X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationExporter.java;h=81960e08a22ba15256ba12bf4750b8ce73576842;hb=3da878124135ff033f42d19d8733891b09e953cd;hp=02758fa80593b17e1dd0c5e10cbe59eb10a2330a;hpb=87ea83af3e209a8c3a4b19f9530a9c05b4541148;p=jalview.git diff --git a/src/jalview/gui/AnnotationExporter.java b/src/jalview/gui/AnnotationExporter.java index 02758fa..81960e0 100644 --- a/src/jalview/gui/AnnotationExporter.java +++ b/src/jalview/gui/AnnotationExporter.java @@ -1,33 +1,53 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8) - * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview. * * Jalview is free software: you can redistribute it and/or * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. + * as published by the Free Software Foundation, either version 3 + * of the License, or (at your option) any later version. * * Jalview is distributed in the hope that it will be useful, but * WITHOUT ANY WARRANTY; without even the implied warranty * of MERCHANTABILITY or FITNESS FOR A PARTICULAR * PURPOSE. See the GNU General Public License for more details. * - * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * You should have received a copy of the GNU General Public License + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. */ package jalview.gui; -import java.util.*; -import java.util.List; - -import java.awt.*; -import java.awt.event.*; -import javax.swing.*; - -import jalview.datamodel.*; -import jalview.io.*; +import jalview.api.FeatureRenderer; +import jalview.bin.Cache; +import jalview.datamodel.AlignmentAnnotation; +import jalview.datamodel.SequenceI; +import jalview.io.AnnotationFile; +import jalview.io.FeaturesFile; +import jalview.io.JalviewFileChooser; +import jalview.io.JalviewFileView; import jalview.util.MessageManager; +import java.awt.BorderLayout; +import java.awt.Color; +import java.awt.FlowLayout; +import java.awt.event.ActionEvent; +import java.awt.event.ActionListener; +import java.io.FileWriter; +import java.io.PrintWriter; + +import javax.swing.BorderFactory; +import javax.swing.ButtonGroup; +import javax.swing.JButton; +import javax.swing.JInternalFrame; +import javax.swing.JLabel; +import javax.swing.JLayeredPane; +import javax.swing.JPanel; +import javax.swing.JRadioButton; +import javax.swing.SwingConstants; + /** * * GUI dialog for exporting features or alignment annotations depending upon @@ -38,20 +58,22 @@ import jalview.util.MessageManager; */ public class AnnotationExporter extends JPanel { - JInternalFrame frame; + private JInternalFrame frame; - AlignmentPanel ap; + private AlignmentPanel ap; - boolean features = true; + /* + * true if exporting features, false if exporting annotations + */ + private boolean exportFeatures = true; - AlignmentAnnotation[] annotations; + private AlignmentAnnotation[] annotations; - List sequenceGroups; + private boolean wholeView; - Hashtable alignmentProperties; - - public AnnotationExporter() + public AnnotationExporter(AlignmentPanel panel) { + this.ap = panel; try { jbInit(); @@ -67,76 +89,69 @@ public class AnnotationExporter extends JPanel frame.getPreferredSize().height); } - public void exportFeatures(AlignmentPanel ap) + /** + * Configures the diglog for options to export visible features + */ + public void exportFeatures() { - this.ap = ap; - features = true; + exportFeatures = true; CSVFormat.setVisible(false); - frame.setTitle("Export Features"); + frame.setTitle(MessageManager.getString("label.export_features")); } - public void exportAnnotations(AlignmentPanel ap, - AlignmentAnnotation[] annotations, List list, - Hashtable alProperties) + /** + * Configures the dialog for options to export all visible annotations + */ + public void exportAnnotations() { - this.ap = ap; - features = false; + boolean showAnnotation = ap.av.isShowAnnotation(); + exportAnnotation(showAnnotation ? null + : ap.av.getAlignment().getAlignmentAnnotation(), true); + } + + /** + * Configures the dialog for options to export the given annotation row + * + * @param toExport + */ + public void exportAnnotation(AlignmentAnnotation toExport) + { + exportAnnotation(new AlignmentAnnotation[] { toExport }, false); + } + + private void exportAnnotation(AlignmentAnnotation[] toExport, + boolean forWholeView) + { + wholeView = forWholeView; + annotations = toExport; + exportFeatures = false; GFFFormat.setVisible(false); CSVFormat.setVisible(true); - this.annotations = annotations; - this.sequenceGroups = list; - this.alignmentProperties = alProperties; - frame.setTitle("Export Annotations"); + frame.setTitle(MessageManager.getString("label.export_annotations")); } - public void toFile_actionPerformed(ActionEvent e) + private void toFile_actionPerformed() { + // TODO: JAL-3048 JalviewFileChooser - Save option JalviewFileChooser chooser = new JalviewFileChooser( - jalview.bin.Cache.getProperty("LAST_DIRECTORY")); + Cache.getProperty("LAST_DIRECTORY")); chooser.setFileView(new JalviewFileView()); - chooser.setDialogTitle(features ? "Save Features to File" - : "Save Annotation to File"); - chooser.setToolTipText("Save"); + chooser.setDialogTitle(exportFeatures + ? MessageManager.getString("label.save_features_to_file") + : MessageManager.getString("label.save_annotation_to_file")); + chooser.setToolTipText(MessageManager.getString("action.save")); int value = chooser.showSaveDialog(this); if (value == JalviewFileChooser.APPROVE_OPTION) { - String text = "No features found on alignment"; - if (features) - { - if (GFFFormat.isSelected()) - { - text = new FeaturesFile().printGFFFormat(ap.av.getAlignment() - .getDataset().getSequencesArray(), - getDisplayedFeatureCols(), true, ap.av.isShowNpFeats());// ap.av.featuresDisplayed//); - } - else - { - text = new FeaturesFile().printJalviewFormat(ap.av.getAlignment() - .getDataset().getSequencesArray(), - getDisplayedFeatureCols(), true, ap.av.isShowNpFeats()); // ap.av.featuresDisplayed); - } - } - else - { - if (CSVFormat.isSelected()) - { - text = new AnnotationFile().printCSVAnnotations(annotations); - } - else - { - text = new AnnotationFile().printAnnotations(annotations, - sequenceGroups, alignmentProperties); - } - } + String text = getText(); try { - java.io.PrintWriter out = new java.io.PrintWriter( - new java.io.FileWriter(chooser.getSelectedFile())); - + PrintWriter out = new PrintWriter( + new FileWriter(chooser.getSelectedFile())); out.print(text); out.close(); } catch (Exception ex) @@ -145,78 +160,106 @@ public class AnnotationExporter extends JPanel } } - close_actionPerformed(null); + close_actionPerformed(); } - public void toTextbox_actionPerformed(ActionEvent e) + /** + * Answers the text to output for either Features (in GFF or Jalview format) or + * Annotations (in CSV or Jalview format) + * + * @return + */ + private String getText() { - String text = "No features found on alignment"; - if (features) + return exportFeatures ? getFeaturesText() : getAnnotationsText(); + } + + /** + * Returns the text contents for output of annotations in either CSV or Jalview + * format + * + * @return + */ + private String getAnnotationsText() + { + String text; + if (CSVFormat.isSelected()) { - if (GFFFormat.isSelected()) - { - text = new FeaturesFile().printGFFFormat(ap.av.getAlignment() - .getDataset().getSequencesArray(), - getDisplayedFeatureCols(), true, ap.av.isShowNpFeats()); - } - else - { - text = new FeaturesFile().printJalviewFormat(ap.av.getAlignment() - .getDataset().getSequencesArray(), - getDisplayedFeatureCols(), true, ap.av.isShowNpFeats()); - } + text = new AnnotationFile().printCSVAnnotations(annotations); } - else if (!features) + else { - if (CSVFormat.isSelected()) + if (wholeView) { - text = new AnnotationFile().printCSVAnnotations(annotations); + text = new AnnotationFile().printAnnotationsForView(ap.av); } else { - text = new AnnotationFile().printAnnotations(annotations, - sequenceGroups, alignmentProperties); + text = new AnnotationFile().printAnnotations(annotations, null, + null); } } + return text; + } - CutAndPasteTransfer cap = new CutAndPasteTransfer(); - try + /** + * Returns the text contents for output of features in either GFF or Jalview + * format + * + * @return + */ + private String getFeaturesText() + { + String text; + SequenceI[] sequences = ap.av.getAlignment().getSequencesArray(); + boolean includeNonPositional = ap.av.isShowNPFeats(); + + FeaturesFile formatter = new FeaturesFile(); + final FeatureRenderer fr = ap.getFeatureRenderer(); + if (GFFFormat.isSelected()) { - cap.setText(text); - Desktop.addInternalFrame(cap, (features ? "Features for - " - : "Annotations for - ") + ap.alignFrame.getTitle(), 600, 500); - } catch (OutOfMemoryError oom) + text = formatter.printGffFormat(sequences, fr, includeNonPositional); + } + else { - new OOMWarning("generating " - + (features ? "Features for - " : "Annotations for - ") - + ap.alignFrame.getTitle(), oom); - cap.dispose(); + text = formatter.printJalviewFormat(sequences, fr, + includeNonPositional); } - - close_actionPerformed(null); + return text; } - private Hashtable getDisplayedFeatureCols() + private void toTextbox_actionPerformed() { - Hashtable fcols = new Hashtable(); - if (ap.av.featuresDisplayed == null) + CutAndPasteTransfer cap = new CutAndPasteTransfer(); + + try { - return fcols; - } - Enumeration en = ap.av.featuresDisplayed.keys(); - FeatureRenderer fr = ap.seqPanel.seqCanvas.getFeatureRenderer(); // consider - // higher - // level - // method ? - while (en.hasMoreElements()) + String text = getText(); + cap.setText(text); + Desktop.addInternalFrame(cap, (exportFeatures ? MessageManager + .formatMessage("label.features_for_params", new String[] + { ap.alignFrame.getTitle() }) + : MessageManager.formatMessage("label.annotations_for_params", + new String[] + { ap.alignFrame.getTitle() })), + 600, 500); + } catch (OutOfMemoryError oom) { - Object col = en.nextElement(); - fcols.put(col, fr.featureColours.get(col)); + new OOMWarning((exportFeatures ? MessageManager.formatMessage( + "label.generating_features_for_params", new String[] + { ap.alignFrame.getTitle() }) + : MessageManager.formatMessage( + "label.generating_annotations_for_params", + new String[] + { ap.alignFrame.getTitle() })), + oom); + cap.dispose(); } - return fcols; + + close_actionPerformed(); } - public void close_actionPerformed(ActionEvent e) + private void close_actionPerformed() { try { @@ -233,25 +276,28 @@ public class AnnotationExporter extends JPanel toFile.setText(MessageManager.getString("label.to_file")); toFile.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { - toFile_actionPerformed(e); + toFile_actionPerformed(); } }); toTextbox.setText(MessageManager.getString("label.to_textbox")); toTextbox.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { - toTextbox_actionPerformed(e); + toTextbox_actionPerformed(); } }); close.setText(MessageManager.getString("action.close")); close.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { - close_actionPerformed(e); + close_actionPerformed(); } }); jalviewFormat.setOpaque(false); @@ -302,5 +348,4 @@ public class AnnotationExporter extends JPanel JPanel jPanel3 = new JPanel(); FlowLayout flowLayout1 = new FlowLayout(); - }