ **
+ ** @param [r] v [ajint] integer
+! ** @return [unsigned char] Unisigned character cast
+ ** @@
+ ******************************************************************************/
+
+--- 259,265 ----
+ ** Needed for very fussy compilers i.e. Digital C
+ **
+ ** @param [r] v [ajint] integer
+! ** @return [unsigned char] Unsigned character cast
+ ** @@
+ ******************************************************************************/
+
+***************
+*** 387,394 ****
+
+ while(1)
+ {
+ ajFmtPrintS(&sysFname,"%s%s%S",p,SLASH_STRING,sysTname);
+!
+ if(ajFilenameExistsExec(sysFname))
+ {
+ ajStrAssignS(Pfilename,sysFname);
+--- 387,398 ----
+
+ while(1)
+ {
++ #if !defined(WIN32) && !defined(__CYGWIN__)
+ ajFmtPrintS(&sysFname,"%s%s%S",p,SLASH_STRING,sysTname);
+! #else
+! ajFmtPrintS(&sysFname,"%s%s%S.exe",p,SLASH_STRING,sysTname);
+! #endif
+!
+ if(ajFilenameExistsExec(sysFname))
+ {
+ 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
+***************
+*** 302,308 ****
+ #endif
+
+ #ifdef PLD_png /* if png/gd/zlib libraries available for png driver */
+! {"png", "png", ".png", 640, 480,
+ AJTRUE, AJFALSE, AJFALSE, AJFALSE, AJFALSE, AJFALSE,
+ GraphxyDisplayToFile, GraphOpenFile,
+ "PNG graphics files"},
+--- 302,308 ----
+ #endif
+
+ #ifdef PLD_png /* if png/gd/zlib libraries available for png driver */
+! {"png", "png", ".png", 800, 600,
+ AJTRUE, AJFALSE, AJFALSE, AJFALSE, AJFALSE, AJFALSE,
+ GraphxyDisplayToFile, GraphOpenFile,
+ "PNG graphics files"},
+***************
+*** 843,849 ****
+ **
+ ** Set internal graph device to that selected for a graph object
+ **
+! ** @param [r] graph [const AjPGraph] Graph object with displaytype set
+ **
+ ** @return [void]
+ ** @@
+--- 843,849 ----
+ **
+ ** Set internal graph device to that selected for a graph object
+ **
+! ** @param [r] graph [const AjPGraph] Graph object with display type set
+ **
+ ** @return [void]
+ ** @@
+***************
+*** 891,897 ****
+ col = colour;
+
+ /* in case of looping through colours */
+! /* start at the begining once past end */
+ while(col > MAXCOL)
+ col -= (MAXCOL+1);
+
+--- 891,897 ----
+ col = colour;
+
+ /* in case of looping through colours */
+! /* start at the beginning once past end */
+ while(col > MAXCOL)
+ col -= (MAXCOL+1);
+
+***************
+*** 1117,1123 ****
+ fold = ajGraphicsSetCharscale(0.0);
+ ajGraphicsSetCharscale(fold/(float)2.0);
+
+! ajDebug("=g= plmtex('t', 1.5, 0.5, 0.5, '%S') [subtitle]\n", strsubtitle);
+ plmtex("t", (PLFLT) 1.5, (PLFLT) 0.5, (PLFLT) 0.5,
+ MAJSTRGETPTR(strsubtitle));
+
+--- 1117,1124 ----
+ fold = ajGraphicsSetCharscale(0.0);
+ ajGraphicsSetCharscale(fold/(float)2.0);
+
+! ajDebug("=g= plmtex('t', 1.5, 0.5, 0.5, '%s') [subtitle]\n",
+! MAJSTRGETPTR(strsubtitle));
+ plmtex("t", (PLFLT) 1.5, (PLFLT) 0.5, (PLFLT) 0.5,
+ MAJSTRGETPTR(strsubtitle));
+
+***************
+*** 1568,1574 ****
+
+ /* @func ajGraphicsBasecolourNewNuc ********************************************
+ **
+! ** Initialize a base colours array for a string of nucleotide
+ ** sequence characters
+ **
+ ** @param [r] codes [const AjPStr] Residue codes for each numbered position
+--- 1569,1575 ----
+
+ /* @func ajGraphicsBasecolourNewNuc ********************************************
+ **
+! ** Initialise a base colours array for a string of nucleotide
+ ** sequence characters
+ **
+ ** @param [r] codes [const AjPStr] Residue codes for each numbered position
+***************
+*** 1635,1641 ****
+ **
+ ** Initialize a base colours array for a string of protein sequence characters
+ ** according to the following colour scheme designed by Toby Gibson (EMBL
+! ** Heidelberg) to show the chemical propoerties important in sequence
+ ** and structure alignment and to be clear to those with common forms
+ ** of colour blindness.
+ **
+--- 1636,1642 ----
+ **
+ ** Initialize a base colours array for a string of protein sequence characters
+ ** according to the following colour scheme designed by Toby Gibson (EMBL
+! ** Heidelberg) to show the chemical properties important in sequence
+ ** and structure alignment and to be clear to those with common forms
+ ** of colour blindness.
+ **
+***************
+*** 2061,2068 ****
+ **
+ ** Draw a portion of a circle (an arc).
+ **
+! ** @param [r] xcentre [PLFLT] x coor for centre.
+! ** @param [r] ycentre [PLFLT] y coor for centre.
+ ** @param [r] radius [PLFLT] radius of the circle.
+ ** @param [r] startangle [PLFLT] angle of the start of the arc.
+ ** @param [r] endangle [PLFLT] angle of the end of the arc.
+--- 2062,2069 ----
+ **
+ ** Draw a portion of a circle (an arc).
+ **
+! ** @param [r] xcentre [PLFLT] x coord for centre.
+! ** @param [r] ycentre [PLFLT] y coord for centre.
+ ** @param [r] radius [PLFLT] radius of the circle.
+ ** @param [r] startangle [PLFLT] angle of the start of the arc.
+ ** @param [r] endangle [PLFLT] angle of the end of the arc.
+***************
+*** 2087,2092 ****
+--- 2088,2096 ----
+ if(endangle < startangle)
+ stopangle += 360.0;
+
++ if((stopangle-startangle)>=360.0)
++ stopangle = startangle + (float) 360.0;
++
+ x[0] = xcentre + ( radius*(float)cos(ajCvtDegToRad(startangle)) );
+ y[0] = ycentre + ( radius*(float)sin(ajCvtDegToRad(startangle)) );
+
+***************
+*** 2126,2133 ****
+ **
+ ** Draw a rectangle along a curve with the current pen colour/style.
+ **
+! ** @param [r] xcentre [PLFLT] x coor for centre.
+! ** @param [r] ycentre [PLFLT] y coor for centre.
+ ** @param [r] radius [PLFLT] radius of the circle.
+ ** @param [r] startangle [PLFLT] angle of the start of the rectangle.
+ ** @param [r] endangle [PLFLT] angle of the end of the rectangle.
+--- 2130,2137 ----
+ **
+ ** Draw a rectangle along a curve with the current pen colour/style.
+ **
+! ** @param [r] xcentre [PLFLT] x coord for centre.
+! ** @param [r] ycentre [PLFLT] y coord for centre.
+ ** @param [r] radius [PLFLT] radius of the circle.
+ ** @param [r] startangle [PLFLT] angle of the start of the rectangle.
+ ** @param [r] endangle [PLFLT] angle of the end of the rectangle.
+***************
+*** 2187,2194 ****
+ ** Draw a rectangle along a curve and fill it with the current pen
+ ** colour/style.
+ **
+! ** @param [r] xcentre [PLFLT] x coor for centre.
+! ** @param [r] ycentre [PLFLT] y coor for centre.
+ ** @param [r] radius [PLFLT] radius of the circle.
+ ** @param [r] startangle [PLFLT] angle of the start of the rectangle.
+ ** @param [r] endangle [PLFLT] angle of the end of the rectangle.
+--- 2191,2198 ----
+ ** Draw a rectangle along a curve and fill it with the current pen
+ ** colour/style.
+ **
+! ** @param [r] xcentre [PLFLT] x coord for centre.
+! ** @param [r] ycentre [PLFLT] y coord for centre.
+ ** @param [r] radius [PLFLT] radius of the circle.
+ ** @param [r] startangle [PLFLT] angle of the start of the rectangle.
+ ** @param [r] endangle [PLFLT] angle of the end of the rectangle.
+***************
+*** 2213,2218 ****
+--- 2217,2225 ----
+ if(endangle < startangle)
+ stopangle += 360.0;
+
++ if((stopangle-startangle)>=360.0)
++ stopangle = startangle + (float) 360.0;
++
+ r1Blocks = radius;
+ r2Blocks = r1Blocks+height;
+
+***************
+*** 2271,2278 ****
+ ** written character by character, forwards or backwards depending on
+ ** the angle.
+ **
+! ** @param [r] xcentre [PLFLT] x coor for centre.
+! ** @param [r] ycentre [PLFLT] y coor for centre.
+ ** @param [r] radius [PLFLT] radius of the circle.
+ ** @param [r] startangle [PLFLT] angle of the start of the arc (in deg).
+ ** @param [r] endangle [PLFLT] angle of the end of the arc (in deg).
+--- 2278,2285 ----
+ ** written character by character, forwards or backwards depending on
+ ** the angle.
+ **
+! ** @param [r] xcentre [PLFLT] x coord for centre.
+! ** @param [r] ycentre [PLFLT] y coord for centre.
+ ** @param [r] radius [PLFLT] radius of the circle.
+ ** @param [r] startangle [PLFLT] angle of the start of the arc (in deg).
+ ** @param [r] endangle [PLFLT] angle of the end of the arc (in deg).
+***************
+*** 2520,2527 ****
+ **
+ ** Draw a circle.
+ **
+! ** @param [r] x [PLFLT] x coor for centre.
+! ** @param [r] y [PLFLT] y coor for centre.
+ ** @param [r] radius [float] radius of the circle.
+ ** @return [void]
+ ** @@
+--- 2527,2534 ----
+ **
+ ** Draw a circle.
+ **
+! ** @param [r] x [PLFLT] x coord for centre.
+! ** @param [r] y [PLFLT] y coord for centre.
+ ** @param [r] radius [float] radius of the circle.
+ ** @return [void]
+ ** @@
+***************
+*** 2710,2719 ****
+ **
+ ** Draw a rectangle with the current pen colour/style.
+ **
+! ** @param [r] x [PLFLT] xx0 coor.
+! ** @param [r] y [PLFLT] yy0 coor.
+! ** @param [r] x2 [PLFLT] xx1 coor.
+! ** @param [r] y2 [PLFLT] yy1 coor.
+ ** @return [void]
+ **
+ ** @@
+--- 2717,2726 ----
+ **
+ ** Draw a rectangle with the current pen colour/style.
+ **
+! ** @param [r] x [PLFLT] xx0 coord.
+! ** @param [r] y [PLFLT] yy0 coord.
+! ** @param [r] x2 [PLFLT] xx1 coord.
+! ** @param [r] y2 [PLFLT] yy1 coord.
+ ** @return [void]
+ **
+ ** @@
+***************
+*** 2768,2777 ****
+ **
+ ** Draw a rectangle and fill it with the current pen colour/style.
+ **
+! ** @param [r] x [PLFLT] xx0 coor.
+! ** @param [r] y [PLFLT] yy0 coor.
+! ** @param [r] x2 [PLFLT] xx1 coor.
+! ** @param [r] y2 [PLFLT] yy1 coor.
+ ** @return [void]
+ **
+ ** @@
+--- 2775,2784 ----
+ **
+ ** Draw a rectangle and fill it with the current pen colour/style.
+ **
+! ** @param [r] x [PLFLT] xx0 coord.
+! ** @param [r] y [PLFLT] yy0 coord.
+! ** @param [r] x2 [PLFLT] xx1 coord.
+! ** @param [r] y2 [PLFLT] yy1 coord.
+ ** @return [void]
+ **
+ ** @@
+***************
+*** 2823,2830 ****
+ **
+ ** Draw text ending at position (xx1,yy1)
+ **
+! ** @param [r] x [PLFLT] xx1 coor.
+! ** @param [r] y [PLFLT] yy1 coor.
+ ** @param [r] txt [const char*] The text to be displayed.
+ ** @return [void]
+ **
+--- 2830,2837 ----
+ **
+ ** Draw text ending at position (xx1,yy1)
+ **
+! ** @param [r] x [PLFLT] xx1 coord.
+! ** @param [r] y [PLFLT] yy1 coord.
+ ** @param [r] txt [const char*] The text to be displayed.
+ ** @return [void]
+ **
+***************
+*** 2863,2872 ****
+ **
+ ** Draw text along a line.
+ **
+! ** @param [r] x [PLFLT] x1 coor.
+! ** @param [r] y [PLFLT] y1 coor.
+! ** @param [r] x2 [PLFLT] x2 coor.
+! ** @param [r] y2 [PLFLT] y2 coor.
+ ** @param [r] txt [const char*] The text to be displayed.
+ ** @param [r] just [PLFLT] justification of the string.
+ ** (0=left,1=right,0.5=middle etc)
+--- 2870,2879 ----
+ **
+ ** Draw text along a line.
+ **
+! ** @param [r] x [PLFLT] x1 coord.
+! ** @param [r] y [PLFLT] y1 coord.
+! ** @param [r] x2 [PLFLT] x2 coord.
+! ** @param [r] y2 [PLFLT] y2 coord.
+ ** @param [r] txt [const char*] The text to be displayed.
+ ** @param [r] just [PLFLT] justification of the string.
+ ** (0=left,1=right,0.5=middle etc)
+***************
+*** 2912,2919 ****
+ **
+ ** For graph data type, writes directly.
+ **
+! ** @param [r] x [PLFLT] xx1 coor.
+! ** @param [r] y [PLFLT] yy1 coor.
+ ** @param [r] txt [const char*] The text to be displayed.
+ ** @return [void]
+ **
+--- 2919,2926 ----
+ **
+ ** For graph data type, writes directly.
+ **
+! ** @param [r] x [PLFLT] xx1 coord.
+! ** @param [r] y [PLFLT] yy1 coord.
+ ** @param [r] txt [const char*] The text to be displayed.
+ ** @return [void]
+ **
+***************
+*** 2994,3001 ****
+ ** Draw text, positioning with respect to (xx1,yy1) by justified as
+ ** defined by just.
+ **
+! ** @param [r] x [PLFLT] xx1 coor.
+! ** @param [r] y [PLFLT] yy1 coor.
+ ** @param [r] txt [const char*] The text to be displayed.
+ ** @param [r] just [PLFLT] justification of the string.
+ ** (0=left,1=right,0.5=middle etc)
+--- 3001,3008 ----
+ ** Draw text, positioning with respect to (xx1,yy1) by justified as
+ ** defined by just.
+ **
+! ** @param [r] x [PLFLT] xx1 coord.
+! ** @param [r] y [PLFLT] yy1 coord.
+ ** @param [r] txt [const char*] The text to be displayed.
+ ** @param [r] just [PLFLT] justification of the string.
+ ** (0=left,1=right,0.5=middle etc)
+***************
+*** 3356,3369 ****
+ ** @suffix C Character data
+ ** @suffix S String object data
+ **
+! ** @argrule Charsize xx1 [PLFLT] xx1 coor.
+! ** @argrule Charsize yy1 [PLFLT] yy1 coor.
+! ** @argrule Charsize xx2 [PLFLT] xx2 coor.
+! ** @argrule Charsize yy2 [PLFLT] yy2 coor.
+ ** @argrule Charsize text [const char*] The text to be displayed.
+ ** @argrule Charsize TextHeight [PLFLT] The height of the text (in user coord).
+! ** @argrule Coord x [PLFLT] x coor for centre.
+! ** @argrule Coord y [PLFLT] y coor for centre.
+ ** @argrule Coord radius [PLFLT] Radius of the circle.
+ ** @argrule Coord angle [PLFLT] angle at which the point is.
+ ** @argrule Distance xx1 [PLFLT] x coord of point 1
+--- 3363,3376 ----
+ ** @suffix C Character data
+ ** @suffix S String object data
+ **
+! ** @argrule Charsize xx1 [PLFLT] xx1 coord.
+! ** @argrule Charsize yy1 [PLFLT] yy1 coord.
+! ** @argrule Charsize xx2 [PLFLT] xx2 coord.
+! ** @argrule Charsize yy2 [PLFLT] yy2 coord.
+ ** @argrule Charsize text [const char*] The text to be displayed.
+ ** @argrule Charsize TextHeight [PLFLT] The height of the text (in user coord).
+! ** @argrule Coord x [PLFLT] x coord for centre.
+! ** @argrule Coord y [PLFLT] y coord for centre.
+ ** @argrule Coord radius [PLFLT] Radius of the circle.
+ ** @argrule Coord angle [PLFLT] angle at which the point is.
+ ** @argrule Distance xx1 [PLFLT] x coord of point 1
+***************
+*** 3372,3378 ****
+ ** @argrule Distance yy2 [PLFLT] y coord of point 2
+ ** @argrule Range array [const float*] array
+ ** @argrule Range npoints [ajuint] Number of data points
+! ** @argrule Range min [float*] min. value ikn array
+ ** @argrule Range max [float*] max. value in array
+ ** @argrule [r] C txt [const char*] Text
+ ** @argrule [r] S str [const AjPStr] Text
+--- 3379,3385 ----
+ ** @argrule Distance yy2 [PLFLT] y coord of point 2
+ ** @argrule Range array [const float*] array
+ ** @argrule Range npoints [ajuint] Number of data points
+! ** @argrule Range min [float*] min. value in array
+ ** @argrule Range max [float*] max. value in array
+ ** @argrule [r] C txt [const char*] Text
+ ** @argrule [r] S str [const AjPStr] Text
+***************
+*** 3395,3404 ****
+ ** TextHeight. If the default size is too large, characters are
+ ** shrunk. If it is too small, characters are enlarged.
+ **
+! ** @param [r] xx1 [PLFLT] xx1 coor.
+! ** @param [r] yy1 [PLFLT] yy1 coor.
+! ** @param [r] xx2 [PLFLT] xx2 coor.
+! ** @param [r] yy2 [PLFLT] yy2 coor.
+ ** @param [r] text [const char*] The text to be displayed.
+ ** @param [r] TextHeight [PLFLT] The height of the text (in user coord).
+ ** @return [PLFLT] The character size (in mm) that fits the specified
+--- 3402,3411 ----
+ ** TextHeight. If the default size is too large, characters are
+ ** shrunk. If it is too small, characters are enlarged.
+ **
+! ** @param [r] xx1 [PLFLT] xx1 coord.
+! ** @param [r] yy1 [PLFLT] yy1 coord.
+! ** @param [r] xx2 [PLFLT] xx2 coord.
+! ** @param [r] yy2 [PLFLT] yy2 coord.
+ ** @param [r] text [const char*] The text to be displayed.
+ ** @param [r] TextHeight [PLFLT] The height of the text (in user coord).
+ ** @return [PLFLT] The character size (in mm) that fits the specified
+***************
+*** 3470,3477 ****
+ **
+ ** compute the coordinates of a point on a circle knowing the angle.
+ **
+! ** @param [r] x [PLFLT] x coor for centre.
+! ** @param [r] y [PLFLT] y coor for centre.
+ ** @param [r] radius [PLFLT] Radius of the circle.
+ ** @param [r] angle [PLFLT] angle at which the point is.
+ ** @return [PLFLT*] The x and y coordinates of the point.
+--- 3477,3484 ----
+ **
+ ** compute the coordinates of a point on a circle knowing the angle.
+ **
+! ** @param [r] x [PLFLT] x coord for centre.
+! ** @param [r] y [PLFLT] y coord for centre.
+ ** @param [r] radius [PLFLT] Radius of the circle.
+ ** @param [r] angle [PLFLT] angle at which the point is.
+ ** @return [PLFLT*] The x and y coordinates of the point.
+***************
+*** 3548,3555 ****
+ {
+ ajuint i;
+
+! *min = 64000.;
+! *max = -64000.;
+
+ for(i=0;i<npoints;++i)
+ {
+--- 3555,3562 ----
+ {
+ ajuint i;
+
+! *min = FLT_MAX;
+! *max = FLT_MIN;
+
+ for(i=0;i<npoints;++i)
+ {
+***************
+*** 3557,3562 ****
+--- 3564,3575 ----
+ *max = (*max > array[i]) ? *max : array[i];
+ }
+
++ if(*min == *max)
++ {
++ *min *= (float) 0.9;
++ *max *= (float) 1.1;
++ }
++
+ return;
+ }
+
+***************
+*** 3767,3773 ****
+ ** @fdata [AjPGraph]
+ ** @fcategory modify
+ **
+! ** @nam3rule Init Initialise a grah object
+ ** @nam4rule InitSeq Initialises using default values based on a sequence.
+ ** @nam3rule Open Open a plot
+ ** @nam3rule Newpage Start a new plot page
+--- 3780,3786 ----
+ ** @fdata [AjPGraph]
+ ** @fcategory modify
+ **
+! ** @nam3rule Init Initialise a graph object
+ ** @nam4rule InitSeq Initialises using default values based on a sequence.
+ ** @nam3rule Open Open a plot
+ ** @nam3rule Newpage Start a new plot page
+***************
+*** 6082,6089 ****
+ ** @nam4rule Yaxis Set the graph is to display a Y axis.
+ ** @nam4rule Xlabel Set whether the graph is to label the x axis.
+ ** @nam4rule Ylabel Set whether the graph is to label the y axis.
+! ** @nam4rule Xtick Set whether the graph is to tickmark the x axis.
+! ** @nam4rule Ytick Set whether the graph is to tickmark the y axis.
+ ** @nam4rule Xend Set the end position for X in the graph.
+ ** @nam4rule Yend Set the end position for Y in the graph.
+ ** @nam4rule Xgrid Whether the graph is to grid the tick marks on the x axis
+--- 6095,6102 ----
+ ** @nam4rule Yaxis Set the graph is to display a Y axis.
+ ** @nam4rule Xlabel Set whether the graph is to label the x axis.
+ ** @nam4rule Ylabel Set whether the graph is to label the y axis.
+! ** @nam4rule Xtick Set whether the graph is to tick mark the x axis.
+! ** @nam4rule Ytick Set whether the graph is to tick mark the y axis.
+ ** @nam4rule Xend Set the end position for X in the graph.
+ ** @nam4rule Yend Set the end position for Y in the graph.
+ ** @nam4rule Xgrid Whether the graph is to grid the tick marks on the x axis
+***************
+*** 7077,7083 ****
+ return;
+ }
+
+! /* @datasection [AjPGraphdata] Graph dataobject ********************************
+ **
+ ** Function is for manipulating an AjPGraphdata object
+ **
+--- 7090,7096 ----
+ return;
+ }
+
+! /* @datasection [AjPGraphdata] Graph data object ********************************
+ **
+ ** Function is for manipulating an AjPGraphdata object
+ **
+***************
+*** 7093,7099 ****
+ **
+ ** @nam3rule New Constructor
+ ** @suffix I Number of points
+! ** @argrule I numofpoints [ajuint] Nuymber of points
+ **
+ ** @valrule * [AjPGraphdata] New graphdata object
+ **
+--- 7106,7112 ----
+ **
+ ** @nam3rule New Constructor
+ ** @suffix I Number of points
+! ** @argrule I numofpoints [ajuint] Number of points
+ **
+ ** @valrule * [AjPGraphdata] New graphdata object
+ **
+***************
+*** 7772,7779 ****
+ {
+ /*
+ ** Use the whole screen. User may add boundaries by
+! ** modifying xmin, xmax et
+ */
+ GraphWind(xmin, xmax, ymin, ymax);
+ }
+
+--- 7785,7793 ----
+ {
+ /*
+ ** Use the whole screen. User may add boundaries by
+! ** modifying xmin, xmax etc.
+ */
++ plvpor (0.0,1.0,0.0,1.0);
+ GraphWind(xmin, xmax, ymin, ymax);
+ }
+
+***************
+*** 8854,8860 ****
+ void ajGraphicsListDevices (AjPList list)
+ {
+ ajint i;
+! AjPStr devname;
+
+ for(i=0;graphType[i].Name;i++)
+ {
+--- 8868,8874 ----
+ void ajGraphicsListDevices (AjPList list)
+ {
+ ajint i;
+! AjPStr devicename;
+
+ for(i=0;graphType[i].Name;i++)
+ {
+***************
+*** 8863,8870 ****
+
+ if(!graphType[i].Alias)
+ {
+! devname = ajStrNewC(graphType[i].Name);
+! ajListstrPushAppend(list, devname);
+ }
+ }
+
+--- 8877,8884 ----
+
+ if(!graphType[i].Alias)
+ {
+! devicename = ajStrNewC(graphType[i].Name);
+! ajListstrPushAppend(list, devicename);
+ }
+ }
+
+***************
+*** 9011,9016 ****
+--- 9025,9032 ----
+ }
+
+
++
++
+ /* @obsolete ajGraphxyDumpDevices
+ ** @rename ajGraphicsxyDumpDevices
+ */
+***************
+*** 9022,9027 ****
+--- 9038,9044 ----
+
+
+
++
+ /* @func ajGraphicsxyListDevices **********************************************
+ **
+ ** Store device names for a graph object in a list
+***************
+*** 9034,9040 ****
+ void ajGraphicsxyListDevices (AjPList list)
+ {
+ ajint i;
+! AjPStr devname;
+
+ for(i=0;graphType[i].Name;i++)
+ {
+--- 9051,9057 ----
+ void ajGraphicsxyListDevices (AjPList list)
+ {
+ ajint i;
+! AjPStr devicename;
+
+ for(i=0;graphType[i].Name;i++)
+ {
+***************
+*** 9043,9056 ****
+
+ if(!graphType[i].Alias)
+ {
+! devname = ajStrNewC(graphType[i].Name);
+! ajListstrPushAppend(list, devname);
+ }
+ }
+
+ return;
+ }
+
+ /* @obsolete ajGraphxyListDevices
+ ** @rename ajGraphicsxyListDevices
+ */
+--- 9060,9076 ----
+
+ if(!graphType[i].Alias)
+ {
+! devicename = ajStrNewC(graphType[i].Name);
+! ajListstrPushAppend(list, devicename);
+ }
+ }
+
+ return;
+ }
+
++
++
++
+ /* @obsolete ajGraphxyListDevices
+ ** @rename ajGraphicsxyListDevices
+ */
+***************
+*** 9061,9066 ****
+--- 9081,9088 ----
+ }
+
+
++
++
+ /* @funcstatic GraphCheckFlags ************************************************
+ **
+ ** Prints the flags defined by bits in the input integer value.
+***************
+*** 9338,9344 ****
+ **
+ ** Test this output
+ ** Check how it handles multiple sequences
+! ** Try to catch the sequnce information
+ **
+ ** Do we want end=start or end=start+1
+ **
+--- 9360,9366 ----
+ **
+ ** Test this output
+ ** Check how it handles multiple sequences
+! ** Try to catch the sequence information
+ **
+ ** Do we want end=start or end=start+1
+ **
+***************
+*** 9566,9572 ****
+ ajFmtPrintF(outf,"%f\t%f\n",graphdata->x[j],graphdata->y[j]);
+
+
+! /* Now for the Data graphobjs */
+ ajFmtPrintF(outf,"##DataObjects\n##Number %d\n",
+ graphdata->numofobjects);
+
+--- 9588,9594 ----
+ ajFmtPrintF(outf,"%f\t%f\n",graphdata->x[j],graphdata->y[j]);
+
+
+! /* Now for the Data graph objects */
+ ajFmtPrintF(outf,"##DataObjects\n##Number %d\n",
+ graphdata->numofobjects);
+
+***************
+*** 9605,9611 ****
+ }
+
+
+! /* Now for the Graph graphobjs */
+ ajFmtPrintF(outf,"##GraphObjects\n##Number %d\n",
+ thys->numofobjects);
+
+--- 9627,9633 ----
+ }
+
+
+! /* Now for the Graph graph objects */
+ ajFmtPrintF(outf,"##GraphObjects\n##Number %d\n",
+ thys->numofobjects);
+
+***************
+*** 10058,10065 ****
+ ** Draw text along a curve (i.e., an arc of a circle).
+ ** The text is written character by character.
+ **
+! ** @param [r] xcentre [PLFLT] x coor for centre.
+! ** @param [r] ycentre [PLFLT] y coor for centre.
+ ** @param [r] Radius [PLFLT] Radius of the circle.
+ ** @param [r] Angle [PLFLT] angle at which a particular character
+ ** will be written (in deg).
+--- 10080,10087 ----
+ ** Draw text along a curve (i.e., an arc of a circle).
+ ** The text is written character by character.
+ **
+! ** @param [r] xcentre [PLFLT] x coord for centre.
+! ** @param [r] ycentre [PLFLT] y coord for centre.
+ ** @param [r] Radius [PLFLT] Radius of the circle.
+ ** @param [r] Angle [PLFLT] angle at which a particular character
+ ** 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
+***************
+*** 0 ****
+--- 1,75 ----
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++ ùžLÂþ¨Wy56©ÑŽ¯Á8|ñ1 ‚ü…ái:
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+\ 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
+***************
+*** 205,213 ****
+ -type string [*] By default every feature in the feature
+ table is extracted. You can set this to be
+ any feature type you wish to extract.
+! See http://www.ebi.ac.uk/Services/WebFeat/
+! for a list of the EMBL feature types and see
+! the Uniprot user manual in
+ http://www.uniprot.org/manual/sequence_annotation
+ for a list of the Uniprot feature types.
+ The type may be wildcarded by using '*'.
+--- 205,213 ----
+ -type string [*] By default every feature in the feature
+ table is extracted. You can set this to be
+ any feature type you wish to extract.
+! See http://www.ebi.ac.uk/embl/WebFeat/ for a
+! list of the EMBL feature types and see the
+! Uniprot user manual in
+ http://www.uniprot.org/manual/sequence_annotation
+ for a list of the Uniprot feature types.
+ The type may be wildcarded by using '*'.
+***************
+*** 264,270 ****
+ '/gene' can have the value of the gene name.
+ By default any feature tag value in the
+ feature table is shown. You can set this to
+! match any feature tag valueyou wish to show.
+ The tag value may be wildcarded by using
+ '*'.
+ If you wish to show more than one tag value,
+--- 264,271 ----
+ '/gene' can have the value of the gene name.
+ By default any feature tag value in the
+ feature table is shown. You can set this to
+! match any feature tag value you wish to
+! show.
+ The tag value may be wildcarded by using
+ '*'.
+ If you wish to show more than one tag value,
+***************
+*** 439,445 ****
+ <td>-type</td>
+ <td>string</td>
+ <td>By default every feature in the feature table is extracted. You can set this to be any feature type you wish to extract.
+! See http://www.ebi.ac.uk/Services/WebFeat/ for a list of the EMBL feature types and see the Uniprot user manual in http://www.uniprot.org/manual/sequence_annotation for a list of the Uniprot feature types.
+ The type may be wildcarded by using '*'.
+ If you wish to extract more than one type, separate their names with the character '|', eg:
+ *UTR | intron</td>
+--- 440,446 ----
+ <td>-type</td>
+ <td>string</td>
+ <td>By default every feature in the feature table is extracted. You can set this to be any feature type you wish to extract.
+! See http://www.ebi.ac.uk/embl/WebFeat/ for a list of the EMBL feature types and see the Uniprot user manual in http://www.uniprot.org/manual/sequence_annotation for a list of the Uniprot feature types.
+ The type may be wildcarded by using '*'.
+ If you wish to extract more than one type, separate their names with the character '|', eg:
+ *UTR | intron</td>
+***************
+*** 487,493 ****
+ <tr bgcolor="#FFFFCC">
+ <td>-value</td>
+ <td>string</td>
+! <td>Tag values are the values associated with a feature tag. Tags are the types of extra values that a feature may have. For example in the EMBL feature table, a 'CDS' type of feature may have the tags '/codon', '/codon_start', '/db_xref', '/EC_number', '/evidence', '/exception', '/function', '/gene', '/label', '/map', '/note', '/number', '/partial', '/product', '/protein_id', '/pseudo', '/standard_name', '/translation', '/transl_except', '/transl_table', or '/usedin'. Only some of these tags can have values, for example '/gene' can have the value of the gene name. By default any feature tag value in the feature table is shown. You can set this to match any feature tag valueyou wish to show.
+ The tag value may be wildcarded by using '*'.
+ If you wish to show more than one tag value, separate their names with a space or the character '|', eg:
+ pax* | 10</td>
+--- 488,494 ----
+ <tr bgcolor="#FFFFCC">
+ <td>-value</td>
+ <td>string</td>
+! <td>Tag values are the values associated with a feature tag. Tags are the types of extra values that a feature may have. For example in the EMBL feature table, a 'CDS' type of feature may have the tags '/codon', '/codon_start', '/db_xref', '/EC_number', '/evidence', '/exception', '/function', '/gene', '/label', '/map', '/note', '/number', '/partial', '/product', '/protein_id', '/pseudo', '/standard_name', '/translation', '/transl_except', '/transl_table', or '/usedin'. Only some of these tags can have values, for example '/gene' can have the value of the gene name. By default any feature tag value in the feature table is shown. You can set this to match any feature tag value you wish to show.
+ The tag value may be wildcarded by using '*'.
+ If you wish to show more than one tag value, separate their names with a space or the character '|', eg:
+ pax* | 10</td>
+***************
+*** 1582,1592 ****
+ Author(s)
+ </H2>
+
+! Gary Williams (gwilliam © rfcgr.mrc.ac.uk)
+ <br>
+ MRC Rosalind Franklin Centre for Genomics Research
+ Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, UK
+
+
+ <H2>
+ History
+--- 1583,1595 ----
+ Author(s)
+ </H2>
+
+! Gary Williams formerly at:
+ <br>
+ MRC Rosalind Franklin Centre for Genomics Research
+ Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, UK
+
++ <p>
++ Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.
+
+ <H2>
+ 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
+***************
+*** 224,230 ****
+ pkgdata_DATA = abiview.1.abiview.gif \
+ banana.1.banana.gif \
+ chaos.1.chaos.gif cirdna.1.cirdna.gif cpgplot.1.cpgplot.gif \
+! dan.2.dan.gif dotmatcher.1.dotmatcher.gif \
+ dotpath.1.dotpath.gif dottup.1.dottup.gif \
+ emboss_icon.gif epestfind.1.epestfind.gif \
+ findkm.1.findkm.gif \
+--- 224,231 ----
+ pkgdata_DATA = abiview.1.abiview.gif \
+ banana.1.banana.gif \
+ chaos.1.chaos.gif cirdna.1.cirdna.gif cpgplot.1.cpgplot.gif \
+! dan.2.dan.gif density.2.density.gif density.3.density.gif \
+! dotmatcher.1.dotmatcher.gif \
+ dotpath.1.dotpath.gif dottup.1.dottup.gif \
+ emboss_icon.gif epestfind.1.epestfind.gif \
+ 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
+***************
+*** 1,7 ****
+ pkgdata_DATA = abiview.1.abiview.gif \
+ banana.1.banana.gif \
+ chaos.1.chaos.gif cirdna.1.cirdna.gif cpgplot.1.cpgplot.gif \
+! dan.2.dan.gif dotmatcher.1.dotmatcher.gif \
+ dotpath.1.dotpath.gif dottup.1.dottup.gif \
+ emboss_icon.gif epestfind.1.epestfind.gif \
+ findkm.1.findkm.gif \
+--- 1,8 ----
+ pkgdata_DATA = abiview.1.abiview.gif \
+ banana.1.banana.gif \
+ chaos.1.chaos.gif cirdna.1.cirdna.gif cpgplot.1.cpgplot.gif \
+! dan.2.dan.gif density.2.density.gif density.3.density.gif \
+! dotmatcher.1.dotmatcher.gif \
+ dotpath.1.dotpath.gif dottup.1.dottup.gif \
+ emboss_icon.gif epestfind.1.epestfind.gif \
+ 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
+***************
+*** 224,230 ****
+ pkgdata_DATA = abiview.1.abiview.gif \
+ banana.1.banana.gif \
+ chaos.1.chaos.gif cirdna.1.cirdna.gif cpgplot.1.cpgplot.gif \
+! dan.2.dan.gif dotmatcher.1.dotmatcher.gif \
+ dotpath.1.dotpath.gif dottup.1.dottup.gif \
+ emboss_icon.gif epestfind.1.epestfind.gif \
+ findkm.1.findkm.gif \
+--- 224,231 ----
+ pkgdata_DATA = abiview.1.abiview.gif \
+ banana.1.banana.gif \
+ chaos.1.chaos.gif cirdna.1.cirdna.gif cpgplot.1.cpgplot.gif \
+! dan.2.dan.gif density.2.density.gif density.3.density.gif \
+! dotmatcher.1.dotmatcher.gif \
+ dotpath.1.dotpath.gif dottup.1.dottup.gif \
+ emboss_icon.gif epestfind.1.epestfind.gif \
+ 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
+***************
+*** 104,114 ****
+ feature table with a type starting 'repeat'
+ is masked. You can set this to be any
+ feature type you wish to mask.
+! See http://www3.ebi.ac.uk/Services/WebFeat/
+! for a list of the EMBL feature types and see
+ Appendix A of the Swissprot user manual in
+! http://www.expasy.ch/txt/userman.txt for a
+! list of the Swissprot feature types.
+ The type may be wildcarded by using '*'.
+ If you wish to mask more than one type,
+ separate their names with spaces or commas,
+--- 104,114 ----
+ feature table with a type starting 'repeat'
+ is masked. You can set this to be any
+ feature type you wish to mask.
+! See http://www.ebi.ac.uk/embl/WebFeat/ for a
+! list of the EMBL feature types and see
+ Appendix A of the Swissprot user manual in
+! http://www.expasy.org/sprot/userman.html for
+! a list of the Swissprot feature types.
+ The type may be wildcarded by using '*'.
+ If you wish to mask more than one type,
+ separate their names with spaces or commas,
+***************
+*** 222,228 ****
+ <td>-type</td>
+ <td>string</td>
+ <td>By default any feature in the feature table with a type starting 'repeat' is masked. You can set this to be any feature type you wish to mask.
+! See http://www3.ebi.ac.uk/Services/WebFeat/ for a list of the EMBL feature types and see Appendix A of the Swissprot user manual in http://www.expasy.ch/txt/userman.txt for a list of the Swissprot feature types.
+ The type may be wildcarded by using '*'.
+ If you wish to mask more than one type, separate their names with spaces or commas, eg:
+ *UTR repeat*</td>
+--- 222,228 ----
+ <td>-type</td>
+ <td>string</td>
+ <td>By default any feature in the feature table with a type starting 'repeat' is masked. You can set this to be any feature type you wish to mask.
+! See http://www.ebi.ac.uk/embl/WebFeat/ for a list of the EMBL feature types and see Appendix A of the Swissprot user manual in http://www.expasy.org/sprot/userman.html for a list of the Swissprot feature types.
+ The type may be wildcarded by using '*'.
+ If you wish to mask more than one type, separate their names with spaces or commas, eg:
+ *UTR repeat*</td>
+***************
+*** 1112,1122 ****
+ </H2>
+
+
+! Gary Williams (gwilliam © rfcgr.mrc.ac.uk)
+ <br>
+ MRC Rosalind Franklin Centre for Genomics Research
+ Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, UK
+
+
+
+ <H2>
+--- 1112,1124 ----
+ </H2>
+
+
+! Gary Williams formerly at:
+ <br>
+ MRC Rosalind Franklin Centre for Genomics Research
+ Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, UK
+
++ <p>
++ Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.
+
+
+ <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
+***************
+*** 126,136 ****
+ -typematch string [*] By default any feature type in the
+ feature table is shown. You can set this to
+ match any feature type you wish to show.
+! See http://www3.ebi.ac.uk/Services/WebFeat/
+! for a list of the EMBL feature types and see
+ Appendix A of the Swissprot user manual in
+! http://www.expasy.ch/txt/userman.txt for a
+! list of the Swissprot feature types.
+ The type may be wildcarded by using '*'.
+ If you wish to show more than one type,
+ separate their names with the character '|',
+--- 126,136 ----
+ -typematch string [*] By default any feature type in the
+ feature table is shown. You can set this to
+ match any feature type you wish to show.
+! See http://www.ebi.ac.uk/embl/WebFeat/ for a
+! list of the EMBL feature types and see
+ Appendix A of the Swissprot user manual in
+! http://www.expasy.org/sprot/userman.html for
+! a list of the Swissprot feature types.
+ The type may be wildcarded by using '*'.
+ If you wish to show more than one type,
+ separate their names with the character '|',
+***************
+*** 173,179 ****
+ '/gene' can have the value of the gene name.
+ By default any feature tag value in the
+ feature table is shown. You can set this to
+! match any feature tag valueyou wish to show.
+ The tag value may be wildcarded by using
+ '*'.
+ If you wish to show more than one tag value,
+--- 173,180 ----
+ '/gene' can have the value of the gene name.
+ By default any feature tag value in the
+ feature table is shown. You can set this to
+! match any feature tag value you wish to
+! show.
+ The tag value may be wildcarded by using
+ '*'.
+ If you wish to show more than one tag value,
+***************
+*** 373,379 ****
+ <td>-typematch</td>
+ <td>string</td>
+ <td>By default any feature type in the feature table is shown. You can set this to match any feature type you wish to show.
+! See http://www3.ebi.ac.uk/Services/WebFeat/ for a list of the EMBL feature types and see Appendix A of the Swissprot user manual in http://www.expasy.ch/txt/userman.txt for a list of the Swissprot feature types.
+ The type may be wildcarded by using '*'.
+ If you wish to show more than one type, separate their names with the character '|', eg:
+ *UTR | intron</td>
+--- 374,380 ----
+ <td>-typematch</td>
+ <td>string</td>
+ <td>By default any feature type in the feature table is shown. You can set this to match any feature type you wish to show.
+! See http://www.ebi.ac.uk/embl/WebFeat/ for a list of the EMBL feature types and see Appendix A of the Swissprot user manual in http://www.expasy.org/sprot/userman.html for a list of the Swissprot feature types.
+ The type may be wildcarded by using '*'.
+ If you wish to show more than one type, separate their names with the character '|', eg:
+ *UTR | intron</td>
+***************
+*** 396,402 ****
+ <tr bgcolor="#FFFFCC">
+ <td>-valuematch</td>
+ <td>string</td>
+! <td>Tag values are the values associated with a feature tag. Tags are the types of extra values that a feature may have. For example in the EMBL feature table, a 'CDS' type of feature may have the tags '/codon', '/codon_start', '/db_xref', '/EC_number', '/evidence', '/exception', '/function', '/gene', '/label', '/map', '/note', '/number', '/partial', '/product', '/protein_id', '/pseudo', '/standard_name', '/translation', '/transl_except', '/transl_table', or '/usedin'. Only some of these tags can have values, for example '/gene' can have the value of the gene name. By default any feature tag value in the feature table is shown. You can set this to match any feature tag valueyou wish to show.
+ The tag value may be wildcarded by using '*'.
+ If you wish to show more than one tag value, separate their names with the character '|', eg:
+ pax* | 10</td>
+--- 397,403 ----
+ <tr bgcolor="#FFFFCC">
+ <td>-valuematch</td>
+ <td>string</td>
+! <td>Tag values are the values associated with a feature tag. Tags are the types of extra values that a feature may have. For example in the EMBL feature table, a 'CDS' type of feature may have the tags '/codon', '/codon_start', '/db_xref', '/EC_number', '/evidence', '/exception', '/function', '/gene', '/label', '/map', '/note', '/number', '/partial', '/product', '/protein_id', '/pseudo', '/standard_name', '/translation', '/transl_except', '/transl_table', or '/usedin'. Only some of these tags can have values, for example '/gene' can have the value of the gene name. By default any feature tag value in the feature table is shown. You can set this to match any feature tag value you wish to show.
+ The tag value may be wildcarded by using '*'.
+ If you wish to show more than one tag value, separate their names with the character '|', eg:
+ pax* | 10</td>
+***************
+*** 953,978 ****
+ X65921
+ H.sapiens fau 1 gene
+ |==========================================================| 2016
+! |----------------------------------------------------------> source
+! |--> exon
+! |--> mRNA
+! |-------> intron
+! |-> exon
+! |-> mRNA
+! |-> CDS
+ |--> intron
+ |---> CDS
+- |---> exon
+- |---> mRNA
+- |-------------> intron
+ |> CDS
+- |> exon
+- |> mRNA
+- |----> intron
+ |--> CDS
+! |--> exon
+ |--> mRNA
+! > polyA_signal
+
+ </pre>
+ </td></tr></table><p>
+--- 954,979 ----
+ X65921
+ H.sapiens fau 1 gene
+ |==========================================================| 2016
+! > polyA_signal
+! |--> exon
+! |----> intron
+! |> exon
+! |-------------> intron
+! |---> exon
+ |--> intron
++ |-> CDS
+ |---> CDS
+ |> CDS
+ |--> CDS
+! |-> exon
+! |-------> intron
+! |--> mRNA
+! |-> mRNA
+! |---> mRNA
+! |> mRNA
+ |--> mRNA
+! |--> exon
+! |----------------------------------------------------------> source
+
+ </pre>
+ </td></tr></table><p>
+***************
+*** 985,1003 ****
+ X65921
+ H.sapiens fau 1 gene
+ |==========================================================| 2016
+- |----------------------------------------------------------> 1-2016 source
+- |--> 408-504 exon
+- |--> 408-504 mRNA
+- |-------> 505-773 intron
+- |-> 774-856,774-856 exon
+- |-> 782-856 CDS
+- |--|---> 857-950,951-1095 intron
+- |---> 951-1095,951-1095 exon
+- |-------------|> 1096-1556,1557-1612 intron
+- |> 1557-1612,1557-1612 exon
+- |----|--> 1613-1786,1787-1912 intron
+- |--> 1787-1912,1787-1912 exon
+ > 1938-1943 polyA_signal
+
+ </pre>
+ </td></tr></table><p>
+--- 986,1004 ----
+ X65921
+ H.sapiens fau 1 gene
+ |==========================================================| 2016
+ > 1938-1943 polyA_signal
++ |--> 1787-1912 exon
++ |----> 1613-1786 intron
++ |> 1557-1612 exon
++ |-------------> 1096-1556 intron
++ |---> 951-1095 exon
++ |--> 857-950 intron
++ |-> |---> |> |--> 782-856,951-1095,1557-1612,1787-1912 CDS
++ |-> 774-856 exon
++ |-------> 505-773 intron
++ |--> |-> |---> |> |--> 408-504,774-856,951-1095,1557-1612,1787-1912 mRNA
++ |--> 408-504 exon
++ |----------------------------------------------------------> 1-2016 source
+
+ </pre>
+ </td></tr></table><p>
+***************
+*** 1175,1185 ****
+ <H2>
+ Author(s)
+ </H2>
+! Gary Williams (gwilliam © rfcgr.mrc.ac.uk)
+ <br>
+ MRC Rosalind Franklin Centre for Genomics Research
+ Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, UK
+
+
+
+
+--- 1176,1188 ----
+ <H2>
+ Author(s)
+ </H2>
+! Gary Williams formerly at:
+ <br>
+ MRC Rosalind Franklin Centre for Genomics Research
+ Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, UK
+
++ <p>
++ Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.
+
+
+
+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
+***************
+*** 285,295 ****
+ -typematch string [*] By default any feature type in the
+ feature table is shown. You can set this to
+ match any feature type you wish to show.
+! See http://www3.ebi.ac.uk/Services/WebFeat/
+! for a list of the EMBL feature types and see
+ Appendix A of the Swissprot user manual in
+! http://www.expasy.ch/txt/userman.txt for a
+! list of the Swissprot feature types.
+ The type may be wildcarded by using '*'.
+ If you wish to show more than one type,
+ separate their names with the character '|',
+--- 285,295 ----
+ -typematch string [*] By default any feature type in the
+ feature table is shown. You can set this to
+ match any feature type you wish to show.
+! See http://www.ebi.ac.uk/embl/WebFeat/ for a
+! list of the EMBL feature types and see
+ Appendix A of the Swissprot user manual in
+! http://www.expasy.org/sprot/userman.html for
+! a list of the Swissprot feature types.
+ The type may be wildcarded by using '*'.
+ If you wish to show more than one type,
+ separate their names with the character '|',
+***************
+*** 316,322 ****
+ extra values that a feature may have. By
+ default any feature tag value in the feature
+ table is shown. You can set this to match
+! any feature tag valueyou wish to show.
+ The tag value may be wildcarded by using
+ '*'.
+ If you wish to show more than one tag value,
+--- 316,322 ----
+ extra values that a feature may have. By
+ default any feature tag value in the feature
+ table is shown. You can set this to match
+! any feature tag value you wish to show.
+ The tag value may be wildcarded by using
+ '*'.
+ If you wish to show more than one tag value,
+***************
+*** 504,510 ****
+ <td>-typematch</td>
+ <td>string</td>
+ <td>By default any feature type in the feature table is shown. You can set this to match any feature type you wish to show.
+! See http://www3.ebi.ac.uk/Services/WebFeat/ for a list of the EMBL feature types and see Appendix A of the Swissprot user manual in http://www.expasy.ch/txt/userman.txt for a list of the Swissprot feature types.
+ The type may be wildcarded by using '*'.
+ If you wish to show more than one type, separate their names with the character '|', eg:
+ *UTR | intron</td>
+--- 504,510 ----
+ <td>-typematch</td>
+ <td>string</td>
+ <td>By default any feature type in the feature table is shown. You can set this to match any feature type you wish to show.
+! See http://www.ebi.ac.uk/embl/WebFeat/ for a list of the EMBL feature types and see Appendix A of the Swissprot user manual in http://www.expasy.org/sprot/userman.html for a list of the Swissprot feature types.
+ The type may be wildcarded by using '*'.
+ If you wish to show more than one type, separate their names with the character '|', eg:
+ *UTR | intron</td>
+***************
+*** 543,549 ****
+ <tr bgcolor="#FFFFCC">
+ <td>-valuematch</td>
+ <td>string</td>
+! <td>Tag values are the values associated with a feature tag. Tags are the types of extra values that a feature may have. By default any feature tag value in the feature table is shown. You can set this to match any feature tag valueyou wish to show.
+ The tag value may be wildcarded by using '*'.
+ If you wish to show more than one tag value, separate their names with the character '|', eg:
+ pax* | 10</td>
+--- 543,549 ----
+ <tr bgcolor="#FFFFCC">
+ <td>-valuematch</td>
+ <td>string</td>
+! <td>Tag values are the values associated with a feature tag. Tags are the types of extra values that a feature may have. By default any feature tag value in the feature table is shown. You can set this to match any feature tag value you wish to show.
+ The tag value may be wildcarded by using '*'.
+ If you wish to show more than one tag value, separate their names with the character '|', eg:
+ pax* | 10</td>
+***************
+*** 1748,1758 ****
+ <H2>
+ Author(s)
+ </H2>
+! Gary Williams (gwilliam © rfcgr.mrc.ac.uk)
+ <br>
+ MRC Rosalind Franklin Centre for Genomics Research
+ Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, UK
+
+
+
+ <H2>
+--- 1748,1760 ----
+ <H2>
+ Author(s)
+ </H2>
+! Gary Williams formerly at:
+ <br>
+ MRC Rosalind Franklin Centre for Genomics Research
+ Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, UK
+
++ <p>
++ Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.
+
+
+ <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
+***************
+*** 382,392 ****
+ -typematch string [*] By default any feature type in the
+ feature table is shown. You can set this to
+ match any feature type you wish to show.
+! See http://www3.ebi.ac.uk/Services/WebFeat/
+! for a list of the EMBL feature types and see
+ Appendix A of the Swissprot user manual in
+! http://www.expasy.ch/txt/userman.txt for a
+! list of the Swissprot feature types.
+ The type may be wildcarded by using '*'.
+ If you wish to show more than one type,
+ separate their names with the character '|',
+--- 382,392 ----
+ -typematch string [*] By default any feature type in the
+ feature table is shown. You can set this to
+ match any feature type you wish to show.
+! See http://www.ebi.ac.uk/embl/WebFeat/ for a
+! list of the EMBL feature types and see
+ Appendix A of the Swissprot user manual in
+! http://www.expasy.org/sprot/userman.html for
+! a list of the Swissprot feature types.
+ The type may be wildcarded by using '*'.
+ If you wish to show more than one type,
+ separate their names with the character '|',
+***************
+*** 397,403 ****
+ in the feature table is shown. You can set
+ this to match any feature sense you wish to
+ show. 0 - any sense, 1 - forward sense, -1 -
+! reverse sense (Any integer value)
+ -minscore float [0.0] Minimum score of feature to display
+ (see also maxscore) (Any numeric value)
+ -maxscore float [0.0] Maximum score of feature to display.
+--- 397,403 ----
+ in the feature table is shown. You can set
+ this to match any feature sense you wish to
+ show. 0 - any sense, 1 - forward sense, -1 -
+! reverse sense (Integer from -1 to 1)
+ -minscore float [0.0] Minimum score of feature to display
+ (see also maxscore) (Any numeric value)
+ -maxscore float [0.0] Maximum score of feature to display.
+***************
+*** 441,447 ****
+ '/gene' can have the value of the gene name.
+ By default any feature tag value in the
+ feature table is shown. You can set this to
+! match any feature tag valueyou wish to show.
+ The tag value may be wildcarded by using
+ '*'.
+ If you wish to show more than one tag value,
+--- 441,448 ----
+ '/gene' can have the value of the gene name.
+ By default any feature tag value in the
+ feature table is shown. You can set this to
+! match any feature tag value you wish to
+! show.
+ The tag value may be wildcarded by using
+ '*'.
+ If you wish to show more than one tag value,
+***************
+*** 473,480 ****
+ -maxcuts integer [2000000000] This sets the maximum number of
+ cuts for any restriction enzyme that will
+ be considered. Any enzymes that cut more
+! times than this will be ignored. (Integer up
+! to 2000000000)
+ -sitelen integer [4] This sets the minimum length of the
+ restriction enzyme recognition site. Any
+ enzymes with sites shorter than this will be
+--- 474,481 ----
+ -maxcuts integer [2000000000] This sets the maximum number of
+ cuts for any restriction enzyme that will
+ be considered. Any enzymes that cut more
+! times than this will be ignored. (Any
+! integer value)
+ -sitelen integer [4] This sets the minimum length of the
+ restriction enzyme recognition site. Any
+ enzymes with sites shorter than this will be
+***************
+*** 495,501 ****
+ pattern to be considered
+ -plasmid boolean [N] If this is set then this allows searches
+ for restriction enzyme recognition site and
+! cut postions that span the end of the
+ sequence to be considered.
+ -methylation boolean [N] If this is set then RE recognition sites
+ will not match methylated bases.
+--- 496,502 ----
+ pattern to be considered
+ -plasmid boolean [N] If this is set then this allows searches
+ for restriction enzyme recognition site and
+! cut positions that span the end of the
+ sequence to be considered.
+ -methylation boolean [N] If this is set then RE recognition sites
+ will not match methylated bases.
+***************
+*** 758,764 ****
+ <td>-typematch</td>
+ <td>string</td>
+ <td>By default any feature type in the feature table is shown. You can set this to match any feature type you wish to show.
+! See http://www3.ebi.ac.uk/Services/WebFeat/ for a list of the EMBL feature types and see Appendix A of the Swissprot user manual in http://www.expasy.ch/txt/userman.txt for a list of the Swissprot feature types.
+ The type may be wildcarded by using '*'.
+ If you wish to show more than one type, separate their names with the character '|', eg:
+ *UTR | intron</td>
+--- 759,765 ----
+ <td>-typematch</td>
+ <td>string</td>
+ <td>By default any feature type in the feature table is shown. You can set this to match any feature type you wish to show.
+! See http://www.ebi.ac.uk/embl/WebFeat/ for a list of the EMBL feature types and see Appendix A of the Swissprot user manual in http://www.expasy.org/sprot/userman.html for a list of the Swissprot feature types.
+ The type may be wildcarded by using '*'.
+ If you wish to show more than one type, separate their names with the character '|', eg:
+ *UTR | intron</td>
+***************
+*** 770,776 ****
+ <td>-sensematch</td>
+ <td>integer</td>
+ <td>By default any feature type in the feature table is shown. You can set this to match any feature sense you wish to show. 0 - any sense, 1 - forward sense, -1 - reverse sense</td>
+! <td>Any integer value</td>
+ <td>0 - any sense, 1 - forward sense, -1 - reverse sense</td>
+ </tr>
+
+--- 771,777 ----
+ <td>-sensematch</td>
+ <td>integer</td>
+ <td>By default any feature type in the feature table is shown. You can set this to match any feature sense you wish to show. 0 - any sense, 1 - forward sense, -1 - reverse sense</td>
+! <td>Integer from -1 to 1</td>
+ <td>0 - any sense, 1 - forward sense, -1 - reverse sense</td>
+ </tr>
+
+***************
+*** 806,812 ****
+ <tr bgcolor="#FFFFCC">
+ <td>-valuematch</td>
+ <td>string</td>
+! <td>Tag values are the values associated with a feature tag. Tags are the types of extra values that a feature may have. For example in the EMBL feature table, a 'CDS' type of feature may have the tags '/codon', '/codon_start', '/db_xref', '/EC_number', '/evidence', '/exception', '/function', '/gene', '/label', '/map', '/note', '/number', '/partial', '/product', '/protein_id', '/pseudo', '/standard_name', '/translation', '/transl_except', '/transl_table', or '/usedin'. Only some of these tags can have values, for example '/gene' can have the value of the gene name. By default any feature tag value in the feature table is shown. You can set this to match any feature tag valueyou wish to show.
+ The tag value may be wildcarded by using '*'.
+ If you wish to show more than one tag value, separate their names with the character '|', eg:
+ pax* | 10</td>
+--- 807,813 ----
+ <tr bgcolor="#FFFFCC">
+ <td>-valuematch</td>
+ <td>string</td>
+! <td>Tag values are the values associated with a feature tag. Tags are the types of extra values that a feature may have. For example in the EMBL feature table, a 'CDS' type of feature may have the tags '/codon', '/codon_start', '/db_xref', '/EC_number', '/evidence', '/exception', '/function', '/gene', '/label', '/map', '/note', '/number', '/partial', '/product', '/protein_id', '/pseudo', '/standard_name', '/translation', '/transl_except', '/transl_table', or '/usedin'. Only some of these tags can have values, for example '/gene' can have the value of the gene name. By default any feature tag value in the feature table is shown. You can set this to match any feature tag value you wish to show.
+ The tag value may be wildcarded by using '*'.
+ If you wish to show more than one tag value, separate their names with the character '|', eg:
+ pax* | 10</td>
+***************
+*** 854,860 ****
+ <td>-maxcuts</td>
+ <td>integer</td>
+ <td>This sets the maximum number of cuts for any restriction enzyme that will be considered. Any enzymes that cut more times than this will be ignored.</td>
+! <td>Integer up to 2000000000</td>
+ <td>2000000000</td>
+ </tr>
+
+--- 855,861 ----
+ <td>-maxcuts</td>
+ <td>integer</td>
+ <td>This sets the maximum number of cuts for any restriction enzyme that will be considered. Any enzymes that cut more times than this will be ignored.</td>
+! <td>Any integer value</td>
+ <td>2000000000</td>
+ </tr>
+
+***************
+*** 901,907 ****
+ <tr bgcolor="#FFFFCC">
+ <td>-plasmid</td>
+ <td>boolean</td>
+! <td>If this is set then this allows searches for restriction enzyme recognition site and cut postions that span the end of the sequence to be considered.</td>
+ <td>Boolean value Yes/No</td>
+ <td>No</td>
+ </tr>
+--- 902,908 ----
+ <tr bgcolor="#FFFFCC">
+ <td>-plasmid</td>
+ <td>boolean</td>
+! <td>If this is set then this allows searches for restriction enzyme recognition site and cut positions that span the end of the sequence to be considered.</td>
+ <td>Boolean value Yes/No</td>
+ <td>No</td>
+ </tr>
+***************
+*** 2197,2207 ****
+ <H2>
+ Author(s)
+ </H2>
+! Gary Williams (gwilliam © rfcgr.mrc.ac.uk)
+ <br>
+ MRC Rosalind Franklin Centre for Genomics Research
+ Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, UK
+
+
+
+ <H2>
+--- 2198,2210 ----
+ <H2>
+ Author(s)
+ </H2>
+! Gary Williams formerly at:
+ <br>
+ MRC Rosalind Franklin Centre for Genomics Research
+ Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, UK
+
++ <p>
++ Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.
+
+
+ <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
+***************
+*** 127,137 ****
+ -atype string [*] By default every feature in the feature
+ table is allowed. You can set this to be any
+ feature type you wish to allow.
+! See http://www3.ebi.ac.uk/Services/WebFeat/
+! for a list of the EMBL feature types and see
+ Appendix A of the Swissprot user manual in
+! http://www.expasy.ch/txt/userman.txt for a
+! list of the Swissprot feature types.
+ The type may be wildcarded by using '*'.
+ If you wish to allow more than one type,
+ separate their names with the character '|',
+--- 127,137 ----
+ -atype string [*] By default every feature in the feature
+ table is allowed. You can set this to be any
+ feature type you wish to allow.
+! See http://www.ebi.ac.uk/embl/WebFeat/ for a
+! list of the EMBL feature types and see
+ Appendix A of the Swissprot user manual in
+! http://www.expasy.org/sprot/userman.html for
+! a list of the Swissprot feature types.
+ The type may be wildcarded by using '*'.
+ If you wish to allow more than one type,
+ separate their names with the character '|',
+***************
+*** 140,150 ****
+ -btype string [*] By default every feature in the feature
+ table is allowed. You can set this to be any
+ feature type you wish to allow.
+! See http://www3.ebi.ac.uk/Services/WebFeat/
+! for a list of the EMBL feature types and see
+ Appendix A of the Swissprot user manual in
+! http://www.expasy.ch/txt/userman.txt for a
+! list of the Swissprot feature types.
+ The type may be wildcarded by using '*'.
+ If you wish to allow more than one type,
+ separate their names with the character '|',
+--- 140,150 ----
+ -btype string [*] By default every feature in the feature
+ table is allowed. You can set this to be any
+ feature type you wish to allow.
+! See http://www.ebi.ac.uk/embl/WebFeat/ for a
+! list of the EMBL feature types and see
+ Appendix A of the Swissprot user manual in
+! http://www.expasy.org/sprot/userman.html for
+! a list of the Swissprot feature types.
+ The type may be wildcarded by using '*'.
+ If you wish to allow more than one type,
+ separate their names with the character '|',
+***************
+*** 334,347 ****
+ then you can specify the 'type' name of the
+ new feature here. By default every feature
+ in the feature table is allowed. See
+! http://www3.ebi.ac.uk/Services/WebFeat/ for
+! a list of the EMBL feature types and see
+ Appendix A of the Swissprot user manual in
+! http://www.expasy.ch/txt/userman.txt for a
+! list of the Swissprot feature types. If you
+! specify an invalid feature type name, then
+! the default name 'misc_feature' is used.
+! (Any string)
+
+ Advanced (Unprompted) qualifiers: (none)
+ Associated qualifiers:
+--- 334,347 ----
+ then you can specify the 'type' name of the
+ new feature here. By default every feature
+ in the feature table is allowed. See
+! http://www.ebi.ac.uk/embl/WebFeat/ for a
+! list of the EMBL feature types and see
+ Appendix A of the Swissprot user manual in
+! http://www.expasy.org/sprot/userman.html for
+! a list of the Swissprot feature types. If
+! you specify an invalid feature type name,
+! then the default name 'misc_feature' is
+! used. (Any string)
+
+ Advanced (Unprompted) qualifiers: (none)
+ Associated qualifiers:
+***************
+*** 420,426 ****
+ <td>-atype</td>
+ <td>string</td>
+ <td>By default every feature in the feature table is allowed. You can set this to be any feature type you wish to allow.
+! See http://www3.ebi.ac.uk/Services/WebFeat/ for a list of the EMBL feature types and see Appendix A of the Swissprot user manual in http://www.expasy.ch/txt/userman.txt for a list of the Swissprot feature types.
+ The type may be wildcarded by using '*'.
+ If you wish to allow more than one type, separate their names with the character '|', eg:
+ *UTR | intron</td>
+--- 420,426 ----
+ <td>-atype</td>
+ <td>string</td>
+ <td>By default every feature in the feature table is allowed. You can set this to be any feature type you wish to allow.
+! See http://www.ebi.ac.uk/embl/WebFeat/ for a list of the EMBL feature types and see Appendix A of the Swissprot user manual in http://www.expasy.org/sprot/userman.html for a list of the Swissprot feature types.
+ The type may be wildcarded by using '*'.
+ If you wish to allow more than one type, separate their names with the character '|', eg:
+ *UTR | intron</td>
+***************
+*** 432,438 ****
+ <td>-btype</td>
+ <td>string</td>
+ <td>By default every feature in the feature table is allowed. You can set this to be any feature type you wish to allow.
+! See http://www3.ebi.ac.uk/Services/WebFeat/ for a list of the EMBL feature types and see Appendix A of the Swissprot user manual in http://www.expasy.ch/txt/userman.txt for a list of the Swissprot feature types.
+ The type may be wildcarded by using '*'.
+ If you wish to allow more than one type, separate their names with the character '|', eg:
+ *UTR | intron</td>
+--- 432,438 ----
+ <td>-btype</td>
+ <td>string</td>
+ <td>By default every feature in the feature table is allowed. You can set this to be any feature type you wish to allow.
+! See http://www.ebi.ac.uk/embl/WebFeat/ for a list of the EMBL feature types and see Appendix A of the Swissprot user manual in http://www.expasy.org/sprot/userman.html for a list of the Swissprot feature types.
+ The type may be wildcarded by using '*'.
+ If you wish to allow more than one type, separate their names with the character '|', eg:
+ *UTR | intron</td>
+***************
+*** 630,636 ****
+ <tr bgcolor="#FFFFCC">
+ <td>-typeout</td>
+ <td>string</td>
+! <td>If you have specified that the pairs of features that are found should be reported as one feature in the ouput, then you can specify the 'type' name of the new feature here. By default every feature in the feature table is allowed. See http://www3.ebi.ac.uk/Services/WebFeat/ for a list of the EMBL feature types and see Appendix A of the Swissprot user manual in http://www.expasy.ch/txt/userman.txt for a list of the Swissprot feature types. If you specify an invalid feature type name, then the default name 'misc_feature' is used.</td>
+ <td>Any string</td>
+ <td>misc_feature</td>
+ </tr>
+--- 630,636 ----
+ <tr bgcolor="#FFFFCC">
+ <td>-typeout</td>
+ <td>string</td>
+! <td>If you have specified that the pairs of features that are found should be reported as one feature in the ouput, then you can specify the 'type' name of the new feature here. By default every feature in the feature table is allowed. See http://www.ebi.ac.uk/embl/WebFeat/ for a list of the EMBL feature types and see Appendix A of the Swissprot user manual in http://www.expasy.org/sprot/userman.html for a list of the Swissprot feature types. If you specify an invalid feature type name, then the default name 'misc_feature' is used.</td>
+ <td>Any string</td>
+ <td>misc_feature</td>
+ </tr>
+***************
+*** 1069,1075 ****
+ The results can be output in one of several styles by using the
+ command-line qualifier <b>-rformat xxx</b>, where 'xxx' is replaced by
+ the name of the required format. The available format names are: embl,
+! genbank, gff, pir, swiss, trace, listfile, dbmotif, diffseq, excel,
+ feattable, motif, regions, seqtable, simple, srs, table, tagseq
+
+ <p>
+--- 1069,1075 ----
+ The results can be output in one of several styles by using the
+ command-line qualifier <b>-rformat xxx</b>, where 'xxx' is replaced by
+ the name of the required format. The available format names are: embl,
+! genbank, gff, pir, swiss, debug, listfile, dbmotif, diffseq, excel,
+ feattable, motif, regions, seqtable, simple, srs, table, tagseq
+
+ <p>
+***************
+*** 1217,1227 ****
+ <H2>
+ Author(s)
+ </H2>
+! Gary Williams (gwilliam © rfcgr.mrc.ac.uk)
+ <br>
+ MRC Rosalind Franklin Centre for Genomics Research
+ Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, UK
+
+
+ <H2>
+ History
+--- 1217,1229 ----
+ <H2>
+ Author(s)
+ </H2>
+! Gary Williams formerly at:
+ <br>
+ MRC Rosalind Franklin Centre for Genomics Research
+ Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, UK
+
++ <p>
++ Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.
+
+ <H2>
+ 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
+***************
+*** 154,162 ****
+ -type string [*] By default every feature in the feature
+ table is extracted. You can set this to be
+ any feature type you wish to extract.
+! See http://www.ebi.ac.uk/Services/WebFeat/
+! for a list of the EMBL feature types and see
+! the Uniprot user manual in
+ http://www.uniprot.org/manual/sequence_annotat
+ ion
+ for a list of the Uniprot feature types.
+--- 154,162 ----
+ -type string [*] By default every feature in the feature
+ table is extracted. You can set this to be
+ any feature type you wish to extract.
+! See http://www.ebi.ac.uk/embl/WebFeat/ for a
+! list of the EMBL feature types and see the
+! Uniprot user manual in
+ http://www.uniprot.org/manual/sequence_annotat
+ ion
+ for a list of the Uniprot feature types.
+***************
+*** 214,220 ****
+ '/gene' can have the value of the gene name.
+ By default any feature tag value in the
+ feature table is shown. You can set this to
+! match any feature tag valueyou wish to show.
+ The tag value may be wildcarded by using
+ '*'.
+ If you wish to show more than one tag value,
+--- 214,221 ----
+ '/gene' can have the value of the gene name.
+ By default any feature tag value in the
+ feature table is shown. You can set this to
+! match any feature tag value you wish to
+! show.
+ The tag value may be wildcarded by using
+ '*'.
+ If you wish to show more than one tag value,
+***************
+*** 855,864 ****
+
+ Author(s)
+
+! Gary Williams (gwilliam (c) rfcgr.mrc.ac.uk)
+ MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust
+ Genome Campus, Hinxton, Cambridge, CB10 1SB, UK
+
+ History
+
+ Written (Dec 12 2001) - Gary Williams
+--- 856,868 ----
+
+ Author(s)
+
+! Gary Williams formerly at:
+ MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust
+ Genome Campus, Hinxton, Cambridge, CB10 1SB, UK
+
++ Please report all bugs to the EMBOSS bug team
++ (emboss-bug (c) emboss.open-bio.org) not to the original author.
++
+ History
+
+ 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
+***************
+*** 68,78 ****
+ feature table with a type starting 'repeat'
+ is masked. You can set this to be any
+ feature type you wish to mask.
+! See http://www3.ebi.ac.uk/Services/WebFeat/
+! for a list of the EMBL feature types and see
+ Appendix A of the Swissprot user manual in
+! http://www.expasy.ch/txt/userman.txt for a
+! list of the Swissprot feature types.
+ The type may be wildcarded by using '*'.
+ If you wish to mask more than one type,
+ separate their names with spaces or commas,
+--- 68,78 ----
+ feature table with a type starting 'repeat'
+ is masked. You can set this to be any
+ feature type you wish to mask.
+! See http://www.ebi.ac.uk/embl/WebFeat/ for a
+! list of the EMBL feature types and see
+ Appendix A of the Swissprot user manual in
+! http://www.expasy.org/sprot/userman.html for
+! a list of the Swissprot feature types.
+ The type may be wildcarded by using '*'.
+ If you wish to mask more than one type,
+ separate their names with spaces or commas,
+***************
+*** 466,475 ****
+
+ Author(s)
+
+! Gary Williams (gwilliam (c) rfcgr.mrc.ac.uk)
+ MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust
+ Genome Campus, Hinxton, Cambridge, CB10 1SB, UK
+
+ History
+
+ Written (2000) - Gary Williams
+--- 466,478 ----
+
+ Author(s)
+
+! Gary Williams formerly at:
+ MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust
+ Genome Campus, Hinxton, Cambridge, CB10 1SB, UK
+
++ Please report all bugs to the EMBOSS bug team
++ (emboss-bug (c) emboss.open-bio.org) not to the original author.
++
+ History
+
+ 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
+***************
+*** 87,97 ****
+ -typematch string [*] By default any feature type in the
+ feature table is shown. You can set this to
+ match any feature type you wish to show.
+! See http://www3.ebi.ac.uk/Services/WebFeat/
+! for a list of the EMBL feature types and see
+ Appendix A of the Swissprot user manual in
+! http://www.expasy.ch/txt/userman.txt for a
+! list of the Swissprot feature types.
+ The type may be wildcarded by using '*'.
+ If you wish to show more than one type,
+ separate their names with the character '|',
+--- 87,97 ----
+ -typematch string [*] By default any feature type in the
+ feature table is shown. You can set this to
+ match any feature type you wish to show.
+! See http://www.ebi.ac.uk/embl/WebFeat/ for a
+! list of the EMBL feature types and see
+ Appendix A of the Swissprot user manual in
+! http://www.expasy.org/sprot/userman.html for
+! a list of the Swissprot feature types.
+ The type may be wildcarded by using '*'.
+ If you wish to show more than one type,
+ separate their names with the character '|',
+***************
+*** 134,140 ****
+ '/gene' can have the value of the gene name.
+ By default any feature tag value in the
+ feature table is shown. You can set this to
+! match any feature tag valueyou wish to show.
+ The tag value may be wildcarded by using
+ '*'.
+ If you wish to show more than one tag value,
+--- 134,141 ----
+ '/gene' can have the value of the gene name.
+ By default any feature tag value in the
+ feature table is shown. You can set this to
+! match any feature tag value you wish to
+! show.
+ The tag value may be wildcarded by using
+ '*'.
+ If you wish to show more than one tag value,
+***************
+*** 412,437 ****
+ X65921
+ H.sapiens fau 1 gene
+ |==========================================================| 2016
+! |----------------------------------------------------------> source
+! |--> exon
+! |--> mRNA
+! |-------> intron
+! |-> exon
+! |-> mRNA
+! |-> CDS
+ |--> intron
+ |---> CDS
+- |---> exon
+- |---> mRNA
+- |-------------> intron
+ |> CDS
+- |> exon
+- |> mRNA
+- |----> intron
+ |--> CDS
+! |--> exon
+ |--> mRNA
+! > polyA_signal
+
+
+ Output files for usage example 2
+--- 413,438 ----
+ X65921
+ H.sapiens fau 1 gene
+ |==========================================================| 2016
+! > polyA_signal
+! |--> exon
+! |----> intron
+! |> exon
+! |-------------> intron
+! |---> exon
+ |--> intron
++ |-> CDS
+ |---> CDS
+ |> CDS
+ |--> CDS
+! |-> exon
+! |-------> intron
+! |--> mRNA
+! |-> mRNA
+! |---> mRNA
+! |> mRNA
+ |--> mRNA
+! |--> exon
+! |----------------------------------------------------------> source
+
+
+ Output files for usage example 2
+***************
+*** 441,467 ****
+ X65921
+ H.sapiens fau 1 gene
+ |==========================================================| 2016
+- |----------------------------------------------------------> 1-2016 source
+- |--> 408-504 exon
+- |--> 408-504 mRNA
+- |-------> 505-773 intron
+- |-> 774-856,774-856 exo
+- n
+- |-> 782-856 CDS
+- |--|---> 857-950,951-1095 in
+- tron
+- |---> 951-1095,951-1095 e
+- xon
+- |-------------|> 1096-1556,1557-1612
+- intron
+- |> 1557-1612,1557-1612
+- exon
+- |----|--> 1613-1786,1787-1912
+- intron
+- |--> 1787-1912,1787-1912
+- exon
+ > 1938-1943 polyA_sig
+ nal
+
+
+ Output files for usage example 3
+--- 442,463 ----
+ X65921
+ H.sapiens fau 1 gene
+ |==========================================================| 2016
+ > 1938-1943 polyA_sig
+ nal
++ |--> 1787-1912 exon
++ |----> 1613-1786 intron
++ |> 1557-1612 exon
++ |-------------> 1096-1556 intron
++ |---> 951-1095 exon
++ |--> 857-950 intron
++ |-> |---> |> |--> 782-856,951-1095,15
++ 57-1612,1787-1912 CDS
++ |-> 774-856 exon
++ |-------> 505-773 intron
++ |--> |-> |---> |> |--> 408-504,774-856,951
++ -1095,1557-1612,1787-1912 mRNA
++ |--> 408-504 exon
++ |----------------------------------------------------------> 1-2016 source
+
+
+ Output files for usage example 3
+***************
+*** 551,560 ****
+
+ Author(s)
+
+! Gary Williams (gwilliam (c) rfcgr.mrc.ac.uk)
+ MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust
+ Genome Campus, Hinxton, Cambridge, CB10 1SB, UK
+
+ History
+
+ Written 1999 - Gary Williams
+--- 547,559 ----
+
+ Author(s)
+
+! Gary Williams formerly at:
+ MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust
+ Genome Campus, Hinxton, Cambridge, CB10 1SB, UK
+
++ Please report all bugs to the EMBOSS bug team
++ (emboss-bug (c) emboss.open-bio.org) not to the original author.
++
+ History
+
+ 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
+***************
+*** 232,242 ****
+ -typematch string [*] By default any feature type in the
+ feature table is shown. You can set this to
+ match any feature type you wish to show.
+! See http://www3.ebi.ac.uk/Services/WebFeat/
+! for a list of the EMBL feature types and see
+ Appendix A of the Swissprot user manual in
+! http://www.expasy.ch/txt/userman.txt for a
+! list of the Swissprot feature types.
+ The type may be wildcarded by using '*'.
+ If you wish to show more than one type,
+ separate their names with the character '|',
+--- 232,242 ----
+ -typematch string [*] By default any feature type in the
+ feature table is shown. You can set this to
+ match any feature type you wish to show.
+! See http://www.ebi.ac.uk/embl/WebFeat/ for a
+! list of the EMBL feature types and see
+ Appendix A of the Swissprot user manual in
+! http://www.expasy.org/sprot/userman.html for
+! a list of the Swissprot feature types.
+ The type may be wildcarded by using '*'.
+ If you wish to show more than one type,
+ separate their names with the character '|',
+***************
+*** 263,269 ****
+ extra values that a feature may have. By
+ default any feature tag value in the feature
+ table is shown. You can set this to match
+! any feature tag valueyou wish to show.
+ The tag value may be wildcarded by using
+ '*'.
+ If you wish to show more than one tag value,
+--- 263,269 ----
+ extra values that a feature may have. By
+ default any feature tag value in the feature
+ table is shown. You can set this to match
+! any feature tag value you wish to show.
+ The tag value may be wildcarded by using
+ '*'.
+ If you wish to show more than one tag value,
+***************
+*** 992,1001 ****
+
+ Author(s)
+
+! Gary Williams (gwilliam (c) rfcgr.mrc.ac.uk)
+ MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust
+ Genome Campus, Hinxton, Cambridge, CB10 1SB, UK
+
+ History
+
+ Target users
+--- 992,1004 ----
+
+ Author(s)
+
+! Gary Williams formerly at:
+ MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust
+ Genome Campus, Hinxton, Cambridge, CB10 1SB, UK
+
++ Please report all bugs to the EMBOSS bug team
++ (emboss-bug (c) emboss.open-bio.org) not to the original author.
++
+ History
+
+ 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
+***************
+*** 327,337 ****
+ -typematch string [*] By default any feature type in the
+ feature table is shown. You can set this to
+ match any feature type you wish to show.
+! See http://www3.ebi.ac.uk/Services/WebFeat/
+! for a list of the EMBL feature types and see
+ Appendix A of the Swissprot user manual in
+! http://www.expasy.ch/txt/userman.txt for a
+! list of the Swissprot feature types.
+ The type may be wildcarded by using '*'.
+ If you wish to show more than one type,
+ separate their names with the character '|',
+--- 327,337 ----
+ -typematch string [*] By default any feature type in the
+ feature table is shown. You can set this to
+ match any feature type you wish to show.
+! See http://www.ebi.ac.uk/embl/WebFeat/ for a
+! list of the EMBL feature types and see
+ Appendix A of the Swissprot user manual in
+! http://www.expasy.org/sprot/userman.html for
+! a list of the Swissprot feature types.
+ The type may be wildcarded by using '*'.
+ If you wish to show more than one type,
+ separate their names with the character '|',
+***************
+*** 342,348 ****
+ in the feature table is shown. You can set
+ this to match any feature sense you wish to
+ show. 0 - any sense, 1 - forward sense, -1 -
+! reverse sense (Any integer value)
+ -minscore float [0.0] Minimum score of feature to display
+ (see also maxscore) (Any numeric value)
+ -maxscore float [0.0] Maximum score of feature to display.
+--- 342,348 ----
+ in the feature table is shown. You can set
+ this to match any feature sense you wish to
+ show. 0 - any sense, 1 - forward sense, -1 -
+! reverse sense (Integer from -1 to 1)
+ -minscore float [0.0] Minimum score of feature to display
+ (see also maxscore) (Any numeric value)
+ -maxscore float [0.0] Maximum score of feature to display.
+***************
+*** 386,392 ****
+ '/gene' can have the value of the gene name.
+ By default any feature tag value in the
+ feature table is shown. You can set this to
+! match any feature tag valueyou wish to show.
+ The tag value may be wildcarded by using
+ '*'.
+ If you wish to show more than one tag value,
+--- 386,393 ----
+ '/gene' can have the value of the gene name.
+ By default any feature tag value in the
+ feature table is shown. You can set this to
+! match any feature tag value you wish to
+! show.
+ The tag value may be wildcarded by using
+ '*'.
+ If you wish to show more than one tag value,
+***************
+*** 418,425 ****
+ -maxcuts integer [2000000000] This sets the maximum number of
+ cuts for any restriction enzyme that will
+ be considered. Any enzymes that cut more
+! times than this will be ignored. (Integer up
+! to 2000000000)
+ -sitelen integer [4] This sets the minimum length of the
+ restriction enzyme recognition site. Any
+ enzymes with sites shorter than this will be
+--- 419,426 ----
+ -maxcuts integer [2000000000] This sets the maximum number of
+ cuts for any restriction enzyme that will
+ be considered. Any enzymes that cut more
+! times than this will be ignored. (Any
+! integer value)
+ -sitelen integer [4] This sets the minimum length of the
+ restriction enzyme recognition site. Any
+ enzymes with sites shorter than this will be
+***************
+*** 440,446 ****
+ pattern to be considered
+ -plasmid boolean [N] If this is set then this allows searches
+ for restriction enzyme recognition site and
+! cut postions that span the end of the
+ sequence to be considered.
+ -methylation boolean [N] If this is set then RE recognition sites
+ will not match methylated bases.
+--- 441,447 ----
+ pattern to be considered
+ -plasmid boolean [N] If this is set then this allows searches
+ for restriction enzyme recognition site and
+! cut positions that span the end of the
+ sequence to be considered.
+ -methylation boolean [N] If this is set then RE recognition sites
+ will not match methylated bases.
+***************
+*** 1207,1216 ****
+
+ Author(s)
+
+! Gary Williams (gwilliam (c) rfcgr.mrc.ac.uk)
+ MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust
+ Genome Campus, Hinxton, Cambridge, CB10 1SB, UK
+
+ History
+
+ Written 1999 - GWW
+--- 1208,1220 ----
+
+ Author(s)
+
+! Gary Williams formerly at:
+ MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust
+ Genome Campus, Hinxton, Cambridge, CB10 1SB, UK
+
++ Please report all bugs to the EMBOSS bug team
++ (emboss-bug (c) emboss.open-bio.org) not to the original author.
++
+ History
+
+ 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
+***************
+*** 107,117 ****
+ -atype string [*] By default every feature in the feature
+ table is allowed. You can set this to be any
+ feature type you wish to allow.
+! See http://www3.ebi.ac.uk/Services/WebFeat/
+! for a list of the EMBL feature types and see
+ Appendix A of the Swissprot user manual in
+! http://www.expasy.ch/txt/userman.txt for a
+! list of the Swissprot feature types.
+ The type may be wildcarded by using '*'.
+ If you wish to allow more than one type,
+ separate their names with the character '|',
+--- 107,117 ----
+ -atype string [*] By default every feature in the feature
+ table is allowed. You can set this to be any
+ feature type you wish to allow.
+! See http://www.ebi.ac.uk/embl/WebFeat/ for a
+! list of the EMBL feature types and see
+ Appendix A of the Swissprot user manual in
+! http://www.expasy.org/sprot/userman.html for
+! a list of the Swissprot feature types.
+ The type may be wildcarded by using '*'.
+ If you wish to allow more than one type,
+ separate their names with the character '|',
+***************
+*** 120,130 ****
+ -btype string [*] By default every feature in the feature
+ table is allowed. You can set this to be any
+ feature type you wish to allow.
+! See http://www3.ebi.ac.uk/Services/WebFeat/
+! for a list of the EMBL feature types and see
+ Appendix A of the Swissprot user manual in
+! http://www.expasy.ch/txt/userman.txt for a
+! list of the Swissprot feature types.
+ The type may be wildcarded by using '*'.
+ If you wish to allow more than one type,
+ separate their names with the character '|',
+--- 120,130 ----
+ -btype string [*] By default every feature in the feature
+ table is allowed. You can set this to be any
+ feature type you wish to allow.
+! See http://www.ebi.ac.uk/embl/WebFeat/ for a
+! list of the EMBL feature types and see
+ Appendix A of the Swissprot user manual in
+! http://www.expasy.org/sprot/userman.html for
+! a list of the Swissprot feature types.
+ The type may be wildcarded by using '*'.
+ If you wish to allow more than one type,
+ separate their names with the character '|',
+***************
+*** 314,327 ****
+ then you can specify the 'type' name of the
+ new feature here. By default every feature
+ in the feature table is allowed. See
+! http://www3.ebi.ac.uk/Services/WebFeat/ for
+! a list of the EMBL feature types and see
+ Appendix A of the Swissprot user manual in
+! http://www.expasy.ch/txt/userman.txt for a
+! list of the Swissprot feature types. If you
+! specify an invalid feature type name, then
+! the default name 'misc_feature' is used.
+! (Any string)
+
+ Advanced (Unprompted) qualifiers: (none)
+ Associated qualifiers:
+--- 314,327 ----
+ then you can specify the 'type' name of the
+ new feature here. By default every feature
+ in the feature table is allowed. See
+! http://www.ebi.ac.uk/embl/WebFeat/ for a
+! list of the EMBL feature types and see
+ Appendix A of the Swissprot user manual in
+! http://www.expasy.org/sprot/userman.html for
+! a list of the Swissprot feature types. If
+! you specify an invalid feature type name,
+! then the default name 'misc_feature' is
+! used. (Any string)
+
+ Advanced (Unprompted) qualifiers: (none)
+ Associated qualifiers:
+***************
+*** 469,475 ****
+ The results can be output in one of several styles by using the
+ command-line qualifier -rformat xxx, where 'xxx' is replaced by the
+ name of the required format. The available format names are: embl,
+! genbank, gff, pir, swiss, trace, listfile, dbmotif, diffseq, excel,
+ feattable, motif, regions, seqtable, simple, srs, table, tagseq
+
+ See: http://emboss.sf.net/docs/themes/ReportFormats.html for further
+--- 469,475 ----
+ The results can be output in one of several styles by using the
+ command-line qualifier -rformat xxx, where 'xxx' is replaced by the
+ name of the required format. The available format names are: embl,
+! genbank, gff, pir, swiss, debug, listfile, dbmotif, diffseq, excel,
+ feattable, motif, regions, seqtable, simple, srs, table, tagseq
+
+ See: http://emboss.sf.net/docs/themes/ReportFormats.html for further
+***************
+*** 568,577 ****
+
+ Author(s)
+
+! Gary Williams (gwilliam (c) rfcgr.mrc.ac.uk)
+ MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust
+ Genome Campus, Hinxton, Cambridge, CB10 1SB, UK
+
+ History
+
+ Written (2002) - Gary Williams
+--- 568,580 ----
+
+ Author(s)
+
+! Gary Williams formerly at:
+ MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust
+ Genome Campus, Hinxton, Cambridge, CB10 1SB, UK
+
++ Please report all bugs to the EMBOSS bug team
++ (emboss-bug (c) emboss.open-bio.org) not to the original author.
++
+ History
+
+ 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
+***************
+*** 13,19 ****
+ parameter: "Y"
+ default: "inputfile"
+ information: "Commands to the cirdna drawing program file"
+! knowntype: "lindna mapping commands"
+ relations: ""
+ ]
+
+--- 13,19 ----
+ parameter: "Y"
+ default: "inputfile"
+ information: "Commands to the cirdna drawing program file"
+! knowntype: "cirdna mapping commands"
+ relations: ""
+ ]
+
+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
+***************
+*** 83,89 ****
+ information: "Type of feature to extract"
+ help: "By default every feature in the feature table is extracted.
+ You can set this to be any feature type you wish to extract. \
+! See http://www.ebi.ac.uk/Services/WebFeat/ for a list of the EMBL
+ feature types and see the Uniprot user manual in
+ http://www.uniprot.org/manual/sequence_annotation
+ for a list of the Uniprot feature types. \
+--- 83,89 ----
+ information: "Type of feature to extract"
+ help: "By default every feature in the feature table is extracted.
+ You can set this to be any feature type you wish to extract. \
+! See http://www.ebi.ac.uk/embl/WebFeat/ for a list of the EMBL
+ feature types and see the Uniprot user manual in
+ http://www.uniprot.org/manual/sequence_annotation
+ 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
+***************
+*** 15,23 ****
+ directory: directory [
+ parameter: "Y"
+ information: "JASPAR database directory"
+! help: "The directory containing the unzipped and untarred
+! JASPAR_CORE, JASPAR_FAM and JASPAR_PHYLOFACTS
+! subdirectories"
+ knowntype: "Jaspar database"
+ relations: "EDAM: Directory"
+ ]
+--- 15,22 ----
+ directory: directory [
+ parameter: "Y"
+ information: "JASPAR database directory"
+! help: "The FlatFileDir directory containing the .pfm files
+! and the matrix_list.txt file"
+ knowntype: "Jaspar database"
+ relations: "EDAM: Directory"
+ ]
+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
+***************
+*** 21,27 ****
+ default: "C"
+ minimum: "1"
+ maximum: "1"
+! values: "C:Core,F:Fam,P:Phylofacts,N:CNE,O:POLII,S:SPLICE"
+ delimiter: ","
+ codedelimiter: ":"
+ header: "Jaspar matrix set"
+--- 21,27 ----
+ default: "C"
+ minimum: "1"
+ maximum: "1"
+! values: "C:Core,F:Fam,P:Phylofacts,N:CNE,O:POLII,S:SPLICE,B:PBM,L:PBM_HLH,H:PBM_HOMEO"
+ delimiter: ","
+ codedelimiter: ":"
+ header: "Jaspar matrix set"
+***************
+*** 38,44 ****
+ help: "The name 'all' reads in all matrix files from the selected \
+ JASPAR matrix set. You can specify individual matrices by giving \
+ their names with commas between then, such as: \
+! 'ma0001,ma0015'. \
+ The case of the names is not important. You can specify a file of \
+ matrix names to read in by giving the name of the file holding the \
+ matrix names with a '@' character in front of it, for example, \
+--- 38,44 ----
+ help: "The name 'all' reads in all matrix files from the selected \
+ JASPAR matrix set. You can specify individual matrices by giving \
+ their names with commas between then, such as: \
+! 'ma0001.1,ma0015*'. \
+ The case of the names is not important. You can specify a file of \
+ matrix names to read in by giving the name of the file holding the \
+ matrix names with a '@' character in front of it, for example, \
+***************
+*** 49,59 ****
+ for. \
+ An example of a file of matrix names is: \
+ ! my matrices \
+! ma0001, ma0002 \
+ ! other matrices \
+! ma0010 \
+! ma0032 \
+! ma0053"
+ knowntype: "jaspar matrix id"
+ relations: "EDAM: JASPAR profile identifier"
+ ]
+--- 49,59 ----
+ for. \
+ An example of a file of matrix names is: \
+ ! my matrices \
+! ma0001.1, ma0002.1 \
+ ! other matrices \
+! ma0010.1 \
+! ma0032* \
+! ma0053.1"
+ knowntype: "jaspar matrix id"
+ relations: "EDAM: JASPAR profile identifier"
+ ]
+***************
+*** 115,123 ****
+ multiple: "Y"
+ taglist: "float:pc=Score_Percent
+ str:id=ID str:name=Name str:species=Species str:class=Class
+! str:supergroup=Supergroup str:pseq=Protein_Seq
+! str:exp=Experiment str:pmid=Source_PMID float:info=Info_Content
+! str:jaspar=Closest_Jaspar str:transfac=Closest_Transfac
+ float:mcs=MCS_Score str:built=Built_From"
+ relations: "EDAM: EMBOSS report"
+ ]
+--- 115,124 ----
+ multiple: "Y"
+ taglist: "float:pc=Score_Percent
+ str:id=ID str:name=Name str:species=Species str:class=Class
+! str:supergroup=Supergroup str:fam=Family str:paz=Pazar_TF_ID
+! str:pseq=Protein_Seq str:exp=Experiment str:pmid=Source_PMID
+! float:info=Info_Content str:jaspar=Closest_Jaspar
+! str:transfac=Closest_Transfac
+ float:mcs=MCS_Score str:built=Built_From"
+ relations: "EDAM: EMBOSS report"
+ ]
+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
+***************
+*** 20,25 ****
+--- 20,26 ----
+ blast_protein_dbname | string | "EDAM: BLAST database name" | Blast protein database name
+ caf_project | file | "EDAM: Common Assembly Format (CAF) project file" | CAF assembly project file
+ cds_sequence | sequence | "EDAM: Nucleotide sequence" | Coding
++ cirdna_mapping_commands | file | | Commands to the cirdna drawing program
+ clique_input | file | "EDAM: PHYLIP discrete states file" | Phylip clique program input
+ clique_output | file | "EDAM: PHYLIP cliques file" | Phylip clique program output
+ 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
+***************
+*** 31,39 ****
+ help: "By default any feature in the feature table with a type
+ starting 'repeat' is masked. You can set this to be any feature
+ type you wish to mask. \
+! See http://www3.ebi.ac.uk/Services/WebFeat/ for a list of the EMBL
+ feature types and see Appendix A of the Swissprot user manual in
+! http://www.expasy.ch/txt/userman.txt for a list of the Swissprot
+ feature types. \
+ The type may be wildcarded by using '*'. \
+ If you wish to mask more than one type, separate their names with
+--- 31,39 ----
+ help: "By default any feature in the feature table with a type
+ starting 'repeat' is masked. You can set this to be any feature
+ type you wish to mask. \
+! See http://www.ebi.ac.uk/embl/WebFeat/ for a list of the EMBL
+ feature types and see Appendix A of the Swissprot user manual in
+! http://www.expasy.org/sprot/userman.html for a list of the Swissprot
+ feature types. \
+ The type may be wildcarded by using '*'. \
+ 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
+***************
+*** 91,97 ****
+ integer: maxcuts [
+ additional: "Y"
+ minimum: "$(mincuts)"
+- maximum: "2000000000"
+ default: "2000000000"
+ information: "Maximum cuts per RE"
+ help: "This sets the maximum number of cuts for any restriction
+--- 91,96 ----
+diff -c -N --recursive -a EMBOSS-6.2.0old/emboss/acd/restover.acd EMBOSS-6.2.0/emboss/acd/restover.acd
+*** EMBOSS-6.2.0old/emboss/acd/restover.acd 2009-10-12 15:42:43.000000000 +0100
+--- EMBOSS-6.2.0/emboss/acd/restover.acd 2010-03-02 09:34:07.000000000 +0000
+***************
+*** 61,67 ****
+
+ integer: max [
+ minimum: "$(min)"
+- maximum: "2000000000"
+ default: "2000000000"
+ information: "Maximum cuts per RE"
+ relations: "EDAM: Generic integer"
+--- 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
+***************
+*** 97,103 ****
+
+ integer: max [
+ minimum: "$(min)"
+- maximum: "2000000000"
+ default: "2000000000"
+ information: "Maximum cuts per RE"
+ help: "This sets the maximum number of cuts for any restriction
+--- 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
+***************
+*** 47,55 ****
+ information: "Type of feature to display"
+ help: "By default any feature type in the feature table is shown.
+ You can set this to match any feature type you wish to show. \
+! See http://www3.ebi.ac.uk/Services/WebFeat/ for a list of the EMBL
+ feature types and see Appendix A of the Swissprot user manual in
+! http://www.expasy.ch/txt/userman.txt for a list of the Swissprot
+ feature types. \
+ The type may be wildcarded by using '*'. \
+ If you wish to show more than one type, separate their names with
+--- 47,55 ----
+ information: "Type of feature to display"
+ help: "By default any feature type in the feature table is shown.
+ You can set this to match any feature type you wish to show. \
+! See http://www.ebi.ac.uk/embl/WebFeat/ for a list of the EMBL
+ feature types and see Appendix A of the Swissprot user manual in
+! http://www.expasy.org/sprot/userman.html for a list of the Swissprot
+ feature types. \
+ The type may be wildcarded by using '*'. \
+ 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
+***************
+*** 152,161 ****
+ help: "By default any feature type in the feature table is
+ shown. You can set this to match any feature type you wish to
+ show. \
+! See http://www3.ebi.ac.uk/Services/WebFeat/ for a list of the
+ EMBL feature types and see Appendix A of the Swissprot user
+! manual in http://www.expasy.ch/txt/userman.txt for a list of the
+! Swissprot feature types. \
+ The type may be wildcarded by using '*'. \
+ If you wish to show more than one type, separate their names
+ with the character '|', eg: \
+--- 152,161 ----
+ help: "By default any feature type in the feature table is
+ shown. You can set this to match any feature type you wish to
+ show. \
+! See http://www.ebi.ac.uk/embl/WebFeat/ for a list of the
+ EMBL feature types and see Appendix A of the Swissprot user
+! manual in http://www.expasy.org/sprot/userman.html
+! for a list of the Swissprot feature types. \
+ The type may be wildcarded by using '*'. \
+ If you wish to show more than one type, separate their names
+ 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
+***************
+*** 249,258 ****
+ help: "By default any feature type in the feature table is
+ shown. You can set this to match any feature type you wish to
+ show. \
+! See http://www3.ebi.ac.uk/Services/WebFeat/ for a list of the
+ EMBL feature types and see Appendix A of the Swissprot user
+! manual in http://www.expasy.ch/txt/userman.txt for a list of the
+! Swissprot feature types. \
+ The type may be wildcarded by using '*'. \
+ If you wish to show more than one type, separate their names
+ with the character '|', eg: \
+--- 249,258 ----
+ help: "By default any feature type in the feature table is
+ shown. You can set this to match any feature type you wish to
+ show. \
+! See http://www.ebi.ac.uk/embl/WebFeat/ for a list of the
+ EMBL feature types and see Appendix A of the Swissprot user
+! manual in http://www.expasy.org/sprot/userman.html
+! for a list of the Swissprot feature types. \
+ The type may be wildcarded by using '*'. \
+ If you wish to show more than one type, separate their names
+ with the character '|', eg: \
+***************
+*** 264,269 ****
+--- 264,271 ----
+ integer: sensematch [
+ additional: "Y"
+ default: "0"
++ minimum: "-1"
++ maximum: "1"
+ information: "Sense of feature to display"
+ expected: "0 - any sense, 1 - forward sense, -1 - reverse
+ sense"
+***************
+*** 387,393 ****
+
+ integer: maxcuts [
+ minimum: "$(mincuts)"
+- maximum: "2000000000"
+ default: "2000000000"
+ information: "Maximum cuts per RE"
+ help: "This sets the maximum number of cuts for any restriction
+--- 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
+***************
+*** 26,31 ****
+--- 26,32 ----
+ integer: window [
+ additional: "Y"
+ default: "1"
++ maximum: "$(sequence.length)"
+ information: "Window size"
+ help: "This determines the size of the region that is considered
+ 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
+***************
+*** 45,54 ****
+ information: "Type of first feature"
+ help: "By default every feature in the feature table is allowed.
+ You can set this to be any feature type you wish to allow. \
+! See http://www3.ebi.ac.uk/Services/WebFeat/ for a list of the
+ EMBL feature types and see Appendix A of the Swissprot user
+! manual in http://www.expasy.ch/txt/userman.txt for a list of the
+! Swissprot feature types. \
+ The type may be wildcarded by using '*'. \
+ If you wish to allow more than one type, separate their names
+ with the character '|', eg: \
+--- 45,54 ----
+ information: "Type of first feature"
+ help: "By default every feature in the feature table is allowed.
+ You can set this to be any feature type you wish to allow. \
+! See http://www.ebi.ac.uk/embl/WebFeat/ for a list of the
+ EMBL feature types and see Appendix A of the Swissprot user
+! manual in http://www.expasy.org/sprot/userman.html
+! for a list of the Swissprot feature types. \
+ The type may be wildcarded by using '*'. \
+ If you wish to allow more than one type, separate their names
+ with the character '|', eg: \
+***************
+*** 168,177 ****
+ information: "Type of second feature"
+ help: "By default every feature in the feature table is allowed.
+ You can set this to be any feature type you wish to allow. \
+! See http://www3.ebi.ac.uk/Services/WebFeat/ for a list of the
+ EMBL feature types and see Appendix A of the Swissprot user
+! manual in http://www.expasy.ch/txt/userman.txt for a list of the
+! Swissprot feature types. \
+ The type may be wildcarded by using '*'. \
+ If you wish to allow more than one type, separate their names
+ with the character '|', eg: \
+--- 168,177 ----
+ information: "Type of second feature"
+ help: "By default every feature in the feature table is allowed.
+ You can set this to be any feature type you wish to allow. \
+! See http://www.ebi.ac.uk/embl/WebFeat/ for a list of the
+ EMBL feature types and see Appendix A of the Swissprot user
+! manual in http://www.expasy.org/sprot/userman.html
+! for a list of the Swissprot feature types. \
+ The type may be wildcarded by using '*'. \
+ If you wish to allow more than one type, separate their names
+ with the character '|', eg: \
+***************
+*** 385,393 ****
+ found should be reported as one feature in the ouput, then you can
+ specify the 'type' name of the new feature here. By default every
+ feature in the feature table is allowed. See
+! http://www3.ebi.ac.uk/Services/WebFeat/ for a list of the EMBL
+ feature types and see Appendix A of the Swissprot user manual in
+! http://www.expasy.ch/txt/userman.txt for a list of the Swissprot
+ feature types. If you specify an invalid feature type name, then
+ the default name 'misc_feature' is used."
+ knowntype: "feature key"
+--- 385,393 ----
+ found should be reported as one feature in the ouput, then you can
+ specify the 'type' name of the new feature here. By default every
+ feature in the feature table is allowed. See
+! http://www.ebi.ac.uk/embl/WebFeat/ for a list of the EMBL
+ feature types and see Appendix A of the Swissprot user manual in
+! http://www.expasy.org/sprot/userman.html for a list of the Swissprot
+ feature types. If you specify an invalid feature type name, then
+ the default name 'misc_feature' is used."
+ 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
+***************
+*** 121,188 ****
+ imrna = 0;
+ itran = 0;
+ irest = 0;
+ feat = ajSeqGetFeat(seq);
+! if(seqoutrest)
+ {
+! copyseq = ajSeqGetSeqCopyS(seq);
+! ajStrFmtUpper(©seq);
+! }
+
+! iter = ajListIterNewread(feat->Features);
+! while(!ajListIterDone(iter))
+! {
+! gf = ajListIterGet(iter);
+! if(ajFeatIsChild(gf))
+! continue;
+! if(seqoutcds && ajFeatTypeMatchC(gf, "CDS"))
+ {
+! icds++;
+! ret = ajFeatGetSeqJoin(gf, feat, seq, &cds);
+! if(!ret)
+! {
+! ajWarn("Cannot extract %S\n",ajSeqGetNameS(seq));
+! continue;
+! }
+! coderet_put_seq(seq,cds,icds,"cds",0,seqoutcds);
+! }
+
+! if(seqoutmrna && ajFeatTypeMatchC(gf, "mRNA"))
+! {
+! imrna++;
+! ret = ajFeatGetSeqJoin(gf, feat, seq, &mrna);
+! if(!ret)
+ {
+! ajWarn("Cannot extract %s",ajSeqGetNameC(seq));
+! continue;
+ }
+- coderet_put_seq(seq,mrna,imrna,"mrna",0,seqoutmrna);
+- }
+
+
+! if(seqoutrest) /* set feature to lowercase */
+! {
+
+! if(ajFeatTypeMatchC(gf, "CDS") ||
+! ajFeatTypeMatchC(gf, "mRNA") ||
+! ajFeatTypeMatchC(gf, "exon"))
+! ajFeatLocMark(gf, feat, ©seq);
+! else
+! irest++;
+! }
+
+! if(seqoutprot && ajFeatTypeMatchC(gf, "CDS"))
+! {
+! if(ajFeatGetTranslation(gf, &trnseq))
+ {
+! itran++;
+! coderet_put_seq(seq, trnseq, itran,"pro",1,seqoutprot);
+ }
+ }
+ }
+- ajListIterDel(&iter);
+-
+- if(seqoutrest)
+- coderet_put_rest(seq,copyseq,"noncoding",seqoutrest);
+
+ if(seqoutcds)
+ ajFmtPrintF(logf, "%6d", icds);
+--- 121,193 ----
+ imrna = 0;
+ itran = 0;
+ irest = 0;
++
+ feat = ajSeqGetFeat(seq);
+!
+! if(feat)
+ {
+! if(seqoutrest)
+! {
+! copyseq = ajSeqGetSeqCopyS(seq);
+! ajStrFmtUpper(©seq);
+! }
+
+! iter = ajListIterNewread(feat->Features);
+! while(!ajListIterDone(iter))
+ {
+! gf = ajListIterGet(iter);
+! if(ajFeatIsChild(gf))
+! continue;
+! if(seqoutcds && ajFeatTypeMatchC(gf, "CDS"))
+! {
+! icds++;
+! ret = ajFeatGetSeqJoin(gf, feat, seq, &cds);
+! if(!ret)
+! {
+! ajWarn("Cannot extract %S\n",ajSeqGetNameS(seq));
+! continue;
+! }
+! coderet_put_seq(seq,cds,icds,"cds",0,seqoutcds);
+! }
+
+! if(seqoutmrna && ajFeatTypeMatchC(gf, "mRNA"))
+ {
+! imrna++;
+! ret = ajFeatGetSeqJoin(gf, feat, seq, &mrna);
+! if(!ret)
+! {
+! ajWarn("Cannot extract %s",ajSeqGetNameC(seq));
+! continue;
+! }
+! coderet_put_seq(seq,mrna,imrna,"mrna",0,seqoutmrna);
+ }
+
+
+! if(seqoutrest) /* set feature to lowercase */
+! {
+
+! if(ajFeatTypeMatchC(gf, "CDS") ||
+! ajFeatTypeMatchC(gf, "mRNA") ||
+! ajFeatTypeMatchC(gf, "exon"))
+! ajFeatLocMark(gf, feat, ©seq);
+! else
+! irest++;
+! }
+
+! if(seqoutprot && ajFeatTypeMatchC(gf, "CDS"))
+ {
+! if(ajFeatGetTranslation(gf, &trnseq))
+! {
+! itran++;
+! coderet_put_seq(seq, trnseq, itran,"pro",1,seqoutprot);
+! }
+ }
+ }
++ ajListIterDel(&iter);
++
++ if(seqoutrest)
++ coderet_put_rest(seq,copyseq,"noncoding",seqoutrest);
+ }
+
+ if(seqoutcds)
+ 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
+***************
+*** 390,406 ****
+
+ /* ajFmtError("..%s..\n\n", ajStrGetPtr( cmd)); */
+ ajDebug("Executing '%S'\n", cmd);
+! #ifndef WIN32
+! ajSysSystemEnv(cmd, env);
+! #else
+ if(system(ajStrGetPtr(cmd)) == -1)
+ {
+ fprintf(stderr,"Command: %s\n",ajStrGetPtr(cmd));
+ ajFatal("clustalw execution failure");
+ }
+
+- #endif
+-
+ /* produce alignment file only if one was produced */
+ if(!only_dend)
+ {
+--- 390,402 ----
+
+ /* ajFmtError("..%s..\n\n", ajStrGetPtr( cmd)); */
+ ajDebug("Executing '%S'\n", cmd);
+!
+ if(system(ajStrGetPtr(cmd)) == -1)
+ {
+ fprintf(stderr,"Command: %s\n",ajStrGetPtr(cmd));
+ ajFatal("clustalw execution failure");
+ }
+
+ /* produce alignment file only if one was produced */
+ if(!only_dend)
+ {
+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
+***************
+*** 22,70 ****
+
+ #include "emboss.h"
+
+
+
+
+! /* @datastatic JaspDir **************************************************
+ **
+ ** JASPAR data directory structure
+ **
+! ** @alias JaspSDir
+! ** @alias JaspODir
+ **
+! ** @attr namactual [AjPStr] name of Jaspar source subdirectory
+! ** @attr namdata [AjPStr] name of Jaspar subdirectory in EMBOSS_DATA area
+ ** @@
+ ******************************************************************************/
+
+! typedef struct JaspSDir
+ {
+! AjPStr namactual;
+! AjPStr namdata;
+! } JaspODir;
+! #define JaspPDir JaspODir*
+!
+!
+
+
+- static void jaspextract_check(const AjPStr directory, AjPList dlist);
+- static void jaspextract_copy(AjPList dlist);
+-
+- static void jaspextract_jddel(JaspPDir *thys);
+- static JaspPDir jaspextract_jdnew(void);
+
+
+
+!
+! static const char *jdirnames[] = {
+! "JASPAR_CORE",
+! "JASPAR_FAM",
+! "JASPAR_PHYLOFACTS",
+! "JASPAR_CNE",
+! "JASPAR_POLII",
+! "JASPAR_SPLICE",
+! NULL
+! };
+
+
+
+--- 22,79 ----
+
+ #include "emboss.h"
+
++ #ifdef WIN32
++ #include <direct.h>
++ #endif
+
++ #define PFMNUMGUESS 2000
++ #define MATRIXFILE "matrix_list.txt"
+
+
+!
+!
+! /* @datastatic JaspPrefix **************************************************
+ **
+ ** JASPAR data directory structure
+ **
+! ** @alias SJaspPrefix
+! ** @alias OJaspPrefix
+ **
+! ** @attr Prefix [const char*] Filename prefix of pfm files
+! ** @attr Directory [const char*] Directory name for files of a given prefix
+ ** @@
+ ******************************************************************************/
+
+! typedef struct SJaspPrefix
+ {
+! const char* Prefix;
+! const char* Directory;
+! } OJaspPrefix;
+
++ static OJaspPrefix Jprefix[] =
++ {
++ {"PB", "JASPAR_PBM"},
++ {"PL", "JASPAR_PBM_HLH"},
++ {"PH", "JASPAR_PBM_HOMEO"},
++ {"MA", "JASPAR_CORE"},
++ {"CN", "JASPAR_CNE"},
++ {"MF", "JASPAR_FAM"},
++ {"PF", "JASPAR_PHYLOFACTS"},
++ {"POL", "JASPAR_POLII"},
++ {"SA", "JASPAR_SPLICE"},
++ {"SD", "JASPAR_SPLICE"},
++ {NULL, NULL}
++ };
+
+
+
+
+! static void jaspextract_openoutdirs(void);
+! static void jaspextract_copyfiles(AjPStr directory);
+! static void jaspextract_readmatrixlist(AjPTable mtable, const AjPStr directory);
+! static void jaspextract_getjaspdirs(AjPList jdirlist);
+! static void jaspextract_writematrixfile(const AjPTable mtable,
+! const AjPStr directory);
+
+
+
+***************
+*** 81,101 ****
+
+ int main(int argc, char **argv)
+ {
+ AjPStr directory = NULL;
+! AjPList dlist = NULL;
+
+ embInit("jaspextract",argc,argv);
+
+ directory = ajAcdGetDirectoryName("directory");
+
+! dlist = ajListNew();
+
+! jaspextract_check(directory, dlist);
+
+! jaspextract_copy(dlist);
+
+ ajStrDel(&directory);
+!
+ embExit();
+
+ return 0;
+--- 90,126 ----
+
+ int main(int argc, char **argv)
+ {
++
+ AjPStr directory = NULL;
+! AjPTable mtable = NULL;
+!
+! AjPList jdirlist = NULL;
+! AjPStr jdirloc = NULL;
+
+ embInit("jaspextract",argc,argv);
+
+ directory = ajAcdGetDirectoryName("directory");
+
+! mtable = ajTablestrNewLen(PFMNUMGUESS);
+! jdirlist = ajListNew();
+
+! jaspextract_openoutdirs();
+! jaspextract_copyfiles(directory);
+
+! jaspextract_readmatrixlist(mtable, directory);
+!
+! jaspextract_getjaspdirs(jdirlist);
+
++ while(ajListPop(jdirlist,(void **)&jdirloc))
++ {
++ jaspextract_writematrixfile(mtable, jdirloc);
++ ajStrDel(&jdirloc);
++ }
++
++ ajTablestrFree(&mtable);
+ ajStrDel(&directory);
+! ajListFree(&jdirlist);
+!
+ embExit();
+
+ return 0;
+***************
+*** 104,311 ****
+
+
+
+! /* @funcstatic jaspextract_check ***********************************************
+ **
+! ** Checks whether specific JASPAR subdirectories exist
+! **
+! ** @param [r] directory [const AjPStr] jaspar directory
+! ** @param [w] dlist [AjPList] jaspar directory list
+ **
+ ** @return [void]
+ ** @@
+ ******************************************************************************/
+
+! static void jaspextract_check(const AjPStr directory, AjPList dlist)
+ {
+! AjPStr entry = NULL;
+! AjPStr nbase = NULL;
+
+! AjPList flist = NULL;
+! ajint i = 0;
+
+! JaspPDir jdir = NULL;
+
+
+
+- flist = ajListNew();
+
+
+! ajFilelistAddPathDir(flist, directory);
+
+
+ while(ajListPop(flist,(void **)&entry))
+ {
+! ajDebug("jaspextract_check '%S'\n", entry);
+
+- if(!ajFilenameExistsRead(entry))
+- continue;
+-
+- ajStrAssignS(&nbase,entry);
+- ajFilenameTrimPath(&nbase);
+-
+ i = 0;
+! while(jdirnames[i])
+ {
+! if(ajStrPrefixC(nbase,jdirnames[i]))
+ {
+! jdir = jaspextract_jdnew();
+! ajStrAssignS(&jdir->namactual,entry);
+! ajStrAssignC(&jdir->namdata,jdirnames[i]);
+! ajListPush(dlist,(void *)jdir);
+! ajDebug("found %d: '%s' => '%S' '%S'\n",
+! i, jdirnames[i], jdir->namactual, jdir->namdata);
+ }
+!
+
+ ++i;
+ }
+
+! ajStrDel(&entry);
+! }
+
+
+! ajStrDel(&nbase);
+
+ ajListFree(&flist);
+
+ return;
+ }
+
+
+
+
+! /* @funcstatic jaspextract_copy ***********************************************
+ **
+! ** Copy datafile into the EMBOSS data area
+ **
+! ** @param [u] dlist [AjPList] jaspar directory list
+ **
+ ** @return [void]
+ ** @@
+ ******************************************************************************/
+
+! static void jaspextract_copy(AjPList dlist)
+ {
+! AjPStr wild = NULL;
+! AjPList flist = NULL;
+! AjPStr entry = NULL;
+! AjPStr nbase = NULL;
+! AjPStr dfile = NULL;
+! AjPFile inf = NULL;
+! AjPFile outf = NULL;
+! AjPStr line = NULL;
+
+! JaspPDir jdir = NULL;
+
+
+- wild = ajStrNewC("*");
+- flist = ajListNew();
+- nbase = ajStrNew();
+- dfile = ajStrNew();
+- line = ajStrNew();
+
+
+
+
+! while(ajListPop(dlist,(void **)&jdir))
+ {
+! ajFilelistAddPathWild(flist, jdir->namactual,wild);
+! ajDebug("jaspextract_copy '%S' '%S'\n",
+! jdir->namactual, wild);
+! while(ajListPop(flist,(void **)&entry))
+ {
+! ajStrAssignS(&nbase,entry);
+! ajFilenameTrimPath(&nbase);
+! ajFmtPrintS(&dfile,"%S%c%S",jdir->namdata,SLASH_CHAR,nbase);
+! ajDebug("copying '%S' => '%S'\n",
+! entry, dfile);
+! /* Avoid UNIX copy for portability */
+! inf = ajFileNewInNameS(entry);
+! if(!inf)
+! ajFatal("Cannot open input file: %S",entry);
+!
+! outf = ajDatafileNewOutNameS(dfile);
+! if(!outf)
+! ajFatal("Cannot open output file: %S",dfile);
+!
+! while(ajReadlineTrim(inf,&line))
+! ajFmtPrintF(outf,"%S\n",line);
+!
+! ajFileClose(&inf);
+! ajFileClose(&outf);
+!
+! ajStrDel(&entry);
+ }
+
+! jaspextract_jddel(&jdir);
+ }
+
+
+! ajListFree(&flist);
+! ajListFree(&dlist);
+
+! ajStrDel(&wild);
+! ajStrDel(&dfile);
+! ajStrDel(&nbase);
+ ajStrDel(&line);
+!
+ return;
+ }
+
+
+
+
+! /* @funcstatic jaspextract_jdnew ***********************************************
+ **
+! ** Create a jaspar directory structure
+ **
+! ** @return [JaspPDir] Jaspar directory structure
+ ** @@
+ ******************************************************************************/
+
+! static JaspPDir jaspextract_jdnew(void)
+ {
+! JaspPDir ret = NULL;
+
+! AJNEW(ret);
+
+! ret->namactual = ajStrNew();
+! ret->namdata = ajStrNew();
+
+! return ret;
+ }
+
+
+
+
+! /* @funcstatic jaspextract_jddel ***********************************************
+ **
+! ** Delete a Jaspar directory structure
+ **
+! ** @param [w] thys [JaspPDir*] jaspar directory structure
+ **
+ ** @return [void]
+ ** @@
+ ******************************************************************************/
+
+! static void jaspextract_jddel(JaspPDir *thys)
+ {
+! JaspPDir pthis = NULL;
+
+! if(!thys)
+! return;
+
+! if(!*thys)
+! return;
+!
+! pthis = *thys;
+
+! ajStrDel(&pthis->namactual);
+! ajStrDel(&pthis->namdata);
+! AJFREE(*thys);
+
+! *thys = NULL;
+
+ return;
+ }
+-
+--- 129,477 ----
+
+
+
+! /* @funcstatic jaspextract_openoutdirs **************************************
+ **
+! ** Checks whether JASPAR output subdirectories exist in the current
+! ** EMBOSS data area. Create them if not. Open them.
+ **
+ ** @return [void]
+ ** @@
+ ******************************************************************************/
+
+! static void jaspextract_openoutdirs(void)
+ {
+! const AjPStr datadir = NULL;
+! AjPStr dir = NULL;
+! const char *p = NULL;
+
+! ajuint i = 0;
+!
+! datadir = ajDatafileValuePath();
+! if(!datadir)
+! ajFatal("jaspextract: Cannot determine the EMBOSS data directory");
+!
+! dir = ajStrNew();
+!
+! i = 0;
+!
+! while(Jprefix[i].Directory)
+! {
+! ajFmtPrintS(&dir,"%S%s",datadir,Jprefix[i].Directory);
+!
+! if(!ajFilenameExistsDir(dir))
+! {
+! p = ajStrGetPtr(dir);
+! #ifndef WIN32
+! mkdir(p,0755);
+! #else
+! _mkdir(p);
+! #endif
+! }
+!
+! if(!ajFilenameExistsDir(dir))
+! ajFatal("jaspextract: No such directory %S",
+! dir);
+!
+! ++i;
+! }
+!
+! ajStrDel(&dir);
+!
+! return;
+! }
+!
+!
+!
+!
+! /* @funcstatic jaspextract_copyfiles *****************************************
+! **
+! ** Copy datafiles into the EMBOSS data area
+! **
+! ** @param [u] directory [AjPStr] jaspar source flatfile directory
+! **
+! ** @return [void]
+! ** @@
+! ******************************************************************************/
+
+! static void jaspextract_copyfiles(AjPStr directory)
+! {
+! AjPStr matrixfile = NULL;
+! AjPList flist = NULL;
+
++ AjPStr wild = NULL;
++ AjPStr entry = NULL;
++ AjPStr bname = NULL;
++ AjPStr line = NULL;
++ AjPStr dest = NULL;
++
++ const AjPStr datadir = NULL;
++
++ ajuint preflen = 0;
++ ajuint i = 0;
++ const char *p = NULL;
++
++ AjPFile inf = NULL;
++ AjPFile outf = NULL;
+
++ matrixfile = ajStrNew();
++ flist = ajListNew();
++ wild = ajStrNewC("*.pfm");
++ bname = ajStrNew();
++ line = ajStrNew();
++ dest = ajStrNew();
+
+
++ datadir = ajDatafileValuePath();
++ if(!datadir)
++ ajFatal("jaspextract: Cannot determine the EMBOSS data directory");
++
++ ajFmtPrintS(&matrixfile,"%S%s",directory,MATRIXFILE);
+
+! if(!ajFilenameExistsRead(matrixfile))
+! ajFatal("jaspextract: Directory (%S) doesn't appear to be a JASPAR "
+! "one\nNo matrix_list.txt file found",directory);
+!
+! ajFilelistAddPathWild(flist, directory, wild);
+
+
+ while(ajListPop(flist,(void **)&entry))
+ {
+! ajStrAssignS(&bname,entry);
+! ajFilenameTrimPath(&bname);
+
+ i = 0;
+!
+! while(Jprefix[i].Prefix)
+ {
+! if(!ajStrPrefixC(bname,Jprefix[i].Prefix))
+ {
+! ++i;
+! continue;
+ }
+!
+! preflen = strlen(Jprefix[i].Prefix);
+! p = ajStrGetPtr(bname);
+! if(p[preflen]>='0' && p[preflen]<='9')
+! break;
+
+ ++i;
+ }
+
+! if(!Jprefix[i].Prefix)
+! {
+! ajStrDel(&entry);
+! continue;
+! }
+!
+!
+! ajFmtPrintS(&dest,"%S%s%c%S",datadir,Jprefix[i].Directory,SLASH_CHAR,
+! bname);
+
++ outf = ajFileNewOutNameS(dest);
++ if(!outf)
++ ajFatal("Cannot open output file %S",dest);
++
++ /* Avoid UNIX copy for portability */
++ inf = ajFileNewInNameS(entry);
++ if(!inf)
++ ajFatal("Cannot open input file: %S",entry);
+
+! while(ajReadlineTrim(inf,&line))
+! ajFmtPrintF(outf,"%S\n",line);
+
++ ajFileClose(&inf);
++ ajFileClose(&outf);
++
++ ajStrDel(&entry);
++
++ }
++
+ ajListFree(&flist);
+
++ ajStrDel(&wild);
++ ajStrDel(&dest);
++ ajStrDel(&line);
++ ajStrDel(&bname);
++ ajStrDel(&matrixfile);
++
+ return;
+ }
+
+
+
+
+! /* @funcstatic jaspextract_readmatrixlist *************************************
+ **
+! ** Read the matrix_list.txt file
+ **
+! ** @param [u] mtable [AjPTable] Table for pfm entry descriptions
+! ** @param [r] directory [const AjPStr] Directory containing matrix_list.txt
+ **
+ ** @return [void]
+ ** @@
+ ******************************************************************************/
+
+! static void jaspextract_readmatrixlist(AjPTable mtable, const AjPStr directory)
+ {
+! const AjPStr datadir = NULL;
+!
+! AjPStr matrixfile = NULL;
+! AjPFile inf = NULL;
+
+! AjPStr line = NULL;
+! AjPStr key = NULL;
+! AjPStr value = NULL;
+
++ matrixfile = ajStrNew();
+
+
++ datadir = ajDatafileValuePath();
++ if(!datadir)
++ ajFatal("jaspextract: Cannot determine the EMBOSS data directory");
++
++ ajFmtPrintS(&matrixfile,"%S%s",directory,MATRIXFILE);
++
++ if(!ajFilenameExistsRead(matrixfile))
++ ajFatal("jaspextract: Directory (%S) doesn't appear to be a JASPAR "
++ "one\nNo matrix_list.txt file found",directory);
+
+
++ inf = ajFileNewInNameS(matrixfile);
++ if(!inf)
++ ajFatal("Cannot open input file: %S",matrixfile);
+
+! while(ajReadline(inf,&line))
+ {
+! key = ajStrNew();
+!
+! if(ajFmtScanS(line,"%S",&key) != 1)
+ {
+! ajStrDel(&key);
+! continue;
+ }
+
+! value = ajStrNew();
+! ajStrAssignS(&value,line);
+!
+! ajTablePut(mtable,(void *)key, (void *)value);
+ }
+
+
+! ajFileClose(&inf);
+
+! ajStrDel(&matrixfile);
+ ajStrDel(&line);
+!
+ return;
+ }
+
+
+
+
+! /* @funcstatic jaspextract_getjaspdirs ****************************************
+! **
+! ** Construct a list of JASPAR_ directory locations in the EMBOSS data area
+ **
+! ** @param [u] jdirlist [AjPList] List for JASPAR_ directory locations
+ **
+! ** @return [void]
+ ** @@
+ ******************************************************************************/
+
+! static void jaspextract_getjaspdirs(AjPList jdirlist)
+ {
+! const AjPStr datadir = NULL;
+! AjPStr line = NULL;
+!
+! ajuint n = 0;
+! ajuint i = 0;
+!
+! datadir = ajDatafileValuePath();
+! if(!datadir)
+! ajFatal("jaspextract: Cannot determine the EMBOSS data directory");
+!
+
+! n = ajFilelistAddPathDir(jdirlist, datadir);
+!
+!
+! for(i=0; i < n; ++i)
+! {
+! ajListPop(jdirlist,(void **)&line);
+
+! if(ajStrFindC(line,"JASPAR_") != -1)
+! ajListPushAppend(jdirlist,(void *)line);
+! else
+! ajStrDel(&line);
+! }
+
+! return;
+ }
+
+
+
+
+! /* @funcstatic jaspextract_writematrixfile **********************************
+ **
+! ** Writes a matrix_list.txt file in a JASPAR_ directory
+ **
+! ** @param [r] mtable [const AjPTable] Table of matrix definitions
+! ** @param [r] directory [const AjPStr] JASPAR_ directory location
+ **
+ ** @return [void]
+ ** @@
+ ******************************************************************************/
+
+! static void jaspextract_writematrixfile(const AjPTable mtable,
+! const AjPStr directory)
+ {
+! AjPStr wild = NULL;
+! AjPList flist = NULL;
+! AjPStr key = NULL;
+! AjPStr fname = NULL;
+! AjPStr dest = NULL;
+! AjPStr value = NULL;
+!
+! AjPFile outf = NULL;
+!
+! const char *p = NULL;
+! char *q = NULL;
+!
+! wild = ajStrNewC("*.pfm");
+! flist = ajListNew();
+! key = ajStrNew();
+! dest = ajStrNew();
+!
+! ajFmtPrintS(&dest,"%S%c%s",directory,SLASH_CHAR,MATRIXFILE);
+!
+! outf = ajFileNewOutNameS(dest);
+! if(!outf)
+! ajFatal("Cannot open output file %S",dest);
+
+! ajFilelistAddPathWild(flist, directory, wild);
+
+! while(ajListPop(flist,(void**)&fname))
+! {
+! ajFilenameTrimPath(&fname);
+
+! p = ajStrGetPtr(fname);
+! q = strrchr(p,(int)'.');
+! ajStrAssignSubC(&key,p,0,q-p-1);
+!
+! value = (AjPStr) ajTableFetch(mtable, (const void *)key);
+
+! if(value)
+! ajFmtPrintF(outf,"%S",value);
+
++ ajStrDel(&fname);
++ }
++
++
++ ajFileClose(&outf);
++
++ ajStrDel(&wild);
++ ajStrDel(&dest);
++ ajStrDel(&key);
++ ajListFree(&flist);
++
+ return;
+ }
+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
+***************
+*** 36,53 ****
+ #define JASPTAB_GUESS 1000
+
+
+! /* @datastatic AjPJsphits *****************************************************
+ **
+ ** Jaspar hits object
+ **
+ ** Holds hits from scanning a sequence with a Jaspar matrix
+ ** Also holds matrix information and type.
+ **
+! ** AjPJsphits is implemented as a pointer to a C data structure.
+ **
+ ** @alias AjPPStr
+! ** @alias AjSJsphits
+! ** @alias AjOJsphits
+ **
+ ** @attr matname [AjPStr] matrix name
+ ** @attr start [ajuint] start position
+--- 36,53 ----
+ #define JASPTAB_GUESS 1000
+
+
+! /* @datastatic PJsphits *****************************************************
+ **
+ ** Jaspar hits object
+ **
+ ** Holds hits from scanning a sequence with a Jaspar matrix
+ ** Also holds matrix information and type.
+ **
+! ** PJsphits is implemented as a pointer to a C data structure.
+ **
+ ** @alias AjPPStr
+! ** @alias SJsphits
+! ** @alias OJsphits
+ **
+ ** @attr matname [AjPStr] matrix name
+ ** @attr start [ajuint] start position
+***************
+*** 61,67 ****
+ ** @@
+ ******************************************************************************/
+
+! typedef struct AjSJspHits {
+ AjPStr matname;
+ ajuint start;
+ ajuint end;
+--- 61,67 ----
+ ** @@
+ ******************************************************************************/
+
+! typedef struct SJsphits {
+ AjPStr matname;
+ ajuint start;
+ ajuint end;
+***************
+*** 71,92 ****
+ float maxscore;
+ char type;
+ char Padding[7];
+! } AjOJsphits;
+! #define AjPJsphits AjOJsphits*
+
+
+
+
+! /* @datastatic AjPJspmat ******************************************************
+ **
+ ** Jaspar matrix object
+ **
+ ** Also holds matrix information and type from the matrix_list.txt file
+ **
+! ** AjPJspmat is implemented as a pointer to a C data structure.
+ **
+! ** @alias AjSJspmat
+! ** @alias AjOJspmat
+ **
+ ** @attr id [AjPStr] Identifier
+ ** @attr num [AjPStr] Information content (very close to optional content value)
+--- 71,92 ----
+ float maxscore;
+ char type;
+ char Padding[7];
+! } OJsphits;
+! #define PJsphits OJsphits*
+
+
+
+
+! /* @datastatic PJspmat ******************************************************
+ **
+ ** Jaspar matrix object
+ **
+ ** Also holds matrix information and type from the matrix_list.txt file
+ **
+! ** PJspmat is implemented as a pointer to a C data structure.
+ **
+! ** @alias SJspmat
+! ** @alias OJspmat
+ **
+ ** @attr id [AjPStr] Identifier
+ ** @attr num [AjPStr] Information content (very close to optional content value)
+***************
+*** 112,118 ****
+ ** @@
+ ******************************************************************************/
+
+! typedef struct AjSJspmat {
+ AjPStr id;
+ AjPStr num;
+ AjPStr name;
+--- 112,118 ----
+ ** @@
+ ******************************************************************************/
+
+! typedef struct SJspmat {
+ AjPStr id;
+ AjPStr num;
+ AjPStr name;
+***************
+*** 134,141 ****
+ AjPStr consens;
+ char type;
+ char Padding[7];
+! } AjOJspmat;
+! #define AjPJspmat AjOJspmat*
+
+
+
+--- 134,141 ----
+ AjPStr consens;
+ char type;
+ char Padding[7];
+! } OJspmat;
+! #define PJspmat OJspmat*
+
+
+
+***************
+*** 152,167 ****
+ const AjBool both, AjPList hits);
+
+
+! static AjPJsphits jaspscan_hitsnew(void);
+! static void jaspscan_hitsdel(AjPJsphits *thys);
+
+! static AjPJspmat jaspscan_infonew(void);
+! static void jaspscan_infodel(AjPJspmat *thys);
+
+ static AjPTable jaspscan_ReadCoreList(const AjPStr jaspdir);
+ static AjPTable jaspscan_ReadFamList(const AjPStr jaspdir);
+
+! static void jaspscan_coretoken(AjPJspmat info, const AjPStr str);
+ static ajuint jaspscan_readmatrix(const AjPStr mfname, float ***matrix);
+
+ static void jaspscan_ReportHits(AjPFeattable TabRpt, const AjPTable mattab,
+--- 152,167 ----
+ const AjBool both, AjPList hits);
+
+
+! static PJsphits jaspscan_hitsnew(void);
+! static void jaspscan_hitsdel(PJsphits *thys);
+
+! static PJspmat jaspscan_infonew(void);
+! static void jaspscan_infodel(PJspmat *thys);
+
+ static AjPTable jaspscan_ReadCoreList(const AjPStr jaspdir);
+ static AjPTable jaspscan_ReadFamList(const AjPStr jaspdir);
+
+! static void jaspscan_coretoken(PJspmat info, const AjPStr str);
+ static ajuint jaspscan_readmatrix(const AjPStr mfname, float ***matrix);
+
+ static void jaspscan_ReportHits(AjPFeattable TabRpt, const AjPTable mattab,
+***************
+*** 594,600 ****
+ const float threshold,
+ const AjBool both, AjPList hits)
+ {
+! AjPJsphits val = NULL;
+ AjPStr mname = NULL;
+ float **matrix = NULL;
+ ajuint cols;
+--- 594,600 ----
+ const float threshold,
+ const AjBool both, AjPList hits)
+ {
+! PJsphits val = NULL;
+ AjPStr mname = NULL;
+ float **matrix = NULL;
+ ajuint cols;
+***************
+*** 790,802 ****
+ **
+ ** Creates a hits object
+ **
+! ** @return [AjPJsphits] list of hits
+ ** @@
+ ******************************************************************************/
+
+! static AjPJsphits jaspscan_hitsnew(void)
+ {
+! AjPJsphits thys = NULL;
+
+ AJNEW0(thys);
+ thys->matname = ajStrNew();
+--- 790,802 ----
+ **
+ ** Creates a hits object
+ **
+! ** @return [PJsphits] list of hits
+ ** @@
+ ******************************************************************************/
+
+! static PJsphits jaspscan_hitsnew(void)
+ {
+! PJsphits thys = NULL;
+
+ AJNEW0(thys);
+ thys->matname = ajStrNew();
+***************
+*** 811,825 ****
+ **
+ ** Delete a Jaspar hits object
+ **
+! ** @param [w] thys [AjPJsphits*] Jaspar hits object
+ **
+ ** @return [void]
+ ** @@
+ ******************************************************************************/
+
+! static void jaspscan_hitsdel(AjPJsphits *thys)
+ {
+! AjPJsphits pthis;
+
+ pthis = *thys;
+
+--- 811,825 ----
+ **
+ ** Delete a Jaspar hits object
+ **
+! ** @param [w] thys [PJsphits*] Jaspar hits object
+ **
+ ** @return [void]
+ ** @@
+ ******************************************************************************/
+
+! static void jaspscan_hitsdel(PJsphits *thys)
+ {
+! PJsphits pthis;
+
+ pthis = *thys;
+
+***************
+*** 840,846 ****
+ **
+ ** @param [r] jaspdir [const AjPStr] Jaspar directory
+ **
+! ** @return [AjPTable] AjPJspmat objects with matrix ID keys
+ ** @@
+ ******************************************************************************/
+
+--- 840,846 ----
+ **
+ ** @param [r] jaspdir [const AjPStr] Jaspar directory
+ **
+! ** @return [AjPTable] PJspmat objects with matrix ID keys
+ ** @@
+ ******************************************************************************/
+
+***************
+*** 852,858 ****
+ AjPStr key = NULL;
+ AjPStr str = NULL;
+
+! AjPJspmat info = NULL;
+
+ AjPFile inf = NULL;
+ const char *p = NULL;
+--- 852,858 ----
+ AjPStr key = NULL;
+ AjPStr str = NULL;
+
+! PJspmat info = NULL;
+
+ AjPFile inf = NULL;
+ const char *p = NULL;
+***************
+*** 936,942 ****
+ **
+ ** @param [r] jaspdir [const AjPStr] Jaspar directory
+ **
+! ** @return [AjPTable] AjPJspmat objects with matrix ID keys
+ ** @@
+ ******************************************************************************/
+
+--- 936,942 ----
+ **
+ ** @param [r] jaspdir [const AjPStr] Jaspar directory
+ **
+! ** @return [AjPTable] PJspmat objects with matrix ID keys
+ ** @@
+ ******************************************************************************/
+
+***************
+*** 948,954 ****
+ AjPStr key = NULL;
+ AjPStr str = NULL;
+
+! AjPJspmat info = NULL;
+
+ AjPFile inf = NULL;
+ const char *p = NULL;
+--- 948,954 ----
+ AjPStr key = NULL;
+ AjPStr str = NULL;
+
+! PJspmat info = NULL;
+
+ AjPFile inf = NULL;
+ const char *p = NULL;
+***************
+*** 1036,1049 ****
+ **
+ ** Parse matrix_list.txt key/value pairs
+ **
+! ** @param [u] info [AjPJspmat] Jaspar matrix information
+ ** @param [r] str [const AjPStr] key/value pair
+ **
+ ** @return [void]
+ ** @@
+ ******************************************************************************/
+
+! static void jaspscan_coretoken(AjPJspmat info, const AjPStr str)
+ {
+ const char *p;
+ const char *q;
+--- 1036,1049 ----
+ **
+ ** Parse matrix_list.txt key/value pairs
+ **
+! ** @param [u] info [PJspmat] Jaspar matrix information
+ ** @param [r] str [const AjPStr] key/value pair
+ **
+ ** @return [void]
+ ** @@
+ ******************************************************************************/
+
+! static void jaspscan_coretoken(PJspmat info, const AjPStr str)
+ {
+ const char *p;
+ const char *q;
+***************
+*** 1123,1135 ****
+ **
+ ** Creates a hits object
+ **
+! ** @return [AjPJspmat] matrix information
+ ** @@
+ ******************************************************************************/
+
+! static AjPJspmat jaspscan_infonew(void)
+ {
+! AjPJspmat thys = NULL;
+
+ AJNEW0(thys);
+
+--- 1123,1135 ----
+ **
+ ** Creates a hits object
+ **
+! ** @return [PJspmat] matrix information
+ ** @@
+ ******************************************************************************/
+
+! static PJspmat jaspscan_infonew(void)
+ {
+! PJspmat thys = NULL;
+
+ AJNEW0(thys);
+
+***************
+*** 1163,1177 ****
+ **
+ ** Delete a Jaspar information object
+ **
+! ** @param [w] thys [AjPJspmat*] Jaspar hits object
+ **
+ ** @return [void]
+ ** @@
+ ******************************************************************************/
+
+! static void jaspscan_infodel(AjPJspmat *thys)
+ {
+! AjPJspmat pthis;
+
+ pthis = *thys;
+
+--- 1163,1177 ----
+ **
+ ** Delete a Jaspar information object
+ **
+! ** @param [w] thys [PJspmat*] Jaspar hits object
+ **
+ ** @return [void]
+ ** @@
+ ******************************************************************************/
+
+! static void jaspscan_infodel(PJspmat *thys)
+ {
+! PJspmat pthis;
+
+ pthis = *thys;
+
+***************
+*** 1220,1227 ****
+ static void jaspscan_ReportHits(AjPFeattable TabRpt, const AjPTable mattab,
+ AjPList hits)
+ {
+! AjPJsphits hit = NULL;
+! AjPJspmat info = NULL;
+ AjPFeature feat = NULL;
+ AjPStr str = NULL;
+ float fnum = 0.;
+--- 1220,1227 ----
+ static void jaspscan_ReportHits(AjPFeattable TabRpt, const AjPTable mattab,
+ AjPList hits)
+ {
+! PJsphits hit = NULL;
+! PJspmat info = NULL;
+ AjPFeature feat = NULL;
+ AjPStr str = NULL;
+ float fnum = 0.;
+***************
+*** 1345,1351 ****
+
+ static void jaspscan_ClearTable(void **key, void **value, void *cl)
+ {
+! AjPJspmat info = (AjPJspmat) *value;
+ AjPStr skey = (AjPStr) *key;
+
+ ajStrDel(&skey);
+--- 1345,1351 ----
+
+ static void jaspscan_ClearTable(void **key, void **value, void *cl)
+ {
+! PJspmat info = (PJspmat) *value;
+ AjPStr skey = (AjPStr) *key;
+
+ 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
+***************
+*** 1278,1284 ****
+ return ajFalse;
+ }
+
+!
+ close(errpipe[0]);
+ close(errpipe[1]);
+ close(outpipe[0]);
+--- 1278,1288 ----
+ return ajFalse;
+ }
+
+! /*
+! fprintf(stdout,"%s",ajStrGetPtr(outstd));
+! fprintf(stderr,"%s",ajStrGetPtr(errstd));
+! */
+!
+ close(errpipe[0]);
+ close(errpipe[1]);
+ close(outpipe[0]);
+***************
+*** 1342,1347 ****
+--- 1346,1370 ----
+ return ajFalse;
+ }
+
++ if(ajStrGetLen(errstd))
++ {
++ if(!(fp=fopen("stderrfile","w")))
++ {
++ fprintf(stderr,"errfile fopen error (do_batch)\n");
++ jembossctl_fork_tidy(&cl,&prog,&enviro,&dir,&outstd,&errstd);
++ return ajFalse;
++ }
++
++ fprintf(fp,"%s\n",ajStrGetPtr(errstd));
++
++ if(fclose(fp))
++ {
++ fprintf(stderr,"errfile fclose error (do_batch)\n");
++ jembossctl_fork_tidy(&cl,&prog,&enviro,&dir,&outstd,&errstd);
++ return ajFalse;
++ }
++ }
++
+ jembossctl_fork_tidy(&cl,&prog,&enviro,&dir,&outstd,&errstd);
+
+ return ajTrue;
+***************
+*** 1695,1731 ****
+ /* @funcstatic jembossctl_make_array ******************************************
+ **
+ ** Construct argv and env arrays for Ajax.fork
+ **
+! ** @param [r] str [const AjPStr] space separated tokens
+ **
+ ** @return [char**] env or argv array
+ ******************************************************************************/
+
+ static char** jembossctl_make_array(const AjPStr str)
+ {
+! int n;
+! char **ptr = NULL;
+! AjPStr buf;
+! const char *save = NULL;
+
+! buf = ajStrNew();
+
+- n = ajStrParseCountMultiC(str," \t\n");
+
+ AJCNEW0(ptr,n+1);
+
+ ptr[n] = NULL;
+
+! n = 0;
+
+! if(!ajSysFuncStrtokR(ajStrGetPtr(str)," \t\n",&save,&buf))
+! return ptr;
+! ptr[n++] = ajCharNewS(buf);
+
+! while(ajSysFuncStrtokR(NULL," \t\n",&save,&buf))
+! ptr[n++] = ajCharNewS(buf);
+
+ ajStrDel(&buf);
+
+ return ptr;
+ }
+--- 1718,1856 ----
+ /* @funcstatic jembossctl_make_array ******************************************
+ **
+ ** Construct argv and env arrays for Ajax.fork
++ ** N.B. This function converts tabs to spaces and removes
++ ** excess space characters.
+ **
+! ** @param [r] str [const AjPStr] space or doublequote separated tokens
+ **
+ ** @return [char**] env or argv array
+ ******************************************************************************/
+
+ static char** jembossctl_make_array(const AjPStr str)
+ {
+! ajint n = 0;
+! ajint i = 0;
+! ajint len = 0;
+!
+! char **ptr = NULL;
+! const char *p = NULL;
+! const char *q = NULL;
+! char c;
+! AjPStr stmp = NULL;
+! AjPStr buf = NULL;
+!
+
+! n = 0;
+!
+! stmp = ajStrNewS(str);
+!
+! ajStrRemoveWhiteExcess(&stmp);
+!
+! p = ajStrGetPtr(stmp);
+! q = p;
+!
+! /*
+! ** Count the number of tokens
+! */
+!
+! while((c = *p))
+! {
+! if(c == '"')
+! {
+! ++p;
+!
+! while(*p != '"' && *p)
+! ++p;
+!
+! if(*p)
+! ++p;
+!
+! if(*p == ' ')
+! {
+! ++n;
+! ++p;
+! }
+!
+! continue;
+! }
+!
+! if(c == ' ')
+! ++n;
+!
+! ++p;
+! }
+!
+! if(p != q)
+! ++n;
+
+
+ AJCNEW0(ptr,n+1);
+
+ ptr[n] = NULL;
+
+! /* If there are no tokens return an empty NULL terminated list */
+! if(!n)
+! {
+! ajStrDel(&stmp);
+! return ptr;
+! }
+!
+!
+! /*
+! ** Tokenise and create ptr array strings
+! */
+!
+! buf = ajStrNew();
+
+! p = q;
+! n = 0;
+!
+! while((c = *p))
+! {
+!
+! if(c == '"')
+! {
+! ++p;
+! while(*p != '"' && *p)
+! ++p;
+!
+! len = p-q;
+!
+!
+! if(*p)
+! ++p;
+!
+! if(len > 1)
+! ajStrAssignSubC(&buf,q,1,len-1);
+! else
+! ajStrAssignC(&buf,"");
+!
+! ptr[n++] = ajCharNewS(buf);
+!
+! if(*p == ' ')
+! ++p;
+!
+! q = p;
+! continue;
+! }
+!
+! while(*p != ' ' && *p)
+! ++p;
+!
+! len = p-q;
+!
+! ajStrAssignSubC(&buf,q,0,len-1);
+! ptr[n++] = ajCharNewS(buf);
+!
+! if(*p == ' ')
+! ++p;
+
+! q = p;
+! }
+
++
+ ajStrDel(&buf);
++ ajStrDel(&stmp);
+
+ return ptr;
+ }
+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
+***************
+*** 27,33 ****
+
+
+
+-
+ /* @macro matchergap **********************************************************
+ **
+ ** sets k-symbol indel score
+--- 27,32 ----
+***************
+*** 47,54 ****
+ static ajint last; /* Last script op appended */
+
+ static ajint I, J; /* current positions of A ,B */
+- static ajint no_mat; /* number of matches */
+- static ajint no_mis; /* number of mismatches */
+ static ajint al_len; /* length of alignment */
+
+
+--- 46,51 ----
+***************
+*** 256,262 ****
+
+ static void matcher_Sim(AjPAlign align,
+ const char A[], const char B[],
+! const AjPSeq seq1, const AjPSeq seq2, ajuint K,
+ ajint Q, ajint R, ajint beg, ajint beg2, ajint nseq);
+ static ajint matcher_BigPass(const char A[], const char B[],
+ ajint M, ajint N, ajint K,
+--- 253,259 ----
+
+ static void matcher_Sim(AjPAlign align,
+ const char A[], const char B[],
+! const AjPSeq seq0, const AjPSeq seq1, ajuint K,
+ ajint Q, ajint R, ajint beg, ajint beg2, ajint nseq);
+ static ajint matcher_BigPass(const char A[], const char B[],
+ ajint M, ajint N, ajint K,
+***************
+*** 413,422 ****
+ seq1len = ajSeqGetLen(seq1);
+
+ /* allocate space for consensus */
+! i =(AJMIN(ajSeqGetLen(seq0),ajSeqGetLen(seq1)))*2;
+ AJCNEW(seqc0,i);
+ AJCNEW(seqc1,i);
+-
+ /* allocate space for all vectors */
+
+ j = (seq1len + 1) /* * sizeof(ajint)*/;
+--- 410,418 ----
+ seq1len = ajSeqGetLen(seq1);
+
+ /* allocate space for consensus */
+! i = (seq0len+seq1len+1);
+ AJCNEW(seqc0,i);
+ AJCNEW(seqc1,i);
+ /* allocate space for all vectors */
+
+ j = (seq1len + 1) /* * sizeof(ajint)*/;
+***************
+*** 434,440 ****
+ AJCNEW(JJ, i);
+ AJCNEW(XX, i);
+ AJCNEW(YY, i);
+! AJCNEW(S, AJMIN(i,j)*5/4);
+ AJCNEW0(row,(seq0len + 1));
+
+ /* set up list for each row (already zeroed by AJCNEW0 macro) */
+--- 430,436 ----
+ AJCNEW(JJ, i);
+ AJCNEW(XX, i);
+ AJCNEW(YY, i);
+! AJCNEW(S, (i+j));
+ AJCNEW0(row,(seq0len + 1));
+
+ /* set up list for each row (already zeroed by AJCNEW0 macro) */
+***************
+*** 452,458 ****
+ numnode = lmin = 0;
+ matcher_BigPass(A,B,seq0len,seq1len,K,nseq, &numnode);
+
+- ajDebug("Matcher numnode: %d\n", numnode);
+ /* Report the K best alignments one by one. After each alignment is
+ output, recompute part of the matrix. First determine the size
+ of the area to be recomputed, then do the recomputation */
+--- 448,453 ----
+***************
+*** 478,485 ****
+ sapp = S;
+ last = 0;
+ al_len = 0;
+- no_mat = 0;
+- no_mis = 0;
+ matcher_Diff(&A[stari]-1, &B[starj]-1,rl,cl,q,q);
+
+ min0 = stari-1;
+--- 473,478 ----
+***************
+*** 1359,1368 ****
+ {
+ if(midj > 1) MATCHERINS(midj-1)
+ MATCHERREP
+- if(A[1] == B[midj])
+- no_mat += 1;
+- else
+- no_mis += 1;
+
+ /* mark(A[I],B[J]) as used: put J into list row[I] */
+ I++; J++;
+--- 1352,1357 ----
+***************
+*** 1579,1585 ****
+ }
+ }
+ }
+-
+ *sp0 = '\0';
+ *sp1 = '\0';
+ *nident = nid;
+--- 1568,1573 ----
+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
+***************
+*** 434,457 ****
+
+ ajGraphicsGetCharsize(&defheight,¤tscale);
+
+! ajGraphicsSetCharscale(((float)ixlen/((float)(numres+charlen)*
+! (currentscale+(float)1.0)))/
+ currentscale);
+
+ ajGraphicsGetCharsize(&defheight,¤tscale);
+
+ yincr = (currentscale + (float)3.0)*(float)0.3;
+
+ /*
+! ** If we have titles (now the standard graph title and subtitle)
+! ** leave 5 rows of space for them
+ */
+! y=ystart-(float)6.0;
+
+ if(ajStrGetLen(options))
+ {
+ fold = ajGraphicsSetCharscale(1.0);
+! ajGraphicsDrawposTextAtmid(xmid,1.0,
+ ajStrGetPtr(options));
+ ajGraphicsSetCharscale(fold);
+ }
+--- 434,461 ----
+
+ ajGraphicsGetCharsize(&defheight,¤tscale);
+
+! ajGraphicsSetCharscale(((float)ixlen/((float)(numres+charlen+1)*
+! (currentscale * (float) 1.5)))/
+ currentscale);
+
++ /* ajGraphicsSetCharscale(((float)ixlen/((float)(numres+charlen)*
++ (currentscale+(float)1.0)))/
++ currentscale); */
++
+ ajGraphicsGetCharsize(&defheight,¤tscale);
+
+ yincr = (currentscale + (float)3.0)*(float)0.3;
+
+ /*
+! ** If we have titles (now the standard graph title and subtitle and footer)
+! ** leave 7 rows of space for them
+ */
+! y=ystart-(float)7.0;
+
+ if(ajStrGetLen(options))
+ {
+ fold = ajGraphicsSetCharscale(1.0);
+! ajGraphicsDrawposTextAtmid(xmid,2.0,
+ ajStrGetPtr(options));
+ ajGraphicsSetCharscale(fold);
+ }
+***************
+*** 1267,1274 ****
+ if(consensus && (numseq==seqend))
+ {
+ res[0] = constr[k];
+! ajGraphicsDrawposTextAtstart((float)(count+gapcount),
+! y-(yincr*((seqend-seqstart)+1)),res);
+ }
+ }
+
+--- 1271,1280 ----
+ if(consensus && (numseq==seqend))
+ {
+ res[0] = constr[k];
+!
+! /* start -> mid */
+! ajGraphicsDrawposTextAtmid((float) 0.5 + (float)(count+gapcount),
+! y-(yincr*((seqend-seqstart)+1)),res);
+ }
+ }
+
+***************
+*** 1339,1346 ****
+ res[0] = seqcharptr[j][k];
+ else
+ res[0] = '-';
+! ajGraphicsDrawposTextAtstart((float)(count+gapcount),
+! y-(yincr*l),res);
+ }
+ }
+ }
+--- 1345,1354 ----
+ res[0] = seqcharptr[j][k];
+ else
+ res[0] = '-';
+! /* start -> mid */
+! ajGraphicsDrawposTextAtmid((float) 0.5 +
+! (float) (count+gapcount),
+! y-(yincr*l),res);
+ }
+ }
+ }
+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
+***************
+*** 33,44 ****
+
+
+
+! /* @datastatic AjPRinfo *******************************************************
+ **
+ ** recoder internals for RE information
+ **
+! ** @alias AjSRinfo
+! ** @alias AjORinfo
+ **
+ ** @attr code [AjPStr] Undocumented
+ ** @attr site [AjPStr] Undocumented
+--- 33,44 ----
+
+
+
+! /* @datastatic PRinfo *******************************************************
+ **
+ ** recoder internals for RE information
+ **
+! ** @alias SRinfo
+! ** @alias ORinfo
+ **
+ ** @attr code [AjPStr] Undocumented
+ ** @attr site [AjPStr] Undocumented
+***************
+*** 50,56 ****
+ ** @attr Padding [char[4]] Padding to alignment boundary
+ ******************************************************************************/
+
+! typedef struct AjSRinfo
+ {
+ AjPStr code;
+ AjPStr site;
+--- 50,56 ----
+ ** @attr Padding [char[4]] Padding to alignment boundary
+ ******************************************************************************/
+
+! typedef struct SRinfo
+ {
+ AjPStr code;
+ AjPStr site;
+***************
+*** 60,77 ****
+ ajint cut3;
+ ajint cut4;
+ char Padding[4];
+! } AjORinfo;
+! #define AjPRinfo AjORinfo*
+
+
+
+
+! /* @datastatic Mutant *********************************************************
+ **
+ ** recoder internals for mutation sites
+ **
+! ** @alias AjSRinfo
+! ** @alias AjORinfo
+ **
+ ** @attr code [AjPStr] Undocumented
+ ** @attr site [AjPStr] Undocumented
+--- 60,77 ----
+ ajint cut3;
+ ajint cut4;
+ char Padding[4];
+! } ORinfo;
+! #define PRinfo ORinfo*
+
+
+
+
+! /* @datastatic PMutant *********************************************************
+ **
+ ** recoder internals for mutation sites
+ **
+! ** @alias SMutant
+! ** @alias OMutant
+ **
+ ** @attr code [AjPStr] Undocumented
+ ** @attr site [AjPStr] Undocumented
+***************
+*** 84,90 ****
+ ** @attr Padding [char[6]] Padding to alignment boudnary
+ ******************************************************************************/
+
+! typedef struct Mutant
+ {
+ AjPStr code;
+ AjPStr site;
+--- 84,90 ----
+ ** @attr Padding [char[6]] Padding to alignment boudnary
+ ******************************************************************************/
+
+! typedef struct SMutant
+ {
+ AjPStr code;
+ AjPStr site;
+***************
+*** 96,102 ****
+ char nbase;
+ char Padding[6];
+ } OMutant;
+! #define Mutant OMutant*
+
+
+ static AjPTrn recoderTable = NULL; /* translation table object */
+--- 96,102 ----
+ char nbase;
+ char Padding[6];
+ } OMutant;
+! #define PMutant OMutant*
+
+
+ static AjPTrn recoderTable = NULL; /* translation table object */
+***************
+*** 109,122 ****
+ AjBool rev, ajint begin, ajint end,
+ AjBool tshow);
+ static AjPList recoder_checkTrans(const AjPStr seq,const EmbPMatMatch match,
+! const AjPRinfo rlp, ajint begin, ajint radj,
+ AjBool rev, ajint end, ajint pos,
+ AjBool* empty);
+ static AjBool recoder_checkPat(const EmbPMatMatch match,
+! const AjPRinfo rlp, ajint radj, AjBool rev,
+ ajint begin, ajint end);
+ static ajint recoder_changebase(char pbase, char* tbase);
+! static void recoder_mutFree(Mutant* mut);
+ static ajint recoder_basecompare(const void *a, const void *b);
+
+ static void recoder_fmt_seq(const char* title, const AjPStr seq,
+--- 109,122 ----
+ AjBool rev, ajint begin, ajint end,
+ AjBool tshow);
+ static AjPList recoder_checkTrans(const AjPStr seq,const EmbPMatMatch match,
+! const PRinfo rlp, ajint begin, ajint radj,
+ AjBool rev, ajint end, ajint pos,
+ AjBool* empty);
+ static AjBool recoder_checkPat(const EmbPMatMatch match,
+! const PRinfo rlp, ajint radj, AjBool rev,
+ ajint begin, ajint end);
+ static ajint recoder_changebase(char pbase, char* tbase);
+! static void recoder_mutFree(PMutant* mut);
+ static ajint recoder_basecompare(const void *a, const void *b);
+
+ static void recoder_fmt_seq(const char* title, const AjPStr seq,
+***************
+*** 155,161 ****
+ AjPList relist = NULL;
+ AjPList muts;
+ AjPList nmuts;
+! AjPRinfo re;
+ AjPStr tailstr = NULL;
+
+ embInit("recoder", argc, argv);
+--- 155,161 ----
+ AjPList relist = NULL;
+ AjPList muts;
+ AjPList nmuts;
+! PRinfo re;
+ AjPStr tailstr = NULL;
+
+ embInit("recoder", argc, argv);
+***************
+*** 297,303 ****
+
+ AjPList patlist = NULL; /* list for pattern matches of.. */
+ EmbPMatMatch match; /* ..AjMatMatch structures*/
+! AjPRinfo rlp = NULL;
+
+ str = ajStrNew();
+ tstr = ajStrNew();
+--- 297,303 ----
+
+ AjPList patlist = NULL; /* list for pattern matches of.. */
+ EmbPMatMatch match; /* ..AjMatMatch structures*/
+! PRinfo rlp = NULL;
+
+ str = ajStrNew();
+ tstr = ajStrNew();
+***************
+*** 410,416 ****
+ AjPFile fin = NULL; /* file pointer to RE file data */
+ AjPStr refilename = NULL; /* .. & string for the filename */
+ register ajint RStotal = 0; /* counts no of RE */
+! AjPRinfo rinfo = NULL;
+ AjBool isall = ajFalse;
+ ajint ne = 0;
+ ajint i;
+--- 410,416 ----
+ AjPFile fin = NULL; /* file pointer to RE file data */
+ AjPStr refilename = NULL; /* .. & string for the filename */
+ register ajint RStotal = 0; /* counts no of RE */
+! PRinfo rinfo = NULL;
+ AjBool isall = ajFalse;
+ ajint ne = 0;
+ ajint i;
+***************
+*** 445,452 ****
+
+ /* read RE data into AjPRestrict obj */
+
+! while(embPatRestrictReadEntry(rptr,fin))
+ {
+ if(!isall) /* only select enzymes on command line */
+ {
+ for(i=0;i<ne;++i)
+--- 445,455 ----
+
+ /* read RE data into AjPRestrict obj */
+
+! while(!ajFileIsEof(fin))
+ {
++ if(!embPatRestrictReadEntry(rptr,fin))
++ continue;
++
+ if(!isall) /* only select enzymes on command line */
+ {
+ for(i=0;i<ne;++i)
+***************
+*** 490,496 ****
+ ** Checks whether the RS pattern falls within the sequence string
+ **
+ ** @param [r] match [const EmbPMatMatch] Match data
+! ** @param [r] rlp [const AjPRinfo] Restriction site info
+ ** @param [r] radj [ajint] Adjustment for reversed sequence
+ ** @param [r] rev [AjBool] Reverse sequence
+ ** @param [r] begin [ajint] Start position
+--- 493,499 ----
+ ** Checks whether the RS pattern falls within the sequence string
+ **
+ ** @param [r] match [const EmbPMatMatch] Match data
+! ** @param [r] rlp [const PRinfo] Restriction site info
+ ** @param [r] radj [ajint] Adjustment for reversed sequence
+ ** @param [r] rev [AjBool] Reverse sequence
+ ** @param [r] begin [ajint] Start position
+***************
+*** 499,505 ****
+ **
+ ******************************************************************************/
+ static AjBool recoder_checkPat(const EmbPMatMatch match,
+! const AjPRinfo rlp, ajint radj, AjBool rev,
+ ajint begin, ajint end)
+ {
+ ajint mpos;
+--- 502,508 ----
+ **
+ ******************************************************************************/
+ static AjBool recoder_checkPat(const EmbPMatMatch match,
+! const PRinfo rlp, ajint radj, AjBool rev,
+ ajint begin, ajint end)
+ {
+ ajint mpos;
+***************
+*** 550,556 ****
+ **
+ ** @param [r] dna [const AjPStr] Sequence as a string
+ ** @param [r] match [const EmbPMatMatch] Match data
+! ** @param [r] rlp [const AjPRinfo] Restriction site info
+ ** @param [r] begin [ajint] Start position
+ ** @param [r] radj [ajint] Adjustment for reversed sequence
+ ** @param [r] rev [AjBool] Reverse sequence
+--- 553,559 ----
+ **
+ ** @param [r] dna [const AjPStr] Sequence as a string
+ ** @param [r] match [const EmbPMatMatch] Match data
+! ** @param [r] rlp [const PRinfo] Restriction site info
+ ** @param [r] begin [ajint] Start position
+ ** @param [r] radj [ajint] Adjustment for reversed sequence
+ ** @param [r] rev [AjBool] Reverse sequence
+***************
+*** 563,569 ****
+ ******************************************************************************/
+
+ static AjPList recoder_checkTrans(const AjPStr dna, const EmbPMatMatch match,
+! const AjPRinfo rlp, ajint begin, ajint radj,
+ AjBool rev, ajint end, ajint pos,
+ AjBool* empty)
+ {
+--- 566,572 ----
+ ******************************************************************************/
+
+ static AjPList recoder_checkTrans(const AjPStr dna, const EmbPMatMatch match,
+! const PRinfo rlp, ajint begin, ajint radj,
+ AjBool rev, ajint end, ajint pos,
+ AjBool* empty)
+ {
+***************
+*** 572,578 ****
+ const char *prs;
+ char *s;
+
+! Mutant tresult;
+ AjPList res;
+
+ ajint mpos;
+--- 575,581 ----
+ const char *prs;
+ char *s;
+
+! PMutant tresult;
+ AjPList res;
+
+ ajint mpos;
+***************
+*** 805,811 ****
+
+ static void recoder_fmt_muts(AjPList muts, AjPFeattable feat, AjBool rev)
+ {
+! Mutant res;
+ AjPFeature sf = NULL;
+ AjPStr tmpFeatStr = NULL;
+
+--- 808,814 ----
+
+ static void recoder_fmt_muts(AjPList muts, AjPFeattable feat, AjBool rev)
+ {
+! PMutant res;
+ AjPFeature sf = NULL;
+ AjPStr tmpFeatStr = NULL;
+
+***************
+*** 857,863 ****
+
+ static ajint recoder_basecompare(const void *a, const void *b)
+ {
+! return((*(Mutant const *)a)->base)-((*(Mutant const *)b)->base);
+ }
+
+
+--- 860,866 ----
+
+ static ajint recoder_basecompare(const void *a, const void *b)
+ {
+! return((*(PMutant const *)a)->base)-((*(PMutant const *)b)->base);
+ }
+
+
+***************
+*** 867,877 ****
+ **
+ ** Free allocated memory for mutant structure
+ **
+! ** @param [d] mut [Mutant*] Mutant structure to be deleted
+ ** @return [void]
+ ******************************************************************************/
+
+! static void recoder_mutFree(Mutant* mut)
+ {
+ ajStrDel(&(*mut)->code);
+ ajStrDel(&(*mut)->site);
+--- 870,880 ----
+ **
+ ** Free allocated memory for mutant structure
+ **
+! ** @param [d] mut [PMutant*] Mutant structure to be deleted
+ ** @return [void]
+ ******************************************************************************/
+
+! static void recoder_mutFree(PMutant* mut)
+ {
+ ajStrDel(&(*mut)->code);
+ 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
+***************
+*** 777,784 ****
+ /* push all enzyme names without the required criteria onto nocutlist */
+
+ enz = embPatRestrictNew();
+! while(embPatRestrictReadEntry(enz, enzfile))
+ {
+ /*
+ ** If user entered explicit enzyme list, then check to see if
+ ** this is one of that explicit list
+--- 777,787 ----
+ /* push all enzyme names without the required criteria onto nocutlist */
+
+ enz = embPatRestrictNew();
+! while(!ajFileIsEof(enzfile))
+ {
++ if(!embPatRestrictReadEntry(enz, enzfile))
++ continue;
++
+ /*
+ ** If user entered explicit enzyme list, then check to see if
+ ** 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
+***************
+*** 951,958 ****
+
+ ne = ajArrCommaList(enzymes,&ea);
+
+! while(embPatRestrictReadEntry(enz,enzfile))
+ {
+ key = ajStrNew();
+ ajStrAssignS(&key,enz->cod);
+ ajStrFmtUpper(&key);
+--- 951,961 ----
+
+ ne = ajArrCommaList(enzymes,&ea);
+
+! while(!ajFileIsEof(enzfile))
+ {
++ if(!embPatRestrictReadEntry(enz,enzfile))
++ continue;
++
+ key = ajStrNew();
+ ajStrAssignS(&key,enz->cod);
+ 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
+***************
+*** 266,272 ****
+ {
+ AjIList iter = NULL ;
+ AjPFeature gf = NULL ;
+! AjPFeattable feat;
+ AjPStr lineout;
+ char strandout = '\0';
+ AjBool first = ajTrue;
+--- 266,277 ----
+ {
+ AjIList iter = NULL ;
+ AjPFeature gf = NULL ;
+! void **array = NULL ;
+! AjPFeature *fullfeats = NULL ;
+! ajuint *featindex = NULL;
+! const AjPFeattable feat;
+! AjPList featlist = NULL;
+! AjPList fullfeatlist = NULL;
+ AjPStr lineout;
+ char strandout = '\0';
+ AjBool first = ajTrue;
+***************
+*** 290,301 ****
+ AjPStr key = NULL;
+ AjBool val = ajFalse;
+
+ /* get the feature table of the sequence */
+! feat = ajSeqGetFeatCopy(seq);
+ if(!feat)
+ return;
+
+-
+ lineout = ajStrNew();
+ tagstmp = ajStrNewC("");
+ tagsout = ajStrNewC("");
+--- 295,310 ----
+ AjPStr key = NULL;
+ AjBool val = ajFalse;
+
++ ajuint i;
++ ajuint isize;
++ ajuint jsize;
++ ajuint j = 0;
++
+ /* get the feature table of the sequence */
+! feat = ajSeqGetFeat(seq);
+ if(!feat)
+ return;
+
+ lineout = ajStrNew();
+ tagstmp = ajStrNewC("");
+ tagsout = ajStrNewC("");
+***************
+*** 303,326 ****
+
+ if(ajFeattableGetSize(feat))
+ {
+ if(!ajStrCmpC(sortlist, "source"))
+ /* sort by: sense, source, type, start */
+! ajListSort(feat->Features, showfeat_CompareFeatSource);
+ else if(!ajStrCmpC(sortlist, "start"))
+! /* sort by: sense, start, type, source, source */
+! ajListSort(feat->Features, showfeat_CompareFeatPos);
+ else if(!ajStrCmpC(sortlist, "type"))
+ /* type */
+ /* sort by: sense, type, source, start */
+! ajListSort(feat->Features, showfeat_CompareFeatType);
+ /* else - no sort */
+
+! iter = ajListIterNewread(feat->Features) ;
+
+ while(!ajListIterDone(iter))
+ {
+ gf = ajListIterGet(iter);
+-
+ /* see if its a child of a multiple join */
+ child = ajFalse;
+ if(ajFeatIsMultiple(gf))
+--- 312,366 ----
+
+ if(ajFeattableGetSize(feat))
+ {
++ isize = ajListToarray(feat->Features, (void***) &array);
++ fullfeats = (AjPFeature*) array;
++
++ featlist = ajListNew();
++ AJCNEW0(featindex, isize);
++
++ jsize = 0;
++ for(i=0;fullfeats[i];i++)
++ {
++ if(ajFeatIsChild(fullfeats[i]))
++ continue;
++ ajListPushAppend(featlist, fullfeats[i]);
++ featindex[jsize++] = i;
++ }
++
+ if(!ajStrCmpC(sortlist, "source"))
+ /* sort by: sense, source, type, start */
+! ajListToindex(featlist, featindex, showfeat_CompareFeatSource);
+ else if(!ajStrCmpC(sortlist, "start"))
+! /* sort by: sense, start, type, source */
+! ajListToindex(featlist, featindex, showfeat_CompareFeatPos);
+ else if(!ajStrCmpC(sortlist, "type"))
+ /* type */
+ /* sort by: sense, type, source, start */
+! ajListToindex(featlist, featindex, showfeat_CompareFeatType);
+ /* else - no sort */
+
+! if(!ajStrCmpC(sortlist, "nosort"))
+! {
+! iter = ajListIterNewread(feat->Features);
+! }
+! else
+! {
+! fullfeatlist = ajListNew();
+! j = 0;
+! for(i=0;i<jsize;i++)
+! {
+! j = featindex[i];
+! ajListPushAppend(fullfeatlist, fullfeats[j++]);
+! while(j < isize && ajFeatIsChild(fullfeats[j]))
+! ajListPushAppend(fullfeatlist, fullfeats[j++]);
+! }
+! iter = ajListIterNewread(fullfeatlist);
+! }
+! AJFREE(featindex);
+
+ while(!ajListIterDone(iter))
+ {
+ gf = ajListIterGet(iter);
+ /* see if its a child of a multiple join */
+ child = ajFalse;
+ if(ajFeatIsMultiple(gf))
+***************
+*** 339,345 ****
+ else
+ want_multiple_line = ajFalse;
+
+-
+ /* check that the feature is within the range we wish to display */
+ if(beg+1 > (ajint)ajFeatGetEnd(gf) ||
+ end+1 < (ajint)ajFeatGetStart(gf))
+--- 379,384 ----
+***************
+*** 510,524 ****
+
+ }
+
+-
+- ajFeattableDel(&feat);
+-
+ ajStrDel(&tagstmp);
+ ajStrDel(&tagsout);
+ ajStrDel(&posout);
+ ajStrDel(&lineout);
+ ajStrDel(&sourceout);
+ ajStrDel(&typeout);
+
+ return;
+ }
+--- 549,563 ----
+
+ }
+
+ ajStrDel(&tagstmp);
+ ajStrDel(&tagsout);
+ ajStrDel(&posout);
+ ajStrDel(&lineout);
+ ajStrDel(&sourceout);
+ ajStrDel(&typeout);
++ ajListFree(&featlist);
++ ajListFree(&fullfeatlist);
++ AJFREE(array);
+
+ return;
+ }
+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
+***************
+*** 238,244 ****
+ ajFmtPrintF(outfile, "\n");
+
+ if(html)
+! ajFmtPrintF(outfile, "<PRE>");
+ }
+
+
+--- 238,244 ----
+ ajFmtPrintF(outfile, "\n");
+
+ if(html)
+! ajFmtPrintF(outfile, "</PRE>\n");
+ }
+
+
+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
+***************
+*** 380,386 ****
+ ajFmtPrintF(outfile, "\n");
+
+ if(html)
+! ajFmtPrintF(outfile, "<PRE>");
+ }
+
+
+--- 380,386 ----
+ ajFmtPrintF(outfile, "\n");
+
+ if(html)
+! ajFmtPrintF(outfile, "</PRE>\n");
+ }
+
+
+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
+***************
+*** 27,38 ****
+
+
+
+! /* @datastatic AjPRinfo *******************************************************
+ **
+ ** recoder internals for RE information
+ **
+! ** @alias AjSRinfo
+! ** @alias AjORinfo
+ **
+ ** @attr code [AjPStr] structure for silent mutation info
+ ** @attr site [AjPStr] Undocumented
+--- 27,38 ----
+
+
+
+! /* @datastatic PRinfo *******************************************************
+ **
+ ** recoder internals for RE information
+ **
+! ** @alias SRinfo
+! ** @alias ORinfo
+ **
+ ** @attr code [AjPStr] structure for silent mutation info
+ ** @attr site [AjPStr] Undocumented
+***************
+*** 44,50 ****
+ ** @attr Padding [char[4]] Padding to alignment boundary
+ ******************************************************************************/
+
+! typedef struct AjSRinfo
+ {
+ AjPStr code;
+ AjPStr site;
+--- 44,50 ----
+ ** @attr Padding [char[4]] Padding to alignment boundary
+ ******************************************************************************/
+
+! typedef struct SRinfo
+ {
+ AjPStr code;
+ AjPStr site;
+***************
+*** 54,71 ****
+ ajint cut3;
+ ajint cut4;
+ char Padding[4];
+! } AjORinfo;
+! #define AjPRinfo AjORinfo*
+
+
+
+
+! /* @datastatic AjPSilent ******************************************************
+ **
+ ** recoder internals for silent sites
+ **
+! ** @alias AjSSilent
+! ** @alias AjOSilent
+ **
+ ** @attr code [AjPStr] Undocumented
+ ** @attr site [AjPStr] Undocumented
+--- 54,71 ----
+ ajint cut3;
+ ajint cut4;
+ char Padding[4];
+! } ORinfo;
+! #define PRinfo ORinfo*
+
+
+
+
+! /* @datastatic PSilent ******************************************************
+ **
+ ** recoder internals for silent sites
+ **
+! ** @alias SSilent
+! ** @alias OSilent
+ **
+ ** @attr code [AjPStr] Undocumented
+ ** @attr site [AjPStr] Undocumented
+***************
+*** 79,85 ****
+ ** @attr Padding [char[2]] Padding to alignment boundary
+ ******************************************************************************/
+
+! typedef struct AjSSilent
+ {
+ AjPStr code;
+ AjPStr site;
+--- 79,85 ----
+ ** @attr Padding [char[2]] Padding to alignment boundary
+ ******************************************************************************/
+
+! typedef struct SSilent
+ {
+ AjPStr code;
+ AjPStr site;
+***************
+*** 91,98 ****
+ char obase;
+ char nbase;
+ char Padding[2];
+! } AjOSilent;
+! #define AjPSilent AjOSilent*
+
+
+
+--- 91,98 ----
+ char obase;
+ char nbase;
+ char Padding[2];
+! } OSilent;
+! #define PSilent OSilent*
+
+
+
+***************
+*** 103,110 ****
+ ajint radj, AjBool rev, ajint end,
+ AjBool tshow);
+ static ajint silent_restr_read(AjPList *relist, const AjPStr enzymes);
+! static AjPSilent silent_checktrans(const AjPStr seq,const EmbPMatMatch match,
+! const AjPRinfo rlp, ajint begin, ajint radj,
+ AjBool rev, ajint end);
+ static void silent_fmt_sequence(const char* title, const AjPStr seq,
+ AjPStr* tailstr,
+--- 103,110 ----
+ ajint radj, AjBool rev, ajint end,
+ AjBool tshow);
+ static ajint silent_restr_read(AjPList *relist, const AjPStr enzymes);
+! static PSilent silent_checktrans(const AjPStr seq,const EmbPMatMatch match,
+! const PRinfo rlp, ajint begin, ajint radj,
+ AjBool rev, ajint end);
+ static void silent_fmt_sequence(const char* title, const AjPStr seq,
+ AjPStr* tailstr,
+***************
+*** 271,277 ****
+
+ static void silent_relistdel(AjPList* relist)
+ {
+! AjPRinfo rlp = NULL;
+
+ while(ajListPop(*relist,(void **)&rlp))
+ {
+--- 271,277 ----
+
+ static void silent_relistdel(AjPList* relist)
+ {
+! PRinfo rlp = NULL;
+
+ while(ajListPop(*relist,(void **)&rlp))
+ {
+***************
+*** 307,313 ****
+ ajint radj,AjBool rev, ajint end,
+ AjBool tshow)
+ {
+! AjPSilent res;
+ AjPList results;
+ AjPStr str; /*holds RS patterns*/
+ AjPStr tstr;
+--- 307,313 ----
+ ajint radj,AjBool rev, ajint end,
+ AjBool tshow)
+ {
+! PSilent res;
+ AjPList results;
+ AjPStr str; /*holds RS patterns*/
+ AjPStr tstr;
+***************
+*** 320,326 ****
+ AjPList patlist = NULL; /*a list for pattern matches.
+ a list of ..*/
+ EmbPMatMatch match; /*..AjMatMatch structures*/
+! AjPRinfo rlp = NULL;
+ AjPStr pep = NULL; /*string to hold protein*/
+ AjPTrn table = NULL; /*object to hold translation table*/
+
+--- 320,326 ----
+ AjPList patlist = NULL; /*a list for pattern matches.
+ a list of ..*/
+ EmbPMatMatch match; /*..AjMatMatch structures*/
+! PRinfo rlp = NULL;
+ AjPStr pep = NULL; /*string to hold protein*/
+ AjPTrn table = NULL; /*object to hold translation table*/
+
+***************
+*** 428,434 ****
+
+ AjPStr refilename = NULL;
+ register ajint RStotal = 0;
+! AjPRinfo rinfo = NULL;
+ AjBool isall = ajFalse;
+ ajint ne = 0;
+ ajint i;
+--- 428,434 ----
+
+ AjPStr refilename = NULL;
+ register ajint RStotal = 0;
+! PRinfo rinfo = NULL;
+ AjBool isall = ajFalse;
+ ajint ne = 0;
+ ajint i;
+***************
+*** 457,464 ****
+ isall = ajFalse;
+ }
+
+! while(embPatRestrictReadEntry(rptr,fin))
+ {
+ if(!isall)
+ {
+ for(i=0;i<ne;++i)
+--- 457,467 ----
+ isall = ajFalse;
+ }
+
+! while(!ajFileIsEof(fin))
+ {
++ if(!embPatRestrictReadEntry(rptr,fin))
++ continue;
++
+ if(!isall)
+ {
+ for(i=0;i<ne;++i)
+***************
+*** 501,520 ****
+ **
+ ** @param [r] seq [const AjPStr] sequence
+ ** @param [r] match [const EmbPMatMatch] pattern match
+! ** @param [r] rlp [const AjPRinfo] RE information
+ ** @param [r] begin [ajint] start position
+ ** @param [r] radj [ajint] reverse numbering adjustment
+ ** @param [r] rev [AjBool] do complement
+ ** @param [r] end [ajint] end position
+! ** @return [AjPSilent] silent mutation object or NULL if not found
+ ** @@
+ ******************************************************************************/
+
+! static AjPSilent silent_checktrans(const AjPStr seq,const EmbPMatMatch match,
+! const AjPRinfo rlp, ajint begin, ajint radj,
+ AjBool rev, ajint end)
+ {
+! AjPSilent ret;
+ const char *p = NULL;
+ const char *q = NULL;
+ const char *s = NULL;
+--- 504,523 ----
+ **
+ ** @param [r] seq [const AjPStr] sequence
+ ** @param [r] match [const EmbPMatMatch] pattern match
+! ** @param [r] rlp [const PRinfo] RE information
+ ** @param [r] begin [ajint] start position
+ ** @param [r] radj [ajint] reverse numbering adjustment
+ ** @param [r] rev [AjBool] do complement
+ ** @param [r] end [ajint] end position
+! ** @return [PSilent] silent mutation object or NULL if not found
+ ** @@
+ ******************************************************************************/
+
+! static PSilent silent_checktrans(const AjPStr seq,const EmbPMatMatch match,
+! const PRinfo rlp, ajint begin, ajint radj,
+ AjBool rev, ajint end)
+ {
+! PSilent ret;
+ const char *p = NULL;
+ const char *q = NULL;
+ const char *s = NULL;
+***************
+*** 721,727 ****
+ static void silent_fmt_hits(AjPList hits, AjPFeattable feat,
+ AjBool silent, AjBool rev)
+ {
+! AjPSilent res;
+ AjPFeature sf = NULL;
+ AjPStr tmpFeatStr = NULL;
+
+--- 724,730 ----
+ static void silent_fmt_hits(AjPList hits, AjPFeattable feat,
+ AjBool silent, AjBool rev)
+ {
+! PSilent res;
+ AjPFeature sf = NULL;
+ AjPStr tmpFeatStr = NULL;
+
+***************
+*** 780,786 ****
+ static void silent_split_hits(AjPList *hits, AjPList *silents,
+ AjPList *nonsilents, AjBool allmut)
+ {
+! AjPSilent res;
+
+ while(ajListPop(*hits,(void **)&res))
+ {
+--- 783,789 ----
+ static void silent_split_hits(AjPList *hits, AjPList *silents,
+ AjPList *nonsilents, AjBool allmut)
+ {
+! PSilent res;
+
+ while(ajListPop(*hits,(void **)&res))
+ {
+***************
+*** 819,823 ****
+
+ static ajint silent_basecompare(const void *a, const void *b)
+ {
+! return((*(AjPSilent const *)a)->base)-((*(AjPSilent const *)b)->base);
+ }
+--- 822,826 ----
+
+ static ajint silent_basecompare(const void *a, const void *b)
+ {
+! return((*(PSilent const *)a)->base)-((*(PSilent const *)b)->base);
+ }
+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
+***************
+*** 102,111 ****
+ pos += size;
+ }
+ }
+ splitter_MakeSubSeqName(&outseq_name, seq, pos, len-1);
+ splitter_ProcessChunk (seqout, seq, pos, len-1,
+ outseq_name, feature);
+! }
+
+ ajSeqoutClose(seqout);
+ ajSeqallDel(&seqall);
+--- 102,112 ----
+ pos += size;
+ }
+ }
++
+ splitter_MakeSubSeqName(&outseq_name, seq, pos, len-1);
+ splitter_ProcessChunk (seqout, seq, pos, len-1,
+ outseq_name, feature);
+! }
+
+ ajSeqoutClose(seqout);
+ ajSeqallDel(&seqall);
+***************
+*** 135,151 ****
+ static void splitter_write(AjPSeqout default_seqout,
+ AjPSeq subseq, const AjPSeq seq)
+ {
+! /* set the description of the subsequence */
+! ajSeqAssignDescS(subseq, ajSeqGetDescS(seq));
+
+! /* set the type of the subsequence */
+! ajSeqType(subseq);
+
+! ajSeqoutWriteSeq(default_seqout, subseq);
+
+! return;
+ }
+
+ /* @funcstatic splitter_MakeSubSeqName ****************************************
+ **
+ ** Undocumented
+--- 136,155 ----
+ static void splitter_write(AjPSeqout default_seqout,
+ AjPSeq subseq, const AjPSeq seq)
+ {
+! /* set the description of the subsequence */
+! ajSeqAssignDescS(subseq, ajSeqGetDescS(seq));
+
+! /* set the type of the subsequence */
+! ajSeqType(subseq);
+
+! ajSeqoutWriteSeq(default_seqout, subseq);
+
+! return;
+ }
+
++
++
++
+ /* @funcstatic splitter_MakeSubSeqName ****************************************
+ **
+ ** Undocumented
+***************
+*** 161,180 ****
+ const AjPSeq seq, ajuint start,
+ ajuint end)
+ {
+! AjPStr value = ajStrNew();
+
+! /* create a nice name for the subsequence */
+! ajStrAssignS(name_ptr, ajSeqGetNameS(seq));
+! ajStrAppendC(name_ptr, "_");
+! ajStrFromUint(&value, ajSeqGetBegin(seq)+start);
+! ajStrAppendS(name_ptr, value);
+! ajStrAppendC(name_ptr, "-");
+! ajStrFromUint(&value, ajSeqGetBegin(seq)+end);
+! ajStrAppendS(name_ptr, value);
+
+! ajStrDel(&value);
+ }
+
+ /* @funcstatic splitter_ProcessChunk ******************************************
+ **
+ ** Undocumented
+--- 165,187 ----
+ const AjPSeq seq, ajuint start,
+ ajuint end)
+ {
+! AjPStr value = ajStrNew();
+
+! /* create a nice name for the subsequence */
+! ajStrAssignS(name_ptr, ajSeqGetNameS(seq));
+! ajStrAppendC(name_ptr, "_");
+! ajStrFromUint(&value, ajSeqGetBegin(seq)+start);
+! ajStrAppendS(name_ptr, value);
+! ajStrAppendC(name_ptr, "-");
+! ajStrFromUint(&value, ajSeqGetBegin(seq)+end);
+! ajStrAppendS(name_ptr, value);
+
+! ajStrDel(&value);
+ }
+
++
++
++
+ /* @funcstatic splitter_ProcessChunk ******************************************
+ **
+ ** Undocumented
+***************
+*** 192,220 ****
+ ajuint start, ajuint end, const AjPStr name,
+ AjBool feature)
+ {
+! AjPStr str = ajStrNew();
+
+! AjPFeattable new_feattable = NULL;
+! AjPSeq subseq = ajSeqNew ();
+
+! ajDebug("splitter_ProcessChunk %d..%d '%S' %B\n",
+! start, end, name, feature);
+
+! new_feattable = ajFeattableNew(name);
+! subseq->Fttable = new_feattable;
+! ajFeattableSetNuc(new_feattable);
+
+! ajStrAssignSubC(&str,ajSeqGetSeqC(seq),start,end);
+! ajSeqAssignSeqS(subseq,str);
+! if (feature)
+! splitter_AddSubSeqFeat(subseq->Fttable,start,end,seq);
+! ajSeqAssignNameS(subseq, name);
+! splitter_write(seqout,subseq,seq);
+
+! ajStrDel(&str);
+! ajSeqDel(&subseq);
+
+! return;
+ }
+
+
+--- 199,233 ----
+ ajuint start, ajuint end, const AjPStr name,
+ AjBool feature)
+ {
+! AjPStr str;
+!
+! AjPFeattable new_feattable = NULL;
+! AjPSeq subseq;
+
+! ajDebug("splitter_ProcessChunk %d..%d '%S' %B\n",
+! start, end, name, feature);
+
+! str = ajStrNew();
+! subseq = ajSeqNew();
+!
+!
+! new_feattable = ajFeattableNew(name);
+! subseq->Fttable = new_feattable;
+! ajFeattableSetNuc(new_feattable);
+
+! ajStrAssignSubC(&str,ajSeqGetSeqC(seq),start,end);
+! ajSeqAssignSeqS(subseq,str);
+
+! if(feature)
+! splitter_AddSubSeqFeat(subseq->Fttable,start,end,seq);
+
+! ajSeqAssignNameS(subseq, name);
+! splitter_write(seqout,subseq,seq);
+
+! ajStrDel(&str);
+! ajSeqDel(&subseq);
+!
+! return;
+ }
+
+
+***************
+*** 233,272 ****
+ static void splitter_AddSubSeqFeat(AjPFeattable ftable, ajuint start,
+ ajuint end, const AjPSeq oldseq)
+ {
+! AjPFeattable old_feattable = NULL;
+! AjIList iter = NULL;
+!
+! old_feattable = ajSeqGetFeatCopy(oldseq);
+! iter = ajListIterNewread(old_feattable->Features);
+
+! while(!ajListIterDone(iter)) {
+! AjPFeature gf = ajListIterGet(iter);
+
+! AjPFeature copy = NULL;
+
+
+! if (((ajFeatGetEnd(gf) < start + 1) &&
+! (gf->End2 == 0 || gf->End2 < start + 1)) ||
+! ((ajFeatGetStart(gf) > end + 1) &&
+! (gf->Start2 == 0 || gf->Start2 > end + 1)))
+ {
+! continue;
+ }
+
+! copy = ajFeatNewFeat(gf);
+! copy->Start = copy->Start - start;
+! copy->End = copy->End - start;
+!
+! if (copy->Start2 > 0)
+! copy->Start2 = copy->Start2 - start;
+!
+! if (copy->End2 > 0)
+! copy->End2 = copy->End2 - start;
+!
+! ajFeatTrimOffRange (copy, 0, 1, end - start + 1, AJTRUE, AJTRUE);
+!
+! ajFeattableAdd(ftable, copy);
+! }
+! ajFeattableDel(&old_feattable);
+! ajListIterDel(&iter);
+ }
+--- 246,293 ----
+ static void splitter_AddSubSeqFeat(AjPFeattable ftable, ajuint start,
+ ajuint end, const AjPSeq oldseq)
+ {
+! AjPFeattable old_feattable = NULL;
+! AjIList iter = NULL;
+
+! old_feattable = ajSeqGetFeatCopy(oldseq);
+
+! if(!old_feattable)
+! return;
+
++ iter = ajListIterNewread(old_feattable->Features);
+
+! while(!ajListIterDone(iter))
+ {
+! AjPFeature gf = ajListIterGet(iter);
+!
+! AjPFeature copy = NULL;
+!
+!
+! if (((ajFeatGetEnd(gf) < start + 1) &&
+! (gf->End2 == 0 || gf->End2 < start + 1)) ||
+! ((ajFeatGetStart(gf) > end + 1) &&
+! (gf->Start2 == 0 || gf->Start2 > end + 1)))
+! {
+! continue;
+! }
+!
+! copy = ajFeatNewFeat(gf);
+! copy->Start = copy->Start - start;
+! copy->End = copy->End - start;
+!
+! if (copy->Start2 > 0)
+! copy->Start2 = copy->Start2 - start;
+!
+! if (copy->End2 > 0)
+! copy->End2 = copy->End2 - start;
+!
+! ajFeatTrimOffRange (copy, 0, 1, end - start + 1, AJTRUE, AJTRUE);
+!
+! ajFeattableAdd(ftable, copy);
+ }
+
+! ajFeattableDel(&old_feattable);
+! ajListIterDel(&iter);
+!
+! return;
+ }
+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
+***************
+*** 1,41 ****
+ PK
+! âV/< META-INF/þÊ PK
+! áV/< ߧ» META-INF/MANIFEST.MF…±ŽÂ0D{Kþ‡-¹Â 9!Ò%ˆ$ërº~p0Nä5üý倂ŽiFšy£±ÜŽ%™ ŽâºC†Šð’=5†!Ê9fZ-"Sâ)o?ʼn©³Œªs ëšØÉMŸV¡ÁʳóéÎ.mùUUð½,¬V–\0 O"9tq|ª;lŸ¾~øpö˜
¥CÞÕã–Ž™È{¾ö&ÃOl)Âiϵÿu|)úÞsºQ+þ PK
+! àV/< org/PK
+! àV/< org/emboss/PK
+! áV/< org/emboss/jemboss/PK
+! áV/< org/emboss/jemboss/draw/PK
+! áV/< org/emboss/jemboss/editor/PK
+! áV/< org/emboss/jemboss/graphics/PK
+! áV/< org/emboss/jemboss/gui/PK
+! áV/< org/emboss/jemboss/gui/filetree/PK
+! áV/< org/emboss/jemboss/gui/form/PK
+! áV/< ' org/emboss/jemboss/gui/sequenceChooser/PK
+! áV/< org/emboss/jemboss/gui/startup/PK
+! áV/< org/emboss/jemboss/parser/PK
+! áV/< org/emboss/jemboss/parser/acd/PK
+! áV/< org/emboss/jemboss/programs/PK
+! áV/< org/emboss/jemboss/server/PK
+! áV/< org/emboss/jemboss/soap/PK
+! àV/<ƒí¼«æ J & org/emboss/jemboss/FileManager$1.class…R]kA=“¯M¶Û6
mêW5¶±&
8•Šˆ_
+ ÅBThjÁÇÉvH6lfÂìÄп⯨ZPðÑ”xg«T%3{ï{Î=wï|ÿñù+€m4KðpËGkEÜöq5w}ä±æaÝƇ:CÁö£¤¾ÍPkkÓãrØÕIÂÓï~Ë—B‰ž4» ¥Î©²}i£pÏ"Ùç YÀæ1CnOŸH†Åv¤ä«ñ°+Í‘èÆ©´u(âca"çOƒ9'Š ÁRÒìÅ"I$EÖgÔª?$™ÕÐHaå›ÃvÇ’5|!ÔI,
o´âà±P=Nw‘êí6/BJZ~@TÅ‘ÑV‡:vBÿÂ2ø =6¡t
+ Êyà’ø˜ 0{ ù¾µ£ÄÃf€ûh0ì„zÈ“±J+'IÌ#e¥Q"æ“É„ÿ*ËS¿ì 6«}Rñ[æëî@†–Pÿmq_„V›S†lÃM©|µEš9é #4ÃÊ¿þßjôΊ4«íŠkÙÍ
nehÏcüE² ‘ï"þVë#ØÖ92 Òœ2Êv°DgÚ>qÀ½*V§ )Ãjë–[•ì'äÞcî òoÏQ8cg—t ÈÒù˜Š?!’§)mõ:¥uÖ5\'â n¤¸›XNË2j']?PK
+! àV/<³kâÔ) Ö $ org/emboss/jemboss/FileManager.classV[SGþ†]˜aXQF1 ‰ñ†,ÊyO% "+ xIzw{apwf2Ó‹¬1‰¹ßÌ=/©ÊcªRæͪ(·’—øJÞò—ä·¤rzvQÔ1ÂÝÓ§Ïå;_Ÿ>3¿ÿ{ë »ñ•Ž$úU h8¡ã$R:ê0¨bHGúåpJðžV1¢£I
+ Ó8£bTG3Îê˜À¤†sÎKó *.êX‡~
/Éùe
LÎY
9 0¨Ë9¯bJô†1
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+--- 1495,1501 ----
+ ôÑGh¬ é)âKOèj® Iú–
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Ûý Éz ¦0 ²UƒÄ`Ô ó5—£è—‚þé þPK
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{m”`ڊŃ›´T¿¥…ã:É»&ä †
ꉰ‘Jòs4 ÚævêÉô‚‚á$é\KƬ5íËaÇ5²¯Û2ÉÌ–ú ©Íˆ‡Ó;bI}K:ÖÍ \)Cy‡Ñ§Å{43Æ×ùMÖGÞ瀴a+§“´ƒI: ÓÛNo”^rJ²úcäÓ¼;L RRKØ:§ØHXƒ •“»™;çÞ
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+***************
+*** 1504,1512 ****
+ |zÆ Úl“¤l¾i·ð•þßôq”…²ðtÆQ rÑ“EE•´ô†Ê\e´¼+ƒ„6“تN£ZþT ‰bWHòàpWÈáÁÙ®Óƒë][ÄfÉ+5ž9Ž½b³ÃëàT§Øìô:9µz ³B^©©Ñë ×Ù”ÅÝ+åqÔ„üUr³WºU® æôú?Fu•ÌéÚÞQ'ûèúg£ÇF%ûÌí=EÁ°‚Æ ú_ð
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+! àV/<Š9ÀuQ ñ ' org/emboss/jemboss/gui/ColumnData.class…PMOÂ@}»¨| ~`¢ñ5±Þ5^0&$Dî lÊ’ÒƲեbBL<øüQÆÙBâÁƒ—7of2ïÍÌ×÷Ç'€s´òÈ`'‡4šv³ØËbŸ!•ö%Cµ?ÂõE๠©À» æ“šè)ë1䄯¼`.͹TÒW Íöß±^¯3d°ºá„dK}ÈÛx>’ѽ±ð‡"R&ß-=U †“~y®œÂÅÂm¢+·úñ<¸ZÐVùAGcy£Ìde bŒe_-ô™YƆYlÙÈ!o£€<Ãñ¿Ê åß[îF39¦KSíÎGô° ½2ËȳŒr I¤‘ë6a‘2 œ:@ÝysNWàNk…”s¸‚µ¤:G‰°AªàÏ°ø rüE¾D¿¡L=g=
+ ª@ÂŒ/K˜qæ 3Þ)ªÖÍúPK
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æ(Iš’ZH'›I:e3“ÎΦ)â}Ÿ Z.Å*J¥•n*‚Š"j½ïï[Q*‡¢¿ß›½²ÉfÓ¿ÜÏgÞüö½ßû¾ßûÝóä‹?à|©Ì‡‹ñZ/6âu>¼ oàá
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+ >¦àã
+--- 1503,1511 ----
+ |zÆ Úl“¤l¾i·ð•þßôq”…²ðtÆQ rÑ“EE•´ô†Ê\e´¼+ƒ„6“تN£ZþT ‰bWHòàpWÈáÁÙ®Óƒë][ÄfÉ+5ž9Ž½b³ÃëàT§Øìô:9µz ³B^©©Ñë ×Ù”ÅÝ+åqÔ„üUr³WºU® æôú?Fu•ÌéÚÞQ'ûèúg£ÇF%ûÌí=EÁ°‚Æ ú_ð
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+ ª@ÂŒ/K˜qæ 3Þ)ªÖÍúPK
+! æcV<Uš+¯
+ ¤ ' org/emboss/jemboss/gui/DragJTable.classÅWy| U ÿÎd“Én&m’–¤4mRZ6›ci¶˜Z ɶ
æ(Iš’ZH'›I:e3“ÎΦ)â}Ÿ Z.Å*J¥•n*‚Š"j½ïï[Q*‡¢¿ß›½²ÉfÓ¿ÜÏgÞüö½ßû¾ßûÝóä‹?à|©Ì‡‹ñZ/6âu>¼ oàá
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+ >¦àã
+***************
+*** 1518,1528 ****
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+--- 1517,1527 ----
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S¸ ß 8 ¤& org/emboss/jemboss/gui/filetree/LocalTreeToolBar$5.classPK
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+! æcV<LJÊy Ç % ¤*d org/emboss/jemboss/draw/Block$7.classPK
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ð¥ # % ¤æf org/emboss/jemboss/draw/Block$8.classPK
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+! æcV<Æj«Ï K / ¤Xß org/emboss/jemboss/server/JembossServer$2.classPK
+! æcV<š-.µ / ¤tá org/emboss/jemboss/server/JembossServer$3.classPK
+! æcV<;ZFüÍ > / ¤vã org/emboss/jemboss/server/JembossServer$4.classPK
+! æcV<ÞØE(Î 0 / ¤å org/emboss/jemboss/server/JembossServer$5.classPK
+! æcV<Ú®· M$ ¿L - ¤«ç org/emboss/jemboss/server/JembossServer.classPK
+! æcV<ÔŠå7 4 - ¤C
+ org/emboss/jemboss/server/JembossThread.classPK
+! æcV<$>7‚í „ 3 ¤Å
+ org/emboss/jemboss/server/TestPrivateServer$1.classPK
+! æcV<Ï:.Áí
+! ¡ 1 ¤
+ org/emboss/jemboss/server/TestPrivateServer.classPK
+! æcV<_ÖýÛí 2 ¤?
+ org/emboss/jemboss/server/TestPublicServer$1.classPK
+! æcV</¯—ÿ¨ 0 ¤|
+ org/emboss/jemboss/server/TestPublicServer.classPK
+! æcV<Ù_Ò¾› È ) ¤r&
+ org/emboss/jemboss/soap/AuthPopup$1.classPK
+! æcV<«átÆ
+! ) ¤T(
+ org/emboss/jemboss/soap/AuthPopup$2.classPK
+! æcV<ˆ.NB ¢ ) ¤a-
+ org/emboss/jemboss/soap/AuthPopup$3.classPK
+! æcV<zêŸH™ È ) ¤»1
+ org/emboss/jemboss/soap/AuthPopup$4.classPK
+! æcV<ø²²ü • ) ¤›3
+ org/emboss/jemboss/soap/AuthPopup$5.classPK
+! æcV<E˜<- • ) ¤æ6
+ org/emboss/jemboss/soap/AuthPopup$6.classPK
+! æcV<{ÍZB % ' ¤3:
+ org/emboss/jemboss/soap/AuthPopup.classPK
+! æcV<ùßaÿf & ¤ºF
+ org/emboss/jemboss/soap/CallAjax.classPK
+! æcV<wU©À O & ¤dK
+ org/emboss/jemboss/soap/FileList.classPK
+! æcV<R2ÚðU ' ¤hQ
+ org/emboss/jemboss/soap/FileRoots.classPK
+! æcV<X¥¯¦Î Á $ ¤W
+ org/emboss/jemboss/soap/GetACD.classPK
+! æcV<å/;Æ _ % ¤[
+ org/emboss/jemboss/soap/GetHelp.classPK
+! æcV<ËýÍ é ( ¤]_
+ org/emboss/jemboss/soap/GetVersion.classPK
+! æcV<d¿ñ»Ä l ) ¤Àc
+ org/emboss/jemboss/soap/GetWossname.classPK
+! æcV<ýæ¶C ¦ ( ¤Ëe
+ org/emboss/jemboss/soap/JembossRun.classPK
+! æcV<eðç Û 2 ¤Tj
+ org/emboss/jemboss/soap/JembossSoapException.classPK
+! æcV<¡BÕv $ * ¤ºk
+ org/emboss/jemboss/soap/MakeFileSafe.classPK
+! æcV<âeN8 W . ¤xn
+ org/emboss/jemboss/soap/PendingResults$1.classPK
+! æcV<bÏÀFU ª . ¤üp
+ org/emboss/jemboss/soap/PendingResults$2.classPK
+! æcV<K˜J•W ‚$ , ¤s
+ org/emboss/jemboss/soap/PendingResults.classPK
+! æcV<¥{ðî Ï , ¤>…
+ org/emboss/jemboss/soap/PrivateRequest.classPK
+! æcV<Xß/½N ~ + ¤v‘
+ org/emboss/jemboss/soap/PublicRequest.classPK
+! æcV<Í?¦ÞÀ ¸ + ¤
š
+ org/emboss/jemboss/soap/ServerSetup$1.classPK
+! æcV<ú90Â$ M + ¤
+ org/emboss/jemboss/soap/ServerSetup$2.classPK
+! æcV<0Òr7B ™ + ¤ƒŸ
+ org/emboss/jemboss/soap/ServerSetup$3.classPK
+! æcV<{xtõt & + ¤¢
+ org/emboss/jemboss/soap/ServerSetup$4.classPK
+! æcV<¡eR˜G ! ) ¤Ë¥
+ org/emboss/jemboss/soap/ServerSetup.classPK
+! æcV<4¹] & $ ¤Y´
+! org/emboss/jemboss/soap/ShowDB.classPK ññó³ ø·
+
+\ 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
+***************
+*** 688,694 ****
+ public static void showFilePane(String filename, JembossParams mysettings)
+ {
+ Hashtable contents = new Hashtable();
+! contents.put(filename,readByteFile(filename));
+ ShowResultSet srs = new ShowResultSet(contents,mysettings);
+ srs.setTitle("Local File");
+ }
+--- 688,701 ----
+ public static void showFilePane(String filename, JembossParams mysettings)
+ {
+ Hashtable contents = new Hashtable();
+! byte[] content = readByteFile(filename);
+! if(content==null)
+! {
+! JOptionPane.showMessageDialog(null, "file \""+filename+"\" was empty",
+! "error", JOptionPane.ERROR_MESSAGE);
+! return;
+! }
+! contents.put(filename, content);
+ ShowResultSet srs = new ShowResultSet(contents,mysettings);
+ srs.setTitle("Local File");
+ }
+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
+***************
+*** 743,748 ****
+--- 743,754 ----
+
+ Hashtable hfile = new Hashtable();
+ Object contents = gReq.getHash().get("contents");
++ if(contents==null)
++ {
++ JOptionPane.showMessageDialog(null, "file was empty", "error",
++ JOptionPane.ERROR_MESSAGE);
++ return;
++ }
+ if(contents instanceof String)
+ hfile.put(filename, ((String)contents).getBytes() );
+ 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
+***************
+*** 469,475 ****
+ {
+ if(batchStart)
+ {
+! BatchSoapProcess bsp = new BatchSoapProcess(embossCommand,filesToMove,mysettings);
+ bsp.setWithSoap(false);
+ bsp.start();
+ if (prfs.getBoolean(DISPLAY_JOB_SUBMITTED_MSG, true)){
+--- 469,476 ----
+ {
+ if(batchStart)
+ {
+! BatchSoapProcess bsp = new BatchSoapProcess(embossCommand,
+! filesToMove, mysettings, commandA);
+ bsp.setWithSoap(false);
+ bsp.start();
+ if (prfs.getBoolean(DISPLAY_JOB_SUBMITTED_MSG, true)){
+***************
+*** 511,519 ****
+ else
+ {
+ JembossServer js = new JembossServer(mysettings.getResultsHome());
+! js.setEmbossCommandA((String[])commandA.toArray(new String[commandA.size()]));
+! Vector result = js.run_prog(embossCommand,
+! mysettings.getCurrentMode(), filesToMove);
+ Hashtable r = convert(result,false);
+ try {
+ resultSetFrame = new ShowResultSet(r,filesToMove,mysettings);
+--- 512,522 ----
+ else
+ {
+ JembossServer js = new JembossServer(mysettings.getResultsHome());
+! // standalone jemboss, no files to move
+! Vector filesToMovev = new Vector();
+! Vector result = js.run_prog_array(
+! new Vector(commandA),
+! mysettings.getCurrentMode(), filesToMovev, "");
+ Hashtable r = convert(result,false);
+ try {
+ resultSetFrame = new ShowResultSet(r,filesToMove,mysettings);
+***************
+*** 528,535 ****
+ }
+ else
+ {
+ Hashtable filesToMove = new Hashtable();
+! String embossCommand = getCommand(filesToMove);
+
+ if(!embossCommand.equals("NOT OK"))
+ {
+--- 531,539 ----
+ }
+ else
+ {
++ List commandA = new ArrayList();
+ Hashtable filesToMove = new Hashtable();
+! String embossCommand = getCommand(filesToMove, commandA);
+
+ if(!embossCommand.equals("NOT OK"))
+ {
+***************
+*** 541,563 ****
+ {
+ if(batchStart)
+ {
+! BatchSoapProcess bsp = new BatchSoapProcess(embossCommand,filesToMove,mysettings);
+ bsp.start();
+ }
+ else
+ {
+! JembossRun thisrun = new JembossRun(embossCommand,"",
+! filesToMove,mysettings);
+! resultSetFrame = new ShowResultSet(thisrun.hash(),filesToMove,mysettings);
+ }
+ }
+ catch (JembossSoapException eae)
+ {
+ AuthPopup ap = new AuthPopup(mysettings,f);
+ ap.setBottomPanel();
+ ap.setSize(380,170);
+ ap.pack();
+ ap.setVisible(true);
+ }
+ }
+ }
+--- 545,581 ----
+ {
+ if(batchStart)
+ {
+! BatchSoapProcess bsp = new BatchSoapProcess(embossCommand,
+! filesToMove, mysettings, commandA);
+ bsp.start();
+ }
+ else
+ {
+! JembossRun thisrun;
+! if(mysettings.getUseAuth())
+! thisrun = new JembossRun(embossCommand, "",filesToMove,
+! mysettings);
+! else
+! thisrun = new JembossRun(commandA, "",filesToMove,mysettings);
+!
+! resultSetFrame = new ShowResultSet(thisrun.hash(),filesToMove,
+! mysettings);
+ }
+ }
+ catch (JembossSoapException eae)
+ {
++ if (mysettings.getUseAuth() == true)
++ {
+ AuthPopup ap = new AuthPopup(mysettings,f);
+ ap.setBottomPanel();
+ ap.setSize(380,170);
+ ap.pack();
+ ap.setVisible(true);
++ }
++ else
++ JOptionPane.showMessageDialog(f,eae.getMessage(),
++ "Problem in executing server job",
++ JOptionPane.ERROR_MESSAGE);
+ }
+ }
+ }
+***************
+*** 594,600 ****
+ if(s.equals("msg"))
+ {
+ String msg = (String)vans.get(j+1);
+! if(msg.startsWith("Error"))
+ JOptionPane.showMessageDialog(null, msg, "alert",
+ JOptionPane.ERROR_MESSAGE);
+ }
+--- 612,618 ----
+ if(s.equals("msg"))
+ {
+ String msg = (String)vans.get(j+1);
+! if(msg.indexOf("Error")!=-1 || msg.indexOf("error")!=-1)
+ JOptionPane.showMessageDialog(null, msg, "alert",
+ JOptionPane.ERROR_MESSAGE);
+ }
+***************
+*** 839,845 ****
+ if(!(textf[h].getText()).equals("") && textf[h].isVisible()
+ && textf[h].isEnabled())
+ {
+! options = options.concat(" -" + val + " " + textf[h].getText());
+ optionsA.add("-" + val);
+ optionsA.add(textf[h].getText());
+
+--- 857,863 ----
+ if(!(textf[h].getText()).equals("") && textf[h].isVisible()
+ && textf[h].isEnabled())
+ {
+! options = options.concat(" -" + val + " \"" + textf[h].getText())+"\"";
+ optionsA.add("-" + val);
+ optionsA.add(textf[h].getText());
+
+***************
+*** 868,874 ****
+
+ if(textFields[0].getText() != null && !textFields[0].getText().trim().equals(""))
+ {
+! options = options.concat(" -" + val + " " + textFields[0].getText());
+ optionsA.add("-" + val);
+ optionsA.add(textFields[0].getText());
+ }
+--- 886,893 ----
+
+ if(textFields[0].getText() != null && !textFields[0].getText().trim().equals(""))
+ {
+! options = options.concat(" -" + val + " \"" +
+! textFields[0].getText()+ "\"");
+ optionsA.add("-" + val);
+ optionsA.add(textFields[0].getText());
+ }
+***************
+*** 1262,1277 ****
+
+ /**
+ *
+! * Get the command line for the Standalone version.
+! * @param Hashtable of the files to be transferrred
+ * @return String command line to use
+ *
+ */
+ private String getCommand(Hashtable filesToMove, List commandA)
+ {
+- String embossBin = mysettings.getEmbossBin();
+ String command = applName;
+! commandA.add(embossBin +(embossBin.endsWith(File.separator)?"":File.separator)+command);
+ int numofFields = parseAcd.getNumofFields();
+
+ String options = checkParameters(parseAcd, numofFields, filesToMove, commandA);
+--- 1281,1295 ----
+
+ /**
+ *
+! * Get the command line for the standalone as well as the client jemboss
+! * @param Hashtable of the files to be transferred
+ * @return String command line to use
+ *
+ */
+ private String getCommand(Hashtable filesToMove, List commandA)
+ {
+ String command = applName;
+! commandA.add(command);
+ int numofFields = parseAcd.getNumofFields();
+
+ String options = checkParameters(parseAcd, numofFields, filesToMove, commandA);
+***************
+*** 1279,1285 ****
+ if(options.equals("NOT OK"))
+ command = "NOT OK";
+ else {
+! command = command.concat(options + " -auto");
+ commandA.add("-auto");
+ }
+
+--- 1297,1308 ----
+ if(options.equals("NOT OK"))
+ command = "NOT OK";
+ else {
+! for (int i=0; i<commandA.size();i++){
+! String s = (String)commandA.get(i);
+! if(s.equals("stdout"))
+! commandA.set(i, "stdoutfile");
+! }
+! command = command.concat(options.replaceAll("\"stdout\"", "stdoutfile") + " -auto");
+ commandA.add("-auto");
+ }
+
+***************
+*** 1287,1315 ****
+ }
+
+
+- /**
+- *
+- * Get the command line for the SOAP version.
+- * @param Hashtable of the files to be transferrred
+- * @return String command line to use
+- *
+- */
+- private String getCommand(Hashtable filesToMove)
+- {
+- String command = applName;
+- int numofFields = parseAcd.getNumofFields();
+-
+- String options = checkParameters(parseAcd, numofFields, filesToMove, new ArrayList());
+-
+- if(options.equals("NOT OK"))
+- command = "NOT OK";
+- else {
+- command = command.concat(options + " -auto");
+- }
+-
+- return command;
+- }
+-
+
+ /**
+ *
+--- 1310,1315 ----
+***************
+*** 1326,1341 ****
+ public class BatchSoapProcess extends Thread
+ {
+ private String embossCommand;
+ private Hashtable filesToMove;
+ private JembossParams mysettings;
+ private boolean withSoap = true;
+
+ public BatchSoapProcess(String embossCommand, Hashtable filesToMove,
+! JembossParams mysettings)
+ {
+ this.embossCommand = embossCommand;
+ this.filesToMove = filesToMove;
+ this.mysettings = mysettings;
+ }
+
+ public void setWithSoap(boolean withSoap)
+--- 1326,1343 ----
+ public class BatchSoapProcess extends Thread
+ {
+ private String embossCommand;
++ List command;
+ private Hashtable filesToMove;
+ private JembossParams mysettings;
+ private boolean withSoap = true;
+
+ public BatchSoapProcess(String embossCommand, Hashtable filesToMove,
+! JembossParams mysettings, List command)
+ {
+ this.embossCommand = embossCommand;
+ this.filesToMove = filesToMove;
+ this.mysettings = mysettings;
++ this.command = command;
+ }
+
+ public void setWithSoap(boolean withSoap)
+***************
+*** 1364,1378 ****
+ final JembossProcess er;
+ if(withSoap)
+ {
+! JembossRun thisrun = new JembossRun(embossCommand,"",
+! filesToMove,mysettings);
+ er = new JembossProcess((String)thisrun.get("jobid"));
+ }
+ else
+ {
+ JembossServer js = new JembossServer(mysettings.getResultsHome());
+! Vector result = js.run_prog(embossCommand,mysettings.getCurrentMode(),
+! filesToMove);
+ Hashtable resultHash = convert(result, false);
+ er = new JembossProcess((String)resultHash.get("jobid"));
+ }
+--- 1366,1388 ----
+ final JembossProcess er;
+ if(withSoap)
+ {
+! JembossRun thisrun;
+! if (mysettings.getUseAuth() == true)
+! thisrun = new JembossRun(embossCommand,"",filesToMove,
+! mysettings);
+! else
+! thisrun = new JembossRun(command,"",filesToMove,mysettings);
+ er = new JembossProcess((String)thisrun.get("jobid"));
+ }
+ else
+ {
+ JembossServer js = new JembossServer(mysettings.getResultsHome());
+! // standalone jemboss, no files to move
+! Vector filesToMovev = new Vector();
+! Vector result = js.run_prog_array(
+! new Vector(command),
+! mysettings.getCurrentMode(),
+! filesToMovev, "");
+ Hashtable resultHash = convert(result, false);
+ er = new JembossProcess((String)resultHash.get("jobid"));
+ }
+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
+***************
+*** 189,194 ****
+--- 189,196 ----
+ public void setJMenuBar()
+ {
+ int index = rtp.getSelectedIndex();
++ if (index == -1)
++ return;
+ String title = rtp.getTitleAt(index);
+ if (toolbar != null)
+ 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
+***************
+*** 22,27 ****
+--- 22,28 ----
+
+ import java.util.*;
+ import java.io.FileInputStream;
++ import java.io.InputStream;
+
+
+ /**
+***************
+*** 280,286 ****
+ // try out of the classpath
+ try
+ {
+! jembossSettings.load(cl.getResourceAsStream("resources/jemboss.properties"));
+ }
+ catch (Exception e)
+ {
+--- 281,289 ----
+ // try out of the classpath
+ try
+ {
+! InputStream is = cl.getResourceAsStream("resources/jemboss.properties");
+! if (is!=null)
+! jembossSettings.load(is);
+ }
+ catch (Exception e)
+ {
+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
+***************
+*** 141,150 ****
+ while((nc = stderrRead.read(c,0,100)) != -1)
+ stderr = stderr.append(new String(c,0,nc));
+ }
+! catch (IOException io)
+ {
+ System.err.println("RunEmbossApplication2: Error in "+
+! "collecting standard out");
+ }
+ finally
+ {
+--- 141,151 ----
+ while((nc = stderrRead.read(c,0,100)) != -1)
+ stderr = stderr.append(new String(c,0,nc));
+ }
+! catch (Exception io)
+ {
++ io.printStackTrace();
+ System.err.println("RunEmbossApplication2: Error in "+
+! "collecting standard error output");
+ }
+ finally
+ {
+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
+***************
+*** 45,53 ****
+ /** Jemboss error log file */
+ private final String errorLog = new String(tmproot+"/jemboss_error.log");
+ /** file separator */
+! private final String fs = new String(System.getProperty("file.separator"));
+ /** path separator */
+! private final String ps = new String(System.getProperty("path.separator"));
+ /** line separator */
+ private final String ls = System.getProperty("line.separator");
+
+--- 45,53 ----
+ /** Jemboss error log file */
+ private final String errorLog = new String(tmproot+"/jemboss_error.log");
+ /** file separator */
+! private final String fs = File.separator;
+ /** path separator */
+! private final String ps = File.pathSeparator;
+ /** line separator */
+ private final String ls = System.getProperty("line.separator");
+
+***************
+*** 666,673 ****
+ catch(Exception exp){}
+
+ //include any stderr from EMBOSS
+ result.add("msg");
+! result.add(aj.getErrStd());
+
+ //add a finished file
+ try
+--- 666,677 ----
+ catch(Exception exp){}
+
+ //include any stderr from EMBOSS
++ String stderr = aj.getErrStd();
+ result.add("msg");
+! result.add(stderr);
+! if (stderr.length()>0)
+! createStderrFile(project, stderr);
+!
+
+ //add a finished file
+ try
+***************
+*** 712,717 ****
+--- 716,740 ----
+ return result;
+ }
+
++
++ /**
++ *
++ * Creates a file named "stderrfile" in the project directory
++ *
++ */
++
++ private void createStderrFile(String project, String stderr)
++ {
++ File finished = new File(project + fs + "stderrfile");
++
++ try
++ {
++ PrintWriter fout = new PrintWriter(new FileWriter(finished));
++ fout.println(stderr);
++ fout.close();
++ }
++ catch (IOException ioe) {}
++ }
+
+ /**
+ *
+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
+***************
+*** 73,79 ****
+ /** user name */
+ private String username = System.getProperty("user.name") + fs;
+ /** results directory */
+! private String tmproot = jp.getResultsHome()+username;
+ /** results directory */
+ private File tmprootDir = new File(tmproot);
+
+--- 73,79 ----
+ /** user name */
+ private String username = System.getProperty("user.name") + fs;
+ /** results directory */
+! private String tmproot = jp.getResultsHome();
+ /** results directory */
+ private File tmprootDir = new File(tmproot);
+
+***************
+*** 320,417 ****
+ return vans;
+ }
+
+- /**
+- * @deprecated
+- * Uses JNI to calculate sequence attributes using EMBOSS library call.
+- * @param fileContent sequence filename or database entry
+- * @param seqtype sequence type (seqset/sequence)
+- * @return sequence length, weight & type (protein/nucleotide)
+- *
+- */
+-
+- /*
+- private Vector call_ajax_(String fileContent, String seqtype)
+- {
+- boolean afile = false;
+- String fn = null;
+- File tf = null;
+-
+- Vector vans = new Vector();
+-
+- // create temporary file
+- if( ((fileContent.indexOf(":") < 0) ||
+- (fileContent.indexOf("\n") > 0) ) &&
+- !((new File(fileContent)).exists()) )
+- {
+- afile = true;
+- try
+- {
+- tf = File.createTempFile("tmp",".jembosstmp", tmprootDir);
+- PrintWriter out = new PrintWriter(new FileWriter(tf));
+- out.println(fileContent);
+- out.close();
+-
+- fn = new String(tf.getCanonicalPath());
+- }
+- catch (IOException ioe)
+- {
+- System.out.println("IOException : STATUS NOT OK");
+- vans.add("status");
+- vans.add("1");
+- return vans;
+- }
+- }
+- else
+- {
+- fn = fileContent; //looks like db entry or local file name
+- }
+-
+- boolean ok = false;
+- Ajax aj = null;
+-
+- if( ((new File(fn)).exists()) || //call ajax if sequence file
+- (fn.indexOf(":") > 0) ) //or db
+- {
+- try
+- {
+- aj = new Ajax();
+- if(seqtype.startsWith("seqset"))
+- ok = aj.seqsetType(fn);
+- else
+- ok = aj.seqType(fn);
+- }
+- catch (Exception e)
+- {
+- System.out.println("AjaxException : STATUS NOT OK");
+- vans.add("status");
+- vans.add("1");
+- return vans;
+- }
+- }
+-
+- if(ok)
+- {
+- vans.add("length");
+- vans.add(new Integer(Ajax.length));
+- vans.add("protein");
+- vans.add(new Boolean(Ajax.protein));
+- vans.add("weight");
+- vans.add(new Float(Ajax.weight));
+- vans.add("status");
+- vans.add("0");
+- }
+- else
+- {
+- vans.add("status");
+- vans.add("1");
+- }
+-
+- if(afile)
+- tf.delete();
+-
+- return vans;
+- }
+- */
+
+
+ /**
+--- 320,325 ----
+***************
+*** 474,501 ****
+ }
+
+
+- /**
+- *
+- * Run an EMBOSS application
+- * @param embossCommand command line to run
+- * @param options unused
+- * @param inFiles input files and names
+- * @return output files from application run
+- *
+- */
+- public Vector run_prog(String embossCommand, String options,
+- String[] inFiles)
+- {
+- Vector result = new Vector();
+-
+- Hashtable inF = new Hashtable();
+- for(int i=0; i<inFiles.length;i+=2)
+- inF.put(inFiles[i],inFiles[i+1]);
+
+- result = run_prog(embossCommand,options,inF);
+-
+- return result;
+- }
+
+ /**
+ *
+--- 382,388 ----
+***************
+*** 503,509 ****
+ * @param embossCommand command line to run
+ * @param options unused
+ * @param inFiles input files and names
+! * @param userName username
+ * @return output files from application run
+ *
+ */
+--- 390,396 ----
+ * @param embossCommand command line to run
+ * @param options unused
+ * @param inFiles input files and names
+! * @param userName user name
+ * @return output files from application run
+ *
+ */
+***************
+*** 513,519 ****
+ Hashtable hashInFiles = getHashtable(inFiles);
+ tmproot = tmproot.concat(userName+fs);
+ return run_prog(embossCommand,options,hashInFiles);
+! /* return run_prog(embossCommand,options,hashInFiles,userName); */
+ }
+
+ /**
+--- 400,454 ----
+ Hashtable hashInFiles = getHashtable(inFiles);
+ tmproot = tmproot.concat(userName+fs);
+ return run_prog(embossCommand,options,hashInFiles);
+! }
+!
+!
+!
+! /**
+! *
+! * Run an EMBOSS application.
+! * Construction of the command line string here is for information only,
+! * jobs are actually executed using the string array representation
+! * of the command line.
+! *
+! * @param embossCommand command line represented as a String array
+! * @param options "interactive" or "batch", i.e sync or async job
+! * @param inFiles input files with names
+! * @param userName user name
+! * @return output files from application run
+! *
+! */
+!
+! public Vector run_prog_array(Vector cmdA, String options,
+! Vector inFiles, String userName)
+! {
+! Hashtable hashInFiles = getHashtable(inFiles);
+! String cmd ="";
+! int i = 0;
+! tmproot = tmproot.concat(userName+fs);
+! embossCommandA = new String[cmdA.size()+hashInFiles.size()];
+!
+! if(cmdA.size()==0)
+! throw new RuntimeException("empty command line array");
+!
+! embossCommandA[0] = embossBin + cmdA.get(0);
+! cmd = (String)cmdA.get(0);
+!
+! for (i=1; i<cmdA.size(); i++)
+! {
+! String s = (String)cmdA.get(i);
+! cmd += " "+(s.indexOf(' ')==-1 ? s : "\""+s+"\"");
+! embossCommandA[i] = s;
+! }
+! Object[] filenames = hashInFiles.keySet().toArray();
+! for (i=0; i<filenames.length; i++)
+! {
+! String s = (String)filenames[i];
+! cmd += " "+s;
+! embossCommandA[cmdA.size()+i] = s;
+! }
+!
+! return run_prog(cmd,options, hashInFiles);
+ }
+
+ /**
+***************
+*** 525,531 ****
+ * @return output files from application run
+ *
+ */
+! public Vector run_prog(String embossCommand, String options,
+ Hashtable inFiles)
+ {
+
+--- 460,466 ----
+ * @return output files from application run
+ *
+ */
+! private Vector run_prog(String embossCommand, String options,
+ Hashtable inFiles)
+ {
+
+***************
+*** 538,557 ****
+ result.add("ERROR: Disallowed command syntax "+embossCommand);
+ result.add("status");
+ result.add("1");
+-
+ return result;
+ }
+
+- //trap anything that is trying to write to stdout
+- int stdIndex = embossCommand.indexOf(" stdout ");
+- if(stdIndex > -1)
+- {
+- String startCmd = embossCommand.substring(0,stdIndex+7);
+- String endCmd = embossCommand.substring(stdIndex+8);
+- embossCommand = startCmd.concat("file ");
+- embossCommand = embossCommand.concat(endCmd);
+- }
+-
+ Enumeration enumFiles = inFiles.keys();
+ String appl = embossCommand.substring(0,embossCommand.indexOf(" "));
+ String rest = embossCommand.substring(embossCommand.indexOf(" "));
+--- 473,481 ----
+***************
+*** 637,643 ****
+ result.add("0");
+
+ if(options.toLowerCase().indexOf("interactive") > -1)
+! {
+ String stdout = "";
+ String stderr = "";
+ try
+--- 561,567 ----
+ result.add("0");
+
+ if(options.toLowerCase().indexOf("interactive") > -1)
+! {
+ String stdout = "";
+ String stderr = "";
+ try
+***************
+*** 659,666 ****
+
+ if(!stderr.equals(""))
+ {
+! result.add("stderr");
+! result.add(stderr);
+ }
+ createFinishedFile(project);
+ }
+--- 583,591 ----
+
+ if(!stderr.equals(""))
+ {
+! result.add("msg");
+! result.add(stderr);
+! createStderrFile(project, stderr);
+ }
+ createFinishedFile(project);
+ }
+***************
+*** 669,677 ****
+ JembossThread jt = new JembossThread(rea,project);
+ jt.start();
+
+- // if(jt.isAlive())
+- // System.out.println("THREAD IS ALIVE!");
+-
+ result.add("job_submitted");
+ result.add("Job " + projectDir.getName() + "submitted.");
+ result.add("jobid");
+--- 594,599 ----
+***************
+*** 681,688 ****
+ }
+
+ //get the output files
+! result = loadFilesContent(projectDir,project,result,inFiles);
+! result = loadPNGContent(projectDir,project,result);
+
+ return result;
+ }
+--- 603,610 ----
+ }
+
+ //get the output files
+! loadFilesContent(projectDir,project,result,inFiles);
+! loadPNGContent(projectDir,project,result);
+
+ return result;
+ }
+***************
+*** 707,712 ****
+--- 629,659 ----
+ }
+
+
++
++
++ /**
++ *
++ * Creates a file named "stderrfile" in the project directory
++ *
++ */
++
++ private void createStderrFile(String project, String stderr)
++ {
++ File finished = new File(project + fs + "stderrfile");
++
++ try
++ {
++ PrintWriter fout = new PrintWriter(new FileWriter(finished));
++ fout.println(stderr);
++ fout.close();
++ }
++ catch (IOException ioe) {}
++ }
++
++
++
++
++
+ /**
+ *
+ * Returns the results for a saved project.
+***************
+*** 744,751 ****
+
+ if(cl.equals(""))
+ {
+! ssr = loadFilesContent(projectDir,project,ssr,null);
+! ssr = loadPNGContent(projectDir,project,ssr);
+ }
+ else
+ {
+--- 691,698 ----
+
+ if(cl.equals(""))
+ {
+! loadFilesContent(projectDir,project,ssr,null);
+! loadPNGContent(projectDir,project,ssr);
+ }
+ else
+ {
+***************
+*** 970,976 ****
+ * @return result
+ *
+ */
+! private Vector loadFilesContent(File projectDir, String project,
+ Vector result, Hashtable inFiles)
+ {
+
+--- 917,923 ----
+ * @return result
+ *
+ */
+! private void loadFilesContent(File projectDir, String project,
+ Vector result, Hashtable inFiles)
+ {
+
+***************
+*** 981,986 ****
+--- 928,936 ----
+ return (!name.startsWith(".") && !name.endsWith(".png"));
+ };
+ });
++
++ if (outFiles == null)
++ return;
+
+ for(int i=0;i<outFiles.length;i++)
+ {
+***************
+*** 1028,1035 ****
+ result.add(fc);
+ }
+ }
+! return result;
+!
+ }
+
+ /**
+--- 978,984 ----
+ result.add(fc);
+ }
+ }
+! return;
+ }
+
+ /**
+***************
+*** 1041,1047 ****
+ * @return result
+ *
+ */
+! private Vector loadPNGContent(File projectDir, String project, Vector result)
+ {
+
+ String pngFiles[] = projectDir.list(new FilenameFilter()
+--- 990,996 ----
+ * @return result
+ *
+ */
+! private void loadPNGContent(File projectDir, String project, Vector result)
+ {
+
+ String pngFiles[] = projectDir.list(new FilenameFilter()
+***************
+*** 1065,1071 ****
+ result.add(data);
+ }
+ }
+! return result;
+ }
+
+ /**
+--- 1014,1020 ----
+ result.add(data);
+ }
+ }
+! return;
+ }
+
+ /**
+***************
+*** 1106,1112 ****
+ * @param prog program
+ * @param opt options
+ * @param resToQuery results to query
+! * @param userName username
+ *
+ */
+ public Vector update_result_status(String prog, String opt,
+--- 1055,1061 ----
+ * @param prog program
+ * @param opt options
+ * @param resToQuery results to query
+! * @param userName user name
+ *
+ */
+ public Vector update_result_status(String prog, String opt,
+***************
+*** 1205,1213 ****
+ throw new java.lang.CloneNotSupportedException();
+ }
+
+- public void setEmbossCommandA(String[] embossCommandA) {
+- this.embossCommandA = embossCommandA;
+- }
+-
+ }
+
+--- 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
+***************
+*** 55,62 ****
+ {
+ rea.waitFor();
+ createFinishedFile();
+ }
+!
+ /**
+ *
+ * Creates a file named "finished" in the project directory,
+--- 55,92 ----
+ {
+ rea.waitFor();
+ createFinishedFile();
++ String stderr;
++ try {
++ stderr = rea.getProcessStderr();
++
++ if (stderr.length()>0)
++ createStderrFile(stderr);
++
++ } catch (Exception e) {
++ System.err.println("Problem while capturing stderr output: " +
++ e.getMessage());
++ }
++
+ }
+!
+! /**
+! *
+! * Creates a file named "stderrfile" in the project directory
+! *
+! */
+! private void createStderrFile(String stderr)
+! {
+! File stderrfile = new File(project + File.separator + "stderrfile");
+!
+! try
+! {
+! PrintWriter fout = new PrintWriter(new FileWriter(stderrfile));
+! fout.println(stderr);
+! fout.close();
+! }
+! catch (IOException ioe) {}
+! }
+!
+ /**
+ *
+ * Creates a file named "finished" in the project directory,
+***************
+*** 65,72 ****
+ */
+ private void createFinishedFile()
+ {
+! String fs = new String(System.getProperty("file.separator"));
+! File finished = new File(project + fs + ".finished");
+
+ try
+ {
+--- 95,101 ----
+ */
+ private void createFinishedFile()
+ {
+! File finished = new File(project + File.separator + ".finished");
+
+ try
+ {
+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
+***************
+*** 176,182 ****
+
+ /**
+ *
+! * Buttons across the bottom
+ *
+ */
+ public void addBottomPanel()
+--- 176,182 ----
+
+ /**
+ *
+! * Buttons across the bottom. Used for the File Manager login only.
+ *
+ */
+ public void addBottomPanel()
+***************
+*** 300,306 ****
+ remove(promptPanel);
+ pack();
+ }
+- else
+ dispose();
+ }
+ });
+--- 300,305 ----
+***************
+*** 328,334 ****
+ remove(promptPanel);
+ pack();
+ }
+- else
+ dispose();
+ }
+ });
+--- 327,332 ----
+***************
+*** 336,345 ****
+ }
+
+
+- //public JButton getOKButton()
+- //{
+- // return okButton;
+- //}
+
+
+ /**
+--- 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
+***************
+*** 44,85 ****
+ private Hashtable proganswer;
+
+ /**
+ *
+! * @param appl defining command
+ * @param options defining options
+ * @param filesToMove Hashtable of filenames and contents
+ * @param mysettings jemboss properties
+ * @throws JembossSoapException if authentication fails
+ *
+ */
+! public JembossRun(String appl, String options, Hashtable filesToMove,
+ JembossParams mysettings) throws JembossSoapException
+ {
+
+ String fulloptions;
+
+ Vector params = new Vector();
+! params.addElement(appl);
+
+ //construct a full options string
+ fulloptions = "mode="+mysettings.getCurrentMode()+" "+options;
+- // if (mysettings.getUseX11())
+- // fulloptions = "display="+mysettings.getX11display()+" "+fulloptions;
+ params.addElement(fulloptions);
+
+ // just pass the hash
+ params.addElement(filesToMove);
+
+ PrivateRequest eRun;
+! try
+! {
+! eRun = new PrivateRequest(mysettings,
+! "run_prog", params);
+! }
+! catch (JembossSoapException e)
+! {
+! throw new JembossSoapException("Authentication Failed");
+! }
+
+ proganswer = eRun.getHash();
+ status = proganswer.get("status").toString();
+--- 44,119 ----
+ private Hashtable proganswer;
+
+ /**
++ * Makes a web service call to run an EMBOSS job.
++ * This constructor is used when user.auth is true.
+ *
+! * @param cmdl command line
+ * @param options defining options
+ * @param filesToMove Hashtable of filenames and contents
+ * @param mysettings jemboss properties
+ * @throws JembossSoapException if authentication fails
+ *
+ */
+! public JembossRun(String cmdl, String options, Hashtable filesToMove,
+ JembossParams mysettings) throws JembossSoapException
+ {
+
+ String fulloptions;
+
+ Vector params = new Vector();
+! params.addElement(cmdl);
+
+ //construct a full options string
+ fulloptions = "mode="+mysettings.getCurrentMode()+" "+options;
+ params.addElement(fulloptions);
+
+ // just pass the hash
+ params.addElement(filesToMove);
+
+ PrivateRequest eRun;
+!
+! eRun = new PrivateRequest(mysettings,"run_prog", params);
+!
+! proganswer = eRun.getHash();
+! status = proganswer.get("status").toString();
+! statusmsg = proganswer.get("msg").toString();
+!
+! proganswer.remove("status"); // delete the status/msg
+! proganswer.remove("msg");
+! }
+!
+!
+! /**
+! * Makes a web service call to run an EMBOSS job.
+! * This constructor is used when user.auth is false.
+! *
+! * @param cmdl command line
+! * @param options defining options
+! * @param filesToMove Hashtable of filenames and contents
+! * @param mysettings jemboss properties
+! * @throws JembossSoapException if authentication fails
+! *
+! */
+! public JembossRun(List cmdl, String options, Hashtable filesToMove,
+! JembossParams mysettings) throws JembossSoapException
+! {
+!
+! String fulloptions;
+!
+! Vector params = new Vector();
+! params.addElement(new Vector(cmdl));
+!
+! //construct a full options string
+! fulloptions = "mode="+mysettings.getCurrentMode()+" "+options;
+! params.addElement(fulloptions);
+!
+! // just pass the hash
+! params.addElement(filesToMove);
+!
+! PrivateRequest eRun;
+!
+! eRun = new PrivateRequest(mysettings,
+! "run_prog_array", params);
+
+ proganswer = eRun.getHash();
+ 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
+***************
+*** 85,91 ****
+ org.apache.axis.client.Service serv =
+ new org.apache.axis.client.Service();
+ Call call = (Call) serv.createCall();
+- //QName qn = new QName(service, method);
+ call.setTargetEndpointAddress( new java.net.URL(endpoint) );
+ call.setOperationName(new QName(service, method));
+ call.setEncodingStyle(org.apache.axis.Constants.URI_SOAP12_ENC);
+--- 85,90 ----
+***************
+*** 110,115 ****
+--- 109,121 ----
+ call.addParameter("Args"+i, XMLType.XSD_STRING,
+ javax.xml.rpc.ParameterMode.IN);
+ }
++ else if(obj.getClass().equals(Vector.class))
++ {
++ params[i] = obj;
++
++ call.addParameter("Args"+i, XMLType.SOAP_VECTOR,
++ javax.xml.rpc.ParameterMode.IN);
++ }
+ else if(obj.getClass().equals(Hashtable.class))
+ {
+ params[i] = getVector((Hashtable)obj);
+***************
+*** 171,177 ****
+ String msg = (String)vans.get(j+1);
+ if(msg.startsWith("Failed Authorisation"))
+ throw new JembossSoapException("Authentication Failed");
+! else if(msg.startsWith("Error"))
+ JOptionPane.showMessageDialog(null, msg, "alert",
+ JOptionPane.ERROR_MESSAGE);
+ }
+--- 177,183 ----
+ String msg = (String)vans.get(j+1);
+ if(msg.startsWith("Failed Authorisation"))
+ throw new JembossSoapException("Authentication Failed");
+! else if(msg.indexOf("Error")!=-1 || msg.indexOf("error")!=-1)
+ JOptionPane.showMessageDialog(null, msg, "alert",
+ JOptionPane.ERROR_MESSAGE);
+ }
+***************
+*** 180,188 ****
+ }
+ catch (Exception e)
+ {
+! System.out.println("Exception in PrivateRequest "+
+ e.getMessage ());
+! throw new JembossSoapException(" Fault Code = " );
+ }
+
+ }
+--- 186,194 ----
+ }
+ catch (Exception e)
+ {
+! System.err.println("Exception in PrivateRequest "+
+ e.getMessage ());
+! throw new JembossSoapException(e.getMessage());
+ }
+
+ }
+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
+***************
+*** 173,179 ****
+ ./configure --with-thread=$PLATFORM \
+ --prefix=$EMBOSS_INSTALL $USER_CONFIG
+ make
+! make install
+ else
+ echo
+ echo "Did not install $dir cannot find"
+--- 173,179 ----
+ ./configure --with-thread=$PLATFORM \
+ --prefix=$EMBOSS_INSTALL $USER_CONFIG
+ make
+! make -j install
+ else
+ echo
+ echo "Did not install $dir cannot find"
+***************
+*** 1079,1084 ****
+--- 1079,1089 ----
+ read DATADIR
+ echo "$DATADIR" >> $RECORD
+
++ if (test "$DATADIR" = ""); then
++ DATADIR="/tmp/SOAP/emboss"
++ fi
++
++
+ echo
+
+ #
+***************
+*** 1210,1216 ****
+ echo
+ sleep 2
+
+! make install
+
+ #
+ #
+--- 1215,1221 ----
+ echo
+ sleep 2
+
+! make -j install
+
+ #
+ #
+***************
+*** 1236,1248 ****
+
+
+
+- #
+- # create wossname.jar
+- #
+- PATH=$EMBOSS_INSTALL/bin:$PATH
+- export PATH
+- $EMBOSS_INSTALL/bin/wossname -colon -gui -outf wossname.out -auto
+- $JAVA_HOME/bin/jar cvf $JEMBOSS/resources/wossname.jar wossname.out
+
+ #
+ # create resources.jar archive of the scoring matrix
+--- 1241,1246 ----
+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
+***************
+*** 800,807 ****
+
+ AjBool embPatRestrictReadEntry(EmbPPatRestrict re, AjPFile inf)
+ {
+! AjPStr line;
+! AjBool ret;
+ const char *p = NULL;
+ char *q = NULL;
+ ajuint i;
+--- 800,807 ----
+
+ AjBool embPatRestrictReadEntry(EmbPPatRestrict re, AjPFile inf)
+ {
+! AjPStr line = NULL;
+! AjBool ret = AJFALSE;
+ const char *p = NULL;
+ char *q = NULL;
+ ajuint i;
+***************
+*** 825,849 ****
+
+
+ p = ajSysFuncStrtok(p,"\t \n");
+ ajStrAssignC(&re->cod,p);
+ p = ajSysFuncStrtok(NULL,"\t \n");
+ ajStrAssignC(&re->pat,p);
+ ajStrAssignC(&re->bin,p);
+
+ p = ajSysFuncStrtok(NULL,"\t \n");
+! sscanf(p,"%d",&re->len);
+ p = ajSysFuncStrtok(NULL,"\t \n");
+! sscanf(p,"%d",&re->ncuts);
+ p = ajSysFuncStrtok(NULL,"\t \n");
+! sscanf(p,"%d",&re->blunt);
+ p = ajSysFuncStrtok(NULL,"\t \n");
+! sscanf(p,"%d",&re->cut1);
+ p = ajSysFuncStrtok(NULL,"\t \n");
+! sscanf(p,"%d",&re->cut2);
+ p = ajSysFuncStrtok(NULL,"\t \n");
+! sscanf(p,"%d",&re->cut3);
+ p = ajSysFuncStrtok(NULL,"\t \n");
+! sscanf(p,"%d",&re->cut4);
+
+ for(i=0,q=ajStrGetuniquePtr(&re->bin);i<re->len;++i)
+ *(q+i)=(char)ajBaseAlphaToBin((int)*(q+i));
+--- 825,882 ----
+
+
+ p = ajSysFuncStrtok(p,"\t \n");
++ if(!p)
++ return ajFalse;
+ ajStrAssignC(&re->cod,p);
++
+ p = ajSysFuncStrtok(NULL,"\t \n");
++ if(!p)
++ return ajFalse;
+ ajStrAssignC(&re->pat,p);
+ ajStrAssignC(&re->bin,p);
+
+ p = ajSysFuncStrtok(NULL,"\t \n");
+! if(!p)
+! return ajFalse;
+! if(!sscanf(p,"%d",&re->len))
+! return ajFalse;
+!
+ p = ajSysFuncStrtok(NULL,"\t \n");
+! if(!p)
+! return ajFalse;
+! if(!sscanf(p,"%d",&re->ncuts))
+! return ajFalse;
+!
+ p = ajSysFuncStrtok(NULL,"\t \n");
+! if(!p)
+! return ajFalse;
+! if(!sscanf(p,"%d",&re->blunt))
+! return ajFalse;
+!
+ p = ajSysFuncStrtok(NULL,"\t \n");
+! if(!p)
+! return ajFalse;
+! if(!sscanf(p,"%d",&re->cut1))
+! return ajFalse;
+!
+ p = ajSysFuncStrtok(NULL,"\t \n");
+! if(!p)
+! return ajFalse;
+! if(!sscanf(p,"%d",&re->cut2))
+! return ajFalse;
+!
+ p = ajSysFuncStrtok(NULL,"\t \n");
+! if(!p)
+! return ajFalse;
+! if(!sscanf(p,"%d",&re->cut3))
+! return ajFalse;
+!
+ p = ajSysFuncStrtok(NULL,"\t \n");
+! if(!p)
+! return ajFalse;
+! if(!sscanf(p,"%d",&re->cut4))
+! return ajFalse;
+!
+
+ for(i=0,q=ajStrGetuniquePtr(&re->bin);i<re->len;++i)
+ *(q+i)=(char)ajBaseAlphaToBin((int)*(q+i));
+***************
+*** 2936,2943 ****
+ {
+ ready[i] = m;
+
+ for(j=m-k-1;j<(ajint)m;++j)
+! skipm[j][i] = m-k-1;
+ }
+
+ p += plen-1;
+--- 2969,2985 ----
+ {
+ ready[i] = m;
+
++ /*
++ ** AJB: Note that if the mismatches are 1 less than the real
++ ** pattern length then the skip value can become 0 - hence
++ ** the use of AJMAX to ensure that the skip value is always
++ ** positive. This prevents a potential infinite loop in the
++ ** upcoming TUBSearch function. Need to check the original
++ ** algorithm to check that nothing is amiss here, then
++ ** delete this comment block.
++ */
+ for(j=m-k-1;j<(ajint)m;++j)
+! skipm[j][i] = AJMAX(m-k-1,1);
+ }
+
+ p += plen-1;
+***************
+*** 4272,4279 ****
+
+ hits = 0;
+
+! while(embPatRestrictReadEntry(enz,enzfile))
+ {
+ if(!enz->ncuts)
+ continue;
+
+--- 4314,4324 ----
+
+ hits = 0;
+
+! while(!ajFileIsEof(enzfile))
+ {
++ if(!embPatRestrictReadEntry(enz,enzfile))
++ continue;
++
+ if(!enz->ncuts)
+ continue;
+
+***************
+*** 4737,4742 ****
+--- 4782,4791 ----
+
+ break;
+ case 6:
++ if(thys->m && mismatch >= thys->m)
++ ajFatal("embPatCompileII: Mismatches (%d) must be less than the "
++ "real pattern length (%d)",mismatch,thys->m);
++
+ if (!thys->skipm)
+ {
+ AJCNEW(thys->skipm,thys->m);
diff --git a/debian/patches/series b/debian/patches/series
index 50db2ce..06a3ea4 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,2 +1,3 @@
+official-upstream-patch.patch
using-pager-in-tfm.patch
tfm-html.patch
--
The European Molecular Biology Open Software Suite.
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