/*
- * 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.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
*/
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<SequenceGroup> sequenceGroups;
+ private boolean wholeView;
- Hashtable alignmentProperties;
-
- public AnnotationExporter()
+ public AnnotationExporter(AlignmentPanel panel)
{
+ this.ap = panel;
try
{
jbInit();
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(MessageManager.getString("label.export_features"));
}
- public void exportAnnotations(AlignmentPanel ap,
- AlignmentAnnotation[] annotations, List<SequenceGroup> 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(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 ? MessageManager.getString("label.save_features_to_file")
+ chooser.setDialogTitle(exportFeatures
+ ? MessageManager.getString("label.save_features_to_file")
: MessageManager.getString("label.save_annotation_to_file"));
chooser.setToolTipText(MessageManager.getString("action.save"));
if (value == JalviewFileChooser.APPROVE_OPTION)
{
- String text = MessageManager.getString("label.no_features_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)
}
}
- 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 = MessageManager.getString("label.no_features_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;
+ }
+
+ /**
+ * 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())
+ {
+ text = formatter.printGffFormat(sequences, fr, includeNonPositional);
+ }
+ else
+ {
+ text = formatter.printJalviewFormat(sequences, fr,
+ includeNonPositional);
+ }
+ return text;
+ }
+ private void toTextbox_actionPerformed()
+ {
CutAndPasteTransfer cap = new CutAndPasteTransfer();
+
try
{
+ String text = getText();
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);
+ 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)
{
- new OOMWarning((features ? MessageManager.formatMessage(
+ 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);
+ { 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.getFeaturesDisplayed() == null)
- {
- return fcols;
- }
- Enumeration en = ap.av.getFeaturesDisplayed().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;
+ close_actionPerformed();
}
- public void close_actionPerformed(ActionEvent e)
+ private void close_actionPerformed()
{
try
{
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);
JPanel jPanel3 = new JPanel();
FlowLayout flowLayout1 = new FlowLayout();
-
}
git://source.jalview.org / jalview.git / blobdiff