Remove redundancy implemented

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index abf4874..3fa1379 100755 (executable)
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -217,35 +217,34 @@ public class Alignment implements AlignmentI
   public Vector removeRedundancy(float threshold, Vector sel) {\r
     Vector del = new Vector();\r
 \r
-    for (int i=1; i < sel.size(); i++) {\r
-      for (int j = 0; j < i; j++) {\r
+    for (int i = 1; i < sel.size(); i++)\r
+    {\r
+      for (int j = 0; j < i; j++)\r
+      {\r
         // Only do the comparison if either have not been deleted\r
-        if (!del.contains((SequenceI)sel.elementAt(i)) ||\r
-            !del.contains((SequenceI)sel.elementAt(j))) {\r
+        if (!del.contains( (SequenceI) sel.elementAt(i)) ||\r
+            !del.contains( (SequenceI) sel.elementAt(j)))\r
+        {\r
 \r
-          float pid = Comparison.compare((SequenceI)sel.elementAt(j),\r
-                                         (SequenceI)sel.elementAt(i));\r
+          float pid = Comparison.compare( (SequenceI) sel.elementAt(j),\r
+                                         (SequenceI) sel.elementAt(i));\r
 \r
-          if (pid >= threshold) {\r
+          if (pid >= threshold)\r
+          {\r
             // Delete the shortest one\r
-            if (((SequenceI)sel.elementAt(j)).getSequence().length() >\r
-                ((SequenceI)sel.elementAt(i)).getSequence().length()) {\r
+            if ( ( (SequenceI) sel.elementAt(j)).getSequence().length() >\r
+                ( (SequenceI) sel.elementAt(i)).getSequence().length())\r
               del.addElement(sel.elementAt(i));\r
-              System.out.println("Deleting sequence " + ((SequenceI)sel.elementAt(i)).getName());\r
-            } else {\r
+            else\r
               del.addElement(sel.elementAt(i));\r
-              System.out.println("Deleting sequence " + ((SequenceI)sel.elementAt(i)).getName());\r
-            }\r
           }\r
         }\r
       }\r
     }\r
 \r
     // Now delete the sequences\r
-    for (int i=0; i < del.size(); i++) {\r
-      System.out.println("Deleting sequence " + ((SequenceI)del.elementAt(i)).getName());\r
+    for (int i=0; i < del.size(); i++)\r
       deleteSequence((SequenceI)del.elementAt(i));\r
-    }\r
 \r
     return del;\r
   }\r

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index ec75ee5..7feadb9 100755 (executable)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -521,6 +521,7 @@ public class AlignFrame extends GAlignFrame
       frame.setContentPane(sp);\r
       Desktop.addInternalFrame(frame, "Conservation Colour Increment", 400, 90);\r
       frame.setMaximizable(false);\r
+      frame.setResizable(false);\r
     }\r
   }\r
 \r
@@ -535,6 +536,7 @@ public class AlignFrame extends GAlignFrame
       frame.setContentPane(sp);\r
       Desktop.addInternalFrame(frame, "Percentage Identity Threshold", 400, 90);\r
       frame.setMaximizable(false);\r
+      frame.setResizable(false);\r
     }\r
   }\r
 \r
@@ -606,6 +608,12 @@ public class AlignFrame extends GAlignFrame
 \r
   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)\r
   {\r
+    RedundancyPanel sp = new RedundancyPanel(alignPanel);\r
+    JInternalFrame frame = new JInternalFrame();\r
+    frame.setContentPane(sp);\r
+    Desktop.addInternalFrame(frame, "Redundancy threshold selection", 400, 100);\r
+    frame.setMaximizable(false);\r
+    frame.setResizable(false);\r
 \r
   }\r
 \r

diff --git a/src/jalview/gui/RedundancyPanel.java b/src/jalview/gui/RedundancyPanel.java
new file mode 100755 (executable)
index 0000000..6cb2c22
--- /dev/null
+++ b/src/jalview/gui/RedundancyPanel.java
@@ -0,0 +1,102 @@
+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

diff --git a/src/jalview/jbgui/GSliderPanel.java b/src/jalview/jbgui/GSliderPanel.java
index e53870f..7921487 100755 (executable)
--- a/src/jalview/jbgui/GSliderPanel.java
+++ b/src/jalview/jbgui/GSliderPanel.java
@@ -6,12 +6,17 @@ import java.awt.event.*;
 
 public class GSliderPanel extends JPanel
 {
+  // this is used for conservation colours, PID colours and redundancy threshold
   protected JSlider slider = new JSlider();
   protected JTextField valueField = new JTextField();
   protected JLabel label = new JLabel();
   JPanel jPanel1 = new JPanel();
   BorderLayout borderLayout1 = new BorderLayout();
   GridLayout gridLayout1 = new GridLayout();
+  JPanel jPanel2 = new JPanel();
+  protected JButton applyButton = new JButton();
+  protected JButton undoButton = new JButton();
+  FlowLayout flowLayout1 = new FlowLayout();
 
   public GSliderPanel()
   {
@@ -28,15 +33,15 @@ public class GSliderPanel extends JPanel
   {
     this.setLayout(gridLayout1);
     slider.setMajorTickSpacing(10);
-    slider.setMaximum(50);
     slider.setMinorTickSpacing(1);
     slider.setPaintTicks(true);
-    slider.setBackground(new Color(212, 208, 236));
+    slider.setBackground(new Color(177, 177, 217));
     slider.setFont(new java.awt.Font("Verdana", 0, 11));
     valueField.setFont(new java.awt.Font("Verdana", 0, 11));
     valueField.setMinimumSize(new Dimension(6, 21));
     valueField.setPreferredSize(new Dimension(60, 21));
     valueField.setText("");
+    valueField.setHorizontalAlignment(SwingConstants.CENTER);
     valueField.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -44,17 +49,41 @@ public class GSliderPanel extends JPanel
         valueField_actionPerformed(e);
       }
     });
-    label.setBackground(new Color(212, 208, 236));
+    label.setBackground(new Color(177, 177, 217));
     label.setFont(new java.awt.Font("Verdana", 0, 11));
     label.setOpaque(true);
     label.setHorizontalAlignment(SwingConstants.CENTER);
     label.setText("set this label text");
     jPanel1.setLayout(borderLayout1);
     gridLayout1.setRows(2);
-    this.add(label, null);
-    this.add(jPanel1, null);
+    jPanel2.setLayout(flowLayout1);
+    applyButton.setBackground(new Color(177, 177, 217));
+    applyButton.setText("Apply");
+    applyButton.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        applyButton_actionPerformed(e);
+      }
+    });
+    undoButton.setBackground(new Color(177, 177, 217));
+    undoButton.setEnabled(false);
+    undoButton.setText("Undo");
+    undoButton.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        undoButton_actionPerformed(e);
+      }
+    });
+    jPanel2.setBackground(new Color(177, 177, 217));
+    this.add(jPanel2, null);
+    jPanel2.add(label, null);
+    jPanel2.add(applyButton, null);
+    jPanel2.add(undoButton, null);this.add(jPanel1, null);
     jPanel1.add(valueField,  BorderLayout.EAST);
     jPanel1.add(slider, BorderLayout.CENTER);
+
   }
 
   protected void valueField_actionPerformed(ActionEvent e)
@@ -62,4 +91,14 @@ public class GSliderPanel extends JPanel
 
   }
 
+  protected void applyButton_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  protected void undoButton_actionPerformed(ActionEvent e)
+  {
+
+  }
+
 }