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Revision 7417db95

Added by Ben Stöver over 7 years ago

Exported single read sequences are now filled up with gaps. (Will be dependent on a parameter in the future.)
Texts in ExportSequenceToFileHandler extzernalized and translated.

View differences:

eu.etaxonomy.taxeditor.molecular/src/main/java/eu/etaxonomy/taxeditor/molecular/handler/ExportSequenceToFileHandler.java
10 10 
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.cdm.model.molecular.Sequence;


  		




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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.Messages;


  		




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


  		




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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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                }


  		




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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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                            file.getAbsolutePath() + "\".", TaxeditorMolecularPlugin.PLUGIN_ID, e, false);  //TODO set pluginID


  		




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                            //TODO Use multi language error message.


  		




  
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                    MessagingUtils.errorDialog(Messages.exportSequenceToFileHandlerIOErrorTitle, this,


  		




  
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                            String.format(Messages.exportSequenceToFileHandlerIOErrorMessage,


  		




  
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                                    file.getAbsolutePath()), TaxeditorMolecularPlugin.PLUGIN_ID, e, false);


  		




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                }


  		




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            }


  		




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        }


  		












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