+/*\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
+\r
package jalview.appletgui;\r
\r
-import jalview.jbappletgui.*;\r
-import jalview.datamodel.*;\r
-import java.awt.event.*;\r
import java.util.*;\r
\r
-public class RedundancyPanel extends GSliderPanel\r
+import java.awt.*;\r
+import java.awt.event.*;\r
+\r
+import jalview.commands.*;\r
+import jalview.datamodel.*;\r
+\r
+public class RedundancyPanel\r
+ extends SliderPanel implements Runnable, WindowListener\r
{\r
AlignmentPanel ap;\r
\r
- SequenceI[] oldAlignment;\r
-\r
+ Stack historyList = new Stack(); // simpler than synching with alignFrame.\r
+ float[] redundancy;\r
+ SequenceI[] originalSequences;\r
+ Frame frame;\r
+ Vector redundantSeqs;\r
\r
public RedundancyPanel(AlignmentPanel ap)\r
{\r
+ super(ap, 0, false, null);\r
+\r
+ redundantSeqs = new Vector();\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(0);\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
+ valueField.setText(slider.getValue() + "");\r
+ sliderValueChanged();\r
}\r
});\r
\r
- slider.setMinimum(0);\r
- slider.setMaximum(100);\r
- slider.setValue(100 );\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
- public void applyButton_actionPerformed(ActionEvent e)\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
- float threshold = slider.getValue();\r
- Vector del;\r
+ label.setText("Calculating....");\r
+\r
+ slider.setVisible(false);\r
+ applyButton.setEnabled(false);\r
+ valueField.setVisible(false);\r
\r
- oldAlignment = new SequenceI[ap.av.alignment.getHeight()];\r
- for (int i = 0; i < ap.av.alignment.getHeight(); i++)\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.getSelectionAsString();\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
+ 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
- oldAlignment[i] = new Sequence(ap.av.alignment.getSequenceAt(i).getName(),\r
- ap.av.alignment.getSequenceAt(i).\r
- getSequence());\r
+ seqi = omitHidden[i];\r
+ seqj = omitHidden[j];\r
}\r
\r
- undoButton.setEnabled(true);\r
-\r
- SequenceGroup sg = ap.av.getSelectionGroup();\r
- if (sg != null && sg.getSize() > 1)\r
- {\r
-\r
- del = ap.av.alignment.removeRedundancy(threshold, sg.sequences);\r
- for (int i = 0; i < del.size(); i++)\r
- if (sg.sequences.contains( (SequenceI) del.elementAt(i)))\r
- sg.deleteSequence( (SequenceI) del.elementAt(i));\r
-\r
- }\r
- else\r
- {\r
- Vector s = new Vector();\r
- int i=0;\r
- while(i < ap.av.alignment.getHeight())\r
- {\r
- s.addElement( ap.av.alignment.getSequenceAt(i) );\r
- i++;\r
- }\r
- del = ap.av.alignment.removeRedundancy(threshold,s);\r
- for (int j=0; j < del.size(); j++)\r
- {\r
- if (sg.sequences.contains((SequenceI)del.elementAt(j)))\r
- sg.deleteSequence((SequenceI)del.elementAt(j));\r
-\r
- }\r
- }\r
-\r
- ap.repaint();\r
+ pid = jalview.util.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
+ 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
- public void undoButton_actionPerformed(ActionEvent e)\r
+ void sliderValueChanged()\r
{\r
- undoButton.setEnabled(false);\r
- ap.av.setAlignment( new Alignment(oldAlignment) );\r
- oldAlignment = null;\r
- ap.repaint();\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.removeElement(originalSequences[i]);\r
+ }\r
+ else if (!redundantSeqs.contains(originalSequences[i]))\r
+ {\r
+ redundantSeqs.addElement(originalSequences[i]);\r
+ }\r
+ }\r
+\r
+ ap.idPanel.idCanvas.setHighlighted(redundantSeqs);\r
+ PaintRefresher.Refresh(this,\r
+ ap.av.getSequenceSetId(),\r
+ true,\r
+ true);\r
+\r
+ }\r
+\r
+ public void applyButton_actionPerformed()\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
+ public void undoButton_actionPerformed()\r
+ {\r
+ CommandI command = (CommandI) historyList.pop();\r
+ command.undoCommand();\r
+\r
+ if (ap.av.historyList.contains(command))\r
+ {\r
+ ap.av.historyList.removeElement(command);\r
+ ap.alignFrame.updateEditMenuBar();\r
+ }\r
+\r
+ ap.paintAlignment(true);\r
+\r
+ if (historyList.size() == 0)\r
+ {\r
+ undoButton.setEnabled(false);\r
+ }\r
+ }\r
\r
public void valueField_actionPerformed(ActionEvent e)\r
{\r
- try{\r
+ try\r
+ {\r
int i = Integer.parseInt(valueField.getText());\r
slider.setValue(i);\r
}\r
- catch(Exception ex)\r
+ catch (Exception ex)\r
{\r
- valueField.setText( slider.getValue()+"" );\r
+ valueField.setText(slider.getValue() + "");\r
}\r
}\r
+\r
+ public void windowOpened(WindowEvent evt)\r
+ {}\r
+\r
+ public void windowClosing(WindowEvent evt)\r
+ {\r
+ ap.idPanel.idCanvas.setHighlighted(null);\r
+ }\r
+\r
+ public void windowClosed(WindowEvent evt)\r
+ {}\r
+\r
+ public void windowActivated(WindowEvent evt)\r
+ {}\r
+\r
+ public void windowDeactivated(WindowEvent evt)\r
+ {}\r
+\r
+ public void windowIconified(WindowEvent evt)\r
+ {}\r
+\r
+ public void windowDeiconified(WindowEvent evt)\r
+ {}\r
}\r
git://source.jalview.org / jalview.git / blobdiff