HomologyAdaptor *HomologyAdaptor_new(ComparaDBAdaptor *dba) {
HomologyAdaptor *ha = NULL;
if ((ha = (HomologyAdaptor *)calloc(1,sizeof(HomologyAdaptor))) == NULL) {
fprintf(stderr,"Error: Failed allocating ha\n");
} else {
BaseComparaAdaptor_init((BaseComparaAdaptor *)ha, dba, HOMOLOGY_ADAPTOR);
}
return ha;
}
SyntenyRegionAdaptor *SyntenyRegionAdaptor_new(ComparaDBAdaptor *dba) {
SyntenyRegionAdaptor *sra = NULL;
if ((sra = (SyntenyRegionAdaptor *)calloc(1,sizeof(SyntenyRegionAdaptor))) == NULL) {
fprintf(stderr,"Error: Failed allocating sra\n");
} else {
BaseComparaAdaptor_init((BaseComparaAdaptor *)sra, dba, SYNTENYREGION_ADAPTOR);
}
return sra;
}
GenomicAlignAdaptor *GenomicAlignAdaptor_new(ComparaDBAdaptor *dba) {
GenomicAlignAdaptor *gaa;
int maxAlLen;
MetaContainer *mc;
if ((gaa = (GenomicAlignAdaptor *)calloc(1,sizeof(GenomicAlignAdaptor))) == NULL) {
fprintf(stderr, "ERROR: Failed allocating space for GenomicAlignAdaptor\n");
return NULL;
}
BaseComparaAdaptor_init((BaseComparaAdaptor *)gaa, dba, GENOMICALIGN_ADAPTOR);
mc = ComparaDBAdaptor_getMetaContainer(gaa->dba);
if (MetaContainer_getIntValueByKey(mc, "max_alignment_length", &maxAlLen)) {
gaa->maxAlignmentLength = maxAlLen;
} else {
fprintf(stderr, "Warning: Meta table key 'max_alignment_length' not defined\n"
"using default value [%d]", DEFAULT_MAX_ALIGNMENT);
gaa->maxAlignmentLength = DEFAULT_MAX_ALIGNMENT;
}
return gaa;
}