public ABITracerCompoundSet() { addNucleotideCompound("A", "T"); addNucleotideCompound("T", "A"); addNucleotideCompound("G", "C"); addNucleotideCompound("C", "G"); addNucleotideCompound("N", "N"); addNucleotideCompound("K", "K"); addNucleotideCompound("Y", "Y"); addNucleotideCompound("R", "R"); addNucleotideCompound("-", "-"); }
/** * Returns the original programmatically determined (unedited) sequence as a <code>AbstractSequence<NucleotideCompound></code>. * * @return AbstractSequence<NucleotideCompound> sequence */ public AbstractSequence<NucleotideCompound> getSequence() throws CompoundNotFoundException { DNASequenceCreator creator = new DNASequenceCreator(ABITracerCompoundSet.getABITracerCompoundSet()); return creator.getSequence(sequence, 0); }
@Override public NucleotideCompound newNucleotideCompound(String base, String complement, String... equivalents) { if(equivalents.length == 0) { return new NucleotideCompound(base, this, complement); } else { NucleotideCompound[] compounds = new NucleotideCompound[equivalents.length]; for(int i=0; i<compounds.length; i++) { compounds[i] = getCompoundForString(equivalents[i]); } return new NucleotideCompound(base, this, complement, compounds); } } }
/** * Returns the original programmatically determined (unedited) sequence as a <code>AbstractSequence<NucleotideCompound></code>. * * @return AbstractSequence<NucleotideCompound> sequence */ public AbstractSequence<NucleotideCompound> getSequence() throws CompoundNotFoundException { DNASequenceCreator creator = new DNASequenceCreator(ABITracerCompoundSet.getABITracerCompoundSet()); return creator.getSequence(sequence, 0); }
@Override public NucleotideCompound newNucleotideCompound(String base, String complement, String... equivalents) { if(equivalents.length == 0) { return new NucleotideCompound(base, this, complement); } else { NucleotideCompound[] compounds = new NucleotideCompound[equivalents.length]; for(int i=0; i<compounds.length; i++) { compounds[i] = getCompoundForString(equivalents[i]); } return new NucleotideCompound(base, this, complement, compounds); } } }
public ABITracerCompoundSet() { addNucleotideCompound("A", "T"); addNucleotideCompound("T", "A"); addNucleotideCompound("G", "C"); addNucleotideCompound("C", "G"); addNucleotideCompound("N", "N"); addNucleotideCompound("K", "K"); addNucleotideCompound("Y", "Y"); addNucleotideCompound("R", "R"); addNucleotideCompound("-", "-"); }