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Revision 00d1a6ce

Added by Ben Stöver over 7 years ago

Export single read alignment wizard separated into two pages.
Option to elongate sequences added.
Application information parameters of JPhyloIO set.

View differences:

eu.etaxonomy.taxeditor.molecular/src/main/java/eu/etaxonomy/taxeditor/molecular/handler/ExportSequenceToFileHandler.java
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package eu.etaxonomy.taxeditor.molecular.handler;
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import info.bioinfweb.commons.bio.SequenceUtils;


  		




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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 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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import eu.etaxonomy.taxeditor.util.ApplicationUtil;


  		




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/**


  		




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 * Allows to export a single read alignment to various alignment formats using


  		




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 * <a href="http://bioinfweb.info/JPhyloIO/">JPhyloIO</a>.


  		




  
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 * <a href="http://bioinfweb.info/JPhyloIO/"><i>JPhyloIO</i>


  		




  
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 * </a>.


  		




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 *


  		




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 * @author Ben Stöver


  		




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 * @date 24.04.2016


  		




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            if (dialog.open() == IStatus.OK) {


  		




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                // Prepare writer parameters:


  		




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                ReadWriteParameterMap parameters = new ReadWriteParameterMap();


  		




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                parameters.put(ReadWriteParameterNames.KEY_SEQUENCE_EXTENSION_TOKEN, Character.toString(SequenceUtils.GAP_CHAR));


  		




  
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                parameters.put(ReadWriteParameterNames.KEY_APPLICATION_NAME, ApplicationUtil.getTitle());


  		




  
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                parameters.put(ReadWriteParameterNames.KEY_APPLICATION_VERSION, ApplicationUtil.getVersion());


  		




  
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                parameters.put(ReadWriteParameterNames.KEY_APPLICATION_URL, "http://cybertaxonomy.eu/taxeditor/");  //TODO Specify URL obtained from a central class?


  		




  
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                parameters.put(ReadWriteParameterNames.KEY_SEQUENCE_EXTENSION_TOKEN, wizard.getModel().getElongationToken());


  		




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                // Create and register object translator for writing pherogram alignment shifts:


  		




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                ObjectTranslatorFactory translatorFactory = new ObjectTranslatorFactory();


  		












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