import jalview.analysis.AlignmentSorter;
import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
import jalview.analysis.TreeBuilder;
+import jalview.analysis.scoremodels.PIDModel;
+import jalview.analysis.scoremodels.ScoreModels;
import jalview.api.AlignViewControllerGuiI;
import jalview.api.AlignViewControllerI;
import jalview.api.AlignViewportI;
{
delete_actionPerformed();
}
+ else if (source == createGroup)
+ {
+ createGroup_actionPerformed();
+ }
+ else if (source == unGroup)
+ {
+ unGroup_actionPerformed();
+ }
else if (source == grpsFromSelection)
{
makeGrpsFromSelection_actionPerformed();
boolean selected = conservationMenuItem.getState();
modifyConservation.setEnabled(selected);
viewport.setConservationSelected(selected);
-
- // viewport.setAbovePIDThreshold(false);
- // abovePIDThreshold.setState(false);
+ viewport.getResidueShading().setConservationApplied(selected);
changeColour(viewport.getGlobalColourScheme());
boolean selected = abovePIDThreshold.getState();
modifyPID.setEnabled(selected);
viewport.setAbovePIDThreshold(selected);
- // conservationMenuItem.setState(false);
- // viewport.setConservationSelected(false);
+ if (!selected)
+ {
+ viewport.getResidueShading().setThreshold(0,
+ viewport.isIgnoreGapsConsensus());
+ }
changeColour(viewport.getGlobalColourScheme());
public void averageDistanceTreeMenuItem_actionPerformed()
{
- NewTreePanel(TreeBuilder.AVERAGE_DISTANCE, "PID",
+ newTreePanel(TreeBuilder.AVERAGE_DISTANCE, new PIDModel().getName(),
"Average distance tree using PID");
}
public void neighbourTreeMenuItem_actionPerformed()
{
- NewTreePanel(TreeBuilder.NEIGHBOUR_JOINING, "PID",
+ newTreePanel(TreeBuilder.NEIGHBOUR_JOINING, new PIDModel().getName(),
"Neighbour joining tree using PID");
}
protected void njTreeBlosumMenuItem_actionPerformed()
{
- NewTreePanel(TreeBuilder.NEIGHBOUR_JOINING, "BL",
+ newTreePanel(TreeBuilder.NEIGHBOUR_JOINING, ScoreModels.getInstance()
+ .getBlosum62().getName(),
"Neighbour joining tree using BLOSUM62");
}
protected void avTreeBlosumMenuItem_actionPerformed()
{
- NewTreePanel(TreeBuilder.AVERAGE_DISTANCE, "BL",
+ newTreePanel(TreeBuilder.AVERAGE_DISTANCE, ScoreModels.getInstance()
+ .getBlosum62().getName(),
"Average distance tree using BLOSUM62");
}
- void NewTreePanel(String type, String pwType, String title)
+ void newTreePanel(String type, String pwType, String title)
{
// are the sequences aligned?
if (!viewport.getAlignment().isAligned(false))
.getString("action.make_groups_selection"));
grpsFromSelection.addActionListener(this);
createGroup.setLabel(MessageManager.getString("action.create_group"));
+ createGroup.addActionListener(this);
unGroup.setLabel(MessageManager.getString("action.remove_group"));
+ unGroup.addActionListener(this);
+
annotationColumnSelection.setLabel(MessageManager
.getString("action.select_by_annotation"));
annotationColumnSelection.addActionListener(this);