public ResidueInfo getResidue(PolymerType pt, Character oneLetterCode) {
String monId;
Map<Character, String> theMapToUse;
switch (pt) {
case peptide:
theMapToUse = ResidueTools.AMINO_ACID_LOOKUP_1TO3;
break;
case dna:
theMapToUse = ResidueTools.DNA_LOOKUP_1TO2;
break;
case rna:
return ResidueProvider.getResidue(oneLetterCode.toString().toUpperCase());
default:
theMapToUse = Collections.emptyMap();
break;
}
if ((monId = theMapToUse.get(oneLetterCode)) != null) {
return ResidueProvider.getResidue(monId);
} else if ((monId = theMapToUse.get(oneLetterCode.toString().toUpperCase().charAt(0)))
!= null) // TODO find an efficient way to convert Character to upper-case equiv
{
return ResidueProvider.getResidue(monId);
} else {
throw new RuntimeException("Could not find " + pt.toString() + " with code " + oneLetterCode);
}
}
/**
* provide a default view using BioJava.. could be done using some proper configuration
* managment...
*/
public void initBioJavaView() {
// first the Residue Provider
ResidueInfoFactory refactory = new BioJavaResidueInfoFactory();
ResidueProvider.setResidueInfoFactory(refactory);
// next the SequenceCollection Provider
SequenceCollectionFactory sfactory = new BioJavaSequenceCollectionFactory();
SequenceCollectionProvider.setSequenceCollectionFactory(sfactory);
BioJavaPubMedFactory pfactory = new BioJavaPubMedFactory();
PubMedProvider.setPubMedFactory(pfactory);
}