import jalview.analysis.AlignmentAnnotationUtils;
import jalview.analysis.AlignmentUtils;
import jalview.analysis.Conservation;
+import jalview.bin.JalviewLite;
import jalview.commands.ChangeCaseCommand;
import jalview.commands.EditCommand;
import jalview.commands.EditCommand.Action;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.io.AppletFormatAdapter;
+import jalview.io.DataSourceType;
+import jalview.io.FileFormat;
import jalview.io.SequenceAnnotationReport;
import jalview.schemes.Blosum62ColourScheme;
import jalview.schemes.BuriedColourScheme;
MenuItem item = new MenuItem(label);
item.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
ap.alignFrame.showURL(url, target);
linkMenu.add(item);
}
+ @Override
public void itemStateChanged(ItemEvent evt)
{
if (evt.getSource() == abovePIDColour)
}
}
+ @Override
public void actionPerformed(ActionEvent evt)
{
Object source = evt.getSource();
Frame frame = new Frame();
frame.add(cap);
- jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
+ JalviewLite.addFrame(frame, MessageManager.formatMessage(
"label.selection_output_command",
new Object[] { e.getActionCommand() }), 600, 500);
// JBPNote: getSelectionAsNewSequence behaviour has changed - this method
// now returns a full copy of sequence data
// TODO consider using getSequenceSelection instead here
- cap.setText(new jalview.io.AppletFormatAdapter().formatSequences(
- e.getActionCommand(), ap.av.getShowJVSuffix(), ap, true));
+ FileFormat fileFormat = FileFormat.valueOf(e.getActionCommand());
+ cap.setText(new AppletFormatAdapter().formatSequences(fileFormat,
+ ap.av.getShowJVSuffix(), ap, true));
}
if (ap.av.applet.jmolAvailable)
{
new jalview.appletgui.AppletJmol(entry, new SequenceI[] { seq },
- null, ap, AppletFormatAdapter.URL);
+ null, ap, DataSourceType.URL);
}
else
{
new MCview.AppletPDBViewer(entry, new SequenceI[] { seq }, null,
- ap, AppletFormatAdapter.URL);
+ ap, DataSourceType.URL);
}
}
void hideSequences(boolean representGroup)
{
- SequenceGroup sg = ap.av.getSelectionGroup();
- if (sg == null || sg.getSize() < 1)
- {
- ap.av.hideSequence(new SequenceI[] { seq });
- return;
- }
-
- ap.av.setSelectionGroup(null);
-
- if (representGroup)
- {
- ap.av.hideRepSequences(seq, sg);
-
- return;
- }
-
- int gsize = sg.getSize();
- SequenceI[] hseqs;
-
- hseqs = new SequenceI[gsize];
-
- int index = 0;
- for (int i = 0; i < gsize; i++)
- {
- hseqs[index++] = sg.getSequenceAt(i);
- }
-
- ap.av.hideSequence(hseqs);
- ap.av.sendSelection();
+ ap.av.hideSequences(seq, representGroup);
}
/**