Modified for hidden region/group calculation

[jalview.git] / src / jalview / appletgui / RedundancyPanel.java

diff --git a/src/jalview/appletgui/RedundancyPanel.java b/src/jalview/appletgui/RedundancyPanel.java
index c71fe29..7608cb9 100755 (executable)
--- a/src/jalview/appletgui/RedundancyPanel.java
+++ b/src/jalview/appletgui/RedundancyPanel.java
@@ -33,10 +33,9 @@ public class RedundancyPanel extends SliderPanel implements Runnable, WindowList
   AlignmentPanel ap;\r
 \r
   Stack historyList = new Stack(); // simpler than synching with alignFrame.\r
-  Vector originalSequences;\r
-  Hashtable originalColours;\r
-  SequenceI[] oldAlignment;\r
   float [] redundancy;\r
+  SequenceI [] originalSequences;\r
+  Hashtable originalColours;\r
   Frame frame;\r
 \r
   public RedundancyPanel(AlignmentPanel ap)\r
@@ -95,65 +94,69 @@ public class RedundancyPanel extends SliderPanel implements Runnable, WindowList
 \r
       validate();\r
 \r
-      Vector sel = new Vector();\r
+      String[] omitHidden = null;\r
+\r
       SequenceGroup sg = ap.av.getSelectionGroup();\r
       int height;\r
-      originalSequences = new Vector();\r
+\r
       originalColours = new Hashtable();\r
+      int start, end;\r
 \r
       if ( (sg != null) && (sg.getSize(false) >= 1))\r
       {\r
-         height = sg.getSize(false);\r
-        for (int i = 0; i < sg.getSize(false); i++)\r
-        {\r
-          sel.addElement(sg.getSequenceAt(i));\r
-        }\r
+         originalSequences = sg.getSequencesInOrder(ap.av.alignment);\r
+         start = sg.getStartRes();\r
+         end = sg.getEndRes();\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
+        originalSequences = ap.av.alignment.getSequencesArray();\r
+        start = 0;\r
+        end = ap.av.alignment.getWidth();\r
       }\r
 \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
 \r
+    //  if (ap.av.hasHiddenColumns)\r
+      {\r
+     //   omitHidden = ap.av.getSelectionAsString();\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
+      String seqi, seqj;\r
+      for (int i = 0; i < height; i++)\r
       {\r
-          originalSequences.addElement(sel.elementAt(i));\r
-          originalColours.put(sel.elementAt(i),\r
-                             ((SequenceI) sel.elementAt(i)).getColor());\r
+          originalColours.put(originalSequences[i],\r
+                             originalSequences[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
+            if(omitHidden==null)\r
             {\r
-              pid = jalview.util.Comparison.PID(seqi,\r
-                                                seqj,\r
-                                                sg.getStartRes(), sg.getEndRes());\r
+              seqi = originalSequences[i].getSequence(start, end);\r
+              seqj = originalSequences[j].getSequence(start, end);\r
             }\r
             else\r
-              pid = jalview.util.Comparison.PID( seqi,  seqj );\r
+            {\r
+              seqi = omitHidden[i];\r
+              seqj = omitHidden[j];\r
+            }\r
 \r
+            pid = jalview.util.Comparison.PID( seqi,  seqj );\r
 \r
-            if(seqj.getLength() < seqi.getLength())\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
@@ -181,9 +184,9 @@ public class RedundancyPanel extends SliderPanel implements Runnable, WindowList
     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
+         originalSequences[i].setColor(java.awt.Color.white);\r
       else\r
-         ((SequenceI)originalSequences.elementAt(i)).setColor(java.awt.Color.red);\r
+         originalSequences[i].setColor(java.awt.Color.red);\r
     }\r
 \r
     PaintRefresher.Refresh(null,ap.av.alignment);\r
@@ -212,7 +215,7 @@ public class RedundancyPanel extends SliderPanel implements Runnable, WindowList
             {\r
               if (value <= redundancy[i])\r
               {\r
-                SequenceI seq = (SequenceI) originalSequences.elementAt(i);\r
+                SequenceI seq = originalSequences[i];\r
                 ap.av.alignment.deleteSequence(seq);\r
                 del.addElement(seq);\r
                 if (sg != null)\r
@@ -270,9 +273,9 @@ public class RedundancyPanel extends SliderPanel implements Runnable, WindowList
 \r
   public void windowClosing(WindowEvent evt)\r
   {\r
-    for(int i=0; i<originalSequences.size(); i++)\r
+    for(int i=0; i<originalSequences.length; i++)\r
     {\r
-      SequenceI seq = (SequenceI)originalSequences.elementAt(i);\r
+      SequenceI seq = originalSequences[i];\r
       seq.setColor( (java.awt.Color)originalColours.get(seq));\r
     }\r
 \r