@Override
	public AbstractSequence<AminoAcidCompound> getSequence(
			List<AminoAcidCompound> list) {
		AbstractSequence<AminoAcidCompound> seq =super.getSequence(list);
		Collection<Object> strCase = new ArrayList<Object>(seq.getLength());
		for(int i=0;i<seq.getLength();i++) {
			strCase.add(true);
		}
		seq.setUserCollection(strCase);
		return seq;
	}
@ Override public AbstractSequence < AminoAcidCompound > getSequence ( List < AminoAcidCompound > list ) { AbstractSequence < AminoAcidCompound > seq = super . getSequence ( list ) ; Collection < Object > strCase = new ArrayList < Object > ( seq . getLength ( ) ) ; for ( int i = 0 ; i < seq . getLength ( ) ; i ++ ) { strCase . add ( true ) ; } seq . setUserCollection ( strCase ) ; return seq ; }
Assumes all compounds were uppercase
@see org.biojava.nbio.core.sequence.io.ProteinSequenceCreator#getSequence(java.util.List)