[med-svn] r3495 - in trunk/packages/emboss/trunk/debian: . patches
Charles Plessy
plessy at alioth.debian.org
Wed Jun 17 14:01:18 UTC 2009
Author: plessy
Date: 2009-06-17 14:01:16 +0000 (Wed, 17 Jun 2009)
New Revision: 3495
Removed:
trunk/packages/emboss/trunk/debian/patches/upstream.patch
Modified:
trunk/packages/emboss/trunk/debian/changelog
trunk/packages/emboss/trunk/debian/patches/series
Log:
New upstream release candidate.
Modified: trunk/packages/emboss/trunk/debian/changelog
===================================================================
--- trunk/packages/emboss/trunk/debian/changelog 2009-06-16 10:37:15 UTC (rev 3494)
+++ trunk/packages/emboss/trunk/debian/changelog 2009-06-17 14:01:16 UTC (rev 3495)
@@ -1,3 +1,10 @@
+emboss (6.1.0~rc1-1) UNRELEASED; urgency=low
+
+ * New upstream relase candidate.
+ * Dropped patch against previous release.
+
+ -- Charles Plessy <plessy at debian.org> Wed, 17 Jun 2009 22:38:53 +0900
+
emboss (6.0.1-11) unstable; urgency=low
* New upstream patch (patch-1-12):
Modified: trunk/packages/emboss/trunk/debian/patches/series
===================================================================
--- trunk/packages/emboss/trunk/debian/patches/series 2009-06-16 10:37:15 UTC (rev 3494)
+++ trunk/packages/emboss/trunk/debian/patches/series 2009-06-17 14:01:16 UTC (rev 3495)
@@ -1,2 +1 @@
using-pager-in-tfm.patch
-upstream.patch
Deleted: trunk/packages/emboss/trunk/debian/patches/upstream.patch
===================================================================
--- trunk/packages/emboss/trunk/debian/patches/upstream.patch 2009-06-16 10:37:15 UTC (rev 3494)
+++ trunk/packages/emboss/trunk/debian/patches/upstream.patch 2009-06-17 14:01:16 UTC (rev 3495)
@@ -1,1644 +0,0 @@
-Author: Upstream
-Forwarded: no
- This is an upstream patch, it does not need to be forwarded.
-Description: Official upstream patch.
- This patch was downloaded from:
- ftp://emboss.open-bio.org/pub/EMBOSS/fixes/patches/patch-1-12.gz
-diff -c -N --recursive EMBOSS-6.0.1old/ajax/ajacd.c EMBOSS-6.0.1/ajax/ajacd.c
-*** EMBOSS-6.0.1old/ajax/ajacd.c 2008-07-14 15:47:38.000000000 +0100
---- EMBOSS-6.0.1/ajax/ajacd.c 2009-05-14 15:34:27.000000000 +0100
-***************
-*** 8256,8263 ****
---- 8256,8271 ----
- acdReplyInit(thys, ajStrGetPtr(gdev), &acdReplyDef);
- else
- #ifndef WIN32
-+ #ifndef X_DISPLAY_MISSING /* X11 is available */
- acdReplyInit(thys, "x11", &acdReplyDef);
- #else
-+ #ifdef PLD_png /* if png/gd/zlib libraries available for png driver */
-+ acdReplyInit(thys, "png", &acdReplyDef);
-+ #else
-+ acdReplyInit(thys, "ps", &acdReplyDef);
-+ #endif
-+ #endif
-+ #else
- acdReplyInit(thys, "win3", &acdReplyDef);
- #endif
- }
-***************
-*** 8426,8433 ****
---- 8434,8449 ----
- acdReplyInit(thys, ajStrGetPtr(gdev), &acdReplyDef);
- else
- #ifndef WIN32
-+ #ifndef X_DISPLAY_MISSING /* X11 is available */
- acdReplyInit(thys, "x11", &acdReplyDef);
- #else
-+ #ifdef PLD_png /* if png/gd/zlib libraries available for png driver */
-+ acdReplyInit(thys, "png", &acdReplyDef);
-+ #else
-+ acdReplyInit(thys, "ps", &acdReplyDef);
-+ #endif
-+ #endif
-+ #else
- acdReplyInit(thys, "win3", &acdReplyDef);
- #endif
- }
-***************
-*** 11433,11443 ****
-
- if(ajSeqIsNuc(val))
- {
-- if(seqin->Rev)
-- {
-- okrev = ajTrue;
-- }
--
- for(itry=acdPromptTry; itry && !okrev; itry--)
- {
- ajStrAssignC(&acdReplyPrompt, "N");
---- 11449,11454 ----
-***************
-*** 11631,11637 ****
- okend = acdQualToSeqend(thys, "send", 0,
- &seqin->End, &acdTmpStr);
- okrev = acdQualToBool(thys, "sreverse", ajFalse,
-! &seqin->Rev, &acdTmpStr);
-
- if(snuc)
- ajSeqinSetNuc(seqin);
---- 11642,11648 ----
- okend = acdQualToSeqend(thys, "send", 0,
- &seqin->End, &acdTmpStr);
- okrev = acdQualToBool(thys, "sreverse", ajFalse,
-! &sreverse, &acdTmpStr);
-
- if(snuc)
- ajSeqinSetNuc(seqin);
-***************
-*** 11723,11734 ****
-
- if(ajSeqIsNuc(seq))
- {
-- if(seqin->Rev)
-- {
-- okrev = ajTrue;
-- val->Rev = seq->Rev = seqin->Rev;
-- }
--
- for(itry=acdPromptTry; itry && !okrev; itry--)
- {
- ajStrAssignC(&acdReplyPrompt, "N");
---- 11734,11739 ----
-***************
-*** 11753,11759 ****
- }
- }
-
-! /* no need to reverse - it should happen in ajSeqallNext */
-
- acdLog("sbegin: %d, send: %d, sreverse: %B\n",
- sbegin, send, sreverse);
---- 11758,11764 ----
- }
- }
-
-!
-
- acdLog("sbegin: %d, send: %d, sreverse: %B\n",
- sbegin, send, sreverse);
-***************
-*** 11906,11912 ****
- okend = acdQualToSeqend(thys, "send", 0,
- &seqin->End, &acdTmpStr);
- okrev = acdQualToBool(thys, "sreverse", ajFalse,
-! &seqin->Rev, &acdTmpStr);
-
- if(snuc)
- ajSeqinSetNuc(seqin);
---- 11911,11917 ----
- okend = acdQualToSeqend(thys, "send", 0,
- &seqin->End, &acdTmpStr);
- okrev = acdQualToBool(thys, "sreverse", ajFalse,
-! &sreverse, &acdTmpStr);
-
- if(snuc)
- ajSeqinSetNuc(seqin);
-***************
-*** 12003,12015 ****
-
- if(ajSeqsetIsNuc(val[0]))
- {
-- if(seqin->Rev)
-- {
-- okrev = ajTrue;
-- for(iset=0;iset<nsets;iset++)
-- val[iset]->Rev = seqin->Rev;
-- }
--
- for(itry=acdPromptTry; itry && !okrev; itry--)
- {
- ajStrAssignC(&acdReplyPrompt, "N");
---- 12008,12013 ----
-***************
-*** 12788,12794 ****
- okend = acdQualToSeqend(thys, "send", 0,
- &seqin->End, &acdTmpStr);
- okrev = acdQualToBool(thys, "sreverse", ajFalse,
-! &seqin->Rev, &acdTmpStr);
-
- if(snuc)
- ajSeqinSetNuc(seqin);
---- 12786,12792 ----
- okend = acdQualToSeqend(thys, "send", 0,
- &seqin->End, &acdTmpStr);
- okrev = acdQualToBool(thys, "sreverse", ajFalse,
-! &sreverse, &acdTmpStr);
-
- if(snuc)
- ajSeqinSetNuc(seqin);
-***************
-*** 12876,12887 ****
-
- if(ajSeqsetGetSize(val) && ajSeqsetIsNuc(val))
- {
-- if(seqin->Rev)
-- {
-- okrev = ajTrue;
-- val->Rev = seqin->Rev;
-- }
--
- for(itry=acdPromptTry; itry && !okrev; itry--)
- {
- ajStrAssignC(&acdReplyPrompt, "N");
---- 12874,12879 ----
-***************
-*** 15461,15479 ****
-
- static void acdHelpExpectGraph(const AcdPAcd thys, AjBool table, AjPStr* str)
- {
-- if(!thys) return;
--
- #ifndef WIN32
-! if(table)
-! ajStrAppendC(str, "<i>EMBOSS_GRAPHICS</i> value, or x11");
-! else
-! ajStrAppendC(str, "$EMBOSS_GRAPHICS value, or x11");
- #else
- if(table)
-! ajStrAppendC(str, "<i>EMBOSS_GRAPHICS</i> value, or win3");
- else
-! ajStrAppendC(str, "$EMBOSS_GRAPHICS value, or win3");
-! #endif
- return;
- }
-
---- 15453,15478 ----
-
- static void acdHelpExpectGraph(const AcdPAcd thys, AjBool table, AjPStr* str)
- {
- #ifndef WIN32
-! #ifndef X_DISPLAY_MISSING /* X11 is available */
-! const char* defdev = "x11";
-! #else
-! #ifdef PLD_png /* if png/gd/zlib libraries available for png driver */
-! const char* defdev = "png";
-! #else
-! const char* defdev = "ps";
-! #endif
-! #endif
- #else
-+ const char* defdev = "win3";
-+ #endif
-+
-+ if(!thys) return;
-+
- if(table)
-! ajFmtPrintAppS(str, "<i>EMBOSS_GRAPHICS</i> value, or %s"), defdev;
- else
-! ajFmtPrintAppS(str, "$EMBOSS_GRAPHICS value, or %s", defdev);
- return;
- }
-
-***************
-*** 19171,19177 ****
- acdLog("number: %d jparam: %d acd->PNum: %d acdNParam: %d\n",
- number, jparam, acd->PNum, acdNParam);
-
-! if(!number && !jparam && acd->PNum)
- {
- for(itestparam = acd->PNum+1; itestparam <= acdNParam;
- itestparam++)
---- 19170,19176 ----
- acdLog("number: %d jparam: %d acd->PNum: %d acdNParam: %d\n",
- number, jparam, acd->PNum, acdNParam);
-
-! if(!ajStrGetLen(master) && !number && !jparam && acd->PNum)
- {
- for(itestparam = acd->PNum+1; itestparam <= acdNParam;
- itestparam++)
-diff -c -N --recursive EMBOSS-6.0.1old/ajax/ajphylo.c EMBOSS-6.0.1/ajax/ajphylo.c
-*** EMBOSS-6.0.1old/ajax/ajphylo.c 2008-06-26 09:38:43.000000000 +0100
---- EMBOSS-6.0.1/ajax/ajphylo.c 2009-05-14 15:34:41.000000000 +0100
-***************
-*** 402,408 ****
- AjPStr tmpval = NULL;
- AjBool lowertri = ajFalse;
- AjBool uppertri = ajFalse;
-!
- if(!phyloRegDistFloat)
- phyloRegDistFloat =
- ajRegCompC("^\\s*([0-9]+[.]?[0-9]*)\\s+(([0-9]+)[^0-9.])?");
---- 402,412 ----
- AjPStr tmpval = NULL;
- AjBool lowertri = ajFalse;
- AjBool uppertri = ajFalse;
-! AjPStr name = NULL;
-! AjPStr rest = NULL;
-! ajuint imaxlen;
-! ajuint linenum = 0;
-!
- if(!phyloRegDistFloat)
- phyloRegDistFloat =
- ajRegCompC("^\\s*([0-9]+[.]?[0-9]*)\\s+(([0-9]+)[^0-9.])?");
-***************
-*** 413,439 ****
- if(!distfile)
- return NULL;
-
-- ajReadlineTrim(distfile, &rdline);
-- if(!ajStrToInt(rdline, &count))
-- {
-- ajErr("Distance file '%S' bad header record '%S'",
-- filename, rdline);
-- return NULL;
-- }
-- ajDebug("DistRead: row count: %d\n", count);
--
-- if(size && (count != size))
-- {
-- ajErr("Distance file '%S' found %d expected %d rows '%S'",
-- filename, count, size);
-- return NULL;
-- }
--
--
- done = ajTrue;
- while(ajReadline(distfile, &rdline))
- {
- if(done) {
- irow = -1;
- icol = 0;
-
---- 417,445 ----
- if(!distfile)
- return NULL;
-
- done = ajTrue;
- while(ajReadline(distfile, &rdline))
- {
-+ linenum++;
-+ if(ajStrIsWhite(rdline)) continue;
- if(done) {
-+ ajStrTrimWhite(&rdline);
-+ if(!ajStrToInt(rdline, &count))
-+ {
-+ ajErr("Distance file '%S' line %u bad header record '%S'",
-+ filename, linenum, rdline);
-+ return NULL;
-+ }
-+ ajDebug("DistRead: row count: %d\n", count);
-+
-+ if(size && (count != size))
-+ {
-+ ajErr("Distance file '%S' line %u "
-+ "found %d expected %d rows '%S'",
-+ filename, linenum, count, size);
-+ return NULL;
-+ }
-+
- irow = -1;
- icol = 0;
-
-***************
-*** 446,458 ****
- ncells = count*count;
- AJCNEW0(dist->Data,ncells);
- AJCNEW0(dist->Replicates,ncells);
- }
-
- /*ajDebug("DistRead line: %S", rdline); */
- if(!i || !ajRegExec(phyloRegDistFloat, rdline))
- {
-- if(ajStrGetLen(rdline) < 11) /* skip this line? */
-- continue;
- if(!irow) /* how long was that first row */
- {
- if(!icol) /* empty - lower triangular */
---- 452,463 ----
- ncells = count*count;
- AJCNEW0(dist->Data,ncells);
- AJCNEW0(dist->Replicates,ncells);
-+ continue;
- }
-
- /*ajDebug("DistRead line: %S", rdline); */
- if(!i || !ajRegExec(phyloRegDistFloat, rdline))
- {
- if(!irow) /* how long was that first row */
- {
- if(!icol) /* empty - lower triangular */
-***************
-*** 475,482 ****
- }
- else if(icol != count) /* something wrong */
- {
-! ajErr("Distance file %S: Row '%S' has %d values",
-! filename, dist->Names[irow], icol);
- }
- }
- else if(irow > 0) /* later rows - we know what to expect */
---- 480,487 ----
- }
- else if(icol != count) /* something wrong */
- {
-! ajErr("Distance file %S: line %u Row '%S' has %d values",
-! filename, linenum, dist->Names[irow], icol);
- }
- }
- else if(irow > 0) /* later rows - we know what to expect */
-***************
-*** 486,523 ****
- /*ajDebug("DistRead Lower irow: %d i: %d\n",
- irow, i);*/
- if(icol != irow)
-! ajErr("Distance file %S: Row '%S' has %d values"
- " in lower-triangular format",
-! filename, dist->Names[irow], icol);
- }
- else if(uppertri)
- {
- /*ajDebug("DistRead Upper irow: %d i: %d\n",
- irow, i);*/
- if(i)
-! ajErr("Distance file %S: Row '%S' has %d values"
- " in upper-triangular format",
-! filename, dist->Names[irow], icol - irow - 1);
- }
- else
- {
- /*ajDebug("DistRead Square irow: %d i: %d\n",
- irow, i);*/
- if(icol != count)
-! ajErr("Distance file %S: Row '%S' has %d values"
- " in square format",
-! filename, dist->Names[irow], icol);
- }
- }
-
- irow++;
- if(irow > count)
- {
-! ajErr("Distances file read beyond %d rows", count);
- return NULL;
- }
-! ajStrAssignSubS(&dist->Names[irow], rdline, 0, 9);
-! ajStrCutStart(&rdline, 10);
- ajStrTrimWhiteEnd(&dist->Names[irow]);
- ajDebug("DistRead name [%d] '%S' i: %d\n",
- irow, dist->Names[irow], i);
---- 491,536 ----
- /*ajDebug("DistRead Lower irow: %d i: %d\n",
- irow, i);*/
- if(icol != irow)
-! ajErr("Distance file %S: line %u Row '%S' has %d values"
- " in lower-triangular format",
-! filename, linenum, dist->Names[irow], icol);
- }
- else if(uppertri)
- {
- /*ajDebug("DistRead Upper irow: %d i: %d\n",
- irow, i);*/
- if(i)
-! ajErr("Distance file %S: line %u Row '%S' has %d values"
- " in upper-triangular format",
-! filename, linenum,
-! dist->Names[irow], icol - irow - 1);
- }
- else
- {
- /*ajDebug("DistRead Square irow: %d i: %d\n",
- irow, i);*/
- if(icol != count)
-! ajErr("Distance file %S: line %u Row '%S' has %d values"
- " in square format",
-! filename, linenum, dist->Names[irow], icol);
- }
- }
-
- irow++;
- if(irow > count)
- {
-! ajErr("Distances file line %u read beyond %d rows",
-! linenum, count);
- return NULL;
- }
-! ajStrExtractWord(rdline, &rest, &name);
-! if(ajStrGetLen(name) >= 10)
-! imaxlen = 10;
-! else
-! imaxlen = ajStrGetLen(name);
-! ajStrAssignSubS(&dist->Names[irow], rdline, 0, imaxlen-1);
-!
-! ajStrCutStart(&rdline, imaxlen);
- ajStrTrimWhiteEnd(&dist->Names[irow]);
- ajDebug("DistRead name [%d] '%S' i: %d\n",
- irow, dist->Names[irow], i);
-***************
-*** 548,555 ****
- {
- if(!missing)
- {
-! ajErr("Distances file %S: Zero (%S) replicates for %S",
-! filename, tmpval, dist->Names[irow]);
- return NULL;
- }
- dist->HasMissing = ajTrue;
---- 561,569 ----
- {
- if(!missing)
- {
-! ajErr("Distances file %S: line %u "
-! "Zero (%S) replicates for %S",
-! filename, linenum, tmpval, dist->Names[irow]);
- return NULL;
- }
- dist->HasMissing = ajTrue;
-***************
-*** 576,584 ****
- }
- if(irow == (count-1))
- {
-! done = ajTrue;
-!
-! if(lowertri) /* fill in the rest */
- {
- for(k=0; k < count; k++)
- {
---- 590,596 ----
- }
- if(irow == (count-1))
- {
-! if(lowertri) /* fill in the rest */
- {
- for(k=0; k < count; k++)
- {
-***************
-*** 596,607 ****
- jpos += count;
- }
- }
- }
-! if(uppertri) /* fill in the rest */
- {
- for(k=0; k < count; k++)
- {
-! idiag = k*count + i; /* diagonal */
- dist->Data[idiag] = 0.0;
- dist->Replicates[idiag] = 1;
- ipos = k*count; /* start of row*/
---- 608,620 ----
- jpos += count;
- }
- }
-+ done = ajTrue;
- }
-! else if(uppertri) /* fill in the rest */
- {
- for(k=0; k < count; k++)
- {
-! idiag = k*count + k; /* diagonal */
- dist->Data[idiag] = 0.0;
- dist->Replicates[idiag] = 1;
- ipos = k*count; /* start of row*/
-***************
-*** 614,623 ****
- jpos += count;
- }
- }
- }
-!
-! ajListPushAppend(distlist, dist);
-! dist = NULL;
- }
- }
-
---- 627,643 ----
- jpos += count;
- }
- }
-+ done = ajTrue;
- }
-! else if(icol == count)
-! {
-! done = ajTrue;
-! }
-!
-! if(done){
-! ajListPushAppend(distlist, dist);
-! dist = NULL;
-! }
- }
- }
-
-***************
-*** 627,634 ****
- return NULL;
- }
-
-! ajDebug("Distances file '%S' has %d (%d) distance matrices\n",
-! filename, i, ajListGetLength(distlist));
- ajFileClose(&distfile);
- ajListToarray(distlist, (void***) &ret);
- /*ret = (AjPPhyloTree*) trees;*/
---- 647,654 ----
- return NULL;
- }
-
-! ajDebug("Distances file '%S' has %u distance matrices\n",
-! filename, ajListGetLength(distlist));
- ajFileClose(&distfile);
- ajListToarray(distlist, (void***) &ret);
- /*ret = (AjPPhyloTree*) trees;*/
-***************
-*** 636,641 ****
---- 656,663 ----
- for(i=0; ret[i]; i++)
- ajPhyloDistTrace(ret[i]);
-
-+ ajStrDel(&name);
-+ ajStrDel(&rest);
- return ret;
- }
-
-diff -c -N --recursive EMBOSS-6.0.1old/ajax/ajseq.c EMBOSS-6.0.1/ajax/ajseq.c
-*** EMBOSS-6.0.1old/ajax/ajseq.c 2008-07-14 15:54:44.000000000 +0100
---- EMBOSS-6.0.1/ajax/ajseq.c 2009-05-14 15:34:27.000000000 +0100
-***************
-*** 287,292 ****
---- 287,293 ----
- pthis->Sv = ajStrNew();
- pthis->Gi = ajStrNew();
- pthis->Tax = ajStrNew();
-+ pthis->Organelle = ajStrNew();
- pthis->Type = ajStrNew();
- pthis->Db = ajStrNew();
- pthis->Full = ajStrNew();
-***************
-*** 317,322 ****
---- 318,326 ----
- pthis->Acclist = ajListstrNew();
- pthis->Keylist = ajListstrNew();
- pthis->Taxlist = ajListstrNew();
-+ pthis->Cmtlist = ajListstrNew();
-+ pthis->Xreflist = ajListstrNew();
-+ pthis->Reflist = ajListstrNew();
-
- return pthis;
- }
-***************
-*** 344,349 ****
---- 348,354 ----
- pthis->Sv = ajStrNew();
- pthis->Gi = ajStrNew();
- pthis->Tax = ajStrNew();
-+ pthis->Organelle = ajStrNew();
- pthis->Type = ajStrNew();
- pthis->Db = ajStrNew();
- pthis->Full = ajStrNew();
-***************
-*** 374,379 ****
---- 379,387 ----
- pthis->Acclist = ajListstrNew();
- pthis->Keylist = ajListstrNew();
- pthis->Taxlist = ajListstrNew();
-+ pthis->Cmtlist = ajListstrNew();
-+ pthis->Xreflist = ajListstrNew();
-+ pthis->Reflist = ajListstrNew();
-
- return pthis;
- }
-***************
-*** 435,440 ****
---- 443,449 ----
- pthis->Sv = ajStrNew();
- pthis->Gi = ajStrNew();
- pthis->Tax = ajStrNew();
-+ pthis->Organelle = ajStrNew();
- pthis->Type = ajStrNew();
- pthis->Db = ajStrNew();
- pthis->Full = ajStrNew();
-***************
-*** 473,478 ****
---- 482,490 ----
- pthis->Acclist = ajListstrNew();
- pthis->Keylist = ajListstrNew();
- pthis->Taxlist = ajListstrNew();
-+ pthis->Cmtlist = ajListstrNew();
-+ pthis->Xreflist = ajListstrNew();
-+ pthis->Reflist = ajListstrNew();
-
- ajDebug("ajSeqNewRangeC rev:%B offset:%d/%d offend:%d/%d\n",
- rev, offset, pthis->Offset, offend, pthis->Offend);
-***************
-*** 552,557 ****
---- 564,570 ----
- pthis->Sv = ajStrNew();
- pthis->Gi = ajStrNew();
- pthis->Tax = ajStrNew();
-+ pthis->Organelle = ajStrNew();
- pthis->Type = ajStrNew();
- pthis->Db = ajStrNew();
- pthis->Full = ajStrNew();
-***************
-*** 623,628 ****
---- 636,642 ----
- ajStrAssignS(&pthis->Sv, seq->Sv);
- ajStrAssignS(&pthis->Gi, seq->Gi);
- ajStrAssignS(&pthis->Tax, seq->Tax);
-+ ajStrAssignS(&pthis->Organelle, seq->Organelle);
- ajStrAssignS(&pthis->Type, seq->Type);
-
- pthis->EType = seq->EType;
-***************
-*** 662,667 ****
---- 676,688 ----
-
- pthis->Taxlist = ajListstrNewList(seq->Taxlist);
-
-+ pthis->Cmtlist = ajListstrNewList(seq->Cmtlist);
-+
-+ pthis->Xreflist = ajListstrNewList(seq->Xreflist);
-+
-+ pthis->Reflist = ajListstrNew();
-+ ajSeqreflistClone(seq->Reflist, pthis->Reflist);
-+
- ajStrAssignS(&pthis->Seq, seq->Seq);
- if (seq->Fttable)
- pthis->Fttable = ajFeattableCopy(seq->Fttable);
-***************
-*** 730,735 ****
---- 751,757 ----
- ajStrDel(&seq->Sv);
- ajStrDel(&seq->Gi);
- ajStrDel(&seq->Tax);
-+ ajStrDel(&seq->Organelle);
- ajStrDel(&seq->Type);
- ajStrDel(&seq->Molecule);
- ajStrDel(&seq->Class);
-***************
-*** 1591,1596 ****
---- 1613,1619 ----
- ajStrSetClear(&seq->Sv);
- ajStrSetClear(&seq->Gi);
- ajStrSetClear(&seq->Tax);
-+ ajStrSetClear(&seq->Organelle);
- ajStrSetClear(&seq->Type);
- ajStrSetClear(&seq->Molecule);
- ajStrSetClear(&seq->Class);
-***************
-*** 5364,5370 ****
---- 5387,5396 ----
- seq->Begin = -(iend);
-
- for(i=0; i < seq->Size; i++)
-+ {
-+ seq->Seq[i]->Rev = ajTrue;
- ajSeqReverseDo(seq->Seq[i]);
-+ }
-
- ajDebug(" set result len: %d Begin: %d End: %d\n",
- ajSeqsetGetLen(seq), seq->Begin, seq->End);
-diff -c -N --recursive EMBOSS-6.0.1old/ajax/ajseqdb.c EMBOSS-6.0.1/ajax/ajseqdb.c
-*** EMBOSS-6.0.1old/ajax/ajseqdb.c 2008-07-14 15:52:03.000000000 +0100
---- EMBOSS-6.0.1/ajax/ajseqdb.c 2009-05-14 15:34:27.000000000 +0100
-***************
-*** 2005,2011 ****
---- 2005,2014 ----
- {
- ajStrTrimWhite(&seqline);
- if(!ajStrGetLen(seqline))
-+ {
-+ ajBuffreadLine(seqfile, &seqline);
- ihead=0;
-+ }
- }
- else
- {
-diff -c -N --recursive EMBOSS-6.0.1old/ajax/ajseqread.c EMBOSS-6.0.1/ajax/ajseqread.c
-*** EMBOSS-6.0.1old/ajax/ajseqread.c 2008-07-14 15:52:48.000000000 +0100
---- EMBOSS-6.0.1/ajax/ajseqread.c 2009-05-14 15:34:27.000000000 +0100
-***************
-*** 1617,1623 ****
- ajDebug("ready to start reading format '%S' '%S' %d..%d\n",
- seqin->Formatstr, seq->Formatstr, seqin->Begin, seqin->End);
-
-! while(ajSeqRead(seq, seqin))
- {
- if (seqin->List)
- ajSeqinClearPos(seqin);
---- 1617,1623 ----
- ajDebug("ready to start reading format '%S' '%S' %d..%d\n",
- seqin->Formatstr, seq->Formatstr, seqin->Begin, seqin->End);
-
-! while(!seqin->multidone && ajSeqRead(seq, seqin))
- {
- if (seqin->List)
- ajSeqinClearPos(seqin);
-diff -c -N --recursive EMBOSS-6.0.1old/ajax/ajseqwrite.c EMBOSS-6.0.1/ajax/ajseqwrite.c
-*** EMBOSS-6.0.1old/ajax/ajseqwrite.c 2008-07-14 15:58:07.000000000 +0100
---- EMBOSS-6.0.1/ajax/ajseqwrite.c 2009-05-14 15:34:27.000000000 +0100
-***************
-*** 451,456 ****
---- 451,457 ----
- pthis->Sv = ajStrNew();
- pthis->Gi = ajStrNew();
- pthis->Tax = ajStrNew();
-+ pthis->Organelle = ajStrNew();
- pthis->Desc = ajStrNew();
- pthis->Type = ajStrNew();
- pthis->EType = 0;
-***************
-*** 3743,3749 ****
- ajFmtPrintF(outseq->File, "DE %S\n", outseq->Desc);
-
- if(ajStrGetLen(outseq->Tax))
-! ajFmtPrintF(outseq->File, "OS %S\n", outseq->Tax);
-
- if(ajListGetLength(outseq->Taxlist) > 1)
- {
---- 3744,3750 ----
- ajFmtPrintF(outseq->File, "DE %S\n", outseq->Desc);
-
- if(ajStrGetLen(outseq->Tax))
-! ajFmtPrintF(outseq->File, "OS %S.\n", outseq->Tax);
-
- if(ajListGetLength(outseq->Taxlist) > 1)
- {
-***************
-*** 6175,6180 ****
---- 6176,6182 ----
- static void seqDeclone(AjPSeqout outseq)
- {
- AjPStr ptr = NULL;
-+ AjPSeqRef tmpref = NULL;
-
- ajStrSetClear(&outseq->Db);
- ajStrSetClear(&outseq->Setdb);
-***************
-*** 6200,6205 ****
---- 6202,6216 ----
- while(ajListstrPop(outseq->Taxlist,&ptr))
- ajStrDel(&ptr);
-
-+ while(ajListstrPop(outseq->Cmtlist,&ptr))
-+ ajStrDel(&ptr);
-+
-+ while(ajListstrPop(outseq->Xreflist,&ptr))
-+ ajStrDel(&ptr);
-+
-+ while(ajListPop(outseq->Reflist,(void **)&tmpref))
-+ ajSeqrefDel(&tmpref);
-+
- ajStrSetClear(&outseq->Seq);
- AJFREE(outseq->Accuracy);
-
-diff -c -N --recursive EMBOSS-6.0.1old/emboss/acd/edialign.acd EMBOSS-6.0.1/emboss/acd/edialign.acd
-*** EMBOSS-6.0.1old/emboss/acd/edialign.acd 2008-04-04 16:54:03.000000000 +0100
---- EMBOSS-6.0.1/emboss/acd/edialign.acd 2009-05-14 15:34:27.000000000 +0100
-***************
-*** 26,32 ****
- information: "Nucleic acid sequence alignment mode"
- help: "Nucleic acid sequence alignment mode (simple, translated or
- mixed)"
-! values: "n : simple ; nt : translation ; ma : mixed alignments"
- default: "n"
- ]
-
---- 26,32 ----
- information: "Nucleic acid sequence alignment mode"
- help: "Nucleic acid sequence alignment mode (simple, translated or
- mixed)"
-! values: "n: simple; nt: translation; ma: mixed alignments"
- default: "n"
- ]
-
-***************
-*** 50,56 ****
- information: "Clustering method to construct sequence tree"
- help: "Clustering method to construct sequence tree (UPGMA,
- minimum linkage or maximum linkage)"
-! values: "UPGMA : UPGMA ; max : maximum linkage ; min : minimum
- linkage"
- default: "UPGMA"
- ]
---- 50,56 ----
- information: "Clustering method to construct sequence tree"
- help: "Clustering method to construct sequence tree (UPGMA,
- minimum linkage or maximum linkage)"
-! values: "UPGMA: UPGMA; max: maximum linkage; min: minimum
- linkage"
- default: "UPGMA"
- ]
-diff -c -N --recursive EMBOSS-6.0.1old/emboss/acd/Makefile.am EMBOSS-6.0.1/emboss/acd/Makefile.am
-*** EMBOSS-6.0.1old/emboss/acd/Makefile.am 2008-07-14 16:46:31.000000000 +0100
---- EMBOSS-6.0.1/emboss/acd/Makefile.am 2009-05-14 15:34:27.000000000 +0100
-***************
-*** 21,27 ****
- fuzznuc.acd fuzzpro.acd fuzztran.acd \
- garnier.acd geecee.acd getorf.acd giep.acd \
- helixturnhelix.acd histogramtest.acd \
-! hmoment.acd iep.acd infoalign.acd infoseq.acd intconv.acd \
- isochore.acd jaspextract.acd jaspscan.acd lindna.acd listor.acd \
- makenucseq.acd makeprotseq.acd marscan.acd \
- maskambignuc.acd maskambigprot.acd maskfeat.acd maskseq.acd \
---- 21,28 ----
- fuzznuc.acd fuzzpro.acd fuzztran.acd \
- garnier.acd geecee.acd getorf.acd giep.acd \
- helixturnhelix.acd histogramtest.acd \
-! hmoment.acd iep.acd infoalign.acd infobase.acd inforesidue.acd \
-! infoseq.acd intconv.acd \
- isochore.acd jaspextract.acd jaspscan.acd lindna.acd listor.acd \
- makenucseq.acd makeprotseq.acd marscan.acd \
- maskambignuc.acd maskambigprot.acd maskfeat.acd maskseq.acd \
-***************
-*** 48,55 ****
- splitter.acd stretcher.acd stssearch.acd supermatcher.acd syco.acd \
- tcode.acd testplot.acd textsearch.acd tfextract.acd tfm.acd \
- tfscan.acd tmap.acd tranalign.acd transeq.acd treetypedisplay.acd \
-! trimest.acd trimseq.acd twofeat.acd union.acd vectorstrip.acd \
-! water.acd whichdb.acd wobble.acd \
- wordcount.acd wordfinder.acd wordmatch.acd \
- wossname.acd yank.acd
-
---- 49,56 ----
- splitter.acd stretcher.acd stssearch.acd supermatcher.acd syco.acd \
- tcode.acd testplot.acd textsearch.acd tfextract.acd tfm.acd \
- tfscan.acd tmap.acd tranalign.acd transeq.acd treetypedisplay.acd \
-! trimest.acd trimseq.acd trimspace.acd twofeat.acd union.acd \
-! vectorstrip.acd water.acd whichdb.acd wobble.acd \
- wordcount.acd wordfinder.acd wordmatch.acd \
- wossname.acd yank.acd
-
-diff -c -N --recursive EMBOSS-6.0.1old/emboss/acd/Makefile.in EMBOSS-6.0.1/emboss/acd/Makefile.in
-*** EMBOSS-6.0.1old/emboss/acd/Makefile.in 2008-07-16 19:33:19.000000000 +0100
---- EMBOSS-6.0.1/emboss/acd/Makefile.in 2009-05-14 15:34:27.000000000 +0100
-***************
-*** 209,215 ****
- fuzznuc.acd fuzzpro.acd fuzztran.acd \
- garnier.acd geecee.acd getorf.acd giep.acd \
- helixturnhelix.acd histogramtest.acd \
-! hmoment.acd iep.acd infoalign.acd infoseq.acd intconv.acd \
- isochore.acd jaspextract.acd jaspscan.acd lindna.acd listor.acd \
- makenucseq.acd makeprotseq.acd marscan.acd \
- maskambignuc.acd maskambigprot.acd maskfeat.acd maskseq.acd \
---- 209,216 ----
- fuzznuc.acd fuzzpro.acd fuzztran.acd \
- garnier.acd geecee.acd getorf.acd giep.acd \
- helixturnhelix.acd histogramtest.acd \
-! hmoment.acd iep.acd infoalign.acd infobase.acd inforesidue.acd \
-! infoseq.acd intconv.acd \
- isochore.acd jaspextract.acd jaspscan.acd lindna.acd listor.acd \
- makenucseq.acd makeprotseq.acd marscan.acd \
- maskambignuc.acd maskambigprot.acd maskfeat.acd maskseq.acd \
-***************
-*** 236,243 ****
- splitter.acd stretcher.acd stssearch.acd supermatcher.acd syco.acd \
- tcode.acd testplot.acd textsearch.acd tfextract.acd tfm.acd \
- tfscan.acd tmap.acd tranalign.acd transeq.acd treetypedisplay.acd \
-! trimest.acd trimseq.acd twofeat.acd union.acd vectorstrip.acd \
-! water.acd whichdb.acd wobble.acd \
- wordcount.acd wordfinder.acd wordmatch.acd \
- wossname.acd yank.acd
-
---- 237,244 ----
- splitter.acd stretcher.acd stssearch.acd supermatcher.acd syco.acd \
- tcode.acd testplot.acd textsearch.acd tfextract.acd tfm.acd \
- tfscan.acd tmap.acd tranalign.acd transeq.acd treetypedisplay.acd \
-! trimest.acd trimseq.acd trimspace.acd twofeat.acd union.acd \
-! vectorstrip.acd water.acd whichdb.acd wobble.acd \
- wordcount.acd wordfinder.acd wordmatch.acd \
- wossname.acd yank.acd
-
-diff -c -N --recursive EMBOSS-6.0.1old/emboss/data/Makefile.am EMBOSS-6.0.1/emboss/data/Makefile.am
-*** EMBOSS-6.0.1old/emboss/data/Makefile.am 2008-07-14 16:09:23.000000000 +0100
---- EMBOSS-6.0.1/emboss/data/Makefile.am 2009-05-14 15:34:27.000000000 +0100
-***************
-*** 30,36 ****
- Epprofile Eprior1.plib Eprior30.plib Erna.melt Eresidues.iub \
- Esig.euk Esig.pro \
- Etags.embl Etags.emboss \
-! Etags.gff Etags.gff3 Etags.gffprotein \
- Etags.pir Etags.protein Etags.swiss \
- Etcode.dat Evdw.dat Ewhite-wimley.dat \
- embossre.equ Emwfilter.dat Emass.dat Emassmod.dat \
---- 30,36 ----
- Epprofile Eprior1.plib Eprior30.plib Erna.melt Eresidues.iub \
- Esig.euk Esig.pro \
- Etags.embl Etags.emboss \
-! Etags.gff Etags.gff3 Etags.gffprotein Etags.gff3protein \
- Etags.pir Etags.protein Etags.swiss \
- Etcode.dat Evdw.dat Ewhite-wimley.dat \
- embossre.equ Emwfilter.dat Emass.dat Emassmod.dat \
-diff -c -N --recursive EMBOSS-6.0.1old/emboss/data/Makefile.in EMBOSS-6.0.1/emboss/data/Makefile.in
-*** EMBOSS-6.0.1old/emboss/data/Makefile.in 2008-07-16 19:33:20.000000000 +0100
---- EMBOSS-6.0.1/emboss/data/Makefile.in 2009-05-14 15:34:27.000000000 +0100
-***************
-*** 228,234 ****
- Epprofile Eprior1.plib Eprior30.plib Erna.melt Eresidues.iub \
- Esig.euk Esig.pro \
- Etags.embl Etags.emboss \
-! Etags.gff Etags.gff3 Etags.gffprotein \
- Etags.pir Etags.protein Etags.swiss \
- Etcode.dat Evdw.dat Ewhite-wimley.dat \
- embossre.equ Emwfilter.dat Emass.dat Emassmod.dat \
---- 228,234 ----
- Epprofile Eprior1.plib Eprior30.plib Erna.melt Eresidues.iub \
- Esig.euk Esig.pro \
- Etags.embl Etags.emboss \
-! Etags.gff Etags.gff3 Etags.gffprotein Etags.gff3protein \
- Etags.pir Etags.protein Etags.swiss \
- Etcode.dat Evdw.dat Ewhite-wimley.dat \
- embossre.equ Emwfilter.dat Emass.dat Emassmod.dat \
-diff -c -N --recursive EMBOSS-6.0.1old/emboss/edialign.c EMBOSS-6.0.1/emboss/edialign.c
-*** EMBOSS-6.0.1old/emboss/edialign.c 2008-06-26 09:39:09.000000000 +0100
---- EMBOSS-6.0.1/emboss/edialign.c 2009-05-14 15:34:27.000000000 +0100
-***************
-*** 627,632 ****
---- 627,634 ----
- ajSeqsetFmtUpper(seqset);
- n = ajSeqsetGetSize(seqset);
-
-+ max_dia = lmax;
-+
- AJCNEW0(seq,n);
- AJCNEW0(seq_name,n);
- AJCNEW0(full_name,n);
-diff -c -N --recursive EMBOSS-6.0.1old/emboss/jaspscan.c EMBOSS-6.0.1/emboss/jaspscan.c
-*** EMBOSS-6.0.1old/emboss/jaspscan.c 2008-06-26 09:39:09.000000000 +0100
---- EMBOSS-6.0.1/emboss/jaspscan.c 2009-05-14 15:34:27.000000000 +0100
-***************
-*** 293,299 ****
-
- jaspscan_scan(substr,begin,mfname, cp, thresh, both, hits);
-
-! ajStrDel(&mfname);
- }
-
- jaspscan_ReportHits(TabRpt,mattab,hits);
---- 293,299 ----
-
- jaspscan_scan(substr,begin,mfname, cp, thresh, both, hits);
-
-! ajListPushAppend(flist, (void **)mfname);
- }
-
- jaspscan_ReportHits(TabRpt,mattab,hits);
-***************
-*** 303,308 ****
---- 303,312 ----
- }
-
-
-+ while(ajListPop(flist,(void **)&mfname))
-+ ajStrDel(&mfname);
-+
-+
- ajStrDel(&dir);
- ajStrDel(&menu);
- ajStrDel(&excl);
-diff -c -N --recursive EMBOSS-6.0.1old/emboss/needle.c EMBOSS-6.0.1/emboss/needle.c
-*** EMBOSS-6.0.1old/emboss/needle.c 2008-06-10 13:48:04.000000000 +0100
---- EMBOSS-6.0.1/emboss/needle.c 2009-05-14 15:34:27.000000000 +0100
-***************
-*** 151,157 ****
- {
- embAlignCalcSimilarity(m,n,sub,cvt,lena,lenb,&id,&sim,&idx,
- &simx);
-! ajFmtPrintAppS(&tmpstr,"Longest_Identity = %5.2f%%\n",
- id);
- ajFmtPrintAppS(&tmpstr,"Longest_Similarity = %5.2f%%\n",
- sim);
---- 151,157 ----
- {
- embAlignCalcSimilarity(m,n,sub,cvt,lena,lenb,&id,&sim,&idx,
- &simx);
-! ajFmtPrintS(&tmpstr,"Longest_Identity = %5.2f%%\n",
- id);
- ajFmtPrintAppS(&tmpstr,"Longest_Similarity = %5.2f%%\n",
- sim);
-diff -c -N --recursive EMBOSS-6.0.1old/emboss/remap.c EMBOSS-6.0.1/emboss/remap.c
-*** EMBOSS-6.0.1old/emboss/remap.c 2008-06-26 09:39:09.000000000 +0100
---- EMBOSS-6.0.1/emboss/remap.c 2009-05-14 15:34:27.000000000 +0100
-***************
-*** 618,624 ****
-
- for(i = 0; keyarray[i]; i++)
- {
-! value = (PValue) valarray[i];
- if(value->count > maxcuts)
- ajFmtPrintF(outfile, "%10S\t %d\t%S\n",
- (AjPStr) keyarray[i], value->count,
---- 618,624 ----
-
- for(i = 0; keyarray[i]; i++)
- {
-! value = ajTableFetch(hittable,keyarray[i]);
- if(value->count > maxcuts)
- ajFmtPrintF(outfile, "%10S\t %d\t%S\n",
- (AjPStr) keyarray[i], value->count,
-diff -c -N --recursive EMBOSS-6.0.1old/emboss/vectorstrip.c EMBOSS-6.0.1/emboss/vectorstrip.c
-*** EMBOSS-6.0.1old/emboss/vectorstrip.c 2008-06-26 09:39:09.000000000 +0100
---- EMBOSS-6.0.1/emboss/vectorstrip.c 2009-05-14 15:34:27.000000000 +0100
-***************
-*** 174,180 ****
- vectorlist = ajListNew();
-
- /* data from command line or file? */
-! if(vec == AJTRUE)
- vectorstrip_read_vector_data(vectorfile, vectorlist);
- else
- {
---- 174,180 ----
- vectorlist = ajListNew();
-
- /* data from command line or file? */
-! if(vec && vectorfile)
- vectorstrip_read_vector_data(vectorfile, vectorlist);
- else
- {
-diff -c -N --recursive EMBOSS-6.0.1old/emboss/water.c EMBOSS-6.0.1/emboss/water.c
-*** EMBOSS-6.0.1old/emboss/water.c 2008-06-26 09:39:09.000000000 +0100
---- EMBOSS-6.0.1/emboss/water.c 2009-05-14 15:34:27.000000000 +0100
-***************
-*** 159,165 ****
- {
- embAlignCalcSimilarity(m,n,sub,cvt,lena,lenb,&id,&sim,&idx,
- &simx);
-! ajFmtPrintAppS(&tmpstr,"Longest_Identity = %5.2f%%\n",
- id);
- ajFmtPrintAppS(&tmpstr,"Longest_Similarity = %5.2f%%\n",
- sim);
---- 159,165 ----
- {
- embAlignCalcSimilarity(m,n,sub,cvt,lena,lenb,&id,&sim,&idx,
- &simx);
-! ajFmtPrintS(&tmpstr,"Longest_Identity = %5.2f%%\n",
- id);
- ajFmtPrintAppS(&tmpstr,"Longest_Similarity = %5.2f%%\n",
- sim);
-diff -c -N --recursive EMBOSS-6.0.1old/nucleus/embaln.c EMBOSS-6.0.1/nucleus/embaln.c
-*** EMBOSS-6.0.1old/nucleus/embaln.c 2008-07-15 15:41:05.000000000 +0100
---- EMBOSS-6.0.1/nucleus/embaln.c 2009-05-14 15:34:27.000000000 +0100
-***************
-*** 69,79 ****
- ajint i;
- ajint j;
-
-! float match;
-! float mscore;
-! float fnew;
-! float *maxa;
-! float maxb;
-
- static AjPStr outstr = NULL;
- char compasschar;
---- 69,79 ----
- ajint i;
- ajint j;
-
-! double match;
-! double mscore;
-! double fnew;
-! double *maxa;
-! double maxb;
-
- static AjPStr outstr = NULL;
- char compasschar;
-***************
-*** 84,90 ****
-
- /* Create stores for the maximum values in a row or column */
-
-! maxa = AJALLOC(lena*sizeof(float));
-
-
- /* First initialise the first column and row */
---- 84,90 ----
-
- /* Create stores for the maximum values in a row or column */
-
-! maxa = AJALLOC(lena*sizeof(double));
-
-
- /* First initialise the first column and row */
-***************
-*** 249,262 ****
- ajint i;
- ajint j;
-
-! float match;
-! float mscore;
-! float result;
-! float fnew;
-! float *maxa;
-
- static AjPStr outstr = NULL;
-! float bx;
- char compasschar;
-
- ajDebug("embAlignPathCalcSW\n");
---- 249,262 ----
- ajint i;
- ajint j;
-
-! double match;
-! double mscore;
-! double result;
-! double fnew;
-! double *maxa;
-
- static AjPStr outstr = NULL;
-! double bx;
- char compasschar;
-
- ajDebug("embAlignPathCalcSW\n");
-***************
-*** 265,271 ****
-
- /* Create stores for the maximum values in a row or column */
-
-! maxa = AJALLOC(lena*sizeof(float));
-
-
- /* First initialise the first column and row */
---- 265,271 ----
-
- /* Create stores for the maximum values in a row or column */
-
-! maxa = AJALLOC(lena*sizeof(double));
-
-
- /* First initialise the first column and row */
-***************
-*** 426,435 ****
- ajint i;
- ajint j;
- ajint k;
-! float pmax;
-! float score;
-! float gapcnt;
-! float bimble;
-
- ajint ix;
- ajint iy;
---- 426,435 ----
- ajint i;
- ajint j;
- ajint k;
-! ajint gapcnt;
-! double pmax;
-! double score;
-! double bimble;
-
- ajint ix;
- ajint iy;
-***************
-*** 439,451 ****
- const char *p;
- const char *q;
-
-! float ic;
-! float errbounds;
-
- ajDebug("embAlignWalkSWMatrix\n");
-
-! errbounds = gapextend;
-! errbounds = (float) 0.01;
-
- /* Get maximum path score and save position */
- pmax = -FLT_MAX;
---- 439,451 ----
- const char *p;
- const char *q;
-
-! ajint ic;
-! double errbounds;
-
- ajDebug("embAlignWalkSWMatrix\n");
-
-! /* errbounds = gapextend; */
-! errbounds = (double) 0.01;
-
- /* Get maximum path score and save position */
- pmax = -FLT_MAX;
-***************
-*** 480,486 ****
- else if(compass[ypos*lenb+xpos]==1) /* Left, gap(s) in vertical */
- {
- score = path[ypos*lenb+xpos];
-! gapcnt = 0.;
- ix = xpos-1;
- while(1)
- {
---- 480,486 ----
- else if(compass[ypos*lenb+xpos]==1) /* Left, gap(s) in vertical */
- {
- score = path[ypos*lenb+xpos];
-! gapcnt = 0;
- ix = xpos-1;
- while(1)
- {
-***************
-*** 504,510 ****
- else if(compass[ypos*lenb+xpos]==2) /* Down, gap(s) in horizontal */
- {
- score = path[ypos*lenb+xpos];
-! gapcnt = 0.;
- iy = ypos-1;
-
- while(1)
---- 504,510 ----
- else if(compass[ypos*lenb+xpos]==2) /* Down, gap(s) in horizontal */
- {
- score = path[ypos*lenb+xpos];
-! gapcnt = 0;
- iy = ypos-1;
-
- while(1)
-***************
-*** 575,584 ****
- {
- ajint i;
- ajint j;
-! float pmax;
-! float score;
-! float gapcnt;
-! float bimble;
-
- ajint ix;
- ajint iy;
---- 575,584 ----
- {
- ajint i;
- ajint j;
-! ajint gapcnt;
-! double pmax;
-! double score;
-! double bimble;
-
- ajint ix;
- ajint iy;
-***************
-*** 588,603 ****
- const char *p;
- const char *q;
-
-! float ic;
-! float errbounds;
-
- ajDebug("embAlignWalkNWMatrix\n");
-
-! errbounds=gapextend;
-! errbounds = (float) 0.01;
-
- /* Get maximum path axis score and save position */
-! pmax = (float) (-1*INT_MAX);
- for(i=0;i<lenb;++i)
- if(path[(lena-1)*lenb+i]>=pmax)
- {
---- 588,603 ----
- const char *p;
- const char *q;
-
-! ajint ic;
-! double errbounds;
-
- ajDebug("embAlignWalkNWMatrix\n");
-
-! /*errbounds=gapextend;*/
-! errbounds = (double) 0.01;
-
- /* Get maximum path axis score and save position */
-! pmax = (double) (-1*INT_MAX);
- for(i=0;i<lenb;++i)
- if(path[(lena-1)*lenb+i]>=pmax)
- {
-***************
-*** 631,637 ****
- else if(compass[ypos*lenb+xpos]==1) /* Left, gap(s) in vertical */
- {
- score = path[ypos*lenb+xpos];
-! gapcnt = 0.;
- ix = xpos-1;
- while(1)
- {
---- 631,637 ----
- else if(compass[ypos*lenb+xpos]==1) /* Left, gap(s) in vertical */
- {
- score = path[ypos*lenb+xpos];
-! gapcnt = 0;
- ix = xpos-1;
- while(1)
- {
-***************
-*** 652,658 ****
- else if(compass[ypos*lenb+xpos]==2) /* Down, gap(s) in horizontal */
- {
- score = path[ypos*lenb+xpos];
-! gapcnt = 0.;
- iy = ypos-1;
-
- while(1)
---- 652,658 ----
- else if(compass[ypos*lenb+xpos]==2) /* Down, gap(s) in horizontal */
- {
- score = path[ypos*lenb+xpos];
-! gapcnt = 0;
- iy = ypos-1;
-
- while(1)
-***************
-*** 1271,1281 ****
- ajint k;
- ajint ip; /* position in path matrix */
-
-! float match;
-! float mscore;
-! float fnew;
-! float maxa;
-! float *maxb;
-
- ajint jlena;
- ajint jlenb;
---- 1271,1281 ----
- ajint k;
- ajint ip; /* position in path matrix */
-
-! double match;
-! double mscore;
-! double fnew;
-! double maxa;
-! double *maxb;
-
- ajint jlena;
- ajint jlenb;
-***************
-*** 1288,1294 ****
- ajint xmax; /* last x position for this row */
- ajint ymax;
-
-! float max;
- static AjPStr outstr = NULL;
-
- char compasschar;
---- 1288,1294 ----
- ajint xmax; /* last x position for this row */
- ajint ymax;
-
-! double max;
- static AjPStr outstr = NULL;
-
- char compasschar;
-***************
-*** 1347,1353 ****
-
- /* Create stores for the maximum values in a row or column */
-
-! maxb = AJALLOC(lenb*sizeof(float));
-
- /* First initialise the first column and row */
- for(i=0;i<lena;++i)
---- 1347,1353 ----
-
- /* Create stores for the maximum values in a row or column */
-
-! maxb = AJALLOC(lenb*sizeof(double));
-
- /* First initialise the first column and row */
- for(i=0;i<lena;++i)
-***************
-*** 1379,1385 ****
- maxb[j] = path[j]-(gapopen);
-
- for(j=rightwidth;j<lenb;++j)
-! maxb[j] = (float) -999.9;
-
- /* ajDebug("2 %d %d\n",lena,lenb);*/
-
---- 1379,1385 ----
- maxb[j] = path[j]-(gapopen);
-
- for(j=rightwidth;j<lenb;++j)
-! maxb[j] = (double) -999.9;
-
- /* ajDebug("2 %d %d\n",lena,lenb);*/
-
-***************
-*** 1540,1549 ****
- ajint j;
- ajint k;
- ajint ip; /* position in path matrix */
-! float pmax;
-! float score;
-! float gapcnt;
-! float bimble;
-
- ajint ix;
- ajint iy;
---- 1540,1549 ----
- ajint j;
- ajint k;
- ajint ip; /* position in path matrix */
-! ajint gapcnt;
-! double pmax;
-! double score;
-! double bimble;
-
- ajint ix;
- ajint iy;
-***************
-*** 1554,1561 ****
- const char *p;
- const char *q;
-
-! float ic;
-! float errbounds;
-
- ajint width;
- ajint leftwidth;
---- 1554,1561 ----
- const char *p;
- const char *q;
-
-! ajint ic;
-! double errbounds;
-
- ajint width;
- ajint leftwidth;
-***************
-*** 1567,1573 ****
-
- ajDebug("embAlignWalkSWMatrixFast\n");
-
-! errbounds = (float) 0.01;
- width = pathwidth;
-
- if(lena < width)
---- 1567,1573 ----
-
- ajDebug("embAlignWalkSWMatrixFast\n");
-
-! errbounds = (double) 0.01;
- width = pathwidth;
-
- if(lena < width)
-***************
-*** 1633,1639 ****
- else if(compass[ip]==1) /* Left, horizontal gap(s): step through xpos */
- {
- score = path[ip];
-! gapcnt = 0.;
- ix = xpos-1;
- while(1)
- {
---- 1633,1639 ----
- else if(compass[ip]==1) /* Left, horizontal gap(s): step through xpos */
- {
- score = path[ip];
-! gapcnt = 0;
- ix = xpos-1;
- while(1)
- {
-***************
-*** 1661,1667 ****
- else if(compass[ip]==2) /* Down, vertical gap(s): step through ypos */
- {
- score = path[ip];
-! gapcnt = 0.;
- iy = ypos-1;
-
- while(1)
---- 1661,1667 ----
- else if(compass[ip]==2) /* Down, vertical gap(s): step through ypos */
- {
- score = path[ip];
-! gapcnt = 0;
- iy = ypos-1;
-
- while(1)
-***************
-*** 1735,1750 ****
-
- static AjPStr outstr = NULL;
-
-! float fmscore;
-! float mscore;
-! float fnew;
-! float maxp;
-! float *maxs;
-
- ret = -FLT_MAX;
- ajDebug("embAlignProfilePathCalc\n");
-
-! maxs = AJALLOC(seqlen*sizeof(float));
-
- /* First initialise the first column and row */
- for(column=0;column<seqlen;++column)
---- 1735,1750 ----
-
- static AjPStr outstr = NULL;
-
-! double fmscore;
-! double mscore;
-! double fnew;
-! double maxp;
-! double *maxs;
-
- ret = -FLT_MAX;
- ajDebug("embAlignProfilePathCalc\n");
-
-! maxs = AJALLOC(seqlen*sizeof(double));
-
- /* First initialise the first column and row */
- for(column=0;column<seqlen;++column)
-***************
-*** 1889,1899 ****
- ajint *start1, ajint *start2)
- {
- ajint i;
-- float pathmax;
-- float score;
--
- ajint gapcnt;
-! float bimble;
-
- ajint ix;
- ajint iy;
---- 1889,1899 ----
- ajint *start1, ajint *start2)
- {
- ajint i;
- ajint gapcnt;
-! double pathmax;
-! double score;
-!
-! double bimble;
-
- ajint ix;
- ajint iy;
-***************
-*** 1909,1922 ****
- const char *p;
- const char *q;
-
-! float errbounds;
-
- ajDebug("embAlignWalkProfileMatrix\n");
-
-! errbounds = (float) 0.01;
-
- /* Get maximum path score and save position */
-! pathmax = -(float) INT_MAX;
- for(row=0;row<proflen;++row)
- for(column=0;column<seqlen;++column)
- if(path[row*seqlen+column] > pathmax)
---- 1909,1922 ----
- const char *p;
- const char *q;
-
-! double errbounds;
-
- ajDebug("embAlignWalkProfileMatrix\n");
-
-! errbounds = (double) 0.01;
-
- /* Get maximum path score and save position */
-! pathmax = -(double) INT_MAX;
- for(row=0;row<proflen;++row)
- for(column=0;column<seqlen;++column)
- if(path[row*seqlen+column] > pathmax)
-diff -c -N --recursive EMBOSS-6.0.1old/nucleus/embprop.c EMBOSS-6.0.1/nucleus/embprop.c
-*** EMBOSS-6.0.1old/nucleus/embprop.c 2008-07-14 23:13:33.000000000 +0100
---- EMBOSS-6.0.1/nucleus/embprop.c 2009-05-14 15:34:27.000000000 +0100
-***************
-*** 880,885 ****
---- 880,886 ----
-
- if(allpartials)
- {
-+ lim = defcnt;
- for(i=0;i<lim;++i)
- for(j=i+1;j<lim;++j)
- {
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