[med-svn] r3716 - in trunk/packages/emboss/trunk/debian: . patches
Charles Plessy
plessy at alioth.debian.org
Fri Jul 31 12:33:36 UTC 2009
Author: plessy
Date: 2009-07-31 12:33:35 +0000 (Fri, 31 Jul 2009)
New Revision: 3716
Added:
trunk/packages/emboss/trunk/debian/patches/official-upstream-patch.patch
Modified:
trunk/packages/emboss/trunk/debian/changelog
trunk/packages/emboss/trunk/debian/patches/series
Log:
New upstream patch.
Modified: trunk/packages/emboss/trunk/debian/changelog
===================================================================
--- trunk/packages/emboss/trunk/debian/changelog 2009-07-30 10:21:44 UTC (rev 3715)
+++ trunk/packages/emboss/trunk/debian/changelog 2009-07-31 12:33:35 UTC (rev 3716)
@@ -1,5 +1,12 @@
emboss (6.1.0-2) UNRELEASED; urgency=low
+ * New upstream patch (patch-1-1):
+ - Fix feature specification problems in Jemboss.
+ - Use version number to point to documentation URLs
+ - Remove standalone option from server script.
+ - Correct FASTQ input searching for '@' to start next sequence
+ - Standardize FASTQ sequence formats with other OpenBio projects
+ - Correct issues in igstrict, genpept and refseqp formats
* debian/control:
- Incremented Standards-Version to reflect conformance with Policy 3.8.2
(no changes needed).
Added: trunk/packages/emboss/trunk/debian/patches/official-upstream-patch.patch
===================================================================
--- trunk/packages/emboss/trunk/debian/patches/official-upstream-patch.patch (rev 0)
+++ trunk/packages/emboss/trunk/debian/patches/official-upstream-patch.patch 2009-07-31 12:33:35 UTC (rev 3716)
@@ -0,0 +1,1552 @@
+Description: Official upstream patch.
+ 29 Jul 2009: Fix feature specification problems in Jemboss.
+ Use version number to point to documentation URLs
+ Remove standalone option from server script.
+ Correct FASTQ input searching for '@' to start next sequence
+ Standardize FASTQ sequence formats with other OpenBio projects
+ Correct issues in igstrict, genpept and refseqp formats
+Origin: ftp://emboss.open-bio.org/pub/EMBOSS/fixes/patches/patch-1-1.gz
+Forwarded: not-needed
+diff -c -N --recursive EMBOSS-6.1.0orig/ajax/ajfeat.c EMBOSS-6.1.0/ajax/ajfeat.c
+*** EMBOSS-6.1.0orig/ajax/ajfeat.c 2009-07-06 16:48:46.000000000 +0100
+--- EMBOSS-6.1.0/ajax/ajfeat.c 2009-07-30 15:28:13.000000000 +0100
+***************
+*** 9517,9528 ****
+ ajint i;
+
+ if(!featRegUfoFmt)
+! featRegUfoFmt = ajRegCompC("^([A-Za-z0-9]+):+(.*)$");
+ /* \1 format */
+ /* \2 remainder */
+
+ if(!featRegUfoFile)
+! featRegUfoFile = ajRegCompC("^([^:]+)$");
+
+ /*ajDebug("ajFeatUfoRead UFO '%S'\n", ufo);*/
+
+--- 9517,9528 ----
+ ajint i;
+
+ if(!featRegUfoFmt)
+! featRegUfoFmt = ajRegCompC("^([A-Za-z0-9][A-Za-z0-9]+):+(.*)$");
+ /* \1 format */
+ /* \2 remainder */
+
+ if(!featRegUfoFile)
+! featRegUfoFile = ajRegCompC("^(([A-Za-z]:)?[^:]+)$");
+
+ /*ajDebug("ajFeatUfoRead UFO '%S'\n", ufo);*/
+
+diff -c -N --recursive EMBOSS-6.1.0orig/ajax/ajseqread.c EMBOSS-6.1.0/ajax/ajseqread.c
+*** EMBOSS-6.1.0orig/ajax/ajseqread.c 2009-07-07 00:08:26.000000000 +0100
+--- EMBOSS-6.1.0/ajax/ajseqread.c 2009-07-30 15:27:39.000000000 +0100
+***************
+*** 689,695 ****
+ AJTRUE, AJTRUE, seqReadSwiss, AJFALSE, 0},
+ {"nbrf", "NBRF/PIR entry format",
+ AJFALSE, AJTRUE, AJTRUE, AJTRUE,
+! AJFALSE, AJTRUE, seqReadNbrf, AJFALSE, 0}, /* test before NCBI */
+ {"pir", "NBRF/PIR entry format (alias)",
+ AJTRUE, AJFALSE, AJTRUE, AJTRUE,
+ AJTRUE, AJTRUE, seqReadNbrf, AJFALSE, 0}, /* alias for nbrf */
+--- 689,695 ----
+ AJTRUE, AJTRUE, seqReadSwiss, AJFALSE, 0},
+ {"nbrf", "NBRF/PIR entry format",
+ AJFALSE, AJTRUE, AJTRUE, AJTRUE,
+! AJTRUE, AJTRUE, seqReadNbrf, AJFALSE, 0}, /* test before NCBI */
+ {"pir", "NBRF/PIR entry format (alias)",
+ AJTRUE, AJFALSE, AJTRUE, AJTRUE,
+ AJTRUE, AJTRUE, seqReadNbrf, AJFALSE, 0}, /* alias for nbrf */
+***************
+*** 712,718 ****
+ {"ncbi", "FASTA format including NCBI-style IDs (alias)",
+ AJTRUE, AJFALSE, AJTRUE, AJTRUE,
+ AJFALSE, AJTRUE, seqReadNcbi, AJFALSE, 0}, /* test before pearson */
+! {"gifasta", "FASTA format including NCBI-style IDs (alias)",
+ AJFALSE, AJFALSE, AJTRUE, AJTRUE,
+ AJFALSE, AJTRUE, seqReadGifasta, AJFALSE, 0}, /* NCBI with GI as ID*/
+ {"pearson", "Plain old fasta format with IDs not parsed further",
+--- 712,718 ----
+ {"ncbi", "FASTA format including NCBI-style IDs (alias)",
+ AJTRUE, AJFALSE, AJTRUE, AJTRUE,
+ AJFALSE, AJTRUE, seqReadNcbi, AJFALSE, 0}, /* test before pearson */
+! {"gifasta", "FASTA format including NCBI-style GIs (alias)",
+ AJFALSE, AJFALSE, AJTRUE, AJTRUE,
+ AJFALSE, AJTRUE, seqReadGifasta, AJFALSE, 0}, /* NCBI with GI as ID*/
+ {"pearson", "Plain old fasta format with IDs not parsed further",
+***************
+*** 749,759 ****
+ AJTRUE, AJFALSE, AJTRUE, AJFALSE,
+ AJTRUE, AJTRUE, seqReadRefseq, AJFALSE, 0}, /* alias for genbank */
+ {"refseqp", "Refseq protein entry format",
+! AJFALSE, AJFALSE, AJFALSE, AJTRUE, /* genbank forwards proteins */
+ AJTRUE, AJTRUE, seqReadRefseqp, AJFALSE, 0},
+ {"genpept", "Refseq protein entry format (alias)",
+! AJTRUE, AJFALSE, AJFALSE, AJTRUE,
+! AJTRUE, AJTRUE, seqReadGenpept, AJFALSE, 0}, /* alias for refseqp*/
+ {"codata", "Codata entry format",
+ AJFALSE, AJTRUE, AJTRUE, AJTRUE,
+ AJTRUE, AJTRUE, seqReadCodata, AJFALSE, 0},
+--- 749,759 ----
+ AJTRUE, AJFALSE, AJTRUE, AJFALSE,
+ AJTRUE, AJTRUE, seqReadRefseq, AJFALSE, 0}, /* alias for genbank */
+ {"refseqp", "Refseq protein entry format",
+! AJFALSE, AJFALSE, AJFALSE, AJTRUE, /* genbank format proteins */
+ AJTRUE, AJTRUE, seqReadRefseqp, AJFALSE, 0},
+ {"genpept", "Refseq protein entry format (alias)",
+! AJFALSE, AJFALSE, AJFALSE, AJTRUE,
+! AJTRUE, AJTRUE, seqReadGenpept, AJFALSE, 0},
+ {"codata", "Codata entry format",
+ AJFALSE, AJTRUE, AJTRUE, AJTRUE,
+ AJTRUE, AJTRUE, seqReadCodata, AJFALSE, 0},
+***************
+*** 785,791 ****
+ {"hennig86", "Hennig86 output format",
+ AJFALSE, AJTRUE, AJTRUE, AJTRUE,
+ AJFALSE, AJTRUE, seqReadHennig86, AJFALSE, 0},
+! {"jackknifer", "Jackknifer output interleaved format",
+ AJFALSE, AJTRUE, AJTRUE, AJTRUE,
+ AJFALSE, AJTRUE, seqReadJackknifer, AJFALSE, 0},
+ {"nexus", "Nexus/paup interleaved format",
+--- 785,791 ----
+ {"hennig86", "Hennig86 output format",
+ AJFALSE, AJTRUE, AJTRUE, AJTRUE,
+ AJFALSE, AJTRUE, seqReadHennig86, AJFALSE, 0},
+! {"jackknifer", "Jackknifer interleaved and non-interleaved formats",
+ AJFALSE, AJTRUE, AJTRUE, AJTRUE,
+ AJFALSE, AJTRUE, seqReadJackknifer, AJFALSE, 0},
+ {"nexus", "Nexus/paup interleaved format",
+***************
+*** 797,803 ****
+ {"treecon", "Treecon output format",
+ AJFALSE, AJTRUE, AJTRUE, AJTRUE,
+ AJFALSE, AJTRUE, seqReadTreecon, AJFALSE, 0},
+! {"mega", "Mega interleaved output format",
+ AJFALSE, AJTRUE, AJTRUE, AJTRUE,
+ AJFALSE, AJTRUE, seqReadMega, AJFALSE, 0},
+ {"igstrict", "Intelligenetics sequence format strict parser",
+--- 797,803 ----
+ {"treecon", "Treecon output format",
+ AJFALSE, AJTRUE, AJTRUE, AJTRUE,
+ AJFALSE, AJTRUE, seqReadTreecon, AJFALSE, 0},
+! {"mega", "Mega interleaved and non-interleaved formats",
+ AJFALSE, AJTRUE, AJTRUE, AJTRUE,
+ AJFALSE, AJTRUE, seqReadMega, AJFALSE, 0},
+ {"igstrict", "Intelligenetics sequence format strict parser",
+***************
+*** 813,819 ****
+ AJFALSE, AJFALSE, AJTRUE, AJTRUE,
+ AJFALSE, AJTRUE, seqReadText, AJFALSE, 0},/* can read almost anything */
+ {"plain", "Plain text (alias)",
+! AJFALSE, AJFALSE, AJTRUE, AJTRUE,
+ AJFALSE, AJTRUE, seqReadText, AJFALSE, 0}, /* alias for text */
+ {"gff2", "GFF feature file with sequence in the header",
+ AJFALSE, AJTRUE, AJTRUE, AJTRUE,
+--- 813,819 ----
+ AJFALSE, AJFALSE, AJTRUE, AJTRUE,
+ AJFALSE, AJTRUE, seqReadText, AJFALSE, 0},/* can read almost anything */
+ {"plain", "Plain text (alias)",
+! AJTRUE, AJFALSE, AJTRUE, AJTRUE,
+ AJFALSE, AJTRUE, seqReadText, AJFALSE, 0}, /* alias for text */
+ {"gff2", "GFF feature file with sequence in the header",
+ AJFALSE, AJTRUE, AJTRUE, AJTRUE,
+***************
+*** 822,838 ****
+ AJFALSE, AJTRUE, AJTRUE, AJTRUE,
+ AJTRUE, AJTRUE, seqReadGff3, AJFALSE, 0},
+ {"gff", "GFF3 feature file with sequence",
+! AJTRUE, AJTRUE, AJTRUE, AJTRUE,
+ AJTRUE, AJTRUE, seqReadGff3, AJFALSE, 0},
+ {"stockholm", "Stockholm (pfam) format",
+ AJFALSE, AJTRUE, AJTRUE, AJTRUE,
+ AJFALSE, AJTRUE, seqReadStockholm, AJFALSE, 0},
+- {"selex", "Selex format", /* can read almost anything */
+- AJFALSE, AJFALSE, AJTRUE, AJTRUE,
+- AJFALSE, AJTRUE, seqReadSelex, AJFALSE, 0},
+ {"pfam", "Stockholm (pfam) format (alias)",
+ AJTRUE, AJTRUE, AJTRUE, AJTRUE,
+ AJFALSE, AJTRUE, seqReadStockholm, AJFALSE, 0},
+ {"fitch", "Fitch program format",
+ AJFALSE, AJTRUE, AJTRUE, AJTRUE,
+ AJFALSE, AJTRUE, seqReadFitch, AJFALSE, 0},
+--- 822,838 ----
+ AJFALSE, AJTRUE, AJTRUE, AJTRUE,
+ AJTRUE, AJTRUE, seqReadGff3, AJFALSE, 0},
+ {"gff", "GFF3 feature file with sequence",
+! AJTRUE, AJFALSE, AJTRUE, AJTRUE,
+ AJTRUE, AJTRUE, seqReadGff3, AJFALSE, 0},
+ {"stockholm", "Stockholm (pfam) format",
+ AJFALSE, AJTRUE, AJTRUE, AJTRUE,
+ AJFALSE, AJTRUE, seqReadStockholm, AJFALSE, 0},
+ {"pfam", "Stockholm (pfam) format (alias)",
+ AJTRUE, AJTRUE, AJTRUE, AJTRUE,
+ AJFALSE, AJTRUE, seqReadStockholm, AJFALSE, 0},
++ {"selex", "Selex format", /* can read almost anything */
++ AJFALSE, AJFALSE, AJTRUE, AJTRUE,
++ AJFALSE, AJTRUE, seqReadSelex, AJFALSE, 0},
+ {"fitch", "Fitch program format",
+ AJFALSE, AJTRUE, AJTRUE, AJTRUE,
+ AJFALSE, AJTRUE, seqReadFitch, AJFALSE, 0},
+***************
+*** 2627,2634 ****
+ seqin->Text, &thys->TextPtr);
+
+ while(ok &&
+! (ajStrGetLen(qualstr) < seqlen) &&
+! (!ajStrPrefixC(seqReadLine, "@")))
+ {
+ seqqualAppendWarn(&qualstr, seqReadLine);
+
+--- 2627,2634 ----
+ seqin->Text, &thys->TextPtr);
+
+ while(ok &&
+! ((ajStrGetLen(qualstr) < seqlen) ||
+! ajStrGetCharFirst(seqReadLine) != '@'))
+ {
+ seqqualAppendWarn(&qualstr, seqReadLine);
+
+***************
+*** 2790,2797 ****
+ seqin->Text, &thys->TextPtr);
+
+ while(ok &&
+! (ajStrGetLen(qualstr) < seqlen) &&
+! (!ajStrPrefixC(seqReadLine, "@")))
+ {
+ seqqualAppendWarn(&qualstr, seqReadLine);
+
+--- 2790,2797 ----
+ seqin->Text, &thys->TextPtr);
+
+ while(ok &&
+! ((ajStrGetLen(qualstr) < seqlen) ||
+! ajStrGetCharFirst(seqReadLine) != '@'))
+ {
+ seqqualAppendWarn(&qualstr, seqReadLine);
+
+***************
+*** 3157,3164 ****
+ seqin->Text, &thys->TextPtr);
+
+ while(ok &&
+! (ajStrGetLen(qualstr) < seqlen) &&
+! (!ajStrPrefixC(seqReadLine, "@")))
+ {
+ seqqualAppendWarn(&qualstr, seqReadLine);
+
+--- 3157,3164 ----
+ seqin->Text, &thys->TextPtr);
+
+ while(ok &&
+! ((ajStrGetLen(qualstr) < seqlen) ||
+! ajStrGetCharFirst(seqReadLine) != '@'))
+ {
+ seqqualAppendWarn(&qualstr, seqReadLine);
+
+***************
+*** 3352,3359 ****
+ seqin->Text, &thys->TextPtr);
+
+ while(ok &&
+! (ajStrGetLen(qualstr) < seqlen) &&
+! (!ajStrPrefixC(seqReadLine, "@")))
+ {
+ seqqualAppendWarn(&qualstr, seqReadLine);
+
+--- 3352,3359 ----
+ seqin->Text, &thys->TextPtr);
+
+ while(ok &&
+! ((ajStrGetLen(qualstr) < seqlen) ||
+! ajStrGetCharFirst(seqReadLine) != '@'))
+ {
+ seqqualAppendWarn(&qualstr, seqReadLine);
+
+***************
+*** 5254,5261 ****
+ return ajFalse;
+ }
+
+! ajStrAssignS(&thys->Name, seqReadLine);
+! ajStrCutEnd(&thys->Name, 1);
+ bufflines++;
+
+ while(ajBuffreadLineStore(buff, &seqReadLine,
+--- 5254,5260 ----
+ return ajFalse;
+ }
+
+! seqSetName(&thys->Name, seqReadLine);
+ bufflines++;
+
+ while(ajBuffreadLineStore(buff, &seqReadLine,
+***************
+*** 5330,5337 ****
+ return ajFalse;
+ }
+
+! ajStrAssignS(&thys->Name, seqReadLine);
+! ajStrCutEnd(&thys->Name, 1);
+ bufflines++;
+
+ while(ajBuffreadLineStore(buff, &seqReadLine,
+--- 5329,5335 ----
+ return ajFalse;
+ }
+
+! seqSetName(&thys->Name, seqReadLine);
+ bufflines++;
+
+ while(ajBuffreadLineStore(buff, &seqReadLine,
+***************
+*** 6651,6656 ****
+--- 6649,6655 ----
+ if(ajStrIsWhite(phyitem->Name) ||
+ ajTableFetch(phytable, phyitem->Name))
+ {
++ ajFilebuffSetBuffered(buff);
+ ajFilebuffResetStore(buff, seqin->Text, &thys->TextPtr);
+ ajDebug("phytable repeated name '%S'\n",
+ phyitem->Name);
+***************
+*** 6745,6750 ****
+--- 6744,6750 ----
+ ajDebug("phylip format length mismatch at %d "
+ "(length %d)\n",
+ maxlen, ilen);
++ ajFilebuffSetBuffered(buff);
+ ajFilebuffResetStore(buff,
+ seqin->Text, &thys->TextPtr);
+ seqMsfDataDel((SeqPMsfData*) &seqin->Data);
+***************
+*** 6771,6776 ****
+--- 6771,6777 ----
+ if(!done)
+ {
+ ajDebug("seqReadPhylip read failed, try seqReadPhylipnon\n");
++ ajFilebuffSetBuffered(buff);
+ ajFilebuffResetStore(buff, seqin->Text, &thys->TextPtr);
+ seqMsfDataDel((SeqPMsfData*) &seqin->Data);
+
+***************
+*** 6781,6786 ****
+--- 6782,6788 ----
+ {
+ ajDebug("Phylip format %d sequences partly read at end\n",
+ iseq-jseq);
++ ajFilebuffSetBuffered(buff);
+ ajFilebuffResetStore(buff, seqin->Text, &thys->TextPtr);
+ seqMsfDataDel((SeqPMsfData*) &seqin->Data);
+
+***************
+*** 10973,10978 ****
+--- 10975,10982 ----
+ if(!ajBuffreadLine(buff, &seqReadLine))
+ return ajFalse;
+
++ ajDebug("++seqReadGenbank first line '%S'\n", seqReadLine);
++
+ bufflines++;
+
+ ok = ajTrue;
+***************
+*** 11030,11035 ****
+--- 11034,11040 ----
+
+ if(nfields == 9)
+ {
++ ajFilebuffSetBuffered(buff);
+ ajFilebuffResetStore(buff, seqin->Text, &thys->TextPtr);
+
+ return seqReadGenpept(thys,seqin);
+***************
+*** 11053,11062 ****
+--- 11058,11070 ----
+ case 4:
+ if(ajStrMatchC(token, "aa"))
+ {
++ ajFilebuffSetBuffered(buff);
+ ajFilebuffResetStore(buff, seqin->Text, &thys->TextPtr);
+ ajStrDel(&token);
+ ajStrTokenDel(&handle);
+
++ ajDebug("first line %d aa pass to refseqp '%S'\n",
++ buff->Pos, seqReadLine);
+ return seqReadRefseqp(thys,seqin);
+ }
+ if(!ajStrMatchC(token, "bp"))
+***************
+*** 11521,11526 ****
+--- 11529,11535 ----
+
+ if(nfields == 8)
+ {
++ ajFilebuffSetBuffered(buff);
+ ajFilebuffResetStore(buff, seqin->Text, &thys->TextPtr);
+
+ return seqReadRefseqp(thys,seqin);
+***************
+*** 11916,11921 ****
+--- 11925,11932 ----
+ if(!ajBuffreadLine(buff, &seqReadLine))
+ return ajFalse;
+
++ ajDebug("++seqReadRefseqp %d first line '%S'\n", buff->Pos, seqReadLine);
++
+ bufflines++;
+
+ ok = ajTrue;
+***************
+*** 12303,12310 ****
+ ok = ajBuffreadLineStore(buff,&seqReadLine,
+ seqin->Text, &thys->TextPtr);
+
+-
+ ajFilebuffClear(buff, 0);
+
+ ajStrTokenDel(&handle);
+ ajStrDel(&token);
+--- 12314,12321 ----
+ ok = ajBuffreadLineStore(buff,&seqReadLine,
+ seqin->Text, &thys->TextPtr);
+
+ ajFilebuffClear(buff, 0);
++ ajDebug("++last line %d '%S'\n", buff->Pos, seqReadLine);
+
+ ajStrTokenDel(&handle);
+ ajStrDel(&token);
+diff -c -N --recursive EMBOSS-6.1.0orig/ajax/ajseqwrite.c EMBOSS-6.1.0/ajax/ajseqwrite.c
+*** EMBOSS-6.1.0orig/ajax/ajseqwrite.c 2009-07-06 16:50:31.000000000 +0100
+--- EMBOSS-6.1.0/ajax/ajseqwrite.c 2009-07-30 15:27:55.000000000 +0100
+***************
+*** 231,237 ****
+ AJFALSE, AJFALSE, AJFALSE, AJTRUE, AJTRUE,
+ AJFALSE, AJTRUE, AJFALSE, seqWriteGcg},
+ {"gcg8", "GCG old (version 8) sequence format",
+! AJFALSE, AJFALSE, AJFALSE, AJTRUE, AJTRUE,
+ AJFALSE, AJTRUE, AJFALSE, seqWriteGcg}, /* alias for gcg */
+ {"embl", "EMBL entry format",
+ AJFALSE, AJFALSE, AJFALSE, AJTRUE, AJFALSE,
+--- 231,237 ----
+ AJFALSE, AJFALSE, AJFALSE, AJTRUE, AJTRUE,
+ AJFALSE, AJTRUE, AJFALSE, seqWriteGcg},
+ {"gcg8", "GCG old (version 8) sequence format",
+! AJTRUE, AJFALSE, AJFALSE, AJTRUE, AJTRUE,
+ AJFALSE, AJTRUE, AJFALSE, seqWriteGcg}, /* alias for gcg */
+ {"embl", "EMBL entry format",
+ AJFALSE, AJFALSE, AJFALSE, AJTRUE, AJFALSE,
+***************
+*** 240,246 ****
+ AJTRUE, AJFALSE, AJFALSE, AJTRUE, AJFALSE,
+ AJTRUE, AJTRUE, AJFALSE, seqWriteEmbl},
+ {"emblold", "EMBL entry format (alias)",
+! AJFALSE, AJFALSE, AJFALSE, AJTRUE, AJFALSE,
+ AJTRUE, AJTRUE, AJFALSE, seqWriteEmbl}, /* embl pre-87 format*/
+ {"em", "EMBL entry format (alias)",
+ AJTRUE, AJFALSE, AJFALSE, AJTRUE, AJFALSE,
+--- 240,246 ----
+ AJTRUE, AJFALSE, AJFALSE, AJTRUE, AJFALSE,
+ AJTRUE, AJTRUE, AJFALSE, seqWriteEmbl},
+ {"emblold", "EMBL entry format (alias)",
+! AJTRUE, AJFALSE, AJFALSE, AJTRUE, AJFALSE,
+ AJTRUE, AJTRUE, AJFALSE, seqWriteEmbl}, /* embl pre-87 format*/
+ {"em", "EMBL entry format (alias)",
+ AJTRUE, AJFALSE, AJFALSE, AJTRUE, AJFALSE,
+***************
+*** 255,261 ****
+ AJTRUE, AJFALSE, AJFALSE, AJFALSE, AJTRUE,
+ AJTRUE, AJTRUE, AJFALSE, seqWriteSwiss},
+ {"swissold", "Swissprot entry format", /* format before 2006 release */
+! AJFALSE, AJFALSE, AJFALSE, AJFALSE, AJTRUE,
+ AJTRUE, AJTRUE, AJFALSE, seqWriteSwiss},
+ {"swissprotold","Swissprot entry format",
+ AJTRUE, AJFALSE, AJFALSE, AJFALSE, AJTRUE,
+--- 255,261 ----
+ AJTRUE, AJFALSE, AJFALSE, AJFALSE, AJTRUE,
+ AJTRUE, AJTRUE, AJFALSE, seqWriteSwiss},
+ {"swissold", "Swissprot entry format", /* format before 2006 release */
+! AJTRUE, AJFALSE, AJFALSE, AJFALSE, AJTRUE,
+ AJTRUE, AJTRUE, AJFALSE, seqWriteSwiss},
+ {"swissprotold","Swissprot entry format",
+ AJTRUE, AJFALSE, AJFALSE, AJFALSE, AJTRUE,
+***************
+*** 347,353 ****
+ {"msf", "GCG MSF (mutiple sequence file) file format",
+ AJFALSE, AJFALSE, AJTRUE, AJTRUE, AJTRUE,
+ AJFALSE, AJTRUE, AJFALSE, seqWriteMsf},
+! {"clustal", "Clustalw output format",
+ AJFALSE, AJFALSE, AJTRUE, AJTRUE, AJTRUE,
+ AJFALSE, AJTRUE, AJFALSE, seqWriteClustal},
+ {"aln", "Clustalw output format (alias)",
+--- 347,353 ----
+ {"msf", "GCG MSF (mutiple sequence file) file format",
+ AJFALSE, AJFALSE, AJTRUE, AJTRUE, AJTRUE,
+ AJFALSE, AJTRUE, AJFALSE, seqWriteMsf},
+! {"clustal", "Clustalw multiple alignment format",
+ AJFALSE, AJFALSE, AJTRUE, AJTRUE, AJTRUE,
+ AJFALSE, AJTRUE, AJFALSE, seqWriteClustal},
+ {"aln", "Clustalw output format (alias)",
+***************
+*** 1360,1374 ****
+
+ static void seqWriteFastqSanger(AjPSeqout outseq)
+ {
+- ajuint i;
+ ajuint j;
+ ajuint ilen;
+- ajuint jlen;
+ AjPStr seq = NULL;
+- ajuint linelen = 60;
+- ajuint iend;
+ AjPStr db = NULL;
+! char qchar;
+
+ ajStrAssignS(&db, outseq->Setoutdb);
+ /* ajStrAssignEmptyS(&db, outseq->Db);*/
+--- 1360,1370 ----
+
+ static void seqWriteFastqSanger(AjPSeqout outseq)
+ {
+ ajuint j;
+ ajuint ilen;
+ AjPStr seq = NULL;
+ AjPStr db = NULL;
+! ajint qchar;
+
+ ajStrAssignS(&db, outseq->Setoutdb);
+ /* ajStrAssignEmptyS(&db, outseq->Db);*/
+***************
+*** 1394,1430 ****
+ ajFmtPrintF(outseq->File, "\n");
+ ilen = ajStrGetLen(outseq->Seq);
+
+! for(i=0; i < ilen; i += linelen)
+! {
+! iend = AJMIN(ilen-1, i+linelen-1);
+! ajStrAssignSubS(&seq, outseq->Seq, i, iend);
+! ajFmtPrintF(outseq->File, "%S\n", seq);
+! }
+!
+! ajFmtPrintF(outseq->File, "+%S", outseq->Name);
+!
+! if(ajStrGetLen(outseq->Sv))
+! ajFmtPrintF(outseq->File, " %S", outseq->Sv);
+! else if(ajStrGetLen(outseq->Acc))
+! ajFmtPrintF(outseq->File, " %S", outseq->Acc);
+
+! ajFmtPrintF(outseq->File, "\n");
+
+ ilen = ajStrGetLen(outseq->Seq);
+
+ if(outseq->Accuracy)
+ {
+! for(i=0; i < ilen; i += linelen)
+ {
+! iend = AJMIN(ilen-1, i+linelen-1);
+! ajStrAssignClear(&seq);
+! for(j=i;j<=iend;j++)
+! {
+! qchar = 33 + (int) outseq->Accuracy[j];
+! ajStrAppendK(&seq, qchar);
+! }
+! ajFmtPrintF(outseq->File, "%S\n", seq);
+ }
+ }
+
+ else
+--- 1390,1416 ----
+ ajFmtPrintF(outseq->File, "\n");
+ ilen = ajStrGetLen(outseq->Seq);
+
+! ajFmtPrintF(outseq->File, "%S\n", outseq->Seq);
+
+! ajFmtPrintF(outseq->File, "+\n");
+
+ ilen = ajStrGetLen(outseq->Seq);
+
+ if(outseq->Accuracy)
+ {
+! ajStrAssignClear(&seq);
+!
+! for(j=0;j<ilen;j++)
+ {
+! qchar = 33 + (int) (0.5 + outseq->Accuracy[j]);
+! if(qchar > 126)
+! qchar = 126;
+! if(qchar < 33)
+! qchar = 33;
+! ajStrAppendK(&seq, (char) qchar);
+ }
++
++ ajFmtPrintF(outseq->File, "%S\n", seq);
+ }
+
+ else
+***************
+*** 1433,1447 ****
+ ** default to a score of 1 (0.75 error : 1 base in 4 is right)
+ */
+
+! for(i=0; i < ilen; i += linelen)
+! {
+! iend = AJMIN(ilen-1, i+linelen-1);
+! jlen = (iend - i + 1);
+! ajStrAssignClear(&seq);
+! ajStrAppendCountK(&seq,'\"', jlen);
+! ajFmtPrintF(outseq->File, "%S\n", seq);
+! }
+
+ }
+
+ ajStrDel(&seq);
+--- 1419,1429 ----
+ ** default to a score of 1 (0.75 error : 1 base in 4 is right)
+ */
+
+! ajStrAssignClear(&seq);
+!
+! ajStrAppendCountK(&seq,'\"', ilen);
+
++ ajFmtPrintF(outseq->File, "%S\n", seq);
+ }
+
+ ajStrDel(&seq);
+***************
+*** 1464,1478 ****
+
+ static void seqWriteFastqIllumina(AjPSeqout outseq)
+ {
+- ajuint i;
+ ajuint j;
+ ajuint ilen;
+- ajuint jlen;
+ AjPStr seq = NULL;
+- ajuint linelen = 60;
+- ajuint iend;
+ AjPStr db = NULL;
+! char qchar;
+
+ ajStrAssignS(&db, outseq->Setoutdb);
+ /* ajStrAssignEmptyS(&db, outseq->Db);*/
+--- 1446,1456 ----
+
+ static void seqWriteFastqIllumina(AjPSeqout outseq)
+ {
+ ajuint j;
+ ajuint ilen;
+ AjPStr seq = NULL;
+ AjPStr db = NULL;
+! ajint qchar;
+
+ ajStrAssignS(&db, outseq->Setoutdb);
+ /* ajStrAssignEmptyS(&db, outseq->Db);*/
+***************
+*** 1498,1534 ****
+ ajFmtPrintF(outseq->File, "\n");
+ ilen = ajStrGetLen(outseq->Seq);
+
+! for(i=0; i < ilen; i += linelen)
+! {
+! iend = AJMIN(ilen-1, i+linelen-1);
+! ajStrAssignSubS(&seq, outseq->Seq, i, iend);
+! ajFmtPrintF(outseq->File, "%S\n", seq);
+! }
+!
+! ajFmtPrintF(outseq->File, "+%S", outseq->Name);
+!
+! if(ajStrGetLen(outseq->Sv))
+! ajFmtPrintF(outseq->File, " %S", outseq->Sv);
+! else if(ajStrGetLen(outseq->Acc))
+! ajFmtPrintF(outseq->File, " %S", outseq->Acc);
+!
+! ajFmtPrintF(outseq->File, "\n");
+
+ ilen = ajStrGetLen(outseq->Seq);
+
+ if(outseq->Accuracy)
+ {
+! for(i=0; i < ilen; i += linelen)
+ {
+! iend = AJMIN(ilen-1, i+linelen-1);
+! ajStrAssignClear(&seq);
+! for(j=i;j<=iend;j++)
+! {
+! qchar = 64 + (int) outseq->Accuracy[j];
+! ajStrAppendK(&seq, qchar);
+! }
+! ajFmtPrintF(outseq->File, "%S\n", seq);
+ }
+ }
+
+ else
+--- 1476,1501 ----
+ ajFmtPrintF(outseq->File, "\n");
+ ilen = ajStrGetLen(outseq->Seq);
+
+! ajFmtPrintF(outseq->File, "%S\n", outseq->Seq);
+! ajFmtPrintF(outseq->File, "+\n");
+
+ ilen = ajStrGetLen(outseq->Seq);
+
+ if(outseq->Accuracy)
+ {
+! ajStrAssignClear(&seq);
+!
+! for(j=0;j<ilen;j++)
+ {
+! qchar = 64 + (int) (0.5 + outseq->Accuracy[j]);
+! if(qchar > 126)
+! qchar = 126;
+! else if(qchar < 33)
+! qchar = 33;
+! ajStrAppendK(&seq, (char) qchar);
+ }
++
++ ajFmtPrintF(outseq->File, "%S\n", seq);
+ }
+
+ else
+***************
+*** 1537,1551 ****
+ ** default to a score of 1 (0.75 error : 1 base in 4 is right)
+ */
+
+! for(i=0; i < ilen; i += linelen)
+! {
+! iend = AJMIN(ilen-1, i+linelen-1);
+! jlen = (iend - i + 1);
+! ajStrAssignClear(&seq);
+! ajStrAppendCountK(&seq,'A', jlen);
+! ajFmtPrintF(outseq->File, "%S\n", seq);
+! }
+
+ }
+
+ ajStrDel(&seq);
+--- 1504,1514 ----
+ ** default to a score of 1 (0.75 error : 1 base in 4 is right)
+ */
+
+! ajStrAssignClear(&seq);
+!
+! ajStrAppendCountK(&seq,'A', ilen);
+
++ ajFmtPrintF(outseq->File, "%S\n", seq);
+ }
+
+ ajStrDel(&seq);
+***************
+*** 1568,1582 ****
+
+ static void seqWriteFastqSolexa(AjPSeqout outseq)
+ {
+- ajuint i;
+ ajuint j;
+ ajuint ilen;
+- ajuint jlen;
+ AjPStr seq = NULL;
+- ajuint linelen = 60;
+- ajuint iend;
+ AjPStr db = NULL;
+! char qchar;
+ double sval;
+ double pval;
+ double qval;
+--- 1531,1541 ----
+
+ static void seqWriteFastqSolexa(AjPSeqout outseq)
+ {
+ ajuint j;
+ ajuint ilen;
+ AjPStr seq = NULL;
+ AjPStr db = NULL;
+! ajint qchar;
+ double sval;
+ double pval;
+ double qval;
+***************
+*** 1605,1651 ****
+ ajFmtPrintF(outseq->File, "\n");
+ ilen = ajStrGetLen(outseq->Seq);
+
+! for(i=0; i < ilen; i += linelen)
+! {
+! iend = AJMIN(ilen-1, i+linelen-1);
+! ajStrAssignSubS(&seq, outseq->Seq, i, iend);
+! ajFmtPrintF(outseq->File, "%S\n", seq);
+! }
+
+! ajFmtPrintF(outseq->File, "+%S", outseq->Name);
+!
+! if(ajStrGetLen(outseq->Sv))
+! ajFmtPrintF(outseq->File, " %S", outseq->Sv);
+! else if(ajStrGetLen(outseq->Acc))
+! ajFmtPrintF(outseq->File, " %S", outseq->Acc);
+!
+! ajFmtPrintF(outseq->File, "\n");
+
+ ilen = ajStrGetLen(outseq->Seq);
+
+ if(outseq->Accuracy)
+ {
+! for(i=0; i < ilen; i += linelen)
+ {
+! iend = AJMIN(ilen-1, i+linelen-1);
+! ajStrAssignClear(&seq);
+! for(j=i;j<=iend;j++)
+! {
+! sval = outseq->Accuracy[j];
+! pval = 1.0 / pow(10.0, (sval/10.0));
+
+! /*adjust zero phred score to 0.75 error rate */
+! if(pval == 1.0)
+! pval = 0.75;
+!
+! qval = 0.5 + -10.0 * log10(pval/(1.0 - pval));
+! qchar = 64 + (int) qval;
+! ajStrAppendK(&seq, qchar);
+! ajDebug("[%d] aval:%.4f qval:%.4f %d '%c'\n",
+! j, sval, qval, (int)qval, qchar);
+! }
+! ajFmtPrintF(outseq->File, "%S\n", seq);
+ }
+ }
+
+ else
+--- 1564,1602 ----
+ ajFmtPrintF(outseq->File, "\n");
+ ilen = ajStrGetLen(outseq->Seq);
+
+! ajFmtPrintF(outseq->File, "%S\n", outseq->Seq);
+
+! ajFmtPrintF(outseq->File, "+\n");
+
+ ilen = ajStrGetLen(outseq->Seq);
+
+ if(outseq->Accuracy)
+ {
+! ajStrAssignClear(&seq);
+!
+! for(j=0;j<ilen;j++)
+ {
+! sval = outseq->Accuracy[j];
+! pval = 1.0 / pow(10.0, (sval/10.0));
+
+! /*adjust zero phred score to 0.75 error rate */
+! if(pval > 0.75)
+! pval = 0.75;
+!
+! qval = -10.0 * log10(pval/(1.0 - pval));
+! if(qval >= 0.0)
+! qchar = 64 + (int) (qval + 0.5);
+! else
+! qchar = 64 + (int) (qval - 0.5);
+! if(qchar > 126)
+! qchar = 126;
+! else if(qchar < 33)
+! qchar = 33;
+! ajStrAppendK(&seq, (char) qchar);
+! ajDebug("[%d] aval:%.4f qval:%.4f %d '%c'\n",
+! j, sval, qval, (int)qval, qchar);
+ }
++ ajFmtPrintF(outseq->File, "%S\n", seq);
+ }
+
+ else
+***************
+*** 1654,1668 ****
+ ** default to a score of -5 (0.75 error : 1 base in 4 is right)
+ */
+
+! for(i=0; i < ilen; i += linelen)
+! {
+! iend = AJMIN(ilen-1, i+linelen-1);
+! jlen = (iend - i + 1);
+! ajStrAssignClear(&seq);
+! ajStrAppendCountK(&seq,';', jlen);
+! ajFmtPrintF(outseq->File, "%S\n", seq);
+! }
+
+ }
+
+ ajStrDel(&seq);
+--- 1605,1615 ----
+ ** default to a score of -5 (0.75 error : 1 base in 4 is right)
+ */
+
+! ajStrAssignClear(&seq);
+!
+! ajStrAppendCountK(&seq,';', ilen);
+
++ ajFmtPrintF(outseq->File, "%S\n", seq);
+ }
+
+ ajStrDel(&seq);
+***************
+*** 7798,7803 ****
+--- 7745,7751 ----
+
+
+
++
+ /* @funcstatic seqSeqFormat ***************************************************
+ **
+ ** Initialises sequence output formatting parameters.
+diff -c -N --recursive EMBOSS-6.1.0orig/jemboss/org/emboss/jemboss/gui/Browser.java EMBOSS-6.1.0/jemboss/org/emboss/jemboss/gui/Browser.java
+*** EMBOSS-6.1.0orig/jemboss/org/emboss/jemboss/gui/Browser.java 2009-06-30 17:18:26.000000000 +0100
+--- EMBOSS-6.1.0/jemboss/org/emboss/jemboss/gui/Browser.java 2009-07-30 15:29:18.000000000 +0100
+***************
+*** 68,74 ****
+--- 68,77 ----
+ import javax.swing.tree.DefaultMutableTreeNode;
+ import javax.swing.tree.TreeSelectionModel;
+
++ import org.emboss.jemboss.Jemboss;
+ import org.emboss.jemboss.JembossParams;
++ import org.emboss.jemboss.server.JembossServer;
++ import org.emboss.jemboss.soap.GetVersion;
+
+
+ /**
+***************
+*** 110,115 ****
+--- 113,120 ----
+ private JMenuItem fwdMenu;
+ /** Forward button option */
+ private JButton fwdBt;
++ /** version of EMBOSS programs */
++ String embossVersion = "6.1";
+
+ /**
+ *
+***************
+*** 178,185 ****
+ URL pageURL = new URL(initialURL);
+ setURL(pageURL,initialURL);
+ }
+ }
+!
+
+ /**
+ *
+--- 183,193 ----
+ URL pageURL = new URL(initialURL);
+ setURL(pageURL,initialURL);
+ }
++ if (Jemboss.withSoap){
++ embossVersion = GetVersion.getVersion(mysettings);
++ }
+ }
+!
+
+ /**
+ *
+***************
+*** 712,719 ****
+ loc = "http://emboss.sourceforge.net/Jemboss/";
+ else if(selectedValue.equals("Home") && category.equals("EMBOSS"))
+ loc = "http://emboss.sourceforge.net/";
+! else if(selectedValue.equals("Apps") && category.equals("EMBOSS"))
+! loc = "http://emboss.sourceforge.net/apps/release/6.0/emboss/apps/";
+
+ if(loc != null)
+ {
+--- 720,732 ----
+ loc = "http://emboss.sourceforge.net/Jemboss/";
+ else if(selectedValue.equals("Home") && category.equals("EMBOSS"))
+ loc = "http://emboss.sourceforge.net/";
+! else if(selectedValue.equals("Apps") && category.equals("EMBOSS")){
+! if (!JembossParams.isJembossServer()){
+! embossVersion = new JembossServer().version();
+! embossVersion = embossVersion.split("\\.")[0]+"."+embossVersion.split("\\.")[1];
+! }
+! loc = "http://emboss.sourceforge.net/apps/release/"+embossVersion+"/emboss/apps/";
+! }
+
+ if(loc != null)
+ {
+diff -c -N --recursive EMBOSS-6.1.0orig/jemboss/org/emboss/jemboss/gui/BuildProgramMenu.java EMBOSS-6.1.0/jemboss/org/emboss/jemboss/gui/BuildProgramMenu.java
+*** EMBOSS-6.1.0orig/jemboss/org/emboss/jemboss/gui/BuildProgramMenu.java 2009-07-08 09:45:48.000000000 +0100
+--- EMBOSS-6.1.0/jemboss/org/emboss/jemboss/gui/BuildProgramMenu.java 2009-07-30 15:29:31.000000000 +0100
+***************
+*** 141,146 ****
+--- 141,162 ----
+ return woss;
+ }
+
++ private synchronized void updateConnectionSettings(){
++ splashing.doneSomething("Cannot connect!");
++ ServerSetup ss = new ServerSetup(mysettings);
++ splashThread.setInterval(100000);
++ int sso = JOptionPane.showConfirmDialog(f,ss,
++ "Check Settings",
++ JOptionPane.OK_CANCEL_OPTION,
++ JOptionPane.ERROR_MESSAGE,null);
++ if(sso == JOptionPane.OK_OPTION){
++ ss.setNewSettings();
++ splashThread.setInterval(80);
++ }
++ else
++ System.exit(0);
++ }
++
+ private void constructWithSoap(){
+
+ mainMenu.setEnableFileManagers(false);
+***************
+*** 157,249 ****
+ mysettings.updateJembossPropStrings(settings);
+ }
+
+! SwingWorker databaseworker = new SwingWorker()
+ {
+! public Object construct()
+! {
+! ShowDB showdb = null;
+! try
+! {
+! showdb = new ShowDB(mysettings);
+! }
+! catch (Exception ex)
+! {
+! splashing.doneSomething("Cannot connect!");
+! ServerSetup ss = new ServerSetup(mysettings);
+! int sso = JOptionPane.showConfirmDialog(f,ss,
+! "Check Settings",
+! JOptionPane.OK_CANCEL_OPTION,
+! JOptionPane.ERROR_MESSAGE,null);
+! if(sso == JOptionPane.OK_OPTION)
+! ss.setNewSettings();
+! else
+! System.exit(0);
+
+! try
+! {
+! showdb = new ShowDB(mysettings);
+! }
+! catch (Exception exp)
+! {
+! exp.printStackTrace();
+! }
+! }
+! String showdbOut = showdb.getDBText();
+
+! Database d = new Database(showdbOut);
+! db = d.getDB();
+! mainMenu.setEnableFileManagers(true);
+! mainMenu.setEnableShowResults(true);
+! splashing.doneSomething("");
+! splashThread.setInterval(0);
+!
+! matrices = showdb.getMatrices(); // get the available matrices
+! codons = showdb.getCodonUsage();
+!
+! /*JLabel jl = */new JLabel("<html>"); // not used but speeds first
+! // ACD form loading which
+! // uses html
+! return null;
+! }
+ };
+ databaseworker.start();
+-
+ splashing.doneSomething("");
+-
+- try
+- {
+- try
+- {
+- Hashtable hwoss = (new JembossJarUtil("resources/wossname.jar")).getHash();
+- if(hwoss.containsKey("wossname.out"))
+- woss = new String((byte[])hwoss.get("wossname.out"));
+- }
+- catch (Exception ex){}
+-
+- if(woss.equals(""))
+- {
+- GetWossname ewoss = new GetWossname(mysettings);
+- woss = ewoss.getWossnameText();
+- mainMenu.setEnableFileManagers(true);
+- mainMenu.setEnableShowResults(true);
+- }
+-
+- splashing.doneSomething("");
+- }
+- catch(Exception e)
+- {
+- splashing.doneSomething("Cannot connect!");
+- ServerSetup ss = new ServerSetup(mysettings);
+- int sso = JOptionPane.showConfirmDialog(f,ss,
+- "Check Settings",
+- JOptionPane.OK_CANCEL_OPTION,
+- JOptionPane.ERROR_MESSAGE,null);
+- if(sso == JOptionPane.OK_OPTION)
+- ss.setNewSettings();
+- else
+- System.exit(0);
+- }
+ }
+
+ private void constructWithoutSoap(){
+
+--- 173,237 ----
+ mysettings.updateJembossPropStrings(settings);
+ }
+
+! try
+ {
+! Hashtable hwoss = (new JembossJarUtil("resources/wossname.jar")).getHash();
+! if(hwoss.containsKey("wossname.out"))
+! woss = new String((byte[])hwoss.get("wossname.out"));
+! }
+! catch (Exception ex){}
+! if(woss.equals(""))
+! {
+! boolean connectionmade = false;
+! while (!connectionmade){
+! try
+! {
+! GetWossname ewoss = new GetWossname(mysettings);
+! woss = ewoss.getWossnameText();
+! mainMenu.setEnableFileManagers(true);
+! mainMenu.setEnableShowResults(true);
+! }
+! catch (JembossSoapException ex){
+! updateConnectionSettings();
+! continue;
+! }
+! connectionmade = true;
+! }
+! }
+
+! SwingWorker databaseworker = new SwingWorker()
+! {
+
+! public Object construct() {
+! boolean connectionmade = false;
+! while (!connectionmade) {
+! ShowDB showdb = null;
+! try {
+! showdb = new ShowDB(mysettings);
+! String showdbOut = showdb.getDBText();
+!
+! Database d = new Database(showdbOut);
+! db = d.getDB();
+! mainMenu.setEnableFileManagers(true);
+! mainMenu.setEnableShowResults(true);
+! splashing.doneSomething("");
+! splashThread.setInterval(0);
+!
+! matrices = showdb.getMatrices();
+! codons = showdb.getCodonUsage();
+! } catch (JembossSoapException ex) {
+! updateConnectionSettings();
+! continue;
+! }
+! connectionmade = true;
+! }
+! return null;
+! }
+ };
+ databaseworker.start();
+ splashing.doneSomething("");
+ }
++
+
+ private void constructWithoutSoap(){
+
+***************
+*** 310,316 ****
+ progs = new ProgList(woss,menuBar);
+
+ if(withSoap)
+! splashing.doneSomething("");
+
+ int npG = progs.getNumPrimaryGroups();
+ menuBar.setLayout(new GridLayout(npG,1));
+--- 298,304 ----
+ progs = new ProgList(woss,menuBar);
+
+ if(withSoap)
+! splashing.doneEverything("");
+
+ int npG = progs.getNumPrimaryGroups();
+ menuBar.setLayout(new GridLayout(npG,1));
+diff -c -N --recursive EMBOSS-6.1.0orig/jemboss/org/emboss/jemboss/gui/form/BuildJembossForm.java EMBOSS-6.1.0/jemboss/org/emboss/jemboss/gui/form/BuildJembossForm.java
+*** EMBOSS-6.1.0orig/jemboss/org/emboss/jemboss/gui/form/BuildJembossForm.java 2009-07-13 17:24:04.000000000 +0100
+--- EMBOSS-6.1.0/jemboss/org/emboss/jemboss/gui/form/BuildJembossForm.java 2009-07-30 15:29:52.000000000 +0100
+***************
+*** 100,107 ****
+ private boolean withSoap;
+ private JFrame f;
+ private JPanel p2;
+! private String embossBin;
+!
+ private int numofFields;
+ private JembossParams mysettings;
+
+--- 100,106 ----
+ private boolean withSoap;
+ private JFrame f;
+ private JPanel p2;
+!
+ private int numofFields;
+ private JembossParams mysettings;
+
+***************
+*** 125,131 ****
+ this.mysettings = mysettings;
+ this.withSoap = withSoap;
+
+- embossBin = mysettings.getEmbossBin();
+ this.envp = envp;
+ this.applName = applName;
+
+--- 124,129 ----
+***************
+*** 172,181 ****
+ {
+ String urlEmbassyPrefix = parseAcd.getUrlPrefix();
+ url = mysettings.getembURL();
+ if(urlEmbassyPrefix != null)
+! url = url + "apps/release/6.0/embassy/" +applName+ "/" ;
+ else
+! url = url + "apps/release/6.0/emboss/apps/";
+
+ url = url+applName+".html";
+ }
+--- 170,181 ----
+ {
+ String urlEmbassyPrefix = parseAcd.getUrlPrefix();
+ url = mysettings.getembURL();
++ String version = GetVersion.getVersion(mysettings);
+ if(urlEmbassyPrefix != null)
+! // get the version from server
+! url = url + "apps/release/"+version+"/embassy/"+urlEmbassyPrefix+"/" ;
+ else
+! url = url + "apps/release/"+version+"/emboss/apps/";
+
+ url = url+applName+".html";
+ }
+***************
+*** 893,900 ****
+ }
+ else if ( att.startsWith("float") )
+ {
+! if( (textFloat[h].getText() != null) && textFloat[h].isVisible()
+! && textFloat[h].isEnabled())
+ {
+ options = options.concat(" -" + val + " " + textFloat[h].getValue());
+ optionsA.add("-"+val);
+--- 893,901 ----
+ }
+ else if ( att.startsWith("float") )
+ {
+! if( textFloat[h].getText() != null &&
+! textFloat[h].getText().length()>0 &&
+! textFloat[h].isVisible() && textFloat[h].isEnabled())
+ {
+ options = options.concat(" -" + val + " " + textFloat[h].getValue());
+ optionsA.add("-"+val);
+diff -c -N --recursive EMBOSS-6.1.0orig/jemboss/org/emboss/jemboss/gui/sequenceChooser/InputSequenceAttributes.java EMBOSS-6.1.0/jemboss/org/emboss/jemboss/gui/sequenceChooser/InputSequenceAttributes.java
+*** EMBOSS-6.1.0orig/jemboss/org/emboss/jemboss/gui/sequenceChooser/InputSequenceAttributes.java 2009-07-13 17:23:30.000000000 +0100
+--- EMBOSS-6.1.0/jemboss/org/emboss/jemboss/gui/sequenceChooser/InputSequenceAttributes.java 2009-07-30 15:30:07.000000000 +0100
+***************
+*** 281,287 ****
+ // bx.add(Box.createHorizontalGlue());
+
+
+! UFO = new JTextField(); //sufo
+ UFO.setPreferredSize(new Dimension(100, 30));
+ UFO.setMaximumSize(new Dimension(100, 30));
+
+--- 281,287 ----
+ // bx.add(Box.createHorizontalGlue());
+
+
+! UFO = new JTextField(); //ufo
+ UFO.setPreferredSize(new Dimension(100, 30));
+ UFO.setMaximumSize(new Dimension(100, 30));
+
+***************
+*** 433,440 ****
+
+ /**
+ *
+! * Determine if there is a default -sufo value
+! * @return true if -sufo is set
+ *
+ */
+ public boolean isUFODefault()
+--- 433,440 ----
+
+ /**
+ *
+! * Determine if there is a default -ufo value
+! * @return true if -ufo is set
+ *
+ */
+ public boolean isUFODefault()
+***************
+*** 508,514 ****
+ // sID.getText());
+
+ if(!isUFODefault())
+! options = options.concat(" -sufo" + seq + " " +
+ UFO.getText());
+
+ return options;
+--- 508,514 ----
+ // sID.getText());
+
+ if(!isUFODefault())
+! options = options.concat(" -ufo" + seq + " " +
+ UFO.getText());
+
+ return options;
+***************
+*** 559,565 ****
+ }
+
+ if(!isUFODefault()){
+! optionsA.add("-sufo"+ seq);
+ optionsA.add(UFO.getText());
+ }
+
+--- 559,565 ----
+ }
+
+ if(!isUFODefault()){
+! optionsA.add("-ufo"+ seq);
+ optionsA.add(UFO.getText());
+ }
+
+diff -c -N --recursive EMBOSS-6.1.0orig/jemboss/org/emboss/jemboss/soap/GetVersion.java EMBOSS-6.1.0/jemboss/org/emboss/jemboss/soap/GetVersion.java
+*** EMBOSS-6.1.0orig/jemboss/org/emboss/jemboss/soap/GetVersion.java 1970-01-01 01:00:00.000000000 +0100
+--- EMBOSS-6.1.0/jemboss/org/emboss/jemboss/soap/GetVersion.java 2009-07-30 15:30:24.000000000 +0100
+***************
+*** 0 ****
+--- 1,82 ----
++ /********************************************************************
++ *
++ * This library is free software; you can redistribute it and/or
++ * modify it under the terms of the GNU Library General Public
++ * License as published by the Free Software Foundation; either
++ * version 2 of the License, or (at your option) any later version.
++ *
++ * This library is distributed in the hope that it will be useful,
++ * but WITHOUT ANY WARRANTY; without even the implied warranty of
++ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
++ * Library General Public License for more details.
++ *
++ * You should have received a copy of the GNU Library General Public
++ * License along with this library; if not, write to the
++ * Free Software Foundation, Inc., 59 Temple Place - Suite 330,
++ * Boston, MA 02111-1307, USA.
++ *
++ * @author: Copyright (C) Tim Carver
++ *
++ ********************************************************************/
++
++ package org.emboss.jemboss.soap;
++
++ import javax.xml.namespace.QName;
++
++ import org.apache.axis.client.Call;
++ import org.emboss.jemboss.JembossParams;
++
++ /**
++ *
++ * Get the version of EMBOSS programs used by the Jemboss server connected
++ *
++ */
++ /**
++ * @author uludag
++ *
++ */
++ public class GetVersion {
++
++ private static String version = null;
++
++ /**
++ * returns complete version string of EMBOSS connected Jemboss server is using
++ * @param mysettings
++ * jemboss properties
++ *
++ */
++ public static String getVersionComplete(JembossParams mysettings) {
++
++ if (version != null)
++ return version;
++
++ if (!JembossParams.isJembossServer())
++ return null;
++ try {
++ String endpoint = mysettings.getPublicSoapURL();
++ org.apache.axis.client.Service serv = new org.apache.axis.client.Service();
++
++ Call call = (Call) serv.createCall();
++ call.setTargetEndpointAddress(new java.net.URL(endpoint));
++ call.setOperationName(new QName(mysettings.getPublicSoapService(),
++ "version"));
++ call.setReturnType(org.apache.axis.Constants.SOAP_STRING);
++ version = (String) call.invoke(new Object[] {});
++ } catch (Exception jse) {
++ jse.printStackTrace();
++ }
++ return version;
++ }
++
++
++ /**
++ * returns firt two digits of EMBOSS version connected server has
++ * @param mysettings
++ * @return version of EMBOSS programs such as 5.0, or 6.1
++ */
++ public static String getVersion(JembossParams mysettings){
++ getVersionComplete(mysettings);
++ return version.split("\\.")[0]+"."+version.split("\\.")[1];
++ }
++
++ }
+diff -c -N --recursive EMBOSS-6.1.0orig/jemboss/org/emboss/jemboss/soap/ShowDB.java EMBOSS-6.1.0/jemboss/org/emboss/jemboss/soap/ShowDB.java
+*** EMBOSS-6.1.0orig/jemboss/org/emboss/jemboss/soap/ShowDB.java 2008-06-12 09:19:07.000000000 +0100
+--- EMBOSS-6.1.0/jemboss/org/emboss/jemboss/soap/ShowDB.java 2009-07-30 15:30:32.000000000 +0100
+***************
+*** 50,64 ****
+ * @param mysettings jemboss properties
+ *
+ */
+! public ShowDB(JembossParams mysettings)
+ {
+
+ PublicRequest dbReq = null;
+! try
+! {
+! dbReq = new PublicRequest(mysettings, "show_db");
+! }
+! catch (JembossSoapException jse) {}
+
+ statusmsg = dbReq.getVal("msg");
+ status = dbReq.getVal("status");
+--- 50,61 ----
+ * @param mysettings jemboss properties
+ *
+ */
+! public ShowDB(JembossParams mysettings) throws JembossSoapException
+ {
+
+ PublicRequest dbReq = null;
+!
+! dbReq = new PublicRequest(mysettings, "show_db");
+
+ statusmsg = dbReq.getVal("msg");
+ status = dbReq.getVal("status");
+diff -c -N --recursive EMBOSS-6.1.0orig/jemboss/utils/install-jemboss-server.sh EMBOSS-6.1.0/jemboss/utils/install-jemboss-server.sh
+*** EMBOSS-6.1.0orig/jemboss/utils/install-jemboss-server.sh 2009-06-30 09:31:50.000000000 +0100
+--- EMBOSS-6.1.0/jemboss/utils/install-jemboss-server.sh 2009-07-30 15:30:59.000000000 +0100
+***************
+*** 694,718 ****
+ echo " EMBOSS and Jemboss Server installation script"
+ echo "--------------------------------------------------------------"
+ echo " "
+! echo "Note: any default values are given in square brackets []. "
+ echo " "
+! echo "There are two types of installation see details at: "
+ echo "http://emboss.sourceforge.net/Jemboss/install/setup.html"
+- echo " "
+- echo "(1) CLIENT-SERVER"
+- echo "(2) STANDALONE"
+- echo "Enter type of installation [1] :"
+- read INSTALL_TYPE
+-
+- if (test "$INSTALL_TYPE" != "1") && (test "$INSTALL_TYPE" != "2"); then
+- INSTALL_TYPE="1"
+- fi
+- clear
+-
+ echo
+- echo "--------------------------------------------------------------"
+- echo " EMBOSS and Jemboss Server installation script"
+- echo "--------------------------------------------------------------"
+ echo
+ echo "*** This script needs to be run with permissions to be able"
+ echo "*** to install EMBOSS in the required directories. This may"
+--- 694,709 ----
+ echo " EMBOSS and Jemboss Server installation script"
+ echo "--------------------------------------------------------------"
+ echo " "
+! echo "Note: any default values are given in square brackets []."
+ echo " "
+! echo "This script installs EMBOSS as well as Jemboss."
+! echo "Jemboss is deployed as a Java web application in your tomcat server."
+! echo "A script is prepared to run Jemboss client that by default uses the"
+! echo "above Jemboss web application."
+! echo
+! echo "For detailed information on installing Jemboss see: "
+ echo "http://emboss.sourceforge.net/Jemboss/install/setup.html"
+ echo
+ echo
+ echo "*** This script needs to be run with permissions to be able"
+ echo "*** to install EMBOSS in the required directories. This may"
+***************
+*** 721,735 ****
+ echo "Before running this script you should download the latest:"
+ echo
+ echo "(1) EMBOSS release (contains Jemboss) ftp://emboss.open-bio.org/pub/EMBOSS/"
+!
+!
+! if [ $INSTALL_TYPE = "1" ]; then
+! echo "(2) Tomcat release http://jakarta.apache.org/site/binindex.html"
+! echo "(3) Apache AXIS (SOAP) release http://xml.apache.org/axis/"
+! fi
+
+ echo
+! echo "Has the above been downloaded (y/n)? "
+ read DOWNLOADED
+
+ if (test "$DOWNLOADED" != "y") && (test "$DOWNLOADED" != "Y"); then
+--- 712,722 ----
+ echo "Before running this script you should download the latest:"
+ echo
+ echo "(1) EMBOSS release (contains Jemboss) ftp://emboss.open-bio.org/pub/EMBOSS/"
+! echo "(2) Tomcat 5.5 series release http://tomcat.apache.org/"
+! echo "(3) Apache AXIS (SOAP) release 1.4 http://ws.apache.org/axis/"
+
+ echo
+! echo "Have the above been downloaded (y/n)? "
+ read DOWNLOADED
+
+ if (test "$DOWNLOADED" != "y") && (test "$DOWNLOADED" != "Y"); then
+***************
+*** 831,836 ****
+--- 818,826 ----
+ fi
+
+ SSL="y"
++
++ # keep the following variable for now so we have cvs compare for a while
++ INSTALL_TYPE="1";
+ if [ $INSTALL_TYPE = "1" ]; then
+ #
+ # localhost name
+***************
+*** 1271,1287 ****
+ #cd $EMBOSS_INSTALL/share/EMBOSS/jemboss
+ JEMBOSS=$EMBOSS_INSTALL/share/EMBOSS/jemboss
+
+- #---------------------------------------------------------------------------------
+- # Exit for standalone installations
+- #---------------------------------------------------------------------------------
+- if [ $INSTALL_TYPE = "2" ]; then
+- echo
+- echo "To run Jemboss:"
+- echo "cd $JEMBOSS"
+- echo "./runJemboss.sh"
+- echo
+- exit 0
+- fi
+
+
+ #
+--- 1261,1266 ----
Modified: trunk/packages/emboss/trunk/debian/patches/series
===================================================================
--- trunk/packages/emboss/trunk/debian/patches/series 2009-07-30 10:21:44 UTC (rev 3715)
+++ trunk/packages/emboss/trunk/debian/patches/series 2009-07-31 12:33:35 UTC (rev 3716)
@@ -1 +1,2 @@
using-pager-in-tfm.patch
+official-upstream-patch.patch
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