3 * Copyright (C) 2014 EDIT
4 * European Distributed Institute of Taxonomy
5 * http://www.e-taxonomy.eu
7 * The contents of this file are subject to the Mozilla Public License Version 1.1
8 * See LICENSE.TXT at the top of this package for the full license terms.
10 package eu
.etaxonomy
.taxeditor
.editor
.molecular
;
13 import org
.biojava3
.core
.sequence
.compound
.NucleotideCompound
;
15 import info
.bioinfweb
.commons
.bio
.biojava3
.core
.sequence
.compound
.AlignmentAmbiguityDNACompoundSet
;
16 import info
.bioinfweb
.libralign
.sequenceprovider
.SequenceDataProvider
;
17 import info
.bioinfweb
.libralign
.sequenceprovider
.implementations
.PackedSequenceDataProvider
;
18 import info
.bioinfweb
.libralign
.sequenceprovider
.tokenset
.BioJavaTokenSet
;
23 * The LibrAlign sequence data provider used to edit contig alignments with the {@link AlignmentEditor}.
28 public class ContigSequenceDataProvider
extends PackedSequenceDataProvider
<NucleotideCompound
>
29 implements SequenceDataProvider
<NucleotideCompound
> {
32 public ContigSequenceDataProvider() {
33 super(new BioJavaTokenSet
<NucleotideCompound
>(AlignmentAmbiguityDNACompoundSet
.getAlignmentAmbiguityDNACompoundSet(), true));
37 public void saveToCMD() { //TODO Add cmd node as parameter
42 public void loadFromCMD() { //TODO Add cmd node as parameter