/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
+ * This file is part of Jalview.
*
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
-import java.util.*;
-
-import java.awt.event.*;
-import javax.swing.*;
-import javax.swing.event.*;
-
-import jalview.commands.*;
-import jalview.datamodel.*;
-import jalview.jbgui.*;
-import jalview.util.*;
+import jalview.analysis.AlignSeq;
+import jalview.commands.CommandI;
+import jalview.commands.EditCommand;
+import jalview.commands.EditCommand.Action;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+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;
+
+import javax.swing.JInternalFrame;
+import javax.swing.JProgressBar;
+import javax.swing.event.ChangeEvent;
+import javax.swing.event.ChangeListener;
+import javax.swing.event.InternalFrameAdapter;
+import javax.swing.event.InternalFrameEvent;
/**
* DOCUMENT ME!
AlignmentPanel ap;
- Stack historyList = new Stack(); // simpler than synching with alignFrame.
+ Stack<CommandI> historyList = new Stack<CommandI>();
+
+ // simpler than synching with alignFrame.
float[] redundancy;
Vector redundantSeqs;
+ private SequenceI[] redreps;
+
/**
* Creates a new RedundancyPanel object.
*
* @param ap
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param af
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public RedundancyPanel(final AlignmentPanel ap, AlignFrame af)
{
slider.addChangeListener(new ChangeListener()
{
+ @Override
public void stateChanged(ChangeEvent evt)
{
valueField.setText(slider.getValue() + "");
}
});
- applyButton.setText("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, "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.idPanel.idCanvas.setHighlighted(null);
+ ap.getIdPanel().getIdCanvas().setHighlighted(null);
}
});
* slider to dynamically hide redundant sequences
*
* @param threshold
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param sel
- * DOCUMENT ME!
+ * DOCUMENT ME!
*
* @return DOCUMENT ME!
*/
+ @Override
public void run()
{
JProgressBar progress = new JProgressBar();
progress.setIndeterminate(true);
southPanel.add(progress, java.awt.BorderLayout.SOUTH);
- label.setText("Calculating....");
+ label.setText(MessageManager.getString("label.calculating"));
slider.setVisible(false);
applyButton.setEnabled(false);
if ((sg != null) && (sg.getSize() >= 1))
{
- originalSequences = sg.getSequencesInOrder(ap.av.alignment);
+ originalSequences = sg.getSequencesInOrder(ap.av.getAlignment());
start = sg.getStartRes();
end = sg.getEndRes();
}
else
{
- originalSequences = ap.av.alignment.getSequencesArray();
+ originalSequences = ap.av.getAlignment().getSequencesArray();
start = 0;
- end = ap.av.alignment.getWidth();
+ end = ap.av.getAlignment().getWidth();
}
height = originalSequences.length;
-
- redundancy = new float[height];
- for (int i = 0; i < height; i++)
- {
- redundancy[i] = 0f;
- }
-
- if (ap.av.hasHiddenColumns)
+ if (ap.av.hasHiddenColumns())
{
omitHidden = ap.av.getViewAsString(sg != null);
}
+ Object rr[] = AlignSeq.computeRedundancyMatrixWithRep(
+ originalSequences,
+ omitHidden, start, end, false);
- // long start = System.currentTimeMillis();
-
- float pid;
- String seqi, seqj;
- for (int i = 0; i < height; i++)
- {
-
- for (int j = 0; j < i; j++)
- {
- if (i == j)
- {
- continue;
- }
-
- if (omitHidden == null)
- {
- seqi = originalSequences[i].getSequenceAsString(start, end);
- seqj = originalSequences[j].getSequenceAsString(start, end);
- }
- else
- {
- seqi = omitHidden[i];
- seqj = omitHidden[j];
- }
-
- pid = Comparison.PID(seqi, seqj);
-
- if (seqj.length() < seqi.length())
- {
- redundancy[j] = Math.max(pid, redundancy[j]);
- }
- else
- {
- redundancy[i] = Math.max(pid, redundancy[i]);
- }
-
- }
- }
+ redundancy = (float[]) rr[0];
+ redreps = (SequenceI[]) rr[1];
progress.setIndeterminate(false);
progress.setVisible(false);
progress = null;
- label.setText("Enter the redundancy threshold");
+ label.setText(
+ MessageManager.getString("label.enter_redundancy_threshold"));
slider.setVisible(true);
applyButton.setEnabled(true);
valueField.setVisible(true);
validate();
+ sliderValueChanged();
// System.out.println((System.currentTimeMillis()-start));
}
}
float value = slider.getValue();
-
+ List<SequenceI> redundantSequences = new ArrayList<SequenceI>();
for (int i = 0; i < redundancy.length; i++)
{
- if (value > redundancy[i])
- {
- redundantSeqs.remove(originalSequences[i]);
- }
- else if (!redundantSeqs.contains(originalSequences[i]))
+ if (value <= redundancy[i])
{
- redundantSeqs.add(originalSequences[i]);
+ redundantSequences.add(originalSequences[i]);
}
-
}
-
- ap.idPanel.idCanvas.setHighlighted(redundantSeqs);
+ ap.getIdPanel().getIdCanvas().setHighlighted(redundantSequences);
}
/**
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * 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();
}
}
- EditCommand cut = new EditCommand("Remove Redundancy",
- EditCommand.CUT, deleted, 0, width, ap.av.alignment);
+ EditCommand cut = new EditCommand(
+ MessageManager.getString("action.remove_redundancy"),
+ Action.CUT, deleted, 0, width, ap.av.getAlignment());
for (int i = 0; i < del.size(); i++)
{
- ap.av.alignment.deleteSequence(deleted[i]);
- PaintRefresher.Refresh(this, ap.av.getSequenceSetId(), true, true);
+ ap.av.getAlignment().deleteSequence(deleted[i]);
if (sg != null)
{
sg.deleteSequence(deleted[i], false);
ap.alignFrame.addHistoryItem(cut);
- ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
- .getSequences());
+ PaintRefresher.Refresh(this, ap.av.getSequenceSetId(), true, true);
+ ap.av.firePropertyChange("alignment", null,
+ ap.av.getAlignment().getSequences());
}
}
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
+ @Override
public void undoButton_actionPerformed(ActionEvent e)
{
- CommandI command = (CommandI) historyList.pop();
- command.undoCommand(af.getViewAlignments());
+ if (historyList == null || historyList.isEmpty())
+ {
+ undoButton.setEnabled(false);
+ return;
+ }
- if (ap.av.historyList.contains(command))
+ CommandI command = historyList.pop();
+ if (ap.av.getHistoryList().contains(command))
{
- ap.av.historyList.remove(command);
+ command.undoCommand(af.getViewAlignments());
+ ap.av.getHistoryList().remove(command);
+ ap.av.firePropertyChange("alignment", null,
+ ap.av.getAlignment().getSequences());
af.updateEditMenuBar();
}
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
+ @Override
public void valueField_actionPerformed(ActionEvent e)
{
try
git://source.jalview.org / jalview.git / blobdiff