Revision bcb823d5
Added by Ben Stöver over 7 years ago
| eu.etaxonomy.taxeditor.molecular/src/main/java/eu/etaxonomy/taxeditor/molecular/handler/ExportSequenceToFileHandler.java | ||
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import info.bioinfweb.jphyloio.ReadWriteParameterNames; |
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import info.bioinfweb.jphyloio.dataadapters.implementations.ListBasedDocumentDataAdapter; |
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import info.bioinfweb.jphyloio.factory.JPhyloIOReaderWriterFactory; |
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import info.bioinfweb.jphyloio.formats.JPhyloIOFormatIDs; |
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import info.bioinfweb.jphyloio.objecttranslation.ObjectTranslatorFactory; |
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import java.io.File; |
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import java.io.IOException; |
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import org.eclipse.core.commands.AbstractHandler; |
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import org.eclipse.core.commands.ExecutionEvent; |
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import org.eclipse.core.commands.ExecutionException; |
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import org.eclipse.core.runtime.IStatus; |
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import org.eclipse.jface.viewers.ISelection; |
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import org.eclipse.jface.viewers.TreeNode; |
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import org.eclipse.jface.wizard.WizardDialog; |
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import org.eclipse.ui.handlers.HandlerUtil; |
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import eu.etaxonomy.cdm.model.molecular.Sequence; |
| ... | ... | |
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import eu.etaxonomy.taxeditor.molecular.io.CDMPherogramAlignmentObjectTranslator; |
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import eu.etaxonomy.taxeditor.molecular.io.CDMSequenceMatrixAdapter; |
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import eu.etaxonomy.taxeditor.molecular.io.SingleReadAlignmentRDFXMLConstants; |
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import eu.etaxonomy.taxeditor.molecular.io.wizard.ExportSingleReadAlignmentWizard; |
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|
| ... | ... | |
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if (treeNodeOfSelection != null && treeNodeOfSelection.getValue() instanceof Sequence) {
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Sequence sequence = (Sequence)treeNodeOfSelection.getValue(); |
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//TODO Collect the following information using a wizard. |
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File targetFile = new File("O:\\Projects\\Bereich BBI\\EDIT Campanula\\Testdaten\\NeXMLExport.xml");
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String formatID = JPhyloIOFormatIDs.NEXML_FORMAT_ID; |
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final ExportSingleReadAlignmentWizard wizard = new ExportSingleReadAlignmentWizard(); |
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final WizardDialog dialog = new WizardDialog(HandlerUtil.getActiveShell(event), wizard); |
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if (dialog.open() == IStatus.OK) { //TODO Is the window disposed?
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// Prepare writer parameters: |
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ReadWriteParameterMap parameters = new ReadWriteParameterMap(); |
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ObjectTranslatorFactory translatorFactory = new ObjectTranslatorFactory(); |
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translatorFactory.addXSDTranslators(true); |
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translatorFactory.addTranslator(new CDMPherogramAlignmentObjectTranslator(), true, SingleReadAlignmentRDFXMLConstants.DATA_TYPE_PHERORAGM_ALIGNMENT); |
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parameters.put(ReadWriteParameterNames.KEY_OBJECT_TRANSLATOR_FACTORY, translatorFactory); |
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ReadWriteParameterMap parameters = new ReadWriteParameterMap(); |
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ObjectTranslatorFactory translatorFactory = new ObjectTranslatorFactory(); |
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translatorFactory.addXSDTranslators(true); |
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translatorFactory.addTranslator(new CDMPherogramAlignmentObjectTranslator(), true, SingleReadAlignmentRDFXMLConstants.DATA_TYPE_PHERORAGM_ALIGNMENT); |
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parameters.put(ReadWriteParameterNames.KEY_OBJECT_TRANSLATOR_FACTORY, translatorFactory); |
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// Create writer and document adapters: |
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JPhyloIOEventWriter writer = factory.getWriter(wizard.getSelectedFormat()); |
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ListBasedDocumentDataAdapter document = new ListBasedDocumentDataAdapter(); |
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document.getMatrices().add(new CDMSequenceMatrixAdapter(sequence, wizard.getConsensusSequenceLabel())); |
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String consensusSequenceLabel = "Consensus sequence"; |
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JPhyloIOEventWriter writer = factory.getWriter(formatID); |
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ListBasedDocumentDataAdapter document = new ListBasedDocumentDataAdapter(); |
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document.getMatrices().add(new CDMSequenceMatrixAdapter(sequence, consensusSequenceLabel)); |
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try {
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writer.writeDocument(document, targetFile, parameters); |
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} |
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catch (IOException e) {
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e.printStackTrace(); |
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MessagingUtils.errorDialog("IO error", this,
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"An error occured when trying to export a consensus sequence alignment to the file \"" + |
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targetFile.getAbsolutePath() + "\".", TaxeditorMolecularPlugin.PLUGIN_ID, e, false); //TODO set pluginID |
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//TODO Use multi language error message. |
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// Write document: |
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try {
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writer.writeDocument(document, wizard.getSelectedFile(), parameters); |
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} |
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catch (IOException e) {
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e.printStackTrace(); |
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MessagingUtils.errorDialog("IO error", this,
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"An error occured when trying to export a consensus sequence alignment to the file \"" + |
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wizard.getSelectedFile().getAbsolutePath() + "\".", TaxeditorMolecularPlugin.PLUGIN_ID, e, false); //TODO set pluginID |
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//TODO Use multi language error message. |
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} |
|
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} |
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} |
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return null; |
Also available in: Unified diff
Missing dependency Apache commons.lang added to molecular.lib.
Single read alignment export feature now makes use of wizard. (Selecting which sequences to export is not yet supported.)