/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 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
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
+ * Copyright (C) 2014 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 <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
import javax.swing.*;
import javax.swing.event.*;
+import jalview.analysis.AlignSeq;
import jalview.commands.*;
import jalview.datamodel.*;
import jalview.jbgui.*;
-import jalview.util.*;
+import jalview.util.MessageManager;
/**
* DOCUMENT ME!
- *
+ *
* @author $author$
* @version $Revision$
*/
-public class RedundancyPanel
- extends GSliderPanel implements Runnable
+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;
/**
* Creates a new RedundancyPanel object.
- *
- * @param ap DOCUMENT ME!
- * @param af DOCUMENT ME!
+ *
+ * @param ap
+ * DOCUMENT ME!
+ * @param af
+ * DOCUMENT ME!
*/
public RedundancyPanel(final AlignmentPanel ap, AlignFrame af)
{
}
});
- applyButton.setText("Remove");
+ applyButton.setText(MessageManager.getString("action.remove"));
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()
{
public void internalFrameClosing(InternalFrameEvent evt)
{
ap.idPanel.idCanvas.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!
- *
+ * 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!
*/
public void run()
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);
int start, end;
- if ( (sg != null) && (sg.getSize() >= 1))
+ 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);
}
-
- // 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 = AlignSeq.computeRedundancyMatrix(originalSequences,
+ omitHidden, start, end, false);
progress.setIndeterminate(false);
progress.setVisible(false);
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.idPanel.idCanvas.setHighlighted(redundantSequences);
}
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
public void applyButton_actionPerformed(ActionEvent e)
{
}
}
- // This has to be done before the restoreHistoryItem method of alignFrame will
+ // This has to be done before the restoreHistoryItem method of alignFrame
+ // will
// actually restore these sequences.
if (del.size() > 0)
{
}
EditCommand cut = new EditCommand("Remove Redundancy",
- EditCommand.CUT, deleted, 0, width,
- ap.av.alignment);
+ EditCommand.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!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
public void undoButton_actionPerformed(ActionEvent e)
{
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
public void valueField_actionPerformed(ActionEvent e)
{
{
int i = Integer.parseInt(valueField.getText());
slider.setValue(i);
- }
- catch (Exception ex)
+ } catch (Exception ex)
{
valueField.setText(slider.getValue() + "");
}
git://source.jalview.org / jalview.git / blobdiff