Vector *AssemblyMapper_listIdsImpl(AssemblyMapper *am, char *frmSeqRegionName, long frmStart, long frmEnd, CoordSystem *frmCs) {
IDType seqRegionId = AssemblyMapper_getSeqRegionId(am, frmSeqRegionName, frmCs);
AssemblyMapperAdaptor *adaptor = AssemblyMapper_getAdaptor(am);
if ( !CoordSystem_compare(frmCs, AssemblyMapper_getComponentCoordSystem(am) ) ) {
if ( !AssemblyMapper_haveRegisteredComponent(am, seqRegionId) ) {
AssemblyMapperAdaptor_registerComponent(adaptor, am, seqRegionId);
}
// Pull out the 'from' identifiers of the mapper pairs. The we
// loaded the assembled side as the 'from' side in the constructor.
MapperPairSet *mps = Mapper_listPairs( AssemblyMapper_getMapper(am), seqRegionId, frmStart, frmEnd, "component");
return MapperPairSet_getFromIds(mps);
} else if ( !CoordSystem_compare(frmCs, AssemblyMapper_getAssembledCoordSystem(am) ) ) {
AssemblyMapperAdaptor_registerAssembled(adaptor, am, seqRegionId, frmStart, frmEnd);
// Pull out the 'to' identifiers of the mapper pairs we loaded the
// component side as the 'to' coord system in the constructor.
MapperPairSet *mps = Mapper_listPairs( AssemblyMapper_getMapper(am), seqRegionId, frmStart, frmEnd, "assembled");
return MapperPairSet_getToIds(mps);
} else {
fprintf(stderr, "Coordinate system %s %s is neither the assembled nor the component coordinate system of this AssemblyMapper\n",
CoordSystem_getName(frmCs), CoordSystem_getVersion(frmCs) );
exit(1);
}
}
char *CoordSystem_getNameColonVersion(CoordSystem *cs) {
if (cs && cs->nameColonVersion == NULL) {
char tmpStr[1024];
sprintf(tmpStr,"%s:%s",CoordSystem_getName(cs),CoordSystem_getVersion(cs) ? CoordSystem_getVersion(cs):"");
StrUtil_copyString(&cs->nameColonVersion, tmpStr, 0);
cs->lenNameColonVersion = strlen(tmpStr);
}
return cs? cs->nameColonVersion : NULL;
}
MapperRangeSet *AssemblyMapper_fastMapImpl(AssemblyMapper *am, char *frmSeqRegionName, long frmStart, long frmEnd, int frmStrand, CoordSystem *frmCs, Slice *toSlice) {
Mapper *mapper = AssemblyMapper_getMapper(am);
CoordSystem *asmCs = AssemblyMapper_getAssembledCoordSystem(am);
CoordSystem *cmpCs = AssemblyMapper_getComponentCoordSystem(am);
AssemblyMapperAdaptor *adaptor = AssemblyMapper_getAdaptor(am);
char *frm;
IDType seqRegionId = AssemblyMapper_getSeqRegionId(am, frmSeqRegionName, frmCs);
// Speed critical section:
// Try to do simple pointer equality comparisons of the coord system
// objects first since this is likely to work most of the time and is
// much faster than a function call.
if ( frmCs == cmpCs
|| ( frmCs != asmCs && !CoordSystem_compare(frmCs, cmpCs)) ) {
if ( !IDHash_contains(AssemblyMapper_getComponentRegister(am), seqRegionId) ) {
AssemblyMapperAdaptor_registerComponent( adaptor, am, seqRegionId);
}
frm = "component";
} else if ( frmCs == asmCs || !CoordSystem_compare(frmCs, asmCs) ) {
// This can be probably be sped up some by only calling registered
// assembled if needed.
AssemblyMapperAdaptor_registerAssembled( adaptor, am, seqRegionId, frmStart, frmEnd);
frm = "assembled";
} else {
fprintf(stderr,"Coordinate system %s %s is neither the assembled nor the component coordinate system of this AssemblyMapper\n",
CoordSystem_getName(frmCs), CoordSystem_getVersion(frmCs) );
}
return Mapper_fastMap( mapper, seqRegionId, frmStart, frmEnd, frmStrand, frm );
}
int CoordSystem_compare(CoordSystem *cs1, CoordSystem *cs2) {
/* Dodgy DAS stuff
if (!$cs2 || !ref($cs2) || !$cs2->isa('Bio::EnsEMBL::CoordSystem')) {
if ($cs2->isa('Bio::EnsEMBL::ExternalData::DAS::CoordSystem')) {
return $cs2->equals($self);
}
throw('Argument must be a CoordSystem');
}
*/
if (!EcoString_strcmp(CoordSystem_getVersion(cs1), CoordSystem_getVersion(cs2)) && !EcoString_strcmp(CoordSystem_getName(cs1), CoordSystem_getName(cs2))) {
// Equal, so return 0
return 0;
}
return 1;
}