/ - Diff - EDIT - EDIT Project Management

      eu.etaxonomy.taxeditor.cdmlib,
      eu.etaxonomy.taxeditor.editor,
      eu.etaxonomy.taxeditor.store,
      eu.etaxonomy.taxeditor.molecular.lib
      eu.etaxonomy.taxeditor.molecular.lib,
      org.eclipse.core.databinding.observable;bundle-version="1.4.0",
      org.eclipse.core.databinding;bundle-version="1.4.0",
      org.eclipse.jface.databinding;bundle-version="1.5.0",
      org.eclipse.core.databinding.property;bundle-version="1.4.0"
     Bundle-RequiredExecutionEnvironment: JavaSE-1.7
     Bundle-ActivationPolicy: lazy
     Bundle-Vendor: EDIT

     import info.bioinfweb.jphyloio.factory.JPhyloIOReaderWriterFactory;
     import info.bioinfweb.jphyloio.objecttranslation.ObjectTranslatorFactory;
     import java.io.File;
     import java.io.IOException;
     import org.eclipse.core.commands.AbstractHandler;
-...
                     parameters.put(ReadWriteParameterNames.KEY_OBJECT_TRANSLATOR_FACTORY, translatorFactory);
                     // Create writer and document adapters:
                     JPhyloIOEventWriter writer = factory.getWriter(wizard.getSelectedFormat().getFormatID());
                     JPhyloIOEventWriter writer = factory.getWriter(wizard.getModel().getFormatInfo().getFormatID());
                     ListBasedDocumentDataAdapter document = new ListBasedDocumentDataAdapter();
                     document.getMatrices().add(new CDMSequenceMatrixAdapter(sequence, wizard.getConsensusSequenceLabel()));
                     document.getMatrices().add(new CDMSequenceMatrixAdapter(sequence, wizard.getModel().getConsensusSequenceLabel()));
                     // Write document:
                     File file = new File(wizard.getModel().getFileName());
                     try {
                         writer.writeDocument(document, wizard.getSelectedFile(), parameters);
                         writer.writeDocument(document, file, parameters);
+                    }
                     catch (IOException e) {
                         e.printStackTrace();
                         MessagingUtils.errorDialog("IO error", this,
                                 "An error occured when trying to export a consensus sequence alignment to the file \"" +
                                 wizard.getSelectedFile().getAbsolutePath() + "\".", TaxeditorMolecularPlugin.PLUGIN_ID, e, false);  //TODO set pluginID
                                 file.getAbsolutePath() + "\".", TaxeditorMolecularPlugin.PLUGIN_ID, e, false);  //TODO set pluginID
                                 //TODO Use multi language error message.
+                    }
+                }

     /**
     * Copyright (C) 2016 EDIT
     * European Distributed Institute of Taxonomy
     * http://www.e-taxonomy.eu
+    *
     * The contents of this file are subject to the Mozilla Public License Version 1.1
     * See LICENSE.TXT at the top of this package for the full license terms.
     */
     package eu.etaxonomy.taxeditor.molecular.io.wizard;
     import org.eclipse.core.databinding.validation.IValidator;
     import org.eclipse.core.databinding.validation.ValidationStatus;
     import org.eclipse.core.runtime.IStatus;
     import org.eclipse.jface.databinding.swt.ISWTObservableValue;
     import org.eclipse.swt.events.SelectionAdapter;
     import org.eclipse.swt.events.SelectionEvent;
     import org.eclipse.swt.widgets.Button;
     /**
      * Validator to make sure a non-empty consensus sequence name is provided. It must be registered as a selection listener
      * of the export consensus sequence check box of the wizard page in order to work properly.
+     *
      * @author Ben Stöver
      * @date 16.11.2016
      */
     public class ConsensusSequenceLabelValidator extends SelectionAdapter implements IValidator {
         private boolean exportConsensusSequence = true;
         private ISWTObservableValue checkBoxObersable;
         public ConsensusSequenceLabelValidator(ISWTObservableValue checkBoxObersable) {
             super();
             this.checkBoxObersable = checkBoxObersable;
+        }
         /**
          * {@inheritDoc}
          */
         @Override
         public IStatus validate(Object value) {
             if (exportConsensusSequence && ((value == null) || ((String)value).isEmpty())) {
                 return ValidationStatus.error("The consensus sequence label must not be empty.");  //TODO multi language
+            }
             else {
                 return ValidationStatus.ok();
+            }
+        }
         /**
          * {@inheritDoc}
          */
         @Override
         public void widgetSelected(SelectionEvent event) {
             exportConsensusSequence = ((Button)event.getSource()).getSelection();
             // Trigger validation of label:
             Object value = checkBoxObersable.getValue();
             checkBoxObersable.setValue("");
             checkBoxObersable.setValue(value);
+        }
+    }

     /**
     * Copyright (C) 2016 EDIT
     * European Distributed Institute of Taxonomy
     * http://www.e-taxonomy.eu
+    *
     * The contents of this file are subject to the Mozilla Public License Version 1.1
     * See LICENSE.TXT at the top of this package for the full license terms.
     */
     package eu.etaxonomy.taxeditor.molecular.io.wizard;
     import org.eclipse.core.databinding.validation.MultiValidator;
     import org.eclipse.core.runtime.IStatus;
     /**
      * @author bstoe_01
      * @date 16.11.2016
+     *
      */
     public class ExportSingleReadAlignmentValidator extends MultiValidator {
         /**
          * {@inheritDoc}
          */
         @Override
         protected IStatus validate() {
             // TODO Auto-generated method stub
             return null;
+        }
+    }

     package eu.etaxonomy.taxeditor.molecular.io.wizard;
     import info.bioinfweb.jphyloio.formatinfo.JPhyloIOFormatInfo;
     import java.io.File;
     import org.eclipse.jface.wizard.Wizard;
-...
      * @date 23.06.2016
      */
     public class ExportSingleReadAlignmentWizard extends Wizard {
         private ExportSingleReadAlignmentWizardPage page;
         private ExportSingleReadAlignmentWizardModel model = new ExportSingleReadAlignmentWizardModel();
         private JPhyloIOFormatInfo selectedFormat = null;
         private File selectedFile = null;
         private String consensusSequenceLabel = null;
         private ExportSingleReadAlignmentWizardPage page;
         public ExportSingleReadAlignmentWizard() {
             setWindowTitle("Export single read alignment");  //TODO Use multi languange message
             setWindowTitle("Export single read alignment");  //TODO Use multi language message
+        }
         public ExportSingleReadAlignmentWizardModel getModel() {
             return model;
+        }
-...
         @Override
         public boolean performFinish() {
             if (!page.getConsensusSequenceLabel().isEmpty()) {
                 selectedFormat = page.getSelectedFormat();
                 selectedFile = page.getSelectedFile();
                 consensusSequenceLabel = page.getConsensusSequenceLabel();
                 return true;
+            }
             else {
                 return false;  //TODO Display according error message in wizard heading, as long as valid inputs are not completed.
+            }
+        }
         public JPhyloIOFormatInfo getSelectedFormat() {
             return selectedFormat;
+        }
         public File getSelectedFile() {
             return selectedFile;
+        }
         public String getConsensusSequenceLabel() {
             return consensusSequenceLabel;
             return true;
             //TODO Add default extension to file, if necessary?
+        }
+    }

     /**
     * Copyright (C) 2016 EDIT
     * European Distributed Institute of Taxonomy
     * http://www.e-taxonomy.eu
+    *
     * The contents of this file are subject to the Mozilla Public License Version 1.1
     * See LICENSE.TXT at the top of this package for the full license terms.
     */
     package eu.etaxonomy.taxeditor.molecular.io.wizard;
     import info.bioinfweb.jphyloio.formatinfo.JPhyloIOFormatInfo;
     import org.eclipse.core.databinding.observable.value.IObservableValue;
     import org.eclipse.core.databinding.observable.value.WritableValue;
     /**
      * The data model for a wizard to export single read alignments to different file formats using <i>JPhyloIO</i>.
+     *
      * @author Ben Stöver
      * @date 16.11.2016
      */
     public class ExportSingleReadAlignmentWizardModel {
         private IObservableValue exportSingleReads = new WritableValue(null, Boolean.class);
         private IObservableValue exportConsensusSequence = new WritableValue(null, Boolean.class);
         private IObservableValue consensusSequenceLabel = new WritableValue(null, String.class);
         private IObservableValue formatInfo = new WritableValue(null, JPhyloIOFormatInfo.class);
         private IObservableValue fileName = new WritableValue(null, String.class);
         public boolean isExportSingleReads() {
             return (Boolean)exportSingleReads.getValue();
+        }
         protected IObservableValue getExportSingleReadsObservable() {
             return exportSingleReads;
+        }
         public boolean isExportConsensusSequence() {
             return (Boolean)exportConsensusSequence.getValue();
+        }
         protected IObservableValue getExportConsensusSequenceObservable() {
             return exportConsensusSequence;
+        }
         public String getConsensusSequenceLabel() {
             return (String)consensusSequenceLabel.getValue();
+        }
         protected IObservableValue getConsensusSequenceLabelObservable() {
             return consensusSequenceLabel;
+        }
         public JPhyloIOFormatInfo getFormatInfo() {
             return (JPhyloIOFormatInfo)formatInfo.getValue();
+        }
         protected IObservableValue getFormatInfoObservable() {
             return formatInfo;
+        }
         public String getFileName() {
             return (String)fileName.getValue();
+        }
         protected IObservableValue getFileNameObservable() {
             return fileName;
+        }
+    }

     import info.bioinfweb.jphyloio.factory.JPhyloIOReaderWriterFactory;
     import info.bioinfweb.jphyloio.formatinfo.JPhyloIOFormatInfo;
     import java.io.File;
     import java.util.ArrayList;
     import java.util.Collections;
     import java.util.List;
     import org.eclipse.core.databinding.DataBindingContext;
     import org.eclipse.core.databinding.UpdateValueStrategy;
     import org.eclipse.jface.databinding.swt.ISWTObservableValue;
     import org.eclipse.jface.databinding.swt.SWTObservables;
     import org.eclipse.jface.databinding.wizard.WizardPageSupport;
     import org.eclipse.jface.wizard.WizardPage;
     import org.eclipse.swt.SWT;
     import org.eclipse.swt.events.SelectionAdapter;
-...
          */
         @Override
         public void createControl(Composite parent) {
             DataBindingContext dbc = new DataBindingContext();
             WizardPageSupport.create(this, dbc);
             Composite container = new Composite(parent, SWT.NULL);
             setControl(container);
-...
             fd_exportSingleReadsCB.left = new FormAttachment(0, 10);
             exportSingleReadsCB.setLayoutData(fd_exportSingleReadsCB);
             exportSingleReadsCB.setText("Export single reads");
             dbc.bindValue(SWTObservables.observeSelection(exportSingleReadsCB),
                     ((ExportSingleReadAlignmentWizard)getWizard()).getModel().getExportSingleReadsObservable());
             exportConsensusSequenceCB = new Button(container, SWT.CHECK);
             exportConsensusSequenceCB.setSelection(true);
-...
             fd_exportConsensusSequenceCB.left = new FormAttachment(0, 10);
             exportConsensusSequenceCB.setLayoutData(fd_exportConsensusSequenceCB);
             exportConsensusSequenceCB.setText("Export consensus sequence");
             ISWTObservableValue exportConsensusSequenceObservable = SWTObservables.observeSelection(exportConsensusSequenceCB);
             dbc.bindValue(exportConsensusSequenceObservable,
                     ((ExportSingleReadAlignmentWizard)getWizard()).getModel().getExportConsensusSequenceObservable());
             // Connect validation of check box and text field for consensus sequence label:
             ConsensusSequenceLabelValidator consensusSequenceLabelValidator =
                     new ConsensusSequenceLabelValidator(exportConsensusSequenceObservable);
             exportConsensusSequenceCB.addSelectionListener(consensusSequenceLabelValidator);
             consensusSequenceNameTextField = new Text(container, SWT.BORDER);
             consensusSequenceNameTextField.setText("ConsensusSequence");
-...
             fd_consensusSequenceNameTextField.top = new FormAttachment(exportConsensusSequenceCB, 6);
             fd_consensusSequenceNameTextField.bottom = new FormAttachment(30, 26);
             consensusSequenceNameTextField.setLayoutData(fd_consensusSequenceNameTextField);
             dbc.bindValue(SWTObservables.observeText(consensusSequenceNameTextField, SWT.Modify),  // WidgetProperties.text().observe(consensusSequenceNameTextField) does not perform a refresh, although SWTObservables seems to be deprecated.
                     ((ExportSingleReadAlignmentWizard)getWizard()).getModel().getConsensusSequenceLabelObservable(),
                     new UpdateValueStrategy().setAfterConvertValidator(consensusSequenceLabelValidator), null);
             Label lblFormat = new Label(container, SWT.NONE);
             FormData fd_lblFormat = new FormData();
-...
             fd_text.left = new FormAttachment(lblAlignmentFile, 6);
             fd_text.top = new FormAttachment(lblSelectTheExport, 6);
             fileTextField.setLayoutData(fd_text);
             dbc.bindValue(SWTObservables.observeText(fileTextField, SWT.Modify),
                     ((ExportSingleReadAlignmentWizard)getWizard()).getModel().getFileNameObservable(),
                     new UpdateValueStrategy().setAfterConvertValidator(new FileNameValidator()), null);
             Button btnBrowse = new Button(container, SWT.NONE);
             btnBrowse.addSelectionListener(new SelectionAdapter() {
-...
                 public void widgetSelected(SelectionEvent e) {
                     FileDialog dialog = new FileDialog(getShell(), SWT.OPEN);
                     dialog.setText("Export to");  //TODO Make multi language
                     //fd.setFilterPath("C:/");
                     ContentExtensionFileFilter filter = getSelectedFormat().createFileFilter();
                     dialog.setFilterExtensions(new String[]{filter.getExtensionsAsString()});
                     dialog.setFilterNames(new String[]{filter.getDescription()});
-...
                     if (selectedFile != null) {  // Otherwise selecting was canceled.
                         fileTextField.setText(selectedFile);
+                    }
                     //TODO Add default extension, if necessary.
+                }
             });
             fd_text.right = new FormAttachment(100, -134);
-...
             for (JPhyloIOFormatInfo formatInfo : FORMATS) {
                 formatComboBox.add(formatInfo.getFormatName());
+            }
             //TODO Bind property and somehow handle translation. (Or use model view combo box from JFace.)
             FormData fd_formatComboBox = new FormData();
             fd_formatComboBox.right = new FormAttachment(consensusSequenceNameTextField, 0, SWT.RIGHT);
-...
+         *
          * @return the format info or {@code null}, if none was yet selected
          */
         public JPhyloIOFormatInfo getSelectedFormat() {
         private JPhyloIOFormatInfo getSelectedFormat() {
             if (formatComboBox != null) {
                 int index = formatComboBox.getSelectionIndex();
                 if (index > -1) {
-...
+            }
             return null;
+        }
         public File getSelectedFile() {
             if (fileTextField !=  null) {
                 return new File(fileTextField.getText());
+            }
             else {
                 return null;
+            }
+        }
         public String getConsensusSequenceLabel() {
             if (consensusSequenceNameTextField != null) {
                 return consensusSequenceNameTextField.getText();
+            }
             else {
                 return null;
+            }
+        }
+    }

     /**
     * Copyright (C) 2016 EDIT
     * European Distributed Institute of Taxonomy
     * http://www.e-taxonomy.eu
+    *
     * The contents of this file are subject to the Mozilla Public License Version 1.1
     * See LICENSE.TXT at the top of this package for the full license terms.
     */
     package eu.etaxonomy.taxeditor.molecular.io.wizard;
     import org.eclipse.core.databinding.validation.IValidator;
     import org.eclipse.core.databinding.validation.ValidationStatus;
     import org.eclipse.core.runtime.IStatus;
     /**
      * Validator to make sure a non-empty file name is provided.
+     *
      * @author Ben Stöver
      * @date 16.11.2016
      */
     public class FileNameValidator implements IValidator {
         /**
          * {@inheritDoc}
          */
         @Override
         public IStatus validate(Object value) {
             if ((value == null) || ((String)value).isEmpty()) {
                 return ValidationStatus.error("The file name must not be empty.");
+            }
             else {
                 return ValidationStatus.ok();
+            }
             //TODO Display warning, if the file extension does not match the selected format? (An according listener would have to be registered.)
+        }
+    }

Project

General

Profile

EDIT

Revision 661914be

Added by Ben Stöver over 6 years ago