// New (don't bother caching because its pretty quick to calculate
long Translation_getGenomicStart(Translation *translation) {
long genomicStart;
if (Exon_getStrand(Translation_getStartExon(translation)) >= 0) {
genomicStart = Exon_getStart(Translation_getStartExon(translation)) + (Translation_getStart(translation) - 1);
} else {
genomicStart = Exon_getEnd(Translation_getEndExon(translation)) - (Translation_getEnd(translation) - 1);
}
return genomicStart;
}
void Translation_transform(Translation *translation, IDHash *exonTransforms) {
Exon * startExon = Translation_getStartExon(translation);
Exon * endExon = Translation_getEndExon(translation);
IDType startExonRef = (IDType)startExon;
IDType endExonRef = (IDType)endExon;
/* CHECK */
if (IDHash_contains(exonTransforms,startExonRef)) {
Translation_setStartExon(translation,IDHash_getValue(exonTransforms,startExonRef));
} else {
// do nothing, the start exon wasnt mapped
}
if (IDHash_contains(exonTransforms,endExonRef)) {
Translation_setEndExon(translation,IDHash_getValue(exonTransforms,endExonRef));
} else {
// do nothing, the end exon wasnt mapped
}
}
int dumpGenes(Vector *genes, int withSupport) {
FILE *fp = stderr;
int i;
int failed = 0;
for (i=0;i<Vector_getNumElement(genes) && !failed;i++) {
Gene *g = Vector_getElementAt(genes,i);
fprintf(fp,"Gene %s (%s) coords: %ld %ld %d\n",Gene_getStableId(g),(Gene_getDisplayXref(g) ? DBEntry_getDisplayId(Gene_getDisplayXref(g)) : ""),Gene_getStart(g),Gene_getEnd(g),Gene_getStrand(g));
int j;
for (j=0;j<Gene_getTranscriptCount(g);j++) {
Transcript *t = Gene_getTranscriptAt(g,j);
int k;
fprintf(fp," Trans %s coords: %ld %ld %d biotype: %s\n",Transcript_getStableId(t), Transcript_getStart(t),Transcript_getEnd(t),Transcript_getStrand(t),Transcript_getBiotype(t));
if (withSupport) {
Vector *support = Transcript_getAllSupportingFeatures(t);
for (k=0; k<Vector_getNumElement(support); k++) {
BaseAlignFeature *baf = Vector_getElementAt(support, k);
fprintf(fp," support %s coords: %ld %ld %d\n", BaseAlignFeature_getHitSeqName(baf), BaseAlignFeature_getStart(baf), BaseAlignFeature_getEnd(baf), BaseAlignFeature_getStrand(baf));
}
Vector *intronSupport = Transcript_getAllIntronSupportingEvidence(t);
for (k=0; k<Vector_getNumElement(intronSupport); k++) {
IntronSupportingEvidence *ise = Vector_getElementAt(intronSupport, k);
fprintf(fp," intron support %s coords: %ld %ld %d\n", IntronSupportingEvidence_getHitName(ise), IntronSupportingEvidence_getStart(ise), IntronSupportingEvidence_getEnd(ise), IntronSupportingEvidence_getStrand(ise));
}
}
for (k=0;k<Transcript_getExonCount(t);k++) {
Exon *e = Transcript_getExonAt(t,k);
fprintf(fp," exon %s (%p) coords: %ld %ld %d\n",Exon_getStableId(e), e, Exon_getStart(e), Exon_getEnd(e), Exon_getStrand(e));
if (withSupport) {
Vector *support = Exon_getAllSupportingFeatures(e);
int m;
for (m=0; m<Vector_getNumElement(support); m++) {
BaseAlignFeature *baf = Vector_getElementAt(support, m);
fprintf(fp," support %s coords: %ld %ld %d\n", BaseAlignFeature_getHitSeqName(baf), BaseAlignFeature_getStart(baf), BaseAlignFeature_getEnd(baf), BaseAlignFeature_getStrand(baf));
}
}
}
Translation *tln = Transcript_getTranslation(t);
if (tln) {
fprintf(fp," translation id: %s %s %d %s %d\n",Translation_getStableId(tln),
Exon_getStableId(Translation_getStartExon(tln)), Translation_getStart(tln),
Exon_getStableId(Translation_getEndExon(tln)), Translation_getEnd(tln));
char *tSeq = Transcript_translate(t);
fprintf(fp," translation: %s\n",tSeq);
free(tSeq);
Vector *tlnAttribs = Translation_getAllAttributes(tln, NULL);
if (Vector_getNumElement(tlnAttribs)) {
fprintf(fp, " translation attributes:\n");
int n;
for (n=0; n<Vector_getNumElement(tlnAttribs); n++) {
Attribute *attrib = Vector_getElementAt(tlnAttribs, n);
fprintf(fp, " code %s name %s desc %s value %s\n",
Attribute_getCode(attrib),
Attribute_getName(attrib),
Attribute_getDescription(attrib),
Attribute_getValue(attrib));
}
}
}
}
}
return failed;
}