eu.etaxonomy.taxeditor.molecular/src/main/java/eu/etaxonomy/taxeditor/molecular/io/wizard/ExportSingleReadAlignmentWizardModel.java

   1 /**
   2 * Copyright (C) 2016 EDIT
   3 * European Distributed Institute of Taxonomy
   4 * http://www.e-taxonomy.eu
   5 *
   6 * The contents of this file are subject to the Mozilla Public License Version 1.1
   7 * See LICENSE.TXT at the top of this package for the full license terms.
   8 */
   9 package eu.etaxonomy.taxeditor.molecular.io.wizard;
  10
  11
  12 import info.bioinfweb.commons.bio.SequenceUtils;
  13 import info.bioinfweb.jphyloio.events.type.EventContentType;
  14 import info.bioinfweb.jphyloio.factory.JPhyloIOReaderWriterFactory;
  15 import info.bioinfweb.jphyloio.formatinfo.JPhyloIOFormatInfo;
  16
  17 import java.util.ArrayList;
  18 import java.util.Collections;
  19 import java.util.List;
  20
  21 import org.eclipse.core.databinding.observable.value.IObservableValue;
  22 import org.eclipse.core.databinding.observable.value.WritableValue;
  23
  24
  25
  26 /**
  27  * The data model for a wizard to export single read alignments to different file formats using <i>JPhyloIO</i>.
  28  *
  29  * @author Ben Stöver
  30  * @date 16.11.2016
  31  */
  32 public class ExportSingleReadAlignmentWizardModel {
  33     protected static final JPhyloIOReaderWriterFactory READER_WRITER_FACTORY = new JPhyloIOReaderWriterFactory();
  34     protected static final List<JPhyloIOFormatInfo> FORMATS = createFormatInfoList();
  35
  36
  37     private IObservableValue formatInfo = new WritableValue(0, Integer.class);
  38     private IObservableValue fileName = new WritableValue(null, String.class);
  39     private IObservableValue exportSingleReads = new WritableValue(true, Boolean.class);
  40     private IObservableValue exportConsensusSequence = new WritableValue(true, Boolean.class);
  41     private IObservableValue consensusSequenceLabel = new WritableValue("Consensus", String.class);
  42     private IObservableValue elongateSequences = new WritableValue(false, Boolean.class);
  43     private IObservableValue useGapToken = new WritableValue(true, Boolean.class);
  44
  45
  46     private static List<JPhyloIOFormatInfo> createFormatInfoList() {
  47         List<JPhyloIOFormatInfo> result = new ArrayList<JPhyloIOFormatInfo>();
  48         for (String formatID : READER_WRITER_FACTORY.getFormatIDsSet()) {
  49             JPhyloIOFormatInfo info = READER_WRITER_FACTORY.getFormatInfo(formatID);
  50             if (info.isElementModeled(EventContentType.ALIGNMENT, false)) {  // Check if the current format allows to write alignments.
  51                 result.add(info);
  52             }
  53         }
  54         return Collections.unmodifiableList(result);
  55     }
  56
  57
  58     protected IObservableValue getFormatInfoObservable() {
  59         return formatInfo;
  60     }
  61
  62
  63     /**
  64      * Returns the <i>JPhyloIO</i> format info object to be used for exporting.
  65      *
  66      * @return the format info
  67      */
  68     public JPhyloIOFormatInfo getFormatInfo() {
  69         return FORMATS.get((Integer)formatInfo.getValue());
  70     }
  71
  72
  73     public String getFileName() {
  74         return (String)fileName.getValue();
  75     }
  76
  77
  78     protected IObservableValue getFileNameObservable() {
  79         return fileName;
  80     }
  81
  82
  83     public boolean isExportSingleReads() {
  84         return (Boolean)exportSingleReads.getValue();
  85     }
  86
  87
  88     protected IObservableValue getExportSingleReadsObservable() {
  89         return exportSingleReads;
  90     }
  91
  92
  93     public boolean isExportConsensusSequence() {
  94         return (Boolean)exportConsensusSequence.getValue();
  95     }
  96
  97
  98     protected IObservableValue getExportConsensusSequenceObservable() {
  99         return exportConsensusSequence;
 100     }
 101
 102
 103     public String getConsensusSequenceLabel() {
 104         return (String)consensusSequenceLabel.getValue();
 105     }
 106
 107
 108     protected IObservableValue getConsensusSequenceLabelObservable() {
 109         return consensusSequenceLabel;
 110     }
 111
 112
 113     public String getElongationToken() {
 114         if ((Boolean)elongateSequences.getValue()) {
 115             if ((Boolean)useGapToken.getValue()) {
 116                 return Character.toString(SequenceUtils.GAP_CHAR);
 117             }
 118             else {
 119                 return Character.toString(SequenceUtils.MISSING_DATA_CHAR);
 120             }
 121         }
 122         else {
 123             return null;
 124         }
 125     }
 126
 127
 128     protected IObservableValue getElongateSequencesObservable() {
 129         return elongateSequences;
 130     }
 131
 132
 133     protected IObservableValue getUseGapTokenObservable() {
 134         return useGapToken;
 135     }
 136 }