- protected void sortByDens(String[] typ)
- {
- sortBy(typ, "Sort by Density", AlignmentSorter.FEATURE_DENSITY);
- }
-
- protected void sortBy(String[] typ, String methodText, final String method)
- {
- if (typ == null)
- {
- typ = getDisplayedFeatureTypes();
- }
- String gps[] = null;
- gps = getDisplayedFeatureGroups();
- 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 = af.alignPanel;
- 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);
- af.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);
- }
-
- 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 (af.viewport.featuresDisplayed.get(typ[i]) == null)
- {
- typ[i] = null;
- }
- }
- }
- }
- return typ;
- }
-
- private String[] getDisplayedFeatureGroups()
- {
- String[] gps = null;
- if (fr != null)
- {
-
- if (fr.featureGroups != null)
- {
- Enumeration en = fr.featureGroups.keys();
- gps = new String[fr.featureColours.size()];
- int g = 0;
- boolean valid = false;
- while (en.hasMoreElements())
- {
- String gp = (String) en.nextElement();
- Boolean on = (Boolean) fr.featureGroups.get(gp);
- if (on != null && on.booleanValue())
- {
- valid = true;
- gps[g++] = gp;
- }
- }
- while (g < gps.length)
- {
- gps[g++] = null;
- }
- if (!valid)
- {
- return null;
- }
- }
- }
- return gps;
- }
-