import jalview.datamodel.SequenceI;
import jalview.io.AppletFormatAdapter;
import jalview.io.DataSourceType;
-import jalview.io.FileFormat;
+import jalview.io.FileFormatI;
+import jalview.io.FileFormats;
import jalview.io.SequenceAnnotationReport;
import jalview.schemes.Blosum62ColourScheme;
import jalview.schemes.BuriedColourScheme;
e.printStackTrace();
}
- for (String ff : FileFormat.getWritableFormats(true))
+ for (String ff : FileFormats.getInstance().getWritableFormats(true))
{
MenuItem item = new MenuItem(ff);
{
menu1.setLabel(MessageManager.getString("action.edit_group"));
groupMenu.remove(createGroupMenuItem);
+ if (sg.cs != null)
+ {
+ abovePIDColour.setState(sg.cs.getThreshold() > 0);
+ conservationMenuItem.setState(sg.cs.conservationApplied());
+ }
}
-
}
else
{
@Override
public void itemStateChanged(ItemEvent evt)
{
- if (evt.getSource() == abovePIDColour)
+ Object source = evt.getSource();
+ if (source == abovePIDColour)
{
abovePIDColour_itemStateChanged();
}
- else if (evt.getSource() == showColourText)
+ else if (source == conservationMenuItem)
+ {
+ conservationMenuItem_itemStateChanged();
+ }
+ else if (source == showColourText)
{
showColourText_itemStateChanged();
}
- else if (evt.getSource() == showText)
+ else if (source == showText)
{
showText_itemStateChanged();
}
- else if (evt.getSource() == showBoxes)
+ else if (source == showBoxes)
{
showBoxes_itemStateChanged();
}
- else if (evt.getSource() == displayNonconserved)
+ else if (source == displayNonconserved)
{
this.showNonconserved_itemStateChanged();
}
{
noColourmenuItem_actionPerformed();
}
- else if (source == conservationMenuItem)
- {
- conservationMenuItem_itemStateChanged();
- }
else if (source == unGroupMenuItem)
{
unGroupMenuItem_actionPerformed();
// now returns a full copy of sequence data
// TODO consider using getSequenceSelection instead here
- FileFormat fileFormat = FileFormat.valueOf(e.getActionCommand());
+ FileFormatI fileFormat = FileFormats.getInstance().forName(
+ e.getActionCommand());
cap.setText(new AppletFormatAdapter().formatSequences(fileFormat,
ap.av.getShowJVSuffix(), ap, true));