X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FRedundancyPanel.java;h=37458a711acdcc5cad7c485d1deb4435213aea10;hb=refs%2Fheads%2Ffeatures%2FJAL-250_hideredundantseqs;hp=daee8623f3469e5939ec69d276fa06433e9d7643;hpb=4ebc6d5b362bc093c39312aa1a69836e3dd6ae84;p=jalview.git
diff --git a/src/jalview/gui/RedundancyPanel.java b/src/jalview/gui/RedundancyPanel.java
index daee862..37458a7 100755
--- a/src/jalview/gui/RedundancyPanel.java
+++ b/src/jalview/gui/RedundancyPanel.java
@@ -1,161 +1,415 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * 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 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.
- *
- * 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
- */
-package jalview.gui;
-
-import java.util.*;
-
-import java.awt.event.*;
-import javax.swing.event.*;
-
-import jalview.datamodel.*;
-import jalview.jbgui.*;
-
-public class RedundancyPanel
- extends GSliderPanel
-{
- AlignFrame af;
- AlignmentPanel ap;
- Stack historyList = new Stack(); // simpler than synching with alignFrame.
-
- public RedundancyPanel(AlignmentPanel ap, AlignFrame af)
- {
- this.ap = ap;
- this.af = af;
- label.setText("Enter the redundancy threshold");
-
- slider.addChangeListener(new ChangeListener()
- {
- public void stateChanged(ChangeEvent evt)
- {
- valueField.setText(slider.getValue() + "");
- }
- });
-
- slider.setMinimum(0);
- slider.setMaximum(100);
- slider.setValue(100);
- }
-
- public void applyButton_actionPerformed(ActionEvent e)
- {
- float threshold = slider.getValue();
- Vector del;
- HistoryItem it;
- historyList.push(it = new HistoryItem("Remove redundancy",
- ap.av.alignment, HistoryItem.HIDE));
-
- if ( (historyList.size() == 1) ||
- !af.historyList.contains(historyList.firstElement()))
- {
- af.addHistoryItem( (HistoryItem) historyList.firstElement());
- af.updateEditMenuBar();
- }
-
- undoButton.setEnabled(true);
-
- SequenceGroup sg = ap.av.getSelectionGroup();
-
- if ( (sg != null) && (sg.getSize() >= 1))
- {
- del = ap.av.alignment.removeRedundancy(threshold, sg.sequences);
-
- for (int i = 0; i < del.size(); i++)
- {
- if (sg.sequences.contains( (SequenceI) del.elementAt(i)))
- {
- sg.deleteSequence( (SequenceI) del.elementAt(i), true);
- }
- }
- }
- else
- {
- Vector s = new Vector();
- int i = 0;
-
- while (i < ap.av.alignment.getHeight())
- {
- s.addElement(ap.av.alignment.getSequenceAt(i));
- i++;
- }
-
- del = ap.av.alignment.removeRedundancy(threshold, s);
- }
-
- // This has to be done before the restoreHistoryItem method of alignFrame will
- // actually restore these sequences.
- if (del.size() > 0)
- {
- for (int i = 0, j = del.size(); i < j; i++)
- {
- SequenceI sq = (SequenceI) del.elementAt(i);
- sq.deleteChars(0, sq.getLength());
- }
- }
-
- ap.av.firePropertyChange("alignment", null,
- ap.av.getAlignment().getSequences());
- ap.av.resetSeqLimits(ap.seqPanel.seqCanvas.getHeight());
-
- if (ap.av.getAlignment().getHeight() < 1)
- {
- try
- {
- af.setClosed(true);
- }
- catch (Exception ex)
- {
- }
- }
-
- ap.av.updateConservation();
- ap.av.updateConsensus();
- af.updateEditMenuBar();
- ap.repaint();
- }
-
- public void undoButton_actionPerformed(ActionEvent e)
- {
- HistoryItem hi = (HistoryItem) historyList.pop();
- af.restoreHistoryItem(hi);
-
- if (historyList.size() == 0)
- {
- undoButton.setEnabled(false);
-
- if (af.historyList.contains(hi))
- {
- af.historyList.remove(hi);
- af.updateEditMenuBar();
- }
- }
- }
-
- public void valueField_actionPerformed(ActionEvent e)
- {
- try
- {
- int i = Integer.parseInt(valueField.getText());
- slider.setValue(i);
- }
- catch (Exception ex)
- {
- valueField.setText(slider.getValue() + "");
- }
- }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * 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 Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.gui;
+
+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!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class RedundancyPanel extends GSliderPanel implements Runnable
+{
+ AlignFrame af;
+
+ AlignmentPanel ap;
+
+ Stack historyList = new Stack();
+
+ // simpler than synching with alignFrame.
+
+ float[] redundancy;
+
+ SequenceI[] originalSequences;
+
+ JInternalFrame frame;
+
+ Vector redundantSeqs;
+
+ private SequenceI[] redreps;
+
+ /**
+ * Creates a new RedundancyPanel object.
+ *
+ * @param ap
+ * DOCUMENT ME!
+ * @param af
+ * DOCUMENT ME!
+ */
+ public RedundancyPanel(final AlignmentPanel ap, AlignFrame af)
+ {
+ this.ap = ap;
+ this.af = af;
+ redundantSeqs = new Vector();
+
+ slider.addChangeListener(new ChangeListener()
+ {
+ @Override
+ public void stateChanged(ChangeEvent evt)
+ {
+ valueField.setText(slider.getValue() + "");
+ sliderValueChanged();
+ }
+ });
+
+ applyButton.setText(MessageManager.getString("action.hide"));
+ allGroupsCheck.setVisible(false);
+ slider.setMinimum(0);
+ slider.setMaximum(100);
+ slider.setValue(100);
+
+ Thread worker = new Thread(this);
+ worker.start();
+
+ frame = new JInternalFrame();
+ frame.setContentPane(this);
+ 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);
+ }
+ });
+
+ }
+
+ /**
+ * This is a copy of remove redundancy in jalivew.datamodel.Alignment except
+ * we dont want to remove redundancy, just calculate once so we can use the
+ * slider to dynamically hide redundant sequences
+ *
+ * @param threshold
+ * DOCUMENT ME!
+ * @param sel
+ * 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(MessageManager.getString("label.calculating"));
+
+ slider.setVisible(false);
+ applyButton.setEnabled(false);
+ valueField.setVisible(false);
+
+ validate();
+
+ String[] omitHidden = null;
+
+ SequenceGroup sg = ap.av.getSelectionGroup();
+ int height;
+
+ int start, end;
+
+ if ((sg != null) && (sg.getSize() >= 1))
+ {
+ originalSequences = sg.getSequencesInOrder(ap.av.getAlignment());
+ start = sg.getStartRes();
+ end = sg.getEndRes();
+ }
+ else
+ {
+ originalSequences = ap.av.getAlignment().getSequencesArray();
+ start = 0;
+ end = ap.av.getAlignment().getWidth();
+ }
+
+ height = originalSequences.length;
+ if (ap.av.hasHiddenColumns())
+ {
+ omitHidden = ap.av.getViewAsString(sg != null);
+ }
+ 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_threshold"));
+ slider.setVisible(true);
+ applyButton.setEnabled(true);
+ valueField.setVisible(true);
+
+ validate();
+ sliderValueChanged();
+ // System.out.println((System.currentTimeMillis()-start));
+ }
+
+ void sliderValueChanged()
+ {
+ if (redundancy == null)
+ {
+ return;
+ }
+
+ float value = slider.getValue();
+ List redundantSequences = new ArrayList();
+ for (int i = 0; i < redundancy.length; i++)
+ {
+ if (value <= redundancy[i])
+ {
+ redundantSequences.add(originalSequences[i]);
+ }
+ }
+ ap.getIdPanel().getIdCanvas().setHighlighted(redundantSequences);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ @Override
+ public void applyButton_actionPerformed(ActionEvent e)
+ {
+
+ 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 rep = new HashMap();
+ /**
+ * hash to collect lists of sequences represented by a sequence
+ */
+ HashMap reps = new HashMap();
+ for (int i = 0; i < redundancy.length; i++)
+ {
+ if (value <= redundancy[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 sgs = new ArrayList();
+ 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 del = new ArrayList();
+
+ 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.
+ if (del.size() > 0)
+ {
+ SequenceI[] deleted = new SequenceI[del.size()];
+
+ int width = 0;
+ for (int i = 0; i < del.size(); i++)
+ {
+ deleted[i] = del.get(i);
+ if (deleted[i].getLength() > width)
+ {
+ width = deleted[i].getLength();
+ }
+ }
+
+ 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.getAlignment().deleteSequence(deleted[i]);
+ if (sg != null)
+ {
+ sg.deleteSequence(deleted[i], false);
+ }
+ }
+
+ historyList.push(cut);
+
+ ap.alignFrame.addHistoryItem(cut);
+
+ PaintRefresher.Refresh(this, ap.av.getSequenceSetId(), true, true);
+ ap.av.firePropertyChange("alignment", null,
+ ap.av.getAlignment().getSequences());
+ }
+
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ @Override
+ public void undoButton_actionPerformed(ActionEvent e)
+ {
+ if (historyList == null || historyList.isEmpty())
+ {
+ undoButton.setEnabled(false);
+ return;
+ }
+
+ CommandI command = historyList.pop();
+ if (ap.av.getHistoryList().contains(command))
+ {
+ command.undoCommand(af.getViewAlignments());
+ ap.av.getHistoryList().remove(command);
+ ap.av.firePropertyChange("alignment", null,
+ ap.av.getAlignment().getSequences());
+ af.updateEditMenuBar();
+ }
+
+ ap.paintAlignment(true);
+
+ if (historyList.size() == 0)
+ {
+ undoButton.setEnabled(false);
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ @Override
+ public void valueField_actionPerformed(ActionEvent e)
+ {
+ try
+ {
+ int i = Integer.parseInt(valueField.getText());
+ slider.setValue(i);
+ } catch (Exception ex)
+ {
+ valueField.setText(slider.getValue() + "");
+ }
+ }
+
+}