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/**
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* Copyright (C) 2016 EDIT
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* European Distributed Institute of Taxonomy
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* http://www.e-taxonomy.eu
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*
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* The contents of this file are subject to the Mozilla Public License Version 1.1
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* See LICENSE.TXT at the top of this package for the full license terms.
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*/
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package eu.etaxonomy.taxeditor.molecular.io.wizard;
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import info.bioinfweb.jphyloio.events.type.EventContentType;
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import info.bioinfweb.jphyloio.factory.JPhyloIOReaderWriterFactory;
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import info.bioinfweb.jphyloio.formatinfo.JPhyloIOFormatInfo;
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import java.util.Collections;
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import java.util.Map;
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import java.util.TreeMap;
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import org.eclipse.core.databinding.observable.value.IObservableValue;
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import org.eclipse.core.databinding.observable.value.WritableValue;
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/**
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* The data model for a wizard to export single read alignments to different file formats using <i>JPhyloIO</i>.
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*
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* @author Ben Stöver
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* @date 16.11.2016
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*/
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public class ExportSingleReadAlignmentWizardModel {
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protected static final JPhyloIOReaderWriterFactory READER_WRITER_FACTORY = new JPhyloIOReaderWriterFactory();
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protected static final Map<String, JPhyloIOFormatInfo> FORMAT_NAMES_TO_INFO_MAP = createFormatInfoList();
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private IObservableValue exportSingleReads = new WritableValue(true, Boolean.class);
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private IObservableValue exportConsensusSequence = new WritableValue(true, Boolean.class);
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private IObservableValue consensusSequenceLabel = new WritableValue("ConsensusSequence", String.class);
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private IObservableValue formatInfo = new WritableValue(null, String.class);
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private IObservableValue fileName = new WritableValue(null, String.class);
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private static Map<String, JPhyloIOFormatInfo> createFormatInfoList() {
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Map<String, JPhyloIOFormatInfo> result = new TreeMap<String, JPhyloIOFormatInfo>();
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for (String formatID : READER_WRITER_FACTORY.getFormatIDsSet()) {
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JPhyloIOFormatInfo info = READER_WRITER_FACTORY.getFormatInfo(formatID);
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if (info.isElementModeled(EventContentType.ALIGNMENT, false)) { // Check if the current format allows to write alignments.
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result.put(info.getFormatName(), info);
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}
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}
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return Collections.unmodifiableMap(result);
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}
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public boolean isExportSingleReads() {
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return (Boolean)exportSingleReads.getValue();
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}
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protected IObservableValue getExportSingleReadsObservable() {
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return exportSingleReads;
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}
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public boolean isExportConsensusSequence() {
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return (Boolean)exportConsensusSequence.getValue();
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}
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protected IObservableValue getExportConsensusSequenceObservable() {
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return exportConsensusSequence;
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}
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public String getConsensusSequenceLabel() {
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return (String)consensusSequenceLabel.getValue();
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}
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protected IObservableValue getConsensusSequenceLabelObservable() {
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return consensusSequenceLabel;
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}
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protected IObservableValue getFormatInfoObservable() {
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return formatInfo;
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}
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/**
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* Returns the <i>JPhyloIO</i> format info object to be used for exporting.
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*
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* @return the format info
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*/
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public JPhyloIOFormatInfo getFormatInfo() {
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return FORMAT_NAMES_TO_INFO_MAP.get(formatInfo.getValue());
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}
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public String getFileName() {
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return (String)fileName.getValue();
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}
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protected IObservableValue getFileNameObservable() {
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return fileName;
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}
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}
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