Highlight sequences before seleting

diff --git a/src/jalview/gui/RedundancyPanel.java b/src/jalview/gui/RedundancyPanel.java
index 3901b1f..5dd2fc4 100755 (executable)
--- a/src/jalview/gui/RedundancyPanel.java
+++ b/src/jalview/gui/RedundancyPanel.java
@@ -27,6 +27,8 @@ import java.awt.event.*;
 import java.util.*;\r
 \r
 import javax.swing.event.*;\r
+import jalview.util.Comparison;\r
+import javax.swing.*;\r
 \r
 \r
 /**\r
@@ -35,11 +37,15 @@ import javax.swing.event.*;
  * @author $author$\r
  * @version $Revision$\r
  */\r
-public class RedundancyPanel extends GSliderPanel\r
+public class RedundancyPanel extends GSliderPanel implements Runnable\r
 {\r
     AlignFrame af;\r
     AlignmentPanel ap;\r
     Stack historyList = new Stack(); // simpler than synching with alignFrame.\r
+    float [] redundancy;\r
+    Vector originalSequences;\r
+    Hashtable originalColours;\r
+    JInternalFrame frame;\r
 \r
     /**\r
      * Creates a new RedundancyPanel object.\r
@@ -51,19 +57,160 @@ public class RedundancyPanel extends GSliderPanel
     {\r
         this.ap = ap;\r
         this.af = af;\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
+                    sliderValueChanged();\r
                 }\r
             });\r
 \r
-        slider.setMinimum(0);\r
+        applyButton.setText("Remove");\r
+        allGroupsCheck.setVisible(false);\r
+        slider.setMinimum(60);\r
         slider.setMaximum(100);\r
         slider.setValue(100);\r
+\r
+        Thread worker = new Thread(this);\r
+        worker.start();\r
+\r
+        frame = new JInternalFrame();\r
+        frame.setContentPane(this);\r
+        Desktop.addInternalFrame(frame, "Redundancy threshold selection", 400,\r
+                         100, false);\r
+        frame.addInternalFrameListener(new InternalFrameAdapter()\r
+            {\r
+              public void internalFrameClosing(InternalFrameEvent evt)\r
+              {\r
+                resetColours();\r
+              }\r
+            }\r
+            );\r
+\r
+    }\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
+     * 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
+        JProgressBar progress = new JProgressBar();\r
+        progress.setIndeterminate(true);\r
+        southPanel.add(progress, java.awt.BorderLayout.SOUTH);\r
+\r
+        label.setText("Calculating....");\r
+\r
+        slider.setVisible(false);\r
+        applyButton.setEnabled(false);\r
+        valueField.setVisible(false);\r
+\r
+        validate();\r
+\r
+        Vector sel = new Vector();\r
+        SequenceGroup sg = ap.av.getSelectionGroup();\r
+        int height;\r
+        originalSequences = new Vector();\r
+        originalColours = new Hashtable();\r
+\r
+        if ( (sg != null) && (sg.getSize() >= 1))\r
+        {\r
+           height = sg.getSize();\r
+          for (int i = 0; i < sg.getSize(); i++)\r
+          {\r
+            sel.addElement(sg.getSequenceAt(i));\r
+          }\r
+        }\r
+        else\r
+        {\r
+          height = ap.av.alignment.getHeight();\r
+          for (int i = 0; i < ap.av.alignment.getHeight(); i++)\r
+          {\r
+            sel.addElement(ap.av.alignment.getSequenceAt(i));\r
+          }\r
+        }\r
+\r
+        redundancy = new float[height];\r
+        for (int i = 0; i < height; i++)\r
+        {\r
+          redundancy[i] = 0f;\r
+        }\r
+\r
+\r
+       // long start = System.currentTimeMillis();\r
+\r
+        float pid;\r
+        SequenceI seqi, seqj;\r
+        for (int i = 0; i < sel.size(); i++)\r
+        {\r
+            originalSequences.addElement(sel.elementAt(i));\r
+            originalColours.put(sel.elementAt(i),\r
+                               ((SequenceI) sel.elementAt(i)).getColor());\r
+\r
+            for (int j = 0; j < i; j++)\r
+            {\r
+              if(i==j)\r
+                continue;\r
+\r
+              seqi = (SequenceI) sel.elementAt(i);\r
+              seqj = (SequenceI) sel.elementAt(j);\r
+\r
+              if (sg != null)\r
+                pid = Comparison.PID( seqi,\r
+                                     seqj,\r
+                                     sg.getStartRes(), sg.getEndRes());\r
+              else\r
+                pid = Comparison.PID( seqi,  seqj );\r
+\r
+\r
+              if(seqj.getLength() < seqi.getLength())\r
+                redundancy[j] = Math.max(pid, redundancy[j]);\r
+              else\r
+                redundancy[i] = Math.max(pid, redundancy[i]);\r
+\r
+            }\r
+        }\r
+\r
+\r
+        progress.setIndeterminate(false);\r
+        progress.setVisible(false);\r
+        progress = null;\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
+    void sliderValueChanged()\r
+    {\r
+      if(redundancy==null)\r
+        return;\r
+\r
+      float value = slider.getValue();\r
+\r
+      for(int i=0; i<redundancy.length; i++)\r
+      {\r
+        if (value > redundancy[i])\r
+           ((SequenceI)originalSequences.elementAt(i)).setColor(java.awt.Color.white);\r
+        else\r
+           ((SequenceI)originalSequences.elementAt(i)).setColor(java.awt.Color.red);\r
+      }\r
+\r
+      PaintRefresher.Refresh(null,ap.av.alignment);\r
+\r
     }\r
 \r
     /**\r
@@ -73,8 +220,6 @@ public class RedundancyPanel extends GSliderPanel
      */\r
     public void applyButton_actionPerformed(ActionEvent e)\r
     {\r
-        float threshold = slider.getValue();\r
-        Vector del;\r
         historyList.push(new HistoryItem("Remove redundancy",\r
                     ap.av.alignment, HistoryItem.HIDE));\r
 \r
@@ -85,35 +230,27 @@ public class RedundancyPanel extends GSliderPanel
             af.updateEditMenuBar();\r
         }\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
-        if ((sg != null) && (sg.getSize() >= 1))\r
+        for (int i = 0; i < redundancy.length; i++)\r
         {\r
-            del = ap.av.alignment.removeRedundancy(threshold, sg.sequences);\r
-\r
-            for (int i = 0; i < del.size(); i++)\r
+          if (value <= redundancy[i])\r
+          {\r
+            SequenceI seq = (SequenceI) originalSequences.elementAt(i);\r
+            ap.av.alignment.deleteSequence(seq);\r
+            del.add(seq);\r
+            if (sg != null)\r
             {\r
-                if (sg.sequences.contains((SequenceI) del.elementAt(i)))\r
-                {\r
-                    sg.deleteSequence((SequenceI) del.elementAt(i), true);\r
-                }\r
+              sg.deleteSequence(seq, false);\r
             }\r
+          }\r
         }\r
-        else\r
-        {\r
-            Vector s = new Vector();\r
-            int i = 0;\r
 \r
-            while (i < ap.av.alignment.getHeight())\r
-            {\r
-                s.addElement(ap.av.alignment.getSequenceAt(i));\r
-                i++;\r
-            }\r
-\r
-            del = ap.av.alignment.removeRedundancy(threshold, s);\r
-        }\r
 \r
         // This has to be done before the restoreHistoryItem method of alignFrame will\r
         // actually restore these sequences.\r
@@ -128,18 +265,17 @@ public class RedundancyPanel extends GSliderPanel
 \r
         ap.av.firePropertyChange("alignment", null, ap.av.getAlignment().getSequences());\r
         af.updateEditMenuBar();\r
+    }\r
 \r
+    void resetColours()\r
+    {\r
+      for(int i=0; i<originalSequences.size(); i++)\r
+      {\r
+        SequenceI seq = (SequenceI)originalSequences.elementAt(i);\r
+        seq.setColor( (java.awt.Color)originalColours.get(seq));\r
+      }\r
 \r
-        if (ap.av.getAlignment().getHeight() < 1)\r
-        {\r
-            try\r
-            {\r
-                af.setClosed(true);\r
-            }\r
-            catch (Exception ex)\r
-            {\r
-            }\r
-        }\r
+      PaintRefresher.Refresh(ap.av.alignment);\r
     }\r
 \r
     /**\r
@@ -149,19 +285,19 @@ public class RedundancyPanel extends GSliderPanel
      */\r
     public void undoButton_actionPerformed(ActionEvent e)\r
     {\r
-        HistoryItem hi = (HistoryItem) historyList.pop();\r
-        af.restoreHistoryItem(hi);\r
+      HistoryItem hi = (HistoryItem) historyList.pop();\r
+      af.restoreHistoryItem(hi);\r
 \r
-        if (historyList.size() == 0)\r
-        {\r
-            undoButton.setEnabled(false);\r
+      if (historyList.size() == 0)\r
+      {\r
+        undoButton.setEnabled(false);\r
 \r
-            if (af.historyList.contains(hi))\r
-            {\r
-                af.historyList.remove(hi);\r
-                af.updateEditMenuBar();\r
-            }\r
+        if (af.historyList.contains(hi))\r
+        {\r
+          af.historyList.remove(hi);\r
+          af.updateEditMenuBar();\r
         }\r
+      }\r
     }\r
 \r
     /**\r
@@ -181,4 +317,6 @@ public class RedundancyPanel extends GSliderPanel
             valueField.setText(slider.getValue() + "");\r
         }\r
     }\r
+\r
+\r
 }\r