MapperRangeSet *PredictionTranscript_cDNA2Genomic(PredictionTranscript *trans, int start, int end) {
Mapper *mapper;
mapper = PredictionTranscript_getcDNACoordMapper(trans);
return Mapper_mapCoordinates(mapper, (IDType)trans, start, end, 1, "cdna" );
}
int testTransform(Mapper *mapper, int srcId, int srcStart, int srcEnd, int srcStrand, char *srcType, int dest[][4], int nDest ) {
MapperRangeSet *results = Mapper_mapCoordinates(mapper, srcId, srcStart, srcEnd, srcStrand, srcType);
printf("\nNew test\n");
int diff = 0;
printf("Number of results = %d nDest = %d\n",MapperRangeSet_getNumRange(results), nDest);
if (MapperRangeSet_getNumRange(results) != nDest) {
diff =1;
} else{
int i;
for (i=0;i<MapperRangeSet_getNumRange(results) && !diff;i++) {
MapperRange *range = MapperRangeSet_getRangeAt(results, i);
switch (range->rangeType) {
case MAPPERRANGE_COORD :
{
MapperCoordinate *mc = (MapperCoordinate *)range;
printf("Coord: "IDFMTSTR" %ld %ld %d\n", mc->id, mc->start, mc->end, mc->strand);
if (dest[i][0] != mc->id || dest[i][1] != mc->start || dest[i][2] != mc->end || dest[i][3] != mc->strand) {
diff=1;
}
}
break;
case MAPPERRANGE_GAP :
{
MapperGap *mg = (MapperGap *)range;
printf("Gap: %ld %ld\n", mg->start, mg->end);
if (dest[i][0] != srcId || dest[i][1] != mg->start || dest[i][2] != mg->end || dest[i][3] != 0) {
diff=1;
}
}
break;
default:
{
printf("Unhandled range type %d\n",range->rangeType);
diff=1;
}
break;
}
}
}
if (diff) {
printf("DIFFERENCE\n");
}
return 1;
}
MapperRangeSet *PredictionTranscript_genomic2cDNA(PredictionTranscript *trans, int start, int end, int strand, BaseContig *contig) {
Mapper *mapper;
// "ids" in mapper are contigs of exons, so use the same contig that should
// be attached to all of the exons...
if (!contig) {
Vector *translateable = PredictionTranscript_getAllTranslateableExons(trans);
PredictionExon *firstExon;
if (!Vector_getNumElement(translateable)) {
return MapperRangeSet_new();
}
firstExon = Vector_getElementAt(translateable, 0);
contig = (BaseContig*)PredictionExon_getSlice(firstExon);
Vector_free(translateable);
}
mapper = PredictionTranscript_getcDNACoordMapper(trans);
return Mapper_mapCoordinates(mapper,(IDType)contig, start, end, strand, "genomic");
}
MapperRangeSet *AssemblyMapper_mapImpl(AssemblyMapper *am, char *frmSeqRegionName, long frmStart, long frmEnd, int frmStrand, CoordSystem *frmCs, int fakeFastMapFlag, 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_mapCoordinates( mapper, seqRegionId, frmStart, frmEnd, frmStrand, frm );
}
MapperRangeSet *Mapper_mapInsert(Mapper *m, IDType id, long start, long end, int strand, char *type, int fastmap) {
// swap start/end and map the resultant 2bp coordinate
long tmp;
tmp = start;
start = end;
end = tmp;
MapperRangeSet *coords = Mapper_mapCoordinates(m, id, start, end, strand, type);
MapperRangeSet *retSet = MapperRangeSet_new();
if (MapperRangeSet_getNumRange(coords) == 1) {
// Note assuming its a mapper coordinate - not sure if this is always true
MapperCoordinate *c = (MapperCoordinate *)MapperRangeSet_getRangeAt(coords,0);
// swap start and end to convert back into insert
MapperCoordinate *newC = MapperCoordinate_new(c->id, c->end, c->start, c->strand, c->coordSystem, 0); // Perl didn't set rank so use 0
MapperRangeSet_addRange(retSet, (MapperRange *)newC);
} else {
if (MapperRangeSet_getNumRange(coords) != 2) {
fprintf(stderr, "Unexpected: Got %d expected 2.\n", MapperRangeSet_getNumRange(coords));
exit(1);
}
// adjust coordinates, remove gaps
MapperRange *c1, *c2;
if (strand == -1) {
c1 = MapperRangeSet_getRangeAt(coords,1);
c2 = MapperRangeSet_getRangeAt(coords,0);
} else {
c1 = MapperRangeSet_getRangeAt(coords,0);
c2 = MapperRangeSet_getRangeAt(coords,1);
}
//@coords = ();
// Was ref($c1) eq 'Bio::EnsEMBL::Mapper::Coordinate' so think this WON'T include MAPPERRANGE_INDEL
MapperCoordinate *newC1 = NULL;
if (c1->rangeType == MAPPERRANGE_COORD) {
MapperCoordinate *mcC1 = (MapperCoordinate *)c1;
// insert is after first coord
if (mcC1->strand * strand == -1) {
mcC1->end--;
} else {
mcC1->start++;
}
newC1 = MapperCoordinate_new(mcC1->id, mcC1->start, mcC1->end, mcC1->strand, mcC1->coordSystem, 0); // Perl didn't set rank, so use 0
}
// (see above for note on this condition if (ref($c2) eq 'Bio::EnsEMBL::Mapper::Coordinate')
MapperCoordinate *newC2 = NULL;
if (c2->rangeType == MAPPERRANGE_COORD) {
MapperCoordinate *mcC2 = (MapperCoordinate *)c2;
// insert is before second coord
if(mcC2->strand * strand == -1) {
mcC2->start++;
} else {
mcC2->end--;
}
newC2 = MapperCoordinate_new(mcC2->id, mcC2->start, mcC2->end, mcC2->strand, mcC2->coordSystem, 0); // Perl didn't set rank, so use 0
}
if (strand == -1) { // Add in 2, 1 order
if (newC2) MapperRangeSet_addRange(retSet, (MapperRange *)newC2);
if (newC1) MapperRangeSet_addRange(retSet, (MapperRange *)newC1);
} else { // Add in 1, 2 order
if (newC1) MapperRangeSet_addRange(retSet, (MapperRange *)newC1);
if (newC2) MapperRangeSet_addRange(retSet, (MapperRange *)newC2);
}
}
if (fastmap) {
if (MapperRangeSet_getNumRange(coords) != 1) {
MapperRangeSet_free(retSet);
retSet = NULL;
} else {
MapperRange *c = MapperRangeSet_getRangeAt(coords, 0);
// Type check - not sure what we're supposed to have here so belt and braces seem appropriate
if (c->rangeType != MAPPERRANGE_COORD) {
fprintf(stderr, "Expected a Coordinate range, got a %d range (look up in MapperRange.h)\n", c->rangeType);
exit(1);
}
MapperCoordinate *mcC = (MapperCoordinate *)c;
MapperCoordinate *newC = MapperCoordinate_new(mcC->id, mcC->start, mcC->end, mcC->strand, mcC->coordSystem, 0); // Perl didn't set rank, so use 0
MapperRangeSet_addRange(retSet, (MapperRange *)newC);
/*
return ($c->{'id'}, $c->{'start'}, $c->{'end'},
$c->{'strand'}, $c->{'coord_system'});
*/
}
}
MapperRangeSet_free(coords);
return retSet;
}
