/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
import jalview.jbgui.GSliderPanel;
import jalview.util.MessageManager;
+import java.awt.Color;
import java.awt.event.ActionEvent;
import java.util.ArrayList;
+import java.util.HashMap;
import java.util.List;
import java.util.Stack;
import java.util.Vector;
Vector redundantSeqs;
+ private SequenceI[] redreps;
+
/**
* Creates a new RedundancyPanel object.
*
slider.addChangeListener(new ChangeListener()
{
+ @Override
public void stateChanged(ChangeEvent evt)
{
valueField.setText(slider.getValue() + "");
}
});
- applyButton.setText(MessageManager.getString("action.remove"));
+ applyButton.setText(MessageManager.getString("action.hide"));
allGroupsCheck.setVisible(false);
slider.setMinimum(0);
slider.setMaximum(100);
frame = new JInternalFrame();
frame.setContentPane(this);
- Desktop.addInternalFrame(frame, MessageManager
- .getString("label.redundancy_threshold_selection"), 400, 100,
- false);
+ Desktop.addInternalFrame(frame,
+ MessageManager
+ .getString("label.redundancy_threshold_selection"),
+ 400, 100, false);
frame.addInternalFrameListener(new InternalFrameAdapter()
{
+ @Override
public void internalFrameClosing(InternalFrameEvent evt)
{
ap.getIdPanel().getIdCanvas().setHighlighted(null);
*
* @return DOCUMENT ME!
*/
+ @Override
public void run()
{
JProgressBar progress = new JProgressBar();
{
omitHidden = ap.av.getViewAsString(sg != null);
}
- redundancy = AlignSeq.computeRedundancyMatrix(originalSequences,
+ Object rr[] = AlignSeq.computeRedundancyMatrixWithRep(
+ originalSequences,
omitHidden, start, end, false);
+ redundancy = (float[]) rr[0];
+ redreps = (SequenceI[]) rr[1];
+
progress.setIndeterminate(false);
progress.setVisible(false);
progress = null;
- label.setText(MessageManager
- .getString("label.enter_redundancy_thereshold"));
+ label.setText(
+ MessageManager.getString("label.enter_redundancy_threshold"));
slider.setVisible(true);
applyButton.setEnabled(true);
valueField.setVisible(true);
* @param e
* DOCUMENT ME!
*/
+ @Override
public void applyButton_actionPerformed(ActionEvent e)
{
- Vector del = new Vector();
undoButton.setEnabled(true);
float value = slider.getValue();
SequenceGroup sg = ap.av.getSelectionGroup();
-
+ // delete_seqs(value, sg);
+ hide_seqs(value, sg);
+ }
+ private void hide_seqs(float value, SequenceGroup sg)
+ {
+ /**
+ * hash to look up the representative for a sequence
+ */
+ HashMap<SequenceI, SequenceI> rep = new HashMap<SequenceI, SequenceI>();
+ /**
+ * hash to collect lists of sequences represented by a sequence
+ */
+ HashMap<SequenceI, SequenceGroup> reps = new HashMap<SequenceI, SequenceGroup>();
for (int i = 0; i < redundancy.length; i++)
{
if (value <= redundancy[i])
{
- del.addElement(originalSequences[i]);
+ // does this sequence represent other sequences ?
+ SequenceGroup repset;
+ // is the representative also redundant ?
+ SequenceI repForI = rep.get(redreps[i]);
+ if (repForI==null) {
+ // the representative is still in the alignment.
+ // is it representing anything already ?
+ repset = reps.get(redreps[i]);
+ if (repset==null)
+ {
+ repset = new SequenceGroup();
+ }
+ repset.addSequence(originalSequences[i], false);
+ rep.put(originalSequences[i], redreps[i]);
+ reps.put(redreps[i], repset);
+ // and save the representative sequence for originalSeq
+ repForI = redreps[i];
+ } else {
+ // already hidden the representative for this sequence, so look up its redundant peers
+ repset = reps.get(repForI);
+ if (repset==null)
+ {
+ throw new Error("Implementation failure for redundancy set creation");
+ }
+ // add the sequence to the peerset, and mark sequence's representative in hash
+ repset.addSequence(originalSequences[i], false);
+ rep.put(originalSequences[i], repForI);
+ }
+ // merge any sequences represented by this with its new containing group
+ SequenceGroup existingreps = reps.remove(originalSequences[i]);
+ if (existingreps!=null)
+ {
+ for (SequenceI sq:existingreps.getSequences())
+ {
+ rep.put(sq, repForI);
+ repset.addSequence(sq, false);
+ }
+ }
}
}
+ int s = 0, e = ap.av.getAlignment().getWidth();
+ if (sg != null)
+ {
+ s = sg.getStartRes();
+ e = sg.getEndRes();
+ }
+ List<SequenceGroup> sgs = new ArrayList<SequenceGroup>();
+ for (SequenceI repseq: reps.keySet())
+ {
+ sg = reps.get(repseq);
+ sg.addSequence(repseq, false);
+ sg.setSeqrep(repseq);
+ sg.setStartRes(s);
+ sg.setEndRes(e);
+ sgs.add(sg);
+ }
+ ap.alignFrame.avc.showRandomColoursForGroups(sgs);
+ for (SequenceI repseq : reps.keySet())
+ {
+ sg = reps.get(repseq);
+ ap.av.hideRepSequences(repseq, sg);
+ }
+ }
+ private void delete_seqs(float value, SequenceGroup sg)
+ {
+ ArrayList<SequenceI> del = new ArrayList<SequenceI>();
+
+ for (int i = 0; i < redundancy.length; i++)
+ {
+ if (value <= redundancy[i])
+ {
+ del.add(originalSequences[i]);
+ }
+ }
// This has to be done before the restoreHistoryItem method of alignFrame
// will
// actually restore these sequences.
int width = 0;
for (int i = 0; i < del.size(); i++)
{
- deleted[i] = (SequenceI) del.elementAt(i);
+ deleted[i] = del.get(i);
if (deleted[i].getLength() > width)
{
width = deleted[i].getLength();
ap.alignFrame.addHistoryItem(cut);
PaintRefresher.Refresh(this, ap.av.getSequenceSetId(), true, true);
- ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
- .getSequences());
+ ap.av.firePropertyChange("alignment", null,
+ ap.av.getAlignment().getSequences());
}
}
* @param e
* DOCUMENT ME!
*/
+ @Override
public void undoButton_actionPerformed(ActionEvent e)
{
if (historyList == null || historyList.isEmpty())
{
command.undoCommand(af.getViewAlignments());
ap.av.getHistoryList().remove(command);
- ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
- .getSequences());
+ ap.av.firePropertyChange("alignment", null,
+ ap.av.getAlignment().getSequences());
af.updateEditMenuBar();
}
* @param e
* DOCUMENT ME!
*/
+ @Override
public void valueField_actionPerformed(ActionEvent e)
{
try