Esempio n. 1
0
void vAdd(FIELD* vec1,FIELD* vec2,ulong size)
{
	ulong i;
	for(i=0;i<size;i++)
		vec1[i]=gfadd(vec1[i],vec2[i]);
	return;
}
Esempio n. 2
0
void cAdd(FIELD* vec,ulong size,FIELD coeff)
{
	ulong i;
	for(i=0;i<size;i++)
		vec[i]=gfadd(coeff,vec[i]);
	return;
}
Esempio n. 3
0
void cMulvAdd(FIELD* vec1,FIELD* vec2,ulong size,FIELD coeff)
{
	/*vec1=coeff*vec2+vec1*/
	ulong i;
	for(i=0;i<size;i++)
		vec1[i]=gfadd(vec1[i],gfmul(coeff,vec2[i]));
	return;
}
Esempio n. 4
0
void GffLoader::load(GList<GenomicSeqData>& seqdata, GFValidateFunc* gf_validate, 
                          bool doCluster, bool doCollapseRedundant, 
                          bool matchAllIntrons, bool fuzzSpan, bool forceExons) {
   GffReader* gffr=new GffReader(f, this->transcriptsOnly, false); //not only mRNA features, not sorted
   gffr->showWarnings(this->showWarnings);
   //           keepAttrs   mergeCloseExons  noExonAttr
   gffr->readAll(this->fullAttributes,    this->mergeCloseExons,  this->noExonAttrs);
   GVec<int> pseudoAttrIds;
   GVec<int> pseudoFeatureIds;
   if (this->noPseudo) {
   	 GffNameList& fnames = gffr->names->feats;
   	 for (int i=0;i<fnames.Count();i++) {
   		char* n=fnames[i]->name;
   		if (startsWith(n, "pseudo")) {
   			pseudoFeatureIds.Add(fnames[i]->idx);
   		}
   	 }
  	 GffNameList& attrnames = gffr->names->attrs;
  	 for (int i=0;i<attrnames.Count();i++) {
  		char* n=attrnames[i]->name;
  		char* p=strifind(n, "pseudo");
  		if (p==n || (p==n+2 && tolower(n[0])=='i' && tolower(n[1])=='s')) {
  			pseudoAttrIds.Add(attrnames[i]->idx);
  		}
  	}
   }

  //int redundant=0; //redundant annotation discarded
  if (verbose) GMessage("   .. loaded %d genomic features from %s\n", gffr->gflst.Count(), fname.chars());
  //int rna_deleted=0;
  //add to GenomicSeqData, adding to existing loci and identifying intron-chain duplicates
  for (int k=0;k<gffr->gflst.Count();k++) {
     GffObj* m=gffr->gflst[k];
     if (strcmp(m->getFeatureName(), "locus")==0 && 
          m->getAttr("transcripts")!=NULL) {
        continue; //discard locus meta-features
        }
     if (this->noPseudo) {
    	 bool is_pseudo=false;
    	 for (int i=0;i<pseudoFeatureIds.Count();++i) {
    		 if (pseudoFeatureIds[i]==m->ftype_id) {
    			 is_pseudo=true;
    			 break;
    		 }
    	 }
    	 if (is_pseudo) continue;
    	 for (int i=0;i<pseudoAttrIds.Count();++i) {
    		 char* attrv=NULL;
    		 if (m->attrs!=NULL) attrv=m->attrs->getAttr(pseudoAttrIds[i]);
    		 if (attrv!=NULL) {
    			 char fc=tolower(attrv[0]);
    			 if (fc=='t' || fc=='y' || fc=='1') {
    				 is_pseudo=true;
    				 break;
    			 }
    		 }
    	 }
    	 if (is_pseudo) continue;
     }
     char* rloc=m->getAttr("locus");
     if (rloc!=NULL && startsWith(rloc, "RLOC_")) {
        m->removeAttr("locus", rloc);
        }
    /*
     if (m->exons.Count()==0 && m->children.Count()==0) {
       //a non-mRNA feature with no subfeatures
       //add a dummy exon just to have the generic exon checking work
       m->addExon(m->start,m->end);
       }
     */
     if (forceExons) {  // && m->children.Count()==0) {
       m->exon_ftype_id=gff_fid_exon;
       }
     GList<GffObj> gfadd(false,false);
     if (gf_validate!=NULL && !(*gf_validate)(m, &gfadd)) {
       continue;
       }
     m->isUsed(true); //so the gffreader won't destroy it
     int i=-1;
     GenomicSeqData f(m->gseq_id);
     GenomicSeqData* gdata=NULL;
     if (seqdata.Found(&f,i)) gdata=seqdata[i];
         else { //entry not created yet for this genomic seq
           gdata=new GenomicSeqData(m->gseq_id);
           seqdata.Add(gdata);
           }
    for (int k=0;k<gfadd.Count();k++) {
      placeGf(gfadd[k], gdata, doCluster, doCollapseRedundant, matchAllIntrons, fuzzSpan);
      }
    placeGf(m, gdata, doCluster, doCollapseRedundant, matchAllIntrons, fuzzSpan);
    } //for each read gffObj
   //if (verbose) GMessage("  .. %d records from %s clustered into loci.\n", gffr->gflst.Count(), fname.chars());
   if (f!=stdin) { fclose(f); f=NULL; }
   delete gffr;
}