eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/molecular/ContigSequenceDataProvider.java

   1 // $Id$
   2 /**
   3 * Copyright (C) 2014 EDIT
   4 * European Distributed Institute of Taxonomy
   5 * http://www.e-taxonomy.eu
   6 *
   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.
   9 */
  10 package eu.etaxonomy.taxeditor.editor.molecular;
  11
  12
  13 import org.biojava3.core.sequence.compound.NucleotideCompound;
  14
  15 import info.bioinfweb.commons.bio.biojava3.core.sequence.compound.AlignmentAmbiguityDNACompoundSet;
  16 import info.bioinfweb.libralign.model.AlignmentModel;
  17 import info.bioinfweb.libralign.model.implementations.PackedAlignmentModel;
  18 import info.bioinfweb.libralign.model.tokenset.BioJavaTokenSet;
  19
  20
  21
  22 /**
  23  * The LibrAlign sequence data provider used to edit contig alignments with the {@link AlignmentEditor}.
  24  *
  25  * @author Ben Stöver
  26  * @date 04.08.2014
  27  */
  28 public class ContigSequenceDataProvider extends PackedAlignmentModel<NucleotideCompound>
  29         implements AlignmentModel<NucleotideCompound> {
  30
  31
  32         public ContigSequenceDataProvider() {
  33                 super(new BioJavaTokenSet<NucleotideCompound>(AlignmentAmbiguityDNACompoundSet.getAlignmentAmbiguityDNACompoundSet(), true));
  34         }
  35
  36
  37         public void saveToCMD() {  //TODO Add cmd node as parameter
  38                 //TODO impl.
  39         }
  40
  41
  42         public void loadFromCMD() {  //TODO Add cmd node as parameter
  43                 //TODO impl.
  44         }
  45 }