AjBool ensIntronTrace(const EnsPIntron intron, ajuint level)
{
AjPStr indent = NULL;
if(!intron)
return ajFalse;
indent = ajStrNew();
ajStrAppendCountK(&indent, ' ', level * 2);
ajDebug("%SensIntronTrace %p\n"
"%S Feature %p\n"
"%S PreviousExon %p\n"
"%S NextExon %p\n"
"%S Use %u\n",
indent, intron,
indent, intron->Feature,
indent, intron->PreviousExon,
indent, intron->NextExon,
indent, intron->Use);
ensFeatureTrace(intron->Feature, level + 1);
ensExonTrace(intron->PreviousExon, level + 1);
ensExonTrace(intron->NextExon, level + 1);
ajStrDel(&indent);
return ajTrue;
}
AjBool ensProjectionsegmentTrace(const EnsPProjectionsegment ps, ajuint level)
{
AjPStr indent = NULL;
if(!ps)
return ajFalse;
indent = ajStrNew();
ajStrAppendCountK(&indent, ' ', level * 2);
ajDebug("%SensProjectionsegmentTrace %p\n"
"%S SrcStart %d\n"
"%S SrcEnd %d\n"
"%S TrgSlice %p\n"
"%S Use %u\n",
indent, ps,
indent, ps->SrcStart,
indent, ps->SrcEnd,
indent, ps->TrgSlice,
indent, ps->Use);
ensSliceTrace(ps->TrgSlice, level + 1);
ajStrDel(&indent);
return ajTrue;
}
AjBool ensGvdatabaseadaptorTrace(const EnsPGvdatabaseadaptor gvdba,
ajuint level)
{
AjPStr indent = NULL;
if (!gvdba)
return ajFalse;
indent = ajStrNew();
ajStrAppendCountK(&indent, ' ', level * 2);
ajDebug("%SensGvdatabaseadaptorTrace %p\n"
"%S Databaseadaptor %p\n"
"%S Failedvariations '%B'\n",
indent, gvdba,
indent, gvdba->Adaptor,
indent, gvdba->Failedvariations);
ensDatabaseadaptorTrace(gvdba->Adaptor, level + 1);
ajStrDel(&indent);
return ajTrue;
}
AjBool ensKaryotypebandTrace(const EnsPKaryotypeband kb, ajuint level)
{
AjPStr indent = NULL;
if(!kb)
return ajFalse;
indent = ajStrNew();
ajStrAppendCountK(&indent, ' ', level * 2);
ajDebug("%SensKaryotypebandTrace %p\n"
"%S Adaptor %p\n"
"%S Identifier %u\n"
"%S Feature %p\n"
"%S Name '%S'\n"
"%S Stain '%S'\n",
indent, kb,
indent, kb->Adaptor,
indent, kb->Identifier,
indent, kb->Feature,
indent, kb->Name,
indent, kb->Stain);
ensFeatureTrace(kb->Feature, 1);
ajStrDel(&indent);
return ajTrue;
}
AjBool ensCacheTrace(const EnsPCache cache, ajuint level)
{
double ratio = 0.0;
AjPStr indent = NULL;
if(!cache)
return ajFalse;
indent = ajStrNew();
ajStrAppendCountK(&indent, ' ', level * 2);
if(cache->Hit || cache->Miss)
ratio = (double) cache->Hit /
((double) cache->Hit + (double) cache->Miss);
ajDebug("%SensCache trace %p\n"
"%S Label '%S'\n"
"%S List %p length: %u\n"
"%S Table %p length: %u\n"
"%S Type %d\n"
"%S Synchron %B\n"
"%S MaxBytes %u\n"
"%S MaxCount %u\n"
"%S MaxSize %u\n"
"%S Bytes %u\n"
"%S Count %u\n"
"%S Dropped %u\n"
"%S Removed %u\n"
"%S Stored %u\n"
"%S Hit %u\n"
"%S Miss %u\n"
"%S Hit/(Hit + Miss) %f\n",
indent, cache,
indent, cache->Label,
indent, cache->List, ajListGetLength(cache->List),
indent, cache->Table, ajTableGetLength(cache->Table),
indent, cache->Type,
indent, cache->Synchron,
indent, cache->MaxBytes,
indent, cache->MaxCount,
indent, cache->MaxSize,
indent, cache->Bytes,
indent, cache->Count,
indent, cache->Dropped,
indent, cache->Removed,
indent, cache->Stored,
indent, cache->Hit,
indent, cache->Miss,
indent, ratio);
ajStrDel(&indent);
return ajTrue;
}
AjBool ensAssemblyexceptionTrace(const EnsPAssemblyexception ae, ajuint level)
{
AjPStr indent = NULL;
if(!ae)
return ajFalse;
indent = ajStrNew();
ajStrAppendCountK(&indent, ' ', level * 2);
ajDebug("%SensAssemblyexceptionTrace %p\n"
"%S Identifier %u\n"
"%S SeqregionIdentifier %u\n"
"%S SeqregionStart %u\n"
"%S SeqregionEnd %u\n"
"%S ExcSeqregionIdentifier %u\n"
"%S ExcRegionStart %d\n"
"%S ExcRegionEnd %u\n"
"%S Orientation %d\n"
"%S Type '%s'\n"
"%S Use %u\n",
indent, ae,
indent, ae->Identifier,
indent, ae->SeqregionIdentifier,
indent, ae->SeqregionStart,
indent, ae->SeqregionEnd,
indent, ae->ExcRegionIdentifier,
indent, ae->ExcRegionStart,
indent, ae->ExcRegionEnd,
indent, ensAssemblyexceptionTypeToChar(ae->Type),
indent, ae->Orientation,
indent, ae->Use);
ajStrDel(&indent);
return ajTrue;
}
AjBool ensGvsynonymTrace(const EnsPGvsynonym gvs, ajuint level)
{
AjPStr indent = NULL;
if (!gvs)
return ajFalse;
indent = ajStrNew();
ajStrAppendCountK(&indent, ' ', level * 2);
ajDebug("%SensGvsynonymTrace %p\n"
"%S Use %u\n"
"%S Identifier %u\n"
"%S Adaptor %p\n"
"%S Gvsource %p\n"
"%S Name '%S'\n"
"%S Moleculetype '%S'\n"
"%S Gvvariationidentifier %u\n"
"%S Subidentifier %u\n",
indent, gvs,
indent, gvs->Use,
indent, gvs->Identifier,
indent, gvs->Adaptor,
indent, gvs->Gvsource,
indent, gvs->Name,
indent, gvs->Moleculetype,
indent, gvs->Gvvariationidentifier,
indent, gvs->Subidentifier);
ensGvsourceTrace(gvs->Gvsource, level + 1);
ajStrDel(&indent);
return ajTrue;
}
static void extractfeat_GetRegionPad(const AjPSeq seq, AjPStr *featstr,
ajint start, ajint end, AjBool sense,
AjBool beginning)
{
ajint tmp;
ajint pad;
AjPStr result;
ajDebug("In extractfeat_GetRegionPad start=%d, end=%d\n", start, end);
result = ajStrNew();
if(start > end)
return;
if(start < 0)
{
pad = -start;
if(ajSeqIsNuc(seq))
ajStrAppendCountK(&result, 'N', pad);
else
ajStrAppendCountK(&result, 'X', pad);
start = 0;
}
if(end > (ajint) ajSeqGetLen(seq)-1)
tmp = ajSeqGetLen(seq)-1;
else
tmp = end;
if(start <= (ajint) ajSeqGetLen(seq) && tmp >= 0)
{
ajDebug("Get subsequence %d-%d\n", start, tmp);
ajStrAppendSubS(&result, ajSeqGetSeqS(seq), start, tmp);
ajDebug("result=%S\n", result);
}
if(end > (ajint) ajSeqGetLen(seq)-1)
{
pad = end - ajSeqGetLen(seq)+1;
if(ajSeqIsNuc(seq))
ajStrAppendCountK(&result, 'N', pad);
else
ajStrAppendCountK(&result, 'X', pad);
ajDebug("result=%S\n", result);
}
/* if feature was in reverse sense, then get reverse complement */
if(!sense)
{
ajDebug("get reverse sense of subsequence\n");
ajSeqstrReverse(&result);
ajDebug("result=%S\n", result);
}
if(beginning)
{
ajDebug("Prepend to featstr: %S\n", result);
ajStrInsertS(featstr, 0, result);
}
else
{
ajDebug("Append to featstr: %S\n", result);
ajStrAppendS(featstr, result);
}
ajDebug("featstr=%S\n", *featstr);
ajStrDel(&result);
return;
}
AjBool ensSeqTrace(const AjPSeq seq, ajuint level)
{
AjPStr indent = NULL;
if(!seq)
return ajFalse;
indent = ajStrNew();
ajStrAppendCountK(&indent, ' ', level * 2);
ajDebug("%SensSeqTrace %p\n"
"%S Name '%S'\n"
"%S Acc '%S'\n"
"%S Sv '%S'\n"
"%S Gi '%S'\n"
"%S Tax '%S'\n"
"%S Taxid '%S'\n"
"%S Organelle '%S'\n"
"%S Type '%S'\n"
"%S Molecule '%S'\n"
"%S Class '%S'\n"
"%S Division '%S'\n"
"%S Evidence '%S'\n"
"%S Db '%S'\n"
"%S Setdb '%S'\n"
"%S Full '%S'\n"
"%S Date %p\n"
"%S Desc '%S'\n"
"%S Fulldesc %p\n"
"%S Doc '%S'\n"
"%S Usa '%S'\n"
"%S Ufo '%S'\n"
"%S Formatstr '%S'\n"
"%S Filename '%S'\n"
"%S Entryname '%S'\n"
"%S TextPtr '%S'\n"
"%S Acclist %p\n"
"%S Keylist %p\n"
"%S Taxlist %p\n"
"%S Genelist %p\n"
"%S Reflist %p\n"
"%S Cmtlist %p\n"
"%S Xreflist %p\n"
"%S Seq %p\n"
"%S Fttable %p\n"
"%S Accuracy %p\n"
"%S Fpos %Lu\n"
"%S Rev '%B'\n"
"%S Reversed '%B'\n"
"%S Trimmed '%B'\n"
"%S Circular '%B'\n"
"%S Begin %d\n"
"%S End %d\n"
"%S Offset %u\n"
"%S Offend %u\n"
"%S Qualsize %u\n"
"%S Weight %f\n"
"%S Format %d\n"
"%S Etype %d\n",
indent, seq,
indent, seq->Name,
indent, seq->Acc,
indent, seq->Sv,
indent, seq->Gi,
indent, seq->Tax,
indent, seq->Taxid,
indent, seq->Organelle,
indent, seq->Type,
indent, seq->Molecule,
indent, seq->Type,
indent, seq->Division,
indent, seq->Evidence,
indent, seq->Db,
indent, seq->Setdb,
indent, seq->Full,
indent, seq->Date,
indent, seq->Desc,
indent, seq->Fulldesc,
indent, seq->Doc,
indent, seq->Usa,
indent, seq->Ufo,
indent, seq->Formatstr,
indent, seq->Filename,
indent, seq->Entryname,
indent, seq->TextPtr,
indent, seq->Acclist,
indent, seq->Keylist,
indent, seq->Taxlist,
indent, seq->Genelist,
indent, seq->Reflist,
indent, seq->Cmtlist,
indent, seq->Xreflist,
indent, seq->Seq,
indent, seq->Fttable,
indent, seq->Accuracy,
indent, seq->Fpos,
indent, seq->Rev,
indent, seq->Reversed,
indent, seq->Trimmed,
indent, seq->Circular,
indent, seq->Begin,
indent, seq->End,
indent, seq->Offset,
indent, seq->Offend,
indent, seq->Qualsize,
indent, seq->Weight,
indent, seq->Format,
indent, seq->EType);
ajStrDel(&indent);
return ajTrue;
}
AjBool ensSeqDescTrace(const AjPSeqDesc seqdesc, ajuint level)
{
AjIList iter = NULL;
AjPStr indent = NULL;
AjPStr value = NULL;
if(!seqdesc)
return ajFalse;
indent = ajStrNew();
ajStrAppendCountK(&indent, ' ', level * 2);
ajDebug("%SensSeqDescTrace %p\n"
"%S Name '%S'\n"
"%S Short %p\n"
"%S EC %p\n"
"%S AltNames %p\n"
"%S SubNames %p\n"
"%S Includes %p\n"
"%S Contains %p\n"
"%S Precursor '%B'\n"
"%S Fragments %u\n",
indent, seqdesc,
indent, seqdesc->Name,
indent, seqdesc->Short,
indent, seqdesc->EC,
indent, seqdesc->AltNames,
indent, seqdesc->SubNames,
indent, seqdesc->Includes,
indent, seqdesc->Contains,
indent, seqdesc->Precursor,
indent, seqdesc->Fragments);
/* Trace the AJAX List of AJAX String short names. */
if(seqdesc->Short)
{
ajDebug("%S AJAX List of AJAX String short names:\n", indent);
iter = ajListIterNew(seqdesc->Short);
while(!ajListIterDone(iter))
{
value = (AjPStr) ajListIterGet(iter);
ajDebug("%S '%S'\n", indent, value);
}
ajListIterDel(&iter);
}
/* Trace the AJAX List of AJAX String EC numbers. */
if(seqdesc->EC)
{
ajDebug("%S AJAX List of AJAX String EC numbers:\n", indent);
iter = ajListIterNew(seqdesc->EC);
while(!ajListIterDone(iter))
{
value = (AjPStr) ajListIterGet(iter);
ajDebug("%S '%S'\n", indent, value);
}
ajListIterDel(&iter);
}
ajStrDel(&indent);
return ajTrue;
}
AjBool ensSeqQueryTrace(const AjPSeqQuery seqquery, ajuint level)
{
AjPStr indent = NULL;
indent = ajStrNew();
ajStrAppendCountK(&indent, ' ', level * 2);
ajDebug("%SensSeqQueryTrace %p\n"
"%S DbName '%S'\n"
"%S DbAlias '%S'\n"
"%S DbType '%S'\n"
"%S Id '%S'\n"
"%S Acc '%S'\n"
"%S Des '%S'\n"
"%S Key '%S'\n"
"%S Org '%S'\n"
"%S Sv '%S'\n"
"%S Gi '%S'\n"
"%S CaseId '%B'\n"
"%S HasAcc '%B'\n"
"%S Method '%S'\n"
"%S Formatstr '%S'\n"
"%S IndexDir '%S'\n"
"%S Directory '%S'\n"
"%S Filename '%S'\n"
"%S Exclude '%S'\n"
"%S DbFields '%S'\n"
"%S DbFilter '%S'\n"
"%S DbProxy '%S'\n"
"%S DbHttpVer '%S'\n"
"%S DbIdentifier '%S'\n"
"%S DbAccession '%S'\n"
"%S DbSequence '%S'\n"
"%S DbReturn '%S'\n"
"%S Field '%S'\n"
"%S QryString '%S'\n"
"%S Application '%S'\n"
"%S Fpos %Ld\n"
"%S Type %d\n"
"%S QryDone '%B'\n"
"%S Access %p\n"
"%S QryData %p\n"
"%S Wild '%B'\n",
indent, seqquery,
indent, seqquery->DbName,
indent, seqquery->DbAlias,
indent, seqquery->DbType,
indent, seqquery->Id,
indent, seqquery->Acc,
indent, seqquery->Des,
indent, seqquery->Key,
indent, seqquery->Org,
indent, seqquery->Sv,
indent, seqquery->Gi,
indent, seqquery->CaseId,
indent, seqquery->HasAcc,
indent, seqquery->Method,
indent, seqquery->Formatstr,
indent, seqquery->IndexDir,
indent, seqquery->Directory,
indent, seqquery->Filename,
indent, seqquery->Exclude,
indent, seqquery->DbFields,
indent, seqquery->DbFilter,
indent, seqquery->DbProxy,
indent, seqquery->DbHttpVer,
indent, seqquery->DbIdentifier,
indent, seqquery->DbAccession,
indent, seqquery->DbSequence,
indent, seqquery->DbReturn,
indent, seqquery->Field,
indent, seqquery->QryString,
indent, seqquery->Application,
indent, seqquery->Fpos,
indent, seqquery->Type,
indent, seqquery->QryDone,
indent, seqquery->Access,
indent, seqquery->QryData,
indent, seqquery->Wild);
ajStrDel(&indent);
return ajTrue;
}
AjBool ensSeqinTrace(const AjPSeqin seqin, ajuint level)
{
AjPStr indent = NULL;
indent = ajStrNew();
ajStrAppendCountK(&indent, ' ', level * 2);
ajDebug("%SensSeqinTrace %p\n"
"%S Name '%S'\n"
"%S Acc '%S'\n"
"%S Inputtype '%S'\n"
"%S Type '%S'\n"
"%S Db '%S'\n"
"%S Full '%S'\n"
"%S Date '%S'\n"
"%S Desc '%S'\n"
"%S Doc '%S'\n"
"%S Inseq '%S'\n"
"%S Begin %d\n"
"%S End %d\n"
"%S List %p\n"
"%S Usa '%S'\n"
"%S Ufo '%S'\n"
"%S Fttable %p\n"
"%S Ftquery %p\n"
"%S Formatstr '%S'\n"
"%S Filename '%S'\n"
"%S Entryname '%S'\n"
"%S Filebuff %p\n"
"%S Search '%B'\n"
"%S Single '%B'\n"
"%S CaseId '%B'\n"
"%S Features '%B'\n"
"%S IsNuc '%B'\n"
"%S IsProt '%B'\n"
"%S multi '%B'\n"
"%S multiset '%B'\n"
"%S multidone '%B'\n"
"%S Lower '%B'\n"
"%S Upper '%B'\n"
"%S Text '%B'\n"
"%S Count %d\n"
"%S Filecount %d\n"
"%S Fileseqs %d\n"
"%S Rev '%B'\n"
"%S Fpos %Ld\n"
"%S Query %p\n"
"%S Data %p\n"
"%S Format %d\n"
"%S Records %u\n",
indent, seqin,
indent, seqin->Name,
indent, seqin->Acc,
indent, seqin->Inputtype,
indent, seqin->Type,
indent, seqin->Db,
indent, seqin->Full,
indent, seqin->Date,
indent, seqin->Desc,
indent, seqin->Doc,
indent, seqin->Inseq,
indent, seqin->Begin,
indent, seqin->End,
indent, seqin->List,
indent, seqin->Usa,
indent, seqin->Ufo,
indent, seqin->Fttable,
indent, seqin->Ftquery,
indent, seqin->Formatstr,
indent, seqin->Filename,
indent, seqin->Entryname,
indent, seqin->Filebuff,
indent, seqin->Search,
indent, seqin->Single,
indent, seqin->CaseId,
indent, seqin->Features,
indent, seqin->IsNuc,
indent, seqin->IsProt,
indent, seqin->multi,
indent, seqin->multiset,
indent, seqin->multidone,
indent, seqin->Lower,
indent, seqin->Upper,
indent, seqin->Text,
indent, seqin->Count,
indent, seqin->Filecount,
indent, seqin->Fileseqs,
indent, seqin->Rev,
indent, seqin->Fpos,
indent, seqin->Query,
indent, seqin->Data,
indent, seqin->Format,
indent, seqin->Records);
ajStrDel(&indent);
ensSeqQueryTrace(seqin->Query, level + 1);
return ajTrue;
}
int main(int argc, char **argv)
{
AjPSeqset seqset;
AjPSeqall seqall;
AjPSeq queryseq;
const AjPSeq targetseq;
ajint wordlen;
AjPTable wordsTable = NULL;
AjPList* matchlist = NULL;
AjPFile logfile;
AjPFeattable* seqsetftables = NULL;
AjPFeattable seqallseqftable = NULL;
AjPFeattabOut ftoutforseqsetseq = NULL;
AjPFeattabOut ftoutforseqallseq = NULL;
AjPAlign align = NULL;
AjIList iter = NULL;
ajint targetstart;
ajint querystart;
ajint len;
ajuint i, j;
ajulong nAllMatches = 0;
ajulong sumAllScore = 0;
AjBool dumpAlign = ajTrue;
AjBool dumpFeature = ajTrue;
AjBool checkmode = ajFalse;
EmbPWordRK* wordsw = NULL;
ajuint npatterns = 0;
ajuint seqsetsize;
ajuint nmatches;
ajuint* nmatchesseqset;
ajuint* lastlocation; /* Cursors for Rabin-Karp search. */
/* Shows until what point the query sequence was
* scanned for a pattern sequences in the seqset.
*/
char* paddedheader = NULL;
const char* header;
AjPStr padding;
header = "Pattern %S #pat-sequences #all-matches avg-match-length\n";
padding = ajStrNew();
embInit("wordmatch", argc, argv);
wordlen = ajAcdGetInt("wordsize");
seqset = ajAcdGetSeqset("asequence");
seqall = ajAcdGetSeqall("bsequence");
logfile = ajAcdGetOutfile("logfile");
dumpAlign = ajAcdGetToggle("dumpalign");
dumpFeature = ajAcdGetToggle("dumpfeat");
if(dumpAlign)
{
align = ajAcdGetAlign("outfile");
ajAlignSetExternal(align, ajTrue);
}
seqsetsize = ajSeqsetGetSize(seqset);
ajSeqsetTrim(seqset);
AJCNEW0(matchlist, seqsetsize);
AJCNEW0(seqsetftables, seqsetsize);
AJCNEW0(nmatchesseqset, seqsetsize);
if (dumpFeature)
{
ftoutforseqsetseq = ajAcdGetFeatout("aoutfeat");
ftoutforseqallseq = ajAcdGetFeatout("boutfeat");
}
checkmode = !dumpFeature && !dumpAlign;
embWordLength(wordlen);
ajFmtPrintF(logfile, "Small sequence/file for constructing"
" target patterns: %S\n", ajSeqsetGetUsa(seqset));
ajFmtPrintF(logfile, "Large sequence/file to be scanned"
" for patterns: %S\n", ajSeqallGetUsa(seqall));
ajFmtPrintF(logfile, "Number of sequences in the patterns file: %u\n",
seqsetsize);
ajFmtPrintF(logfile, "Pattern/word length: %u\n", wordlen);
for(i=0;i<seqsetsize;i++)
{
targetseq = ajSeqsetGetseqSeq(seqset, i);
embWordGetTable(&wordsTable, targetseq);
}
AJCNEW0(lastlocation, seqsetsize);
if(ajTableGetLength(wordsTable)>0)
{
npatterns = embWordRabinKarpInit(wordsTable,
&wordsw, wordlen, seqset);
ajFmtPrintF(logfile, "Number of patterns/words found: %u\n", npatterns);
while(ajSeqallNext(seqall,&queryseq))
{
for(i=0;i<seqsetsize;i++)
{
lastlocation[i]=0;
if (!checkmode)
matchlist[i] = ajListstrNew();
}
nmatches = embWordRabinKarpSearch(
ajSeqGetSeqS(queryseq), seqset,
(EmbPWordRK const *)wordsw, wordlen, npatterns,
matchlist, lastlocation, checkmode);
nAllMatches += nmatches;
if (checkmode)
continue;
for(i=0;i<seqsetsize;i++)
{
if(ajListGetLength(matchlist[i])>0)
{
iter = ajListIterNewread(matchlist[i]) ;
while(embWordMatchIter(iter, &targetstart, &querystart, &len,
&targetseq))
{
if(dumpAlign)
{
ajAlignDefineSS(align, targetseq, queryseq);
ajAlignSetScoreI(align, len);
/* ungapped alignment means same length
* for both sequences
*/
ajAlignSetSubRange(align, targetstart, 1, len,
ajSeqIsReversed(targetseq),
ajSeqGetLen(targetseq),
querystart, 1, len,
ajSeqIsReversed(queryseq),
ajSeqGetLen(queryseq));
}
}
if(dumpAlign)
{
ajAlignWrite(align);
ajAlignReset(align);
}
if(ajListGetLength(matchlist[i])>0 && dumpFeature)
{
embWordMatchListConvToFeat(matchlist[i],
&seqsetftables[i],
&seqallseqftable,
targetseq, queryseq);
ajFeattableWrite(ftoutforseqallseq, seqallseqftable);
ajFeattableDel(&seqallseqftable);
}
ajListIterDel(&iter);
}
embWordMatchListDelete(&matchlist[i]);
}
}
/* search completed, now report statistics */
for(i=0;i<npatterns;i++)
{
sumAllScore += wordsw[i]->lenMatches;
for(j=0;j<wordsw[i]->nseqs;j++)
nmatchesseqset[wordsw[i]->seqindxs[j]] +=
wordsw[i]->nSeqMatches[j];
}
ajFmtPrintF(logfile, "Number of sequences in the file scanned "
"for patterns: %u\n", ajSeqallGetCount(seqall));
ajFmtPrintF(logfile, "Number of all matches: %Lu"
" (wordmatch finds exact matches only)\n", nAllMatches);
if(nAllMatches>0)
{
ajFmtPrintF(logfile, "Sum of match lengths: %Lu\n", sumAllScore);
ajFmtPrintF(logfile, "Average match length: %.2f\n",
sumAllScore*1.0/nAllMatches);
ajFmtPrintF(logfile, "\nDistribution of the matches among pattern"
" sequences:\n");
ajFmtPrintF(logfile, "-----------------------------------------"
"-----------\n");
for(i=0;i<ajSeqsetGetSize(seqset);i++)
{
if (nmatchesseqset[i]>0)
ajFmtPrintF(logfile, "%-42s: %8u\n",
ajSeqGetNameC(ajSeqsetGetseqSeq(seqset, i)),
nmatchesseqset[i]);
ajFeattableWrite(ftoutforseqsetseq, seqsetftables[i]);
ajFeattableDel(&seqsetftables[i]);
}
ajFmtPrintF(logfile, "\nPattern statistics:\n");
ajFmtPrintF(logfile, "-------------------\n");
if(wordlen>7)
ajStrAppendCountK(&padding, ' ', wordlen-7);
paddedheader = ajFmtString(header,padding);
ajFmtPrintF(logfile, paddedheader);
for(i=0;i<npatterns;i++)
if (wordsw[i]->nMatches>0)
ajFmtPrintF(logfile, "%-7s: %12u %12u %17.2f\n",
wordsw[i]->word->fword, wordsw[i]->nseqs,
wordsw[i]->nMatches,
wordsw[i]->lenMatches*1.0/wordsw[i]->nMatches);
}
}
for(i=0;i<npatterns;i++)
{
for(j=0;j<wordsw[i]->nseqs;j++)
AJFREE(wordsw[i]->locs[j]);
AJFREE(wordsw[i]->locs);
AJFREE(wordsw[i]->seqindxs);
AJFREE(wordsw[i]->nnseqlocs);
AJFREE(wordsw[i]->nSeqMatches);
AJFREE(wordsw[i]);
}
embWordFreeTable(&wordsTable);
AJFREE(wordsw);
AJFREE(matchlist);
AJFREE(lastlocation);
AJFREE(nmatchesseqset);
AJFREE(seqsetftables);
if(dumpAlign)
{
ajAlignClose(align);
ajAlignDel(&align);
}
if(dumpFeature)
{
ajFeattabOutDel(&ftoutforseqsetseq);
ajFeattabOutDel(&ftoutforseqallseq);
}
ajFileClose(&logfile);
ajSeqallDel(&seqall);
ajSeqsetDel(&seqset);
ajSeqDel(&queryseq);
ajStrDel(&padding);
AJFREE(paddedheader);
embExit();
return 0;
}
