void ajCallExit(void)
{
ajTableMapDel(callTable, callItemDel, NULL);
ajTableMapDel(oldcallTable, callItemDel, NULL);
ajTableMapDel(oldcallCount, callCountDel, NULL);
ajTableFree(&callTable);
ajTableFree(&oldcallTable);
ajTableFree(&oldcallCount);
return;
}
static void remap_DelTable(AjPTable * table)
{
void **keyarray = NULL; /* array for table */
void **valarray = NULL; /* array for table */
ajint i;
PValue value;
if(ajTableGetLength(*table))
{
ajTableToarrayKeysValues(*table, &keyarray, &valarray);
for(i = 0; keyarray[i]; i++)
{
value = (PValue) valarray[i];
ajStrDel(&(value->iso));
AJFREE(valarray[i]); /* free the ajint* value */
ajStrDel((AjPStr*)&keyarray[i]);
}
AJFREE(keyarray);
AJFREE(valarray);
}
ajTableFree(table);
return;
}
static void messTableDelete(AjPTable* table)
{
void **keyarray = NULL;
void **valarray = NULL;
ajint i;
if(!table)
return;
if(!*table)
return;
ajTableToarrayKeysValues(*table, &keyarray, &valarray);
for(i = 0; keyarray[i]; i++)
{
AJFREE(keyarray[i]);
AJFREE(valarray[i]);
}
AJFREE(keyarray);
AJFREE(valarray);
ajTableFree(table);
*table = NULL;
return;
}
static AjBool assemblyexceptionadaptorCacheExit(
EnsPAssemblyexceptionadaptor aea)
{
if(!aea)
return ajFalse;
if(!aea->CacheBySeqregionIdentifier)
return ajTrue;
ajTableMapDel(aea->CacheBySeqregionIdentifier,
assemblyexceptionadaptorClearIdentifierCache,
NULL);
ajTableFree(&aea->CacheBySeqregionIdentifier);
return ajTrue;
}
int main(int argc, char **argv)
{
AjPSeqall seqall;
AjPSeq seq = NULL;
AjPReport report = NULL;
AjPStr jaspdir = NULL;
AjPStr menu = NULL;
AjPStr substr = NULL;
AjPStr mats = NULL;
AjPStr excl = NULL;
float thresh = 0.;
ajuint recurs = 0;
AjPStr dir = NULL;
AjPStr mfname = NULL;
AjPList flist = NULL;
AjPList hits = NULL;
AjPStr head = NULL;
ajint begin;
ajint end;
ajuint mno;
char cp;
ajuint i;
AjPTable mattab = NULL;
AjPFeattable TabRpt = NULL;
AjBool both = ajFalse;
embInit("jaspscan", argc, argv);
seqall = ajAcdGetSeqall("sequence");
menu = ajAcdGetListSingle("menu");
mats = ajAcdGetString("matrices");
excl = ajAcdGetString("exclude");
thresh = ajAcdGetFloat("threshold");
report = ajAcdGetReport("outfile");
both = ajAcdGetBoolean("both");
jaspdir = ajStrNew();
substr = ajStrNew();
flist = ajListNew();
hits = ajListNew();
dir = ajStrNew();
head = ajStrNew();
cp = ajStrGetCharFirst(menu);
if(cp=='C')
ajStrAssignC(&jaspdir,J_COR);
else if(cp=='F')
ajStrAssignC(&jaspdir,J_FAM);
else if(cp=='P')
ajStrAssignC(&jaspdir,J_PHY);
else if(cp=='N')
ajStrAssignC(&jaspdir,J_CNE);
else if(cp=='O')
ajStrAssignC(&jaspdir,J_POL);
else if(cp=='S')
ajStrAssignC(&jaspdir,J_SPL);
else
ajFatal("Invalid JASPAR database selection");
ajStrAssignS(&dir, ajDatafileValuePath());
if(!ajStrGetLen(dir))
ajFatal("EMBOSS DATA directory couldn't be determined");
jaspscan_ParseInput(dir, jaspdir, mats, excl, &recurs, flist);
mno = ajListGetLength(flist);
if(cp == 'C')
mattab = jaspscan_ReadCoreList(jaspdir);
if(cp == 'F')
mattab = jaspscan_ReadFamList(jaspdir);
if(cp == 'P')
mattab = jaspscan_ReadCoreList(jaspdir);
if(cp == 'N')
mattab = jaspscan_ReadCoreList(jaspdir);
if(cp == 'O')
mattab = jaspscan_ReadCoreList(jaspdir);
if(cp == 'S')
mattab = jaspscan_ReadCoreList(jaspdir);
ajFmtPrintS(&head,"Database scanned: %S Threshold: %.3f",jaspdir,thresh);
ajReportSetHeaderS(report,head);
while(ajSeqallNext(seqall, &seq))
{
begin = ajSeqallGetseqBegin(seqall);
end = ajSeqallGetseqEnd(seqall);
ajStrAssignSubC(&substr,ajSeqGetSeqC(seq),begin-1,end-1);
ajStrFmtUpper(&substr);
TabRpt = ajFeattableNewSeq(seq);
for(i=0; i < mno; ++i)
{
ajListPop(flist,(void **)&mfname);
jaspscan_scan(substr,begin,mfname, cp, thresh, both, hits);
ajListPushAppend(flist, (void **)mfname);
}
jaspscan_ReportHits(TabRpt,mattab,hits);
ajReportWrite(report, TabRpt, seq);
ajFeattableDel(&TabRpt);
}
while(ajListPop(flist,(void **)&mfname))
ajStrDel(&mfname);
ajStrDel(&dir);
ajStrDel(&menu);
ajStrDel(&excl);
ajStrDel(&substr);
ajStrDel(&mats);
ajStrDel(&head);
ajStrDel(&jaspdir);
ajSeqDel(&seq);
ajTableMapDel(mattab,jaspscan_ClearTable,NULL);
ajTableFree(&mattab);
ajListFree(&flist);
ajListFree(&hits);
ajSeqallDel(&seqall);
ajReportDel(&report);
embExit();
return 0;
}
void ensCacheDel(EnsPCache* Pcache)
{
AjBool debug = AJFALSE;
EnsPCache pthis = NULL;
CachePNode node = NULL;
if(!Pcache)
return;
if(!*Pcache)
return;
debug = ajDebugTest("ensCacheDel");
if(debug)
ajDebug("ensCacheDel\n"
" *Pcache %p\n",
*Pcache);
pthis = *Pcache;
/* Remove nodes from the AJAX List. */
while(ajListPop(pthis->List, (void **) &node))
{
/* Remove the node from the AJAX Table. */
ajTableRemove(pthis->Table, node->Key);
/* Update the cache statistics. */
pthis->Count--;
pthis->Bytes -= node->Bytes;
/* Write changes of value data to disk if any. */
if(pthis->Write && node->Value && node->Dirty)
(*pthis->Write)(node->Value);
/* Both, key and value data are deleted via cacheNodeDel. */
cacheNodeDel(pthis, &node);
}
if(debug)
ensCacheTrace(pthis, 1);
ajStrDel(&pthis->Label);
ajListFree(&pthis->List);
ajTableFree(&pthis->Table);
AJFREE(pthis);
*Pcache = NULL;
return;
}
int main(int argc, char **argv)
{
const char *codons[]=
{
"TAG","TAA","TGA","GCG","GCA","GCT","GCC","TGT", /* 00-07 */
"TGC","GAT","GAC","GAA","GAG","TTT","TTC","GGT", /* 08-15 */
"GGG","GGA","GGC","CAT","CAC","ATA","ATT","ATC", /* 16-23 */
"AAA","AAG","CTA","TTA","TTG","CTT","CTC","CTG", /* 24-31 */
"ATG","AAT","AAC","CCG","CCA","CCT","CCC","CAA", /* 32-39 */
"CAG","CGT","CGA","CGC","AGG","AGA","CGG","TCG", /* 40-47 */
"TCA","AGT","TCT","TCC","AGC","ACG","ACT","ACA", /* 48-55 */
"ACC","GTA","GTT","GTC","GTG","TGG","TAT","TAC" /* 56-63 */
};
const char *aa=
"***AAAACCDDEEFFGGGGHHIIIKKLLLLLLMNNPPPPQQRRRRRRSSSSSSTTTTVVVVWYY";
AjPFile inf = NULL;
AjPFile outf = NULL;
char *entryname = NULL;
AjPStr fname = NULL;
AjPStr key = NULL;
AjPStr tmpkey = NULL;
AjBool allrecords = AJFALSE;
AjPTable table = NULL;
ajint i = 0;
ajint j = 0;
ajint k = 0;
ajint x = 0;
ajint savecount[3];
AjPStr *keyarray = NULL;
CutgPValues *valarray = NULL;
AjPCod codon = NULL;
ajint sum = 0;
char c;
AjPList flist = NULL;
AjPFile logf = NULL;
AjPStr entry = NULL;
AjPStr baseentry = NULL;
AjPStr wild = NULL;
AjPStr division = NULL;
AjPStr release = NULL;
AjPStr wildspecies = NULL;
CutgPValues value = NULL;
AjPStr docstr = NULL;
AjPStr species = NULL;
AjPStr filename = NULL;
ajint nstops;
embInit("cutgextract",argc,argv);
tmpkey = ajStrNew();
fname = ajStrNew();
table = ajTablestrNewLen(TABLE_ESTIMATE);
flist = ajAcdGetDirlist("directory");
wild = ajAcdGetString("wildspec");
release = ajAcdGetString("release");
logf = ajAcdGetOutfile("outfile");
wildspecies = ajAcdGetString("species");
filename = ajAcdGetString("filename");
allrecords = ajAcdGetBoolean("allrecords");
ajStrInsertC(&release, 0, "CUTG");
ajStrRemoveWhite(&release);
while(ajListPop(flist,(void **)&entry))
{
ajStrAssignS(&baseentry, entry);
ajFilenameTrimPath(&baseentry);
ajDebug("Testing file '%S'\n", entry);
if(!ajStrMatchWildS(baseentry,wild))
{
ajStrDel(&entry);
continue;
}
ajDebug("... matched wildcard '%S'\n", wild);
inf = ajFileNewInNameS(entry);
if(!inf)
ajFatal("cannot open file %S",entry);
ajFmtPrintS(&division, "%F", inf);
ajFilenameTrimAll(&division);
while((entryname = cutgextract_next(inf, wildspecies,
&species, &docstr)))
{
if(ajStrGetLen(filename))
ajStrAssignS(&tmpkey,filename);
else
ajStrAssignC(&tmpkey,entryname);
/* See if organism is already in the table */
value = ajTableFetch(table,tmpkey);
if(!value) /* Initialise */
{
key = ajStrNewS(tmpkey);
AJNEW0(value);
ajStrAssignS(&value->Species,species);
ajStrAssignS(&value->Division, division);
ajTablePut(table,(void *)key,(void *)value);
}
for(k=0;k<3;k++)
savecount[k] = value->Count[k];
nstops = cutgextract_readcodons(inf,allrecords, value->Count);
if(nstops < 1)
{
value->Skip++;
continue;
}
value->CdsCount++;
if(nstops>1)
{
value->CdsCount += (nstops - 1);
value->Warn++;
ajWarn("Found %d stop codons (%d %d %d) for CDS '%S'",
nstops,
value->Count[0] - savecount[0],
value->Count[1] - savecount[1],
value->Count[2] - savecount[2],
cutgextractSavepid);
}
}
ajStrDel(&entry);
ajFileClose(&inf);
}
ajTableToarrayKeysValues(table,(void***) &keyarray, (void***) &valarray);
i = 0;
while(keyarray[i])
{
key = keyarray[i];
value = (CutgPValues) valarray[i++];
codon = ajCodNew();
sum = 0;
for(j=0;j<CODONS;++j)
{
sum += value->Count[j];
x = ajCodIndexC(codons[j]);
codon->num[x] = value->Count[j];
c = aa[j];
if(c=='*')
codon->aa[x] = 27;
else
codon->aa[x] = c-'A';
}
ajCodCalcUsage(codon,sum);
ajStrAppendC(&key, ".cut");
if(allrecords)
{
if(value->Warn)
ajFmtPrintF(logf, "Writing %S CDS: %d Warnings: %d\n",
key, value->CdsCount, value->Warn);
else
ajFmtPrintF(logf, "Writing %S CDS: %d\n",
key, value->CdsCount);
}
else
{
if(value->Skip)
ajFmtPrintF(logf, "Writing %S CDS: %d Skipped: %d\n",
key, value->CdsCount, value->Skip);
else
ajFmtPrintF(logf, "Writing %S CDS: %d\n",
key, value->CdsCount);
}
ajFmtPrintS(&fname,"CODONS/%S",key);
outf = ajDatafileNewOutNameS(fname);
if(!outf)
ajFatal("Cannot open output file %S",fname);
ajCodSetNameS(codon, key);
ajCodSetSpeciesS(codon, value->Species);
ajCodSetDivisionS(codon, value->Division);
ajCodSetReleaseS(codon, release);
ajCodSetNumcds(codon, value->CdsCount);
ajCodSetNumcodons(codon, sum);
ajCodWrite(codon, outf);
ajFileClose(&outf);
ajStrDel(&key);
ajStrDel(&value->Division);
ajStrDel(&value->Doc);
ajStrDel(&value->Species);
AJFREE(value);
ajCodDel(&codon);
}
AJFREE(keyarray);
AJFREE(valarray);
ajTableFree(&table);
ajListFree(&flist);
ajStrDel(&wild);
ajStrDel(&release);
ajStrDel(&wildspecies);
ajStrDel(&filename);
ajFileClose(&logf);
ajStrDel(&cutgextractSavepid);
ajStrDel(&cutgextractLine);
ajStrDel(&cutgextractOrg);
ajStrDel(&fname);
ajStrDel(&tmpkey);
ajStrDel(&species);
ajStrDel(&docstr);
ajStrDel(&division);
ajStrDel(&baseentry);
embExit();
return 0;
}
