Revision 00d1a6ce
Added by Ben Stöver over 7 years ago
| eu.etaxonomy.taxeditor.molecular/src/main/java/eu/etaxonomy/taxeditor/molecular/io/wizard/ExportSingleReadAlignmentWizardModel.java | ||
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package eu.etaxonomy.taxeditor.molecular.io.wizard; |
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import info.bioinfweb.commons.bio.SequenceUtils; |
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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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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 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("Consensus", String.class);
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private IObservableValue elongateSequences = new WritableValue(false, Boolean.class); |
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private IObservableValue useGapToken = new WritableValue(true, Boolean.class); |
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private static Map<String, JPhyloIOFormatInfo> createFormatInfoList() {
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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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public boolean isExportSingleReads() {
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return (Boolean)exportSingleReads.getValue(); |
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} |
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} |
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protected IObservableValue getFormatInfoObservable() {
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return formatInfo; |
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public String getElongationToken() {
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if ((Boolean)elongateSequences.getValue()) {
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if ((Boolean)useGapToken.getValue()) {
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return Character.toString(SequenceUtils.GAP_CHAR); |
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} |
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else {
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return Character.toString(SequenceUtils.MISSING_DATA_CHAR); |
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} |
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} |
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else {
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return null; |
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} |
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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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protected IObservableValue getElongateSequencesObservable() {
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return elongateSequences; |
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} |
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public String getFileName() {
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return (String)fileName.getValue();
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protected IObservableValue getUseGapTokenObservable() {
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return useGapToken;
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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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} |
Also available in: Unified diff
Export single read alignment wizard separated into two pages.
Option to elongate sequences added.
Application information parameters of JPhyloIO set.