src/jalview/appletgui/RedundancyPanel.java

   1 package jalview.appletgui;\r
   2 \r
   3 import jalview.jbappletgui.*;\r
   4 import jalview.datamodel.*;\r
   5 import java.awt.event.*;\r
   6 import java.util.*;\r
   7 \r
   8 public class RedundancyPanel extends GSliderPanel\r
   9 {\r
  10   AlignmentPanel ap;\r
  11 \r
  12   SequenceI[] oldAlignment;\r
  13 \r
  14 \r
  15   public RedundancyPanel(AlignmentPanel ap)\r
  16   {\r
  17     this.ap = ap;\r
  18 \r
  19     label.setText("Enter the redundancy threshold");\r
  20 \r
  21     slider.addAdjustmentListener(new AdjustmentListener()\r
  22     {\r
  23       public void adjustmentValueChanged(AdjustmentEvent evt)\r
  24       {\r
  25         valueField.setText( slider.getValue()+"" );\r
  26       }\r
  27     });\r
  28 \r
  29     slider.setMinimum(0);\r
  30     slider.setMaximum(100);\r
  31     slider.setValue(100 );\r
  32 \r
  33   }\r
  34 \r
  35   public void applyButton_actionPerformed(ActionEvent e)\r
  36   {\r
  37        float threshold = slider.getValue();\r
  38        Vector del;\r
  39 \r
  40        oldAlignment = new SequenceI[ap.av.alignment.getHeight()];\r
  41         for (int i = 0; i < ap.av.alignment.getHeight(); i++)\r
  42         {\r
  43            oldAlignment[i] = new Sequence(ap.av.alignment.getSequenceAt(i).getName(),\r
  44                                 ap.av.alignment.getSequenceAt(i).\r
  45                                 getSequence());\r
  46         }\r
  47 \r
  48         undoButton.setEnabled(true);\r
  49 \r
  50         SequenceGroup sg = ap.av.getSelectionGroup();\r
  51        if (sg != null && sg.getSize() > 1)\r
  52        {\r
  53 \r
  54          del = ap.av.alignment.removeRedundancy(threshold, sg.sequences);\r
  55          for (int i = 0; i < del.size(); i++)\r
  56            if (sg.sequences.contains( (SequenceI) del.elementAt(i)))\r
  57              sg.deleteSequence( (SequenceI) del.elementAt(i));\r
  58 \r
  59          }\r
  60          else\r
  61          {\r
  62            Vector s = new Vector();\r
  63            int i=0;\r
  64            while(i < ap.av.alignment.getHeight())\r
  65            {\r
  66              s.addElement( ap.av.alignment.getSequenceAt(i) );\r
  67              i++;\r
  68            }\r
  69             del = ap.av.alignment.removeRedundancy(threshold,s);\r
  70            for (int j=0; j < del.size(); j++)\r
  71            {\r
  72                if (sg.sequences.contains((SequenceI)del.elementAt(j)))\r
  73                sg.deleteSequence((SequenceI)del.elementAt(j));\r
  74 \r
  75            }\r
  76          }\r
  77 \r
  78          ap.repaint();\r
  79 \r
  80   }\r
  81 \r
  82   public void undoButton_actionPerformed(ActionEvent e)\r
  83   {\r
  84       undoButton.setEnabled(false);\r
  85       ap.av.setAlignment( new Alignment(oldAlignment) );\r
  86       oldAlignment = null;\r
  87       ap.repaint();\r
  88   }\r
  89 \r
  90 \r
  91   public void valueField_actionPerformed(ActionEvent e)\r
  92   {\r
  93     try{\r
  94       int i = Integer.parseInt(valueField.getText());\r
  95       slider.setValue(i);\r
  96     }\r
  97     catch(Exception ex)\r
  98     {\r
  99       valueField.setText( slider.getValue()+"" );\r
 100     }\r
 101   }\r
 102 }\r