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 24-Aug-2009: Fix string extension so that pointers in lists remain valid. This fixes a bug in processing SwissProt complex descriptions. Fix definition of AJRESIZE0 macro. Fix processing of first match in a profile alignment (prophet). Origin: ftp://emboss.open-bio.org/pub/EMBOSS/fixes/patches/patch-1-2.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/ajmem.h EMBOSS-6.1.0/ajax/ajmem.h *** EMBOSS-6.1.0orig/ajax/ajmem.h 2007-12-12 12:46:19.000000000 +0000 --- EMBOSS-6.1.0/ajax/ajmem.h 2009-08-25 09:31:44.000000000 +0100 *************** *** 71,77 **** #define AJFREE(ptr) ((void)(ajMemFree(ptr), (ptr) = 0)) #define AJRESIZE(ptr, nbytes) ((ptr) = ajMemResize((ptr), \ (nbytes), __FILE__, __LINE__, AJFALSE)) ! #define AJRESIZE0(ptr, oldbytes, nbytes) (ptr) = ajMemResizeZero((ptr), \ (oldbytes), (nbytes), __FILE__, __LINE__, AJFALSE)) #define AJCRESIZE(ptr, nbytes) ((ptr) = ajMemResize((ptr), \ (nbytes)*sizeof *(ptr), __FILE__, __LINE__, AJFALSE)) --- 71,77 ---- #define AJFREE(ptr) ((void)(ajMemFree(ptr), (ptr) = 0)) #define AJRESIZE(ptr, nbytes) ((ptr) = ajMemResize((ptr), \ (nbytes), __FILE__, __LINE__, AJFALSE)) ! #define AJRESIZE0(ptr, oldbytes, nbytes) ((ptr) = ajMemResizeZero((ptr), \ (oldbytes), (nbytes), __FILE__, __LINE__, AJFALSE)) #define AJCRESIZE(ptr, nbytes) ((ptr) = ajMemResize((ptr), \ (nbytes)*sizeof *(ptr), __FILE__, __LINE__, AJFALSE)) 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;jAccuracy[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;jAccuracy[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;jAccuracy[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/ajax/ajstr.c EMBOSS-6.1.0/ajax/ajstr.c *** EMBOSS-6.1.0orig/ajax/ajstr.c 2009-06-22 16:51:03.000000000 +0100 --- EMBOSS-6.1.0/ajax/ajstr.c 2009-08-25 09:30:30.000000000 +0100 *************** *** 3,13 **** ** ** AjPStr objects are reference counted strings ** Any change will need a new string object if the use count ! ** is greater than 1, so the original ajStr provided so that it can ! ** be reallocated in any routine where string modification is possible. ** ! ** In many cases ! ** the text is always a copy, even of a constant original, so ** that it can be simply freed. ** ** @author Copyright (C) 1998 Peter Rice --- 3,13 ---- ** ** AjPStr objects are reference counted strings ** Any change will need a new string object if the use count ! ** is greater than 1, so the original AjPStr is provided as a pointer ! ** so that it can be reallocated in any routine where string modification ! ** may be needed. ** ! ** In many cases the text is always a copy, even of a constant original, so ** that it can be simply freed. ** ** @author Copyright (C) 1998 Peter Rice *************** *** 2042,2047 **** --- 2042,2048 ---- ** @nam4rule NewRes Construct with reserved size. ** ** @argrule C txt [const char*] Text string + ** @argrule K ch [char] Single character ** @argrule S str [const AjPStr] Text string ** @argrule NewRes size [ajuint] Reserved size ** @argrule NewRef refstr [AjPStr] Text string to be duplicated *************** *** 2099,2104 **** --- 2100,2132 ---- + /* @func ajStrNewK ************************************************************ + ** + ** String constructor which allocates memory for a string and initialises it + ** with the single character provided. + ** + ** The string size is set just large enough to hold the supplied text. + ** + ** @param [r] ch [char] Null-terminated character string to initialise + ** the new string. + ** @return [AjPStr] Pointer to a string containing the supplied text + ** @@ + ******************************************************************************/ + + AjPStr ajStrNewK(char ch) + { + char txt[2] = " "; + AjPStr thys; + + txt[0] = ch; + thys = ajStrNewResLenC(txt, 2, 1); + + return thys; + } + + + + /* @func ajStrNewS ************************************************************ ** ** String constructor which allocates memory for a string and initialises it *************** *** 6106,6111 **** --- 6134,6157 ---- + /* @func ajStrTrimWhiteStart ************************************************** + ** + ** Removes regions composed of white space characters only from the start of a + ** string. + ** + ** @param [u] Pstr [AjPStr*] String + ** @return [AjBool] ajTrue if string was reallocated + ** @@ + ******************************************************************************/ + + AjBool ajStrTrimWhiteStart(AjPStr* Pstr) + { + return ajStrTrimStartC(Pstr, "\t \n\r"); + } + + + + /* @func ajStrTruncateLen ***************************************************** ** ** Removes the end from a string reducing it to a defined length. *************** *** 8512,8524 **** thys = *Pstr; ! if((thys->Use > 1) || (thys->Res < savesize)) { strCloneL(Pstr, savesize); return ajTrue; } return ajFalse; } --- 8558,8578 ---- thys = *Pstr; ! if(thys->Use > 1) { strCloneL(Pstr, savesize); return ajTrue; } + if(thys->Res < savesize) + { + AJRESIZE(thys->Ptr, savesize); + thys->Res = savesize; + + return ajTrue; + } + return ajFalse; } *************** *** 8565,8570 **** --- 8619,8631 ---- thys = *Pstr; + if(thys->Use > 1) + { + strCloneL(Pstr, size); + + return ajTrue; + } + if(thys->Res < size) { if(size >= LONGSTR) *************** *** 8579,8592 **** else roundsize = ajRound(size, STRSIZE); ! strCloneL(Pstr, roundsize); ! ! return ajTrue; ! } ! ! if(thys->Use > 1) ! { ! strCloneL(Pstr, size); return ajTrue; } --- 8640,8647 ---- else roundsize = ajRound(size, STRSIZE); ! AJRESIZE(thys->Ptr, roundsize); ! thys->Res = roundsize; return ajTrue; } diff -c -N --recursive EMBOSS-6.1.0orig/ajax/ajstr.h EMBOSS-6.1.0/ajax/ajstr.h *** EMBOSS-6.1.0orig/ajax/ajstr.h 2009-06-22 16:51:04.000000000 +0100 --- EMBOSS-6.1.0/ajax/ajstr.h 2009-08-25 09:30:34.000000000 +0100 *************** *** 65,70 **** --- 65,73 ---- ** ** String iterator, used to test iterator functionality. ** + ** @alias AjSStrIter + ** @alias AjOStrIter + ** ** @new ajStrIter Creates and initializes an iterator for a string ** ** @delete ajStrIterFree Destructor for a string iterator *************** *** 192,197 **** --- 195,201 ---- AjPStr ajStrNew (void); AjPStr ajStrNewC (const char *txt); + AjPStr ajStrNewK (char ch); AjPStr ajStrNewS (const AjPStr str); AjPStr ajStrNewRef(AjPStr str); AjPStr ajStrNewRes(ajuint size); *************** *** 296,301 **** --- 300,306 ---- AjBool ajStrTrimStartC (AjPStr* Pstr, const char* txt); AjBool ajStrTrimWhite(AjPStr* Pstr); AjBool ajStrTrimWhiteEnd(AjPStr* Pstr); + AjBool ajStrTrimWhiteStart(AjPStr* Pstr); AjBool ajStrTruncateLen(AjPStr* Pstr, ajuint len); AjBool ajStrTruncatePos(AjPStr* Pstr, ajint pos); 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(""); // 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 ---- diff -c -N --recursive EMBOSS-6.1.0orig/nucleus/embaln.c EMBOSS-6.1.0/nucleus/embaln.c *** EMBOSS-6.1.0orig/nucleus/embaln.c 2009-06-12 19:02:30.000000000 +0100 --- EMBOSS-6.1.0/nucleus/embaln.c 2009-08-25 09:31:28.000000000 +0100 *************** *** 2091,2096 **** --- 2091,2098 ---- ajStrAppendK(m,p[row--]); ajStrAppendK(n,q[column--]); + if(row < 0 || column < 0) + break; if(path[(row)*seqlen+(column)]<=0.) break;