| /dports/biology/stringtie/stringtie-2.1.1/gclib/ |
| H A D | gff.h | 335 setValue(av, is_cds);
340 void setValue(const char* av, bool is_cds=false) {
363 cds=is_cds;
525 this->Add(new GffAttr(nid, attrval, is_cds)); in add_if_new()
556 Get(i)->setValue(val, is_cds); in add_or_update()
564 this->Add(new GffAttr(aid, val, is_cds)); in add_or_update()
567 int haveId(int attr_id, bool is_cds=false) {
607 char* getAttr(int aid, bool is_cds) { in getAttr() argument
610 if (aid==Get(i)->attr_id && Get(i)->cds==is_cds) in getAttr()
615 void copyAttrs(GffAttrs* attrs, bool is_cds=false) {
[all …]
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| H A D | gff.cpp | 466 is_cds=true; //though some place it outside the last CDS segment in GffLine()
473 is_cds=true; in GffLine()
479 is_cds=true; in GffLine()
731 is_cds=true; in GffLine()
904 if (gl.is_cds) { in readExon()
921 parseAttrs((*segs)[eidx]->attrs, gl.info, true, gl.is_cds); in readExon()
1175 isCDSOnly(gffline.is_cds); //for now in GffObj()
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| /dports/biology/libgff/libgff-2.0.0/include/ |
| H A D | gff.h | 335 setValue(av, is_cds);
340 void setValue(const char* av, bool is_cds=false) {
363 cds=is_cds;
525 this->Add(new GffAttr(nid, attrval, is_cds)); in add_if_new()
556 Get(i)->setValue(val, is_cds); in add_or_update()
564 this->Add(new GffAttr(aid, val, is_cds)); in add_or_update()
567 int haveId(int attr_id, bool is_cds=false) {
607 char* getAttr(int aid, bool is_cds) { in getAttr() argument
610 if (aid==Get(i)->attr_id && Get(i)->cds==is_cds) in getAttr()
615 void copyAttrs(GffAttrs* attrs, bool is_cds=false) {
[all …]
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| /dports/biology/gffread/gffread-0.12.7/gclib/ |
| H A D | gff.h | 351 setValue(av, is_cds);
356 void setValue(const char* av, bool is_cds=false) {
379 cds=is_cds;
542 this->Add(new GffAttr(nid, attrval, is_cds)); in add_if_new()
573 Get(i)->setValue(val, is_cds); in add_or_update()
581 this->Add(new GffAttr(aid, val, is_cds)); in add_or_update()
584 int haveId(int attr_id, bool is_cds=false) {
624 char* getAttr(int aid, bool is_cds) { in getAttr() argument
627 if (aid==Get(i)->attr_id && Get(i)->cds==is_cds) in getAttr()
632 void copyAttrs(GffAttrs* attrs, bool is_cds=false) {
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| H A D | gff.cpp | 499 is_cds=true; //though some place it outside the last CDS segment in GffLine()
506 is_cds=true; in GffLine()
512 is_cds=true; in GffLine()
747 is_cds=true; in GffLine()
920 if (gl.is_cds) { in readExon()
937 parseAttrs((*segs)[eidx]->attrs, gl.info, true, gl.is_cds); in readExon()
1191 isCDSOnly(gffline.is_cds); //for now in GffObj()
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| /dports/biology/wise/wise2.4.1/src/dynlibsrc/ |
| H A D | gene.c | 167 int is_cds = 0; in read_EMBL_feature_Gene() local
186 is_cds = TRUE; in read_EMBL_feature_Gene()
319 if( is_cds == TRUE ) { in read_EMBL_feature_Gene()
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| H A D | gene.dy | 189 int is_cds = 0;
208 is_cds = TRUE;
341 if( is_cds == TRUE ) {
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| /dports/biology/cufflinks/cufflinks-2.2.1-89-gdc3b0cb/src/ |
| H A D | gff.cpp | 211 is_cds=true; //though some place it outside the last CDS segment in GffLine()
217 is_cds=true; in GffLine()
222 is_cds=true; in GffLine()
359 is_cds=true; in GffLine()
455 if (!isTranscript() && gl->is_cds) { in addExon()
506 gl->qstart,gl->qend, gl->is_cds, gl->exontype); in addExon()
788 isCDS=gffline->is_cds; //for now in GffObj()
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| H A D | gff.h | 93 bool is_cds:1; //"cds" or "start/stop_codon" features member
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| /dports/biology/libgff/libgff-2.0.0/src/ |
| H A D | gff.cpp | 466 is_cds=true; //though some place it outside the last CDS segment in GffLine()
473 is_cds=true; in GffLine()
479 is_cds=true; in GffLine()
731 is_cds=true; in GffLine()
904 if (gl.is_cds) { in readExon()
921 parseAttrs((*segs)[eidx]->attrs, gl.info, true, gl.is_cds); in readExon()
1175 isCDSOnly(gffline.is_cds); //for now in GffObj()
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| /dports/biology/ncbi-toolkit/ncbi/tools/ |
| H A D | spidey.c | 274 …tAce(FILE *ofp, SPI_RegionInfoPtr srip, BioseqPtr bsp_genomic, BioseqPtr bsp_mrna, Boolean is_cds);
1651 …ntAce(FILE *ofp, SPI_RegionInfoPtr srip, BioseqPtr bsp_genomic, BioseqPtr bsp_mrna, Boolean is_cds) in SPI_PrintAce() argument
1664 fprintf(ofp, "Subsequence Sp_%s.%s", id2, (is_cds == TRUE)?"cds":"mrna"); in SPI_PrintAce()
1669 fprintf(ofp, "Sequence Sp_%s.%s\n", id2, (is_cds == TRUE)?"cds":"mrna"); in SPI_PrintAce()
1672 if (is_cds) in SPI_PrintAce()
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