*/
package jalview.gui;
+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 java.awt.FlowLayout;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
+import java.util.List;
+import java.util.Map;
import javax.swing.BorderFactory;
import javax.swing.ButtonGroup;
public void exportAnnotations(AlignmentPanel ap)
{
this.ap = ap;
- annotations = ap.av.isShowAnnotation() ? null : ap.av.getAlignment()
- .getAlignmentAnnotation();
+ annotations = ap.av.isShowAnnotation() ? null
+ : ap.av.getAlignment().getAlignmentAnnotation();
wholeView = true;
startExportAnnotation();
}
jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle(features ? MessageManager
- .getString("label.save_features_to_file") : MessageManager
- .getString("label.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);
.getString("label.no_features_on_alignment");
if (features)
{
+ FeaturesFile formatter = new FeaturesFile();
+ SequenceI[] sequences = ap.av.getAlignment().getSequencesArray();
+ Map<String, FeatureColourI> featureColours = ap.getFeatureRenderer()
+ .getDisplayedFeatureCols();
+ List<String> featureGroups = ap.getFeatureRenderer()
+ .getDisplayedFeatureGroups();
+ boolean includeNonPositional = ap.av.isShowNPFeats();
if (GFFFormat.isSelected())
{
- text = new FeaturesFile().printGFFFormat(ap.av.getAlignment()
- .getDataset().getSequencesArray(), ap.getFeatureRenderer()
- .getDisplayedFeatureCols(), true, ap.av.isShowNPFeats());// ap.av.featuresDisplayed//);
+ text = formatter.printGffFormat(sequences, featureColours,
+ featureGroups, includeNonPositional);
}
else
{
- text = new FeaturesFile().printJalviewFormat(ap.av.getAlignment()
- .getDataset().getSequencesArray(), ap.getFeatureRenderer()
- .getDisplayedFeatureCols(), true, ap.av.isShowNPFeats()); // ap.av.featuresDisplayed);
+ text = formatter.printJalviewFormat(sequences, featureColours,
+ featureGroups, includeNonPositional);
}
}
else
{
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() })),
+ 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);
} catch (OutOfMemoryError oom)
{
new OOMWarning((features ? MessageManager.formatMessage(
- "label.generating_features_for_params",
- new String[] { ap.alignFrame.getTitle() })
+ "label.generating_features_for_params", new String[]
+ { ap.alignFrame.getTitle() })
: MessageManager.formatMessage(
"label.generating_annotations_for_params",
- new String[] { ap.alignFrame.getTitle() })), oom);
+ new String[]
+ { ap.alignFrame.getTitle() })),
+ oom);
cap.dispose();
}
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);