-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2007 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.*;\r
-import javax.swing.event.*;\r
-\r
-import jalview.commands.*;\r
-import jalview.datamodel.*;\r
-import jalview.jbgui.*;\r
-import jalview.util.*;\r
-\r
-/**\r
- * DOCUMENT ME!\r
- *\r
- * @author $author$\r
- * @version $Revision$\r
- */\r
-public class RedundancyPanel\r
- extends GSliderPanel implements Runnable\r
-{\r
- AlignFrame af;\r
- AlignmentPanel ap;\r
- Stack historyList = new Stack(); // simpler than synching with alignFrame.\r
- float[] redundancy;\r
- SequenceI[] originalSequences;\r
- JInternalFrame frame;\r
- Vector redundantSeqs;\r
-\r
- /**\r
- * Creates a new RedundancyPanel object.\r
- *\r
- * @param ap DOCUMENT ME!\r
- * @param af DOCUMENT ME!\r
- */\r
- public RedundancyPanel(final AlignmentPanel ap, AlignFrame af)\r
- {\r
- this.ap = ap;\r
- this.af = af;\r
- redundantSeqs = new Vector();\r
-\r
- slider.addChangeListener(new ChangeListener()\r
- {\r
- public void stateChanged(ChangeEvent evt)\r
- {\r
- valueField.setText(slider.getValue() + "");\r
- sliderValueChanged();\r
- }\r
- });\r
-\r
- applyButton.setText("Remove");\r
- allGroupsCheck.setVisible(false);\r
- slider.setMinimum(0);\r
- slider.setMaximum(100);\r
- slider.setValue(100);\r
-\r
- Thread worker = new Thread(this);\r
- worker.start();\r
-\r
- frame = new JInternalFrame();\r
- frame.setContentPane(this);\r
- Desktop.addInternalFrame(frame, "Redundancy threshold selection", 400,\r
- 100, false);\r
- frame.addInternalFrameListener(new InternalFrameAdapter()\r
- {\r
- public void internalFrameClosing(InternalFrameEvent evt)\r
- {\r
- ap.idPanel.idCanvas.setHighlighted(null);\r
- }\r
- }\r
- );\r
-\r
- }\r
-\r
- /**\r
- * This is a copy of remove redundancy in jalivew.datamodel.Alignment\r
- * except we dont want to remove redundancy, just calculate once\r
- * so we can use the slider to dynamically hide redundant sequences\r
- *\r
- * @param threshold DOCUMENT ME!\r
- * @param sel DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public void run()\r
- {\r
- JProgressBar progress = new JProgressBar();\r
- progress.setIndeterminate(true);\r
- southPanel.add(progress, java.awt.BorderLayout.SOUTH);\r
-\r
- label.setText("Calculating....");\r
-\r
- slider.setVisible(false);\r
- applyButton.setEnabled(false);\r
- valueField.setVisible(false);\r
-\r
- validate();\r
-\r
- String[] omitHidden = null;\r
-\r
- SequenceGroup sg = ap.av.getSelectionGroup();\r
- int height;\r
-\r
- int start, end;\r
-\r
- if ( (sg != null) && (sg.getSize() >= 1))\r
- {\r
- originalSequences = sg.getSequencesInOrder(ap.av.alignment);\r
- start = sg.getStartRes();\r
- end = sg.getEndRes();\r
- }\r
- else\r
- {\r
- originalSequences = ap.av.alignment.getSequencesArray();\r
- start = 0;\r
- end = ap.av.alignment.getWidth();\r
- }\r
-\r
- height = originalSequences.length;\r
-\r
- redundancy = new float[height];\r
- for (int i = 0; i < height; i++)\r
- {\r
- redundancy[i] = 0f;\r
- }\r
-\r
- if (ap.av.hasHiddenColumns)\r
- {\r
- omitHidden = ap.av.getViewAsString(sg != null);\r
- }\r
-\r
- // long start = System.currentTimeMillis();\r
-\r
- float pid;\r
- String seqi, seqj;\r
- for (int i = 0; i < height; i++)\r
- {\r
-\r
- for (int j = 0; j < i; j++)\r
- {\r
- if (i == j)\r
- {\r
- continue;\r
- }\r
-\r
- if (omitHidden == null)\r
- {\r
- seqi = originalSequences[i].getSequenceAsString(start, end);\r
- seqj = originalSequences[j].getSequenceAsString(start, end);\r
- }\r
- else\r
- {\r
- seqi = omitHidden[i];\r
- seqj = omitHidden[j];\r
- }\r
-\r
- pid = Comparison.PID(seqi, seqj);\r
-\r
- if (seqj.length() < seqi.length())\r
- {\r
- redundancy[j] = Math.max(pid, redundancy[j]);\r
- }\r
- else\r
- {\r
- redundancy[i] = Math.max(pid, redundancy[i]);\r
- }\r
-\r
- }\r
- }\r
-\r
- progress.setIndeterminate(false);\r
- progress.setVisible(false);\r
- progress = null;\r
-\r
- label.setText("Enter the redundancy threshold");\r
- slider.setVisible(true);\r
- applyButton.setEnabled(true);\r
- valueField.setVisible(true);\r
-\r
- validate();\r
- // System.out.println((System.currentTimeMillis()-start));\r
- }\r
-\r
- void sliderValueChanged()\r
- {\r
- if (redundancy == null)\r
- {\r
- return;\r
- }\r
-\r
- float value = slider.getValue();\r
-\r
- for (int i = 0; i < redundancy.length; i++)\r
- {\r
- if (value > redundancy[i])\r
- {\r
- redundantSeqs.remove(originalSequences[i]);\r
- }\r
- else if (!redundantSeqs.contains(originalSequences[i]))\r
- {\r
- redundantSeqs.add(originalSequences[i]);\r
- }\r
-\r
- }\r
-\r
- ap.idPanel.idCanvas.setHighlighted(redundantSeqs);\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void applyButton_actionPerformed(ActionEvent e)\r
- {\r
- Vector del = new Vector();\r
-\r
- undoButton.setEnabled(true);\r
-\r
- float value = slider.getValue();\r
- SequenceGroup sg = ap.av.getSelectionGroup();\r
-\r
- for (int i = 0; i < redundancy.length; i++)\r
- {\r
- if (value <= redundancy[i])\r
- {\r
- del.addElement(originalSequences[i]);\r
- }\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
- SequenceI[] deleted = new SequenceI[del.size()];\r
-\r
- int width = 0;\r
- for (int i = 0; i < del.size(); i++)\r
- {\r
- deleted[i] = (SequenceI) del.elementAt(i);\r
- if (deleted[i].getLength() > width)\r
- {\r
- width = deleted[i].getLength();\r
- }\r
- }\r
-\r
- EditCommand cut = new EditCommand("Remove Redundancy",\r
- EditCommand.CUT, deleted, 0, width,\r
- ap.av.alignment);\r
-\r
- for (int i = 0; i < del.size(); i++)\r
- {\r
- ap.av.alignment.deleteSequence(deleted[i]);\r
- PaintRefresher.Refresh(this,\r
- ap.av.getSequenceSetId(),\r
- true,\r
- true);\r
- if (sg != null)\r
- {\r
- sg.deleteSequence(deleted[i], false);\r
- }\r
- }\r
-\r
- historyList.push(cut);\r
-\r
- ap.alignFrame.addHistoryItem(cut);\r
-\r
- ap.av.firePropertyChange("alignment", null,\r
- ap.av.getAlignment().getSequences());\r
- }\r
-\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void undoButton_actionPerformed(ActionEvent e)\r
- {\r
- CommandI command = (CommandI) historyList.pop();\r
- command.undoCommand();\r
-\r
- if (ap.av.historyList.contains(command))\r
- {\r
- ap.av.historyList.remove(command);\r
- af.updateEditMenuBar();\r
- }\r
-\r
- ap.repaint();\r
-\r
- if (historyList.size() == 0)\r
- {\r
- undoButton.setEnabled(false);\r
- }\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\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
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ *
+ * 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/>.
+ */
+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.*;
+
+/**
+ * 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() >= 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].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]);
+ }
+
+ }
+ }
+
+ 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)
+ {
+ 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])
+ {
+ del.addElement(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] = (SequenceI) del.elementAt(i);
+ if (deleted[i].getLength() > width)
+ {
+ width = deleted[i].getLength();
+ }
+ }
+
+ EditCommand cut = new EditCommand("Remove Redundancy",
+ EditCommand.CUT, deleted, 0, width, ap.av.alignment);
+
+ for (int i = 0; i < del.size(); i++)
+ {
+ ap.av.alignment.deleteSequence(deleted[i]);
+ PaintRefresher.Refresh(this, ap.av.getSequenceSetId(), true, true);
+ if (sg != null)
+ {
+ sg.deleteSequence(deleted[i], false);
+ }
+ }
+
+ historyList.push(cut);
+
+ ap.alignFrame.addHistoryItem(cut);
+
+ ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
+ .getSequences());
+ }
+
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ public void undoButton_actionPerformed(ActionEvent e)
+ {
+ CommandI command = (CommandI) historyList.pop();
+ command.undoCommand(af.getViewAlignments());
+
+ if (ap.av.historyList.contains(command))
+ {
+ ap.av.historyList.remove(command);
+ af.updateEditMenuBar();
+ }
+
+ ap.paintAlignment(true);
+
+ if (historyList.size() == 0)
+ {
+ undoButton.setEnabled(false);
+ }
+ }
+
+ /**
+ * 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