- * Check for any annotations on the underlying dataset sequences (for the
- * current selection group) which are not 'on the alignment'.If any are found,
- * enable the option to add them to the alignment. The criteria for 'on the
- * alignment' is finding an alignment annotation on the alignment, matched on
+ * Builds the group colour sub-menu, including any user-defined colours which
+ * were loaded at startup or during the Jalview session
+ */
+ protected void buildColourMenu()
+ {
+ SequenceGroup sg = ap.av.getSelectionGroup();
+ if (sg == null)
+ {
+ /*
+ * popup menu with no sequence group scope
+ */
+ return;
+ }
+ colourMenu.removeAll();
+ colourMenu.add(textColour);
+ colourMenu.addSeparator();
+
+ ColourMenuHelper.addMenuItems(colourMenu, this, sg, false);
+
+ colourMenu.addSeparator();
+ colourMenu.add(conservationMenuItem);
+ colourMenu.add(modifyConservation);
+ colourMenu.add(abovePIDColour);
+ colourMenu.add(modifyPID);
+ }
+
+ protected void modifyConservation_actionPerformed()
+ {
+ SequenceGroup sg = getGroup();
+ if (sg.cs != null)
+ {
+ SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
+ SliderPanel.showConservationSlider();
+ }
+ }
+
+ protected void modifyPID_actionPerformed()
+ {
+ SequenceGroup sg = getGroup();
+ if (sg.cs != null)
+ {
+ // int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup()
+ // .getName());
+ // sg.cs.setThreshold(threshold, ap.av.isIgnoreGapsConsensus());
+ SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup().getName());
+ SliderPanel.showPIDSlider();
+ }
+ }
+
+ /**
+ * Check for any annotations on the underlying dataset sequences (for the
+ * current selection group) which are not 'on the alignment'.If any are found,
+ * enable the option to add them to the alignment. The criteria for 'on the
+ * alignment' is finding an alignment annotation on the alignment, matched on