+ protected void sortByDens(String[] typ)
+ {
+ sortBy(typ, "Sort by Density", AlignmentSorter.FEATURE_DENSITY);
+ }
+ private String[] getDisplayedFeatureTypes()
+ {
+ String[] typ = null;
+ if (fr != null)
+ {
+ synchronized (fr.renderOrder)
+ {
+ typ = new String[fr.renderOrder.length];
+ System.arraycopy(fr.renderOrder, 0, typ, 0, typ.length);
+ for (int i = 0; i < typ.length; i++)
+ {
+ if (av.featuresDisplayed.get(typ[i]) == null)
+ {
+ typ[i] = null;
+ }
+ }
+ }
+ }
+ return typ;
+ }
+
+
+ protected void sortBy(String[] typ, String methodText, final String method)
+ {
+ if (typ == null)
+ {
+ typ = getDisplayedFeatureTypes();
+ }
+ String gps[] = null;
+ gps = fr.getGroups(true);
+ if (typ != null)
+ {
+ for (int i = 0; i < typ.length; i++)
+ {
+ System.err.println("Sorting on Types:" + typ[i]);
+ }
+ }
+ if (gps != null)
+ {
+
+ for (int i = 0; i < gps.length; i++)
+ {
+ System.err.println("Sorting on groups:" + gps[i]);
+ }
+ }
+ AlignmentPanel alignPanel = ap;
+ AlignmentI al = alignPanel.av.getAlignment();
+
+ int start, stop;
+ SequenceGroup sg = alignPanel.av.getSelectionGroup();
+ if (sg != null)
+ {
+ start = sg.getStartRes();
+ stop = sg.getEndRes();
+ }
+ else
+ {
+ start = 0;
+ stop = al.getWidth();
+ }
+ SequenceI[] oldOrder = al.getSequencesArray();
+ AlignmentSorter.sortByFeature(typ, gps, start, stop, al, method);
+ this.ap.alignFrame.addHistoryItem(new OrderCommand(methodText, oldOrder, alignPanel.av
+ .getAlignment()));
+ alignPanel.paintAlignment(true);
+
+ }
+
+ protected void sortByScore(String[] typ)
+ {
+ sortBy(typ, "Sort by Feature Score", AlignmentSorter.FEATURE_SCORE);
+ }
+