protected void buildTranslators() { Map<NucleotideCompound, NucleotideCompound> localDnaToRna = new HashMap<NucleotideCompound, NucleotideCompound>(); Map<NucleotideCompound, NucleotideCompound> localRnaToDna = new HashMap<NucleotideCompound, NucleotideCompound>(); NucleotideCompound thymine = getViewedSequence().getCompoundSet().getCompoundForString("T"); NucleotideCompound lowerThymine = getViewedSequence().getCompoundSet().getCompoundForString("t"); for (NucleotideCompound dnaBase : getViewedSequence().getCompoundSet().getAllCompounds()) { NucleotideCompound equivalent; if (dnaBase.equals(thymine)) { equivalent = rnaCompounds.getCompoundForString("U"); } else if (dnaBase.equals(lowerThymine)) { equivalent = rnaCompounds.getCompoundForString("u"); } else { equivalent = rnaCompounds.getCompoundForString( dnaBase.toString()); } localDnaToRna.put(dnaBase, equivalent); localRnaToDna.put(equivalent, dnaBase); } this.dnaToRna = localDnaToRna; this.rnaToDna = localRnaToDna; }
protected void buildTranslators() { Map<NucleotideCompound, NucleotideCompound> localDnaToRna = new HashMap<NucleotideCompound, NucleotideCompound>(); Map<NucleotideCompound, NucleotideCompound> localRnaToDna = new HashMap<NucleotideCompound, NucleotideCompound>(); NucleotideCompound thymine = getViewedSequence().getCompoundSet().getCompoundForString("T"); NucleotideCompound lowerThymine = getViewedSequence().getCompoundSet().getCompoundForString("t"); for (NucleotideCompound dnaBase : getViewedSequence().getCompoundSet().getAllCompounds()) { NucleotideCompound equivalent; if (dnaBase.equals(thymine)) { equivalent = rnaCompounds.getCompoundForString("U"); } else if (dnaBase.equals(lowerThymine)) { equivalent = rnaCompounds.getCompoundForString("u"); } else { equivalent = rnaCompounds.getCompoundForString( dnaBase.toString()); } localDnaToRna.put(dnaBase, equivalent); localRnaToDna.put(equivalent, dnaBase); } this.dnaToRna = localDnaToRna; this.rnaToDna = localRnaToDna; }