/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
*/
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.FeatureColourI;
+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.util.Map;
+
+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
boolean features = true;
- AlignmentAnnotation[] annotations;
+ private AlignmentAnnotation[] annotations;
- List<SequenceGroup> sequenceGroups;
-
- Hashtable alignmentProperties;
+ private boolean wholeView;
public AnnotationExporter()
{
this.ap = ap;
features = true;
CSVFormat.setVisible(false);
- frame.setTitle("Export Features");
+ frame.setTitle(MessageManager.getString("label.export_features"));
}
- public void exportAnnotations(AlignmentPanel ap,
- AlignmentAnnotation[] annotations, List<SequenceGroup> list,
- Hashtable alProperties)
+ public void exportAnnotations(AlignmentPanel ap)
{
this.ap = ap;
+ annotations = ap.av.isShowAnnotation() ? null : ap.av.getAlignment()
+ .getAlignmentAnnotation();
+ wholeView = true;
+ startExportAnnotation();
+ }
+
+ public void exportAnnotations(AlignmentPanel alp,
+ AlignmentAnnotation[] toExport)
+ {
+ ap = alp;
+ annotations = toExport;
+ wholeView = false;
+ startExportAnnotation();
+ }
+
+ private void startExportAnnotation()
+ {
features = 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)
jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle(features ? "Save Features to File"
- : "Save Annotation to File");
+ chooser.setDialogTitle(features ? 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 = getFileContents();
try
{
close_actionPerformed(null);
}
- public void toTextbox_actionPerformed(ActionEvent e)
+ private String getFileContents()
{
- String text = "No features found on alignment";
+ String text = MessageManager
+ .getString("label.no_features_on_alignment");
if (features)
{
+ Map<String, FeatureColourI> displayedFeatureColours = ap
+ .getFeatureRenderer().getDisplayedFeatureCols();
+ FeaturesFile formatter = new FeaturesFile();
+ SequenceI[] sequences = ap.av.getAlignment().getSequencesArray();
+ Map<String, FeatureColourI> featureColours = ap.getFeatureRenderer()
+ .getDisplayedFeatureCols();
+ boolean includeNonPositional = ap.av.isShowNPFeats();
if (GFFFormat.isSelected())
{
- text = new FeaturesFile().printGFFFormat(ap.av.getAlignment()
- .getDataset().getSequencesArray(),
- getDisplayedFeatureCols(), true, ap.av.isShowNpFeats());
+ text = new FeaturesFile().printGffFormat(ap.av.getAlignment()
+ .getDataset().getSequencesArray(), displayedFeatureColours,
+ true, ap.av.isShowNPFeats());
+ text = formatter.printGffFormat(sequences, featureColours, true,
+ includeNonPositional);
}
else
{
text = new FeaturesFile().printJalviewFormat(ap.av.getAlignment()
- .getDataset().getSequencesArray(),
- getDisplayedFeatureCols(), true, ap.av.isShowNpFeats());
+ .getDataset().getSequencesArray(), displayedFeatureColours,
+ true, ap.av.isShowNPFeats()); // ap.av.featuresDisplayed);
+ text = formatter.printJalviewFormat(sequences, featureColours,
+ true, includeNonPositional);
}
}
- else if (!features)
+ else
{
if (CSVFormat.isSelected())
{
}
else
{
- text = new AnnotationFile().printAnnotations(annotations,
- sequenceGroups, alignmentProperties);
+ if (wholeView)
+ {
+ text = new AnnotationFile().printAnnotationsForView(ap.av);
+ }
+ else
+ {
+ text = new AnnotationFile().printAnnotations(annotations, null,
+ null);
+ }
}
}
+ return text;
+ }
+ public void toTextbox_actionPerformed(ActionEvent e)
+ {
CutAndPasteTransfer cap = new CutAndPasteTransfer();
+
try
{
+ String text = getFileContents();
cap.setText(text);
Desktop.addInternalFrame(
cap,
(features ? MessageManager.formatMessage(
- "label.features_for_params", new String[]
- { ap.alignFrame.getTitle() }) : MessageManager
- .formatMessage("label.annotations_for_params",
- new String[]
- { ap.alignFrame.getTitle() })), 600, 500);
+ "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)
{
new OOMWarning((features ? 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);
+ "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();
}
close_actionPerformed(null);
}
- private Hashtable getDisplayedFeatureCols()
- {
- Hashtable fcols = new Hashtable();
- if (ap.av.featuresDisplayed == null)
- {
- return fcols;
- }
- Enumeration en = ap.av.featuresDisplayed.keys();
- FeatureRenderer fr = ap.seqPanel.seqCanvas.getFeatureRenderer(); // consider
- // higher
- // level
- // method ?
- while (en.hasMoreElements())
- {
- Object col = en.nextElement();
- fcols.put(col, fr.featureColours.get(col));
- }
- return fcols;
- }
-
public void close_actionPerformed(ActionEvent e)
{
try
toFile.setText(MessageManager.getString("label.to_file"));
toFile.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
toFile_actionPerformed(e);
toTextbox.setText(MessageManager.getString("label.to_textbox"));
toTextbox.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
toTextbox_actionPerformed(e);
close.setText(MessageManager.getString("action.close"));
close.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
close_actionPerformed(e);
JPanel jPanel3 = new JPanel();
FlowLayout flowLayout1 = new FlowLayout();
-
}
git://source.jalview.org / jalview.git / blobdiff