/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
package jalview.gui;
import jalview.datamodel.AlignmentAnnotation;
-import jalview.datamodel.SequenceGroup;
import jalview.io.AnnotationFile;
import jalview.io.FeaturesFile;
import jalview.io.JalviewFileChooser;
import java.awt.FlowLayout;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
-import java.util.Hashtable;
-import java.util.List;
import javax.swing.BorderFactory;
import javax.swing.ButtonGroup;
boolean features = true;
- AlignmentAnnotation[] annotations;
+ private AlignmentAnnotation[] annotations;
- List<SequenceGroup> sequenceGroups;
-
- Hashtable alignmentProperties;
+ private boolean wholeView;
public AnnotationExporter()
{
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(MessageManager.getString("label.export_annotations"));
}
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(), ap
- .getFeatureRenderer().getDisplayedFeatureCols(), true,
- ap.av.isShowNpFeats());// ap.av.featuresDisplayed//);
- }
- else
- {
- text = new FeaturesFile().printJalviewFormat(ap.av.getAlignment()
- .getDataset().getSequencesArray(), ap
- .getFeatureRenderer().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 = MessageManager.getString("label.no_features_on_alignment");
+ String text = MessageManager
+ .getString("label.no_features_on_alignment");
if (features)
{
if (GFFFormat.isSelected())
{
text = new FeaturesFile().printGFFFormat(ap.av.getAlignment()
.getDataset().getSequencesArray(), ap.getFeatureRenderer()
- .getDisplayedFeatureCols(), true, ap.av.isShowNpFeats());
+ .getDisplayedFeatureCols(), true, ap.av.isShowNpFeats());// ap.av.featuresDisplayed//);
}
else
{
text = new FeaturesFile().printJalviewFormat(ap.av.getAlignment()
.getDataset().getSequencesArray(), ap.getFeatureRenderer()
- .getDisplayedFeatureCols(), true, ap.av.isShowNpFeats());
+ .getDisplayedFeatureCols(), true, ap.av.isShowNpFeats()); // ap.av.featuresDisplayed);
}
}
- 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,
JPanel jPanel3 = new JPanel();
FlowLayout flowLayout1 = new FlowLayout();
-
}