SeqFeature *BaseAdaptor_uncachedFetchByDbID(BaseAdaptor *ba, IDType id) {
SeqFeature *feat = NULL;
char constraint[1024];
//construct a constraint like 't1.table1_id = 123'
NameTableType *tables = ba->getTables();
char **t = (*tables)[0];
sprintf(constraint, "%s.%s_id = "IDFMTSTR, t[SYN], t[NAME], id);
//Should only be one
Vector *vec = BaseAdaptor_genericFetch(ba, constraint, NULL, NULL);
if (Vector_getNumElement(vec) > 1) {
fprintf(stderr, "Error: Got more than one feature back in fetch ID call\n");
} else {
if (Vector_getNumElement(vec) == 1) {
feat = Vector_getElementAt(vec, 0);
Object_incRefCount(feat);
}
}
// NIY May want to set a free func???
Vector_free(vec);
return feat;
}
PredictionExon *PredictionExon_new() {
PredictionExon *pe;
if ((pe = (PredictionExon *)calloc(1,sizeof(PredictionExon))) == NULL) {
fprintf(stderr,"ERROR: Failed allocating space for pe\n");
return NULL;
}
pe->objectType = CLASS_PREDICTIONEXON;
Object_incRefCount(pe);
pe->funcs = &predictionExonFuncs;
return pe;
}
GenomeDB *GenomeDB_new() {
GenomeDB *gdb;
if ((gdb = (GenomeDB *)calloc(1,sizeof(GenomeDB))) == NULL) {
fprintf(stderr,"ERROR: Failed allocating space for gdb\n");
return NULL;
}
gdb->objectType = CLASS_GENOMEDB;
gdb->funcs = &genomeDBFuncs;
Object_incRefCount(gdb);
return gdb;
}
SyntenyRegion *SyntenyRegion_new() {
SyntenyRegion *sr;
if ((sr = (SyntenyRegion *)calloc(1,sizeof(SyntenyRegion))) == NULL) {
fprintf(stderr,"ERROR: Failed allocating space for sr\n");
return NULL;
}
sr->objectType = CLASS_SYNTENYREGION;
sr->funcs = &syntenyRegionFuncs;
Object_incRefCount(sr);
return sr;
}
SimpleFeature *SimpleFeature_new() {
SimpleFeature *sf;
if ((sf = (SimpleFeature *)calloc(1,sizeof(SimpleFeature))) == NULL) {
fprintf(stderr,"ERROR: Failed allocating space for sf\n");
return NULL;
}
sf->objectType = CLASS_SIMPLEFEATURE;
Object_incRefCount(sf);
sf->funcs = &simpleFeatureFuncs;
return sf;
}
Clone *Clone_new() {
Clone *cl;
if ((cl = (Clone *)calloc(1,sizeof(Clone))) == NULL) {
fprintf(stderr,"ERROR: Failed allocating space for cl\n");
return NULL;
}
cl->objectType = CLASS_CLONE;
cl->funcs = &cloneFuncs;
Object_incRefCount(cl);
return cl;
}
PredictionTranscript *PredictionTranscript_new() {
PredictionTranscript *transcript;
if ((transcript = (PredictionTranscript *)calloc(1,sizeof(PredictionTranscript))) == NULL) {
fprintf(stderr,"ERROR: Failed allocating space for transcripe\n");
return NULL;
}
transcript->objectType = CLASS_PREDICTIONTRANSCRIPT;
Object_incRefCount(transcript);
transcript->funcs = &predictionTranscriptFuncs;
transcript->exons = Vector_new();
return transcript;
}
Analysis *Analysis_new() {
Analysis *anal;
if ((anal = (Analysis *)calloc(1,sizeof(Analysis))) == NULL) {
fprintf(stderr,"ERROR: Failed allocating space for anal\n");
return NULL;
}
anal->objectType = CLASS_ANALYSIS;
anal->funcs = &analysisFuncs;
Object_incRefCount(anal);
return anal;
}
RawContig *RawContig_new() {
RawContig *rc;
if ((rc = (RawContig *)calloc(1,sizeof(RawContig))) == NULL) {
fprintf(stderr,"ERROR: Failed allocating space for rc\n");
return NULL;
}
rc->length = rc->emblOffset = rc->cloneId = -1;
rc->objectType = CLASS_RAWCONTIG;
Object_incRefCount(rc);
rc->funcs = &rawContigFuncs;
return rc;
}
Translation *Translation_new() {
Translation *t;
if ((t = (Translation *)calloc(1,sizeof(Translation))) == NULL) {
fprintf(stderr,"ERROR: Failed allocating space for t\n");
return NULL;
}
Translation_setVersion(t,-1);
t->objectType = CLASS_TRANSLATION;
t->funcs = &translationFuncs;
Object_incRefCount(t);
return t;
}
AssemblyMapper *AssemblyMapper_new(AssemblyMapperAdaptor *adaptor, Vector *coordSystems) {
AssemblyMapper *am;
if ((am = (AssemblyMapper *)calloc(1, sizeof(AssemblyMapper))) == NULL) {
fprintf(stderr, "ERROR: Failed allocating space for AssemblyMapper\n");
return NULL;
}
am->objectType = CLASS_ASSEMBLYMAPPER;
am->funcs = &assemblyMapperFuncs;
Object_incRefCount(am);
AssemblyMapper_setAdaptor(am, adaptor);
AssemblyMapperAdaptor_cacheSeqIdsWithMultAssemblies(adaptor);
if ( Vector_getNumElement(coordSystems) != 2 ) {
fprintf(stderr, "Can only map between two coordinate systems %d were provided\n", Vector_getNumElement(coordSystems));
exit(1);
}
// Set the component and assembled coordinate systems
AssemblyMapper_setAssembledCoordSystem(am, Vector_getElementAt(coordSystems, 0));
AssemblyMapper_setComponentCoordSystem(am, Vector_getElementAt(coordSystems, 1));
AssemblyMapper_setAssembledRegister(am, IDHash_new(IDHASH_MEDIUM));
AssemblyMapper_setComponentRegister(am, IDHash_new(IDHASH_MEDIUM));
// We load the mapper calling the 'ASSEMBLED' the 'from' coord system
// and the 'COMPONENT' the 'to' coord system.
AssemblyMapper_setMapper(am, Mapper_new("assembled", "component", AssemblyMapper_getAssembledCoordSystem(am),
AssemblyMapper_getComponentCoordSystem(am)));
AssemblyMapper_setMaxPairCount(am, AM_DEFAULT_MAX_PAIR_COUNT);
return am;
}