/*\r
* Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\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
\r
import java.util.*;\r
\r
-import java.awt.event.*;\r
-\r
import java.awt.*;\r
+import java.awt.event.*;\r
\r
-import jalview.datamodel.*;\r
-import jalview.appletgui.PaintRefresher;\r
import jalview.commands.*;\r
+import jalview.datamodel.*;\r
\r
-public class RedundancyPanel extends SliderPanel implements Runnable, WindowListener\r
+public class RedundancyPanel\r
+ extends SliderPanel implements Runnable, WindowListener\r
{\r
AlignmentPanel ap;\r
\r
Stack historyList = new Stack(); // simpler than synching with alignFrame.\r
- float [] redundancy;\r
- SequenceI [] originalSequences;\r
+ float[] redundancy;\r
+ SequenceI[] originalSequences;\r
Frame frame;\r
Vector redundantSeqs;\r
\r
\r
slider.setVisibleAmount(1);\r
slider.setMinimum(0);\r
- slider.setMaximum(100+slider.getVisibleAmount());\r
+ slider.setMaximum(100 + slider.getVisibleAmount());\r
slider.setValue(100);\r
\r
slider.addAdjustmentListener(new AdjustmentListener()\r
Thread worker = new Thread(this);\r
worker.start();\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
*/\r
public void run()\r
{\r
- label.setText("Calculating....");\r
+ label.setText("Calculating....");\r
\r
- slider.setVisible(false);\r
- applyButton.setEnabled(false);\r
- valueField.setVisible(false);\r
+ slider.setVisible(false);\r
+ applyButton.setEnabled(false);\r
+ valueField.setVisible(false);\r
\r
- validate();\r
+ validate();\r
\r
- String[] omitHidden = null;\r
+ String[] omitHidden = null;\r
\r
- SequenceGroup sg = ap.av.getSelectionGroup();\r
- int height;\r
+ SequenceGroup sg = ap.av.getSelectionGroup();\r
+ int height;\r
\r
- int start, end;\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
+ 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
+ height = originalSequences.length;\r
\r
- redundancy = new float[height];\r
- for (int i = 0; i < height; i++)\r
- {\r
- redundancy[i] = 0f;\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
- // omitHidden = ap.av.getSelectionAsString();\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
- // long start = System.currentTimeMillis();\r
+ pid = jalview.util.Comparison.PID(seqi, seqj);\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
- continue;\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 = jalview.util.Comparison.PID( seqi, seqj );\r
-\r
- if(seqj.length() < seqi.length())\r
- redundancy[j] = Math.max(pid, redundancy[j]);\r
- else\r
- redundancy[i] = Math.max(pid, redundancy[i]);\r
-\r
- }\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
+ 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
+ validate();\r
+ // System.out.println("blob done "+ (System.currentTimeMillis()-start));\r
}\r
\r
void sliderValueChanged()\r
{\r
- if(redundancy==null)\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
+ for (int i = 0; i < redundancy.length; i++)\r
{\r
if (value > redundancy[i])\r
- redundantSeqs.removeElement(originalSequences[i]);\r
- else if(!redundantSeqs.contains(originalSequences[i]))\r
- redundantSeqs.addElement(originalSequences[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
true,\r
true);\r
\r
- }\r
+ }\r
+\r
public void applyButton_actionPerformed()\r
- { Vector del = new Vector();\r
+ {\r
+ Vector del = new Vector();\r
+\r
+ undoButton.setEnabled(true);\r
\r
- undoButton.setEnabled(true);\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
- float value = slider.getValue();\r
- SequenceGroup sg = ap.av.getSelectionGroup();\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
- for (int i = 0; i < redundancy.length; i++)\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
- if (value <= redundancy[i])\r
- {\r
- del.addElement(originalSequences[i]);\r
- }\r
+ width = deleted[i].getLength();\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
+ 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
- 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
- width = deleted[i].getLength();\r
- }\r
-\r
- EditCommand cut = new EditCommand("Remove Redundancy",\r
- EditCommand.CUT, deleted,0,width,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, ap.av.getAlignment().getSequences());\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
if (historyList.size() == 0)\r
{\r
undoButton.setEnabled(false);\r
- }\r
+ }\r
}\r
\r
public void valueField_actionPerformed(ActionEvent e)\r
}\r
}\r
\r
-\r
public void windowOpened(WindowEvent evt)\r
{}\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