import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
+import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.SequenceGroup;
-import java.awt.event.ActionEvent;
import java.util.Hashtable;
+import java.util.Map;
import java.util.Vector;
/**
* change colors based on covariation.
*
* @author Lauren Michelle Lui
- *
+ * @deprecated this seems to be unfinished - just use RNAHelicesColour
*/
+@Deprecated
public class RNAHelicesColourChooser
{
ColourSchemeI oldcs;
- Hashtable oldgroupColours;
+ Map<SequenceGroup, ColourSchemeI> oldgroupColours;
- jalview.datamodel.AlignmentAnnotation currentAnnotation;
+ AlignmentAnnotation currentAnnotation;
boolean adjusting = false;
oldcs = av.getGlobalColourScheme();
if (av.getAlignment().getGroups() != null)
{
- oldgroupColours = new Hashtable();
+ oldgroupColours = new Hashtable<SequenceGroup, ColourSchemeI>();
for (SequenceGroup sg : ap.getAlignment().getGroups())
{
- if (sg.cs != null)
+ if (sg.getColourScheme() != null)
{
- oldgroupColours.put(sg, sg.cs);
+ oldgroupColours.put(sg, sg.getColourScheme());
}
}
}
this.av = av;
this.ap = ap;
- if (oldcs instanceof RNAHelicesColour)
- {
- RNAHelicesColour rhc = (RNAHelicesColour) oldcs;
-
- }
-
adjusting = true;
- Vector list = new Vector();
+ Vector<String> list = new Vector<String>();
int index = 1;
- for (int i = 0; i < av.getAlignment().getAlignmentAnnotation().length; i++)
+ AlignmentAnnotation[] anns = av.getAlignment().getAlignmentAnnotation();
+ if (anns != null)
{
- String label = av.getAlignment().getAlignmentAnnotation()[i].label;
- if (!list.contains(label))
+ for (int i = 0; i < anns.length; i++)
{
- list.addElement(label);
- }
- else
- {
- list.addElement(label + "_" + (index++));
+ String label = anns[i].label;
+ if (!list.contains(label))
+ {
+ list.addElement(label);
+ }
+ else
+ {
+ list.addElement(label + "_" + (index++));
+ }
}
}
adjusting = false;
-
changeColour();
-
}
void changeColour()
{
return;
}
- RNAHelicesColour rhc = null;
-
- rhc = new RNAHelicesColour(av.getAlignment());
+ RNAHelicesColour rhc = new RNAHelicesColour(av.getAlignment());
av.setGlobalColourScheme(rhc);
- if (av.getAlignment().getGroups() != null)
- {
- for (SequenceGroup sg : ap.getAlignment().getGroups())
- {
- if (sg.cs == null)
- {
- continue;
- }
-
- sg.cs = new RNAHelicesColour(sg);
-
- }
- }
-
ap.paintAlignment(true);
}
-
- void reset()
- {
- av.setGlobalColourScheme(oldcs);
- if (av.getAlignment().getGroups() != null)
- {
- for (SequenceGroup sg : ap.getAlignment().getGroups())
- {
- sg.cs = (ColourSchemeI) oldgroupColours.get(sg);
- }
- }
- }
-
- public void annotations_actionPerformed(ActionEvent e)
- {
- changeColour();
- }
-
}