Vector *RawContig_getAllRepeatFeatures(RawContig *rc, char *logicName) {
RawContigAdaptor *rca = (RawContigAdaptor *)RawContig_getAdaptor(rc);
RepeatFeatureAdaptor *rfa;
if (!rca) {
fprintf(stderr, "Warning: Contig has no adaptor - cannot retrieve repeat features\n");
return emptyVector;
}
rfa = DBAdaptor_getRepeatFeatureAdaptor(rca->dba);
return RepeatFeatureAdaptor_fetchAllByRawContig(rfa,rc,logicName);
}
int main(int argc, char *argv[]) {
DBAdaptor *dba;
RepeatFeatureAdaptor *rfa;
Slice *slice;
Vector *features;
int i;
int failed;
initEnsC(argc, argv);
dba = Test_initROEnsDB();
slice = Test_getStandardSlice(dba);
ok(1, slice!=NULL);
rfa = DBAdaptor_getRepeatFeatureAdaptor(dba);
ok(2, rfa!=NULL);
features = Slice_getAllRepeatFeatures(slice,NULL,NULL, NULL);
ok(3, features!=NULL);
ok(4, Vector_getNumElement(features)!=0);
failed = 0;
for (i=0;i<Vector_getNumElement(features) && !failed;i++) {
RepeatFeature *rf = Vector_getElementAt(features,i);
int start = RepeatFeature_getStart(rf);
int end = RepeatFeature_getEnd(rf);
Vector *rrfVector;
RepeatFeature *rrf;
printf("slice start = %d end = %d\n",start,end);
/*
rrfVector = RepeatFeature_transformToRawContig(rf);
if (Vector_getNumElement(rrfVector) > 1) {
printf("Feature mapped to more than one rawcontig\n");
failed=1;
}
rrf = Vector_getElementAt(rrfVector,0);
//printf("rc start = %d end = %d\n",RepeatFeature_getStart(rrf),RepeatFeature_getEnd(rrf));
rf = RepeatFeature_transformToSlice(rrf, slice);
if (RepeatFeature_getStart(rf) != start ||
RepeatFeature_getEnd(rf) != end) {
printf("Remapping to slice produced different coords\n");
failed =1;
}
*/
}
ok(5, !failed);
return 0;
}
