-/*\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
-\r
-package jalview.appletgui;\r
-\r
-import java.util.*;\r
-\r
-import java.awt.event.*;\r
-\r
-import java.awt.*;\r
-\r
-import jalview.datamodel.*;\r
-import jalview.appletgui.PaintRefresher;\r
-\r
-public class RedundancyPanel extends SliderPanel implements Runnable, WindowListener\r
-{\r
- AlignmentPanel ap;\r
-\r
- Stack historyList = new Stack(); // simpler than synching with alignFrame.\r
- Vector originalSequences;\r
- Hashtable originalColours;\r
- SequenceI[] oldAlignment;\r
- float [] redundancy;\r
- Frame frame;\r
-\r
- public RedundancyPanel(AlignmentPanel ap)\r
- {\r
- super(ap, 0, false, null);\r
-\r
- this.ap = ap;\r
- undoButton.setVisible(true);\r
- applyButton.setVisible(true);\r
- allGroupsCheck.setVisible(false);\r
-\r
- label.setText("Enter the redundancy threshold");\r
- valueField.setText("100");\r
-\r
- slider.setVisibleAmount(1);\r
- slider.setMinimum(40);\r
- slider.setMaximum(100+slider.getVisibleAmount());\r
- slider.setValue(100);\r
-\r
- slider.addAdjustmentListener(new AdjustmentListener()\r
- {\r
- public void adjustmentValueChanged(AdjustmentEvent evt)\r
- {\r
- valueField.setText(slider.getValue() + "");\r
- sliderValueChanged();\r
- }\r
- });\r
-\r
- frame = new Frame();\r
- frame.add(this);\r
- jalview.bin.JalviewLite.addFrame(frame, "Redundancy threshold selection",\r
- 400, 100);\r
-\r
- frame.addWindowListener(this);\r
-\r
- Thread worker = new Thread(this);\r
- worker.start();\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
- label.setText("Calculating....");\r
-\r
- slider.setVisible(false);\r
- applyButton.setEnabled(false);\r
- valueField.setVisible(false);\r
-\r
- validate();\r
-\r
- Vector sel = new Vector();\r
- SequenceGroup sg = ap.av.getSelectionGroup();\r
- int height;\r
- originalSequences = new Vector();\r
- originalColours = new Hashtable();\r
-\r
- if ( (sg != null) && (sg.getSize() >= 1))\r
- {\r
- height = sg.getSize();\r
- for (int i = 0; i < sg.getSize(); i++)\r
- {\r
- sel.addElement(sg.getSequenceAt(i));\r
- }\r
- }\r
- else\r
- {\r
- height = ap.av.alignment.getHeight();\r
- for (int i = 0; i < ap.av.alignment.getHeight(); i++)\r
- {\r
- sel.addElement(ap.av.alignment.getSequenceAt(i));\r
- }\r
- }\r
-\r
- redundancy = new float[height];\r
- for (int i = 0; i < height; i++)\r
- {\r
- redundancy[i] = 0f;\r
- }\r
-\r
-\r
- // long start = System.currentTimeMillis();\r
-\r
- float pid;\r
- SequenceI seqi, seqj;\r
- for (int i = 0; i < sel.size(); i++)\r
- {\r
- originalSequences.addElement(sel.elementAt(i));\r
- originalColours.put(sel.elementAt(i),\r
- ((SequenceI) sel.elementAt(i)).getColor());\r
-\r
- for (int j = 0; j < i; j++)\r
- {\r
- if(i==j)\r
- continue;\r
-\r
- seqi = (SequenceI) sel.elementAt(i);\r
- seqj = (SequenceI) sel.elementAt(j);\r
-\r
- if (sg != null)\r
- {\r
- pid = jalview.util.Comparison.PID(seqi,\r
- seqj,\r
- sg.getStartRes(), sg.getEndRes());\r
- }\r
- else\r
- pid = jalview.util.Comparison.PID( seqi, seqj );\r
-\r
-\r
- if(seqj.getLength() < seqi.getLength())\r
- redundancy[j] = Math.max(pid, redundancy[j]);\r
- else\r
- redundancy[i] = Math.max(pid, redundancy[i]);\r
-\r
- }\r
- }\r
-\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("blob done "+ (System.currentTimeMillis()-start));\r
- }\r
-\r
- void sliderValueChanged()\r
- {\r
- if(redundancy==null)\r
- return;\r
-\r
- float value = slider.getValue();\r
-\r
- for(int i=0; i<redundancy.length; i++)\r
- {\r
- if (value > redundancy[i])\r
- ((SequenceI)originalSequences.elementAt(i)).setColor(java.awt.Color.white);\r
- else\r
- ((SequenceI)originalSequences.elementAt(i)).setColor(java.awt.Color.red);\r
- }\r
-\r
- PaintRefresher.Refresh(null,ap.av.alignment);\r
-\r
- }\r
- public void applyButton_actionPerformed()\r
- {\r
- historyList.push(new HistoryItem("Remove redundancy",\r
- ap.av.alignment, HistoryItem.HIDE));\r
-\r
- if ((historyList.size() == 1) ||\r
- !ap.alignFrame.historyList.contains(historyList.firstElement()))\r
- {\r
- ap.alignFrame.addHistoryItem((HistoryItem) historyList.firstElement());\r
- ap.alignFrame.updateEditMenuBar();\r
- }\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
- SequenceI seq = (SequenceI) originalSequences.elementAt(i);\r
- ap.av.alignment.deleteSequence(seq);\r
- del.addElement(seq);\r
- if (sg != null)\r
- {\r
- sg.deleteSequence(seq, false);\r
- }\r
- }\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
- 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, ap.av.getAlignment().getSequences());\r
- ap.alignFrame.updateEditMenuBar();\r
-\r
- }\r
-\r
- public void undoButton_actionPerformed()\r
- {\r
- HistoryItem hi = (HistoryItem) historyList.pop();\r
- ap.alignFrame.restoreHistoryItem(hi);\r
-\r
- if (historyList.size() == 0)\r
- {\r
- undoButton.setEnabled(false);\r
- }\r
- ap.alignFrame.updateEditMenuBar();\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
-\r
- public void windowOpened(WindowEvent evt)\r
- {}\r
-\r
- public void windowClosing(WindowEvent evt)\r
- {\r
- for(int i=0; i<originalSequences.size(); i++)\r
- {\r
- SequenceI seq = (SequenceI)originalSequences.elementAt(i);\r
- seq.setColor( (java.awt.Color)originalColours.get(seq));\r
- }\r
-\r
- PaintRefresher.Refresh(ap.av.alignment);\r
- }\r
-\r
- public void windowClosed(WindowEvent evt)\r
- {}\r
-\r
- public void windowActivated(WindowEvent evt)\r
- {}\r
- public void windowDeactivated(WindowEvent evt)\r
- {}\r
- public void windowIconified(WindowEvent evt)\r
- {}\r
- public void windowDeiconified(WindowEvent evt)\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.appletgui;
+
+import java.util.*;
+
+import java.awt.*;
+import java.awt.event.*;
+
+import jalview.commands.*;
+import jalview.datamodel.*;
+
+public class RedundancyPanel extends SliderPanel implements Runnable,
+ WindowListener
+{
+ AlignmentPanel ap;
+
+ Stack historyList = new Stack(); // simpler than synching with alignFrame.
+
+ float[] redundancy;
+
+ SequenceI[] originalSequences;
+
+ Frame frame;
+
+ Vector redundantSeqs;
+
+ public RedundancyPanel(AlignmentPanel ap)
+ {
+ super(ap, 0, false, null);
+
+ redundantSeqs = new Vector();
+ this.ap = ap;
+ undoButton.setVisible(true);
+ applyButton.setVisible(true);
+ allGroupsCheck.setVisible(false);
+
+ label.setText("Enter the redundancy threshold");
+ valueField.setText("100");
+
+ slider.setVisibleAmount(1);
+ slider.setMinimum(0);
+ slider.setMaximum(100 + slider.getVisibleAmount());
+ slider.setValue(100);
+
+ slider.addAdjustmentListener(new AdjustmentListener()
+ {
+ public void adjustmentValueChanged(AdjustmentEvent evt)
+ {
+ valueField.setText(slider.getValue() + "");
+ sliderValueChanged();
+ }
+ });
+
+ frame = new Frame();
+ frame.add(this);
+ jalview.bin.JalviewLite.addFrame(frame,
+ "Redundancy threshold selection", 400, 100);
+
+ frame.addWindowListener(this);
+
+ Thread worker = new Thread(this);
+ worker.start();
+ }
+
+ /**
+ * 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()
+ {
+ 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.getSelectionAsString();
+ }
+
+ // 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 = jalview.util.Comparison.PID(seqi, seqj);
+
+ if (seqj.length() < seqi.length())
+ {
+ redundancy[j] = Math.max(pid, redundancy[j]);
+ }
+ else
+ {
+ redundancy[i] = Math.max(pid, redundancy[i]);
+ }
+
+ }
+ }
+
+ label.setText("Enter the redundancy threshold");
+ slider.setVisible(true);
+ applyButton.setEnabled(true);
+ valueField.setVisible(true);
+
+ validate();
+ // System.out.println("blob done "+ (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.removeElement(originalSequences[i]);
+ }
+ else if (!redundantSeqs.contains(originalSequences[i]))
+ {
+ redundantSeqs.addElement(originalSequences[i]);
+ }
+ }
+
+ ap.idPanel.idCanvas.setHighlighted(redundantSeqs);
+ PaintRefresher.Refresh(this, ap.av.getSequenceSetId(), true, true);
+
+ }
+
+ public void applyButton_actionPerformed()
+ {
+ 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());
+ }
+
+ }
+
+ public void undoButton_actionPerformed()
+ {
+ CommandI command = (CommandI) historyList.pop();
+ command.undoCommand(null);
+
+ if (ap.av.historyList.contains(command))
+ {
+ ap.av.historyList.removeElement(command);
+ ap.alignFrame.updateEditMenuBar();
+ }
+
+ ap.paintAlignment(true);
+
+ if (historyList.size() == 0)
+ {
+ undoButton.setEnabled(false);
+ }
+ }
+
+ public void valueField_actionPerformed(ActionEvent e)
+ {
+ try
+ {
+ int i = Integer.parseInt(valueField.getText());
+ slider.setValue(i);
+ } catch (Exception ex)
+ {
+ valueField.setText(slider.getValue() + "");
+ }
+ }
+
+ public void windowOpened(WindowEvent evt)
+ {
+ }
+
+ public void windowClosing(WindowEvent evt)
+ {
+ ap.idPanel.idCanvas.setHighlighted(null);
+ }
+
+ public void windowClosed(WindowEvent evt)
+ {
+ }
+
+ public void windowActivated(WindowEvent evt)
+ {
+ }
+
+ public void windowDeactivated(WindowEvent evt)
+ {
+ }
+
+ public void windowIconified(WindowEvent evt)
+ {
+ }
+
+ public void windowDeiconified(WindowEvent evt)
+ {
+ }
+}
git://source.jalview.org / jalview.git / blobdiff