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.jphyloio.events.TokenSetType;
  17 import info.bioinfweb.libralign.model.AlignmentModel;
  18 import info.bioinfweb.libralign.model.implementations.PackedAlignmentModel;
  19 import info.bioinfweb.libralign.model.tokenset.BioJavaTokenSet;
  20
  21
  22
  23 /**
  24  * The LibrAlign sequence data provider used to edit contig alignments with the {@link AlignmentEditor}.
  25  *
  26  * @author Ben Stöver
  27  * @date 04.08.2014
  28  */
  29 public class ContigSequenceDataProvider extends PackedAlignmentModel<NucleotideCompound>
  30         implements AlignmentModel<NucleotideCompound> {
  31
  32
  33         public ContigSequenceDataProvider() {
  34                 super(new BioJavaTokenSet<NucleotideCompound>(TokenSetType.NUCLEOTIDE,
  35                                 AlignmentAmbiguityDNACompoundSet.getAlignmentAmbiguityDNACompoundSet(), true));
  36         }
  37
  38
  39         public void saveToCMD() {  //TODO Add cmd node as parameter
  40                 //TODO impl.
  41         }
  42
  43
  44         public void loadFromCMD() {  //TODO Add cmd node as parameter
  45                 //TODO impl.
  46         }
  47 }