+package jalview.gui;\r
+\r
+import jalview.jbgui.*;\r
+import jalview.datamodel.*;\r
+import java.awt.event.*;\r
+import java.util.*;\r
+import javax.swing.event.*;\r
+\r
+public class RedundancyPanel extends GSliderPanel\r
+{\r
+ AlignmentPanel ap;\r
+\r
+ SequenceI[] oldAlignment;\r
+\r
+\r
+ public RedundancyPanel(AlignmentPanel ap)\r
+ {\r
+ this.ap = ap;\r
+\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
+\r
+ public void applyButton_actionPerformed(ActionEvent e)\r
+ {\r
+ float threshold = slider.getValue();\r
+ Vector del;\r
+\r
+ oldAlignment = new SequenceI[ap.av.alignment.getHeight()];\r
+ for (int i = 0; i < ap.av.alignment.getHeight(); i++)\r
+ {\r
+ oldAlignment[i] = new Sequence(ap.av.alignment.getSequenceAt(i).getName(),\r
+ ap.av.alignment.getSequenceAt(i).\r
+ getSequence());\r
+ }\r
+\r
+ undoButton.setEnabled(true);\r
+\r
+ if (ap.av.sel != null && ap.av.sel.size() > 1)\r
+ {\r
+\r
+ del = ap.av.alignment.removeRedundancy(threshold, ap.av.sel.asVector());\r
+ for (int i = 0; i < del.size(); i++)\r
+ if (ap.av.sel.contains( (SequenceI) del.elementAt(i)))\r
+ ap.av.sel.removeElement( (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 (ap.av.sel.contains((SequenceI)del.elementAt(j)))\r
+ ap.av.sel.removeElement((SequenceI)del.elementAt(j));\r
+\r
+ }\r
+ }\r
+\r
+ ap.RefreshPanels();\r
+\r
+ }\r
+\r
+ public void undoButton_actionPerformed(ActionEvent e)\r
+ {\r
+ undoButton.setEnabled(false);\r
+ ap.av.setAlignment( new Alignment(oldAlignment) );\r
+ oldAlignment = null;\r
+ ap.RefreshPanels();\r
+ }\r
+\r
+\r
+ public void valueField_actionPerformed(ActionEvent e)\r
+ {\r
+ try{\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