-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
- *\r
- * This program is free software; you can redistribute it and/or\r
- * modify it under the terms of the GNU General Public License\r
- * as published by the Free Software Foundation; either version 2\r
- * of the License, or (at your option) any later version.\r
- *\r
- * This program is distributed in the hope that it will be useful,\r
- * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
- * GNU General Public License for more details.\r
- *\r
- * You should have received a copy of the GNU General Public License\r
- * along with this program; if not, write to the Free Software\r
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
- */\r
-package jalview.gui;\r
-\r
-import java.util.*;\r
-\r
-import java.awt.event.*;\r
-import javax.swing.event.*;\r
-\r
-import jalview.datamodel.*;\r
-import jalview.jbgui.*;\r
-\r
-public class RedundancyPanel\r
- extends GSliderPanel\r
-{\r
- AlignFrame af;\r
- AlignmentPanel ap;\r
- Stack historyList = new Stack(); // simpler than synching with alignFrame.\r
-\r
- public RedundancyPanel(AlignmentPanel ap, AlignFrame af)\r
- {\r
- this.ap = ap;\r
- this.af = af;\r
- label.setText("Enter the redundancy threshold");\r
-\r
- slider.addChangeListener(new ChangeListener()\r
- {\r
- public void stateChanged(ChangeEvent evt)\r
- {\r
- valueField.setText(slider.getValue() + "");\r
- }\r
- });\r
-\r
- slider.setMinimum(0);\r
- slider.setMaximum(100);\r
- slider.setValue(100);\r
- }\r
-\r
- public void applyButton_actionPerformed(ActionEvent e)\r
- {\r
- float threshold = slider.getValue();\r
- Vector del;\r
- HistoryItem it;\r
- historyList.push(it = new HistoryItem("Remove redundancy",\r
- ap.av.alignment, HistoryItem.HIDE));\r
-\r
- if ( (historyList.size() == 1) ||\r
- !af.historyList.contains(historyList.firstElement()))\r
- {\r
- af.addHistoryItem( (HistoryItem) historyList.firstElement());\r
- af.updateEditMenuBar();\r
- }\r
-\r
- undoButton.setEnabled(true);\r
-\r
- SequenceGroup sg = ap.av.getSelectionGroup();\r
-\r
- if ( (sg != null) && (sg.getSize() >= 1))\r
- {\r
- del = ap.av.alignment.removeRedundancy(threshold, sg.sequences);\r
-\r
- for (int i = 0; i < del.size(); i++)\r
- {\r
- if (sg.sequences.contains( (SequenceI) del.elementAt(i)))\r
- {\r
- sg.deleteSequence( (SequenceI) del.elementAt(i));\r
- }\r
- }\r
- }\r
- else\r
- {\r
- Vector s = new Vector();\r
- int i = 0;\r
-\r
- while (i < ap.av.alignment.getHeight())\r
- {\r
- s.addElement(ap.av.alignment.getSequenceAt(i));\r
- i++;\r
- }\r
-\r
- del = ap.av.alignment.removeRedundancy(threshold, s);\r
- }\r
-\r
- // This has to be done before the restoreHistoryItem method of alignFrame will\r
- // actually restore these sequences.\r
- if (del.size() > 0)\r
- {\r
- for (int i = 0, j = del.size(); i < j; i++)\r
- {\r
- SequenceI sq = (SequenceI) del.elementAt(i);\r
- sq.deleteChars(0, sq.getLength());\r
- }\r
- }\r
-\r
- ap.av.firePropertyChange("alignment", null,\r
- ap.av.getAlignment().getSequences());\r
- ap.av.resetSeqLimits(ap.seqPanel.seqCanvas.getHeight());\r
-\r
- if (ap.av.getAlignment().getHeight() < 1)\r
- {\r
- try\r
- {\r
- af.setClosed(true);\r
- }\r
- catch (Exception ex)\r
- {\r
- }\r
- }\r
-\r
- ap.av.updateConservation();\r
- ap.av.updateConsensus();\r
- af.updateEditMenuBar();\r
- ap.repaint();\r
- }\r
-\r
- public void undoButton_actionPerformed(ActionEvent e)\r
- {\r
- HistoryItem hi = (HistoryItem) historyList.pop();\r
- af.restoreHistoryItem(hi);\r
-\r
- if (historyList.size() == 0)\r
- {\r
- undoButton.setEnabled(false);\r
-\r
- if (af.historyList.contains(hi))\r
- {\r
- af.historyList.remove(hi);\r
- af.updateEditMenuBar();\r
- }\r
- }\r
- }\r
-\r
- public void valueField_actionPerformed(ActionEvent e)\r
- {\r
- try\r
- {\r
- int i = Integer.parseInt(valueField.getText());\r
- slider.setValue(i);\r
- }\r
- catch (Exception ex)\r
- {\r
- valueField.setText(slider.getValue() + "");\r
- }\r
- }\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2006 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 jalview.datamodel.*;
+
+import jalview.jbgui.*;
+
+import java.awt.event.*;
+
+import java.util.*;
+
+import javax.swing.event.*;
+import jalview.util.Comparison;
+import javax.swing.*;
+
+
+/**
+ * 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;
+
+ /**
+ * 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()
+ {
+ public void stateChanged(ChangeEvent evt)
+ {
+ valueField.setText(slider.getValue() + "");
+ sliderValueChanged();
+ }
+ });
+
+ applyButton.setText("Remove");
+ 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, "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!
+ *
+ * @return DOCUMENT ME!
+ */
+ public void run()
+ {
+ JProgressBar progress = new JProgressBar();
+ progress.setIndeterminate(true);
+ southPanel.add(progress, java.awt.BorderLayout.SOUTH);
+
+ label.setText("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(false) >= 1))
+ {
+ originalSequences = sg.getSequencesInOrder(ap.av.alignment);
+ start = sg.getStartRes();
+ end = sg.getEndRes();
+ }
+ else
+ {
+ originalSequences = ap.av.alignment.getSequencesArray();
+ start = 0;
+ end = ap.av.alignment.getWidth();
+ }
+
+ height = originalSequences.length;
+
+ redundancy = new float[height];
+ for (int i = 0; i < height; i++)
+ {
+ redundancy[i] = 0f;
+ }
+
+ 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].getSequence(start, end);
+ seqj = originalSequences[j].getSequence(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]);
+
+ }
+ }
+
+ progress.setIndeterminate(false);
+ progress.setVisible(false);
+ progress = null;
+
+ label.setText("Enter the redundancy threshold");
+ slider.setVisible(true);
+ applyButton.setEnabled(true);
+ valueField.setVisible(true);
+
+ validate();
+ // System.out.println((System.currentTimeMillis()-start));
+ }
+
+ void sliderValueChanged()
+ {
+ if(redundancy==null)
+ return;
+
+ float value = slider.getValue();
+
+ for(int i=0; i<redundancy.length; i++)
+ {
+ if (value > redundancy[i])
+ redundantSeqs.remove(originalSequences[i]);
+ else if(!redundantSeqs.contains(originalSequences[i]))
+ redundantSeqs.add(originalSequences[i]);
+
+ }
+
+ ap.idPanel.idCanvas.setHighlighted(redundantSeqs);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void applyButton_actionPerformed(ActionEvent e)
+ {
+ historyList.push(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();
+ }
+
+ Vector del = new Vector();
+
+ undoButton.setEnabled(true);
+
+ float value = slider.getValue();
+ SequenceGroup sg = ap.av.getSelectionGroup();
+
+ for (int i = 0; i < redundancy.length; i++)
+ {
+ if (value <= redundancy[i])
+ {
+ SequenceI seq = originalSequences[i];
+ ap.av.alignment.deleteSequence(seq);
+ del.add(seq);
+ if (sg != null)
+ {
+ sg.deleteSequence(seq, false);
+ }
+ }
+ }
+
+
+ // 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());
+ af.updateEditMenuBar();
+ }
+
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ 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();
+ }
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void valueField_actionPerformed(ActionEvent e)
+ {
+ try
+ {
+ int i = Integer.parseInt(valueField.getText());
+ slider.setValue(i);
+ }
+ catch (Exception ex)
+ {
+ valueField.setText(slider.getValue() + "");
+ }
+ }
+
+
+}
git://source.jalview.org / jalview.git / blobdiff