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Revision 9a9359ce

Added by Ben Stöver over 7 years ago

New JPhyloIO package now exported by molecular.lib.
SingleReadAlignmentPredicates renamed to SingleReadAlignmentRDFXMLConstants.
Pherogram alignment shifts are now written to single read export unsing a custom ObjectTranslator implementation.

View differences:

eu.etaxonomy.taxeditor.molecular/src/main/java/eu/etaxonomy/taxeditor/molecular/handler/ExportSequenceToFileHandler.java
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import info.bioinfweb.jphyloio.JPhyloIOEventWriter;


  		




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import info.bioinfweb.jphyloio.ReadWriteParameterMap;


  		




  
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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 eu.etaxonomy.taxeditor.editor.EditorUtil;


  		




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import eu.etaxonomy.taxeditor.model.MessagingUtils;


  		




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import eu.etaxonomy.taxeditor.molecular.TaxeditorMolecularPlugin;


  		




  
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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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            //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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            ReadWriteParameterMap parameters = new ReadWriteParameterMap();


  		




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            String consensusSequenceLabel = "Consensus sequence";


  		




  
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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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            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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