Use selection area with hidden columns in calculations

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

diff --git a/src/jalview/gui/RedundancyPanel.java b/src/jalview/gui/RedundancyPanel.java
index 78d8424..b248294 100755 (executable)
--- a/src/jalview/gui/RedundancyPanel.java
+++ b/src/jalview/gui/RedundancyPanel.java
@@ -43,7 +43,7 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
     AlignmentPanel ap;\r
     Stack historyList = new Stack(); // simpler than synching with alignFrame.\r
     float [] redundancy;\r
-    Vector originalSequences;\r
+    SequenceI [] originalSequences;\r
     Hashtable originalColours;\r
     JInternalFrame frame;\r
 \r
@@ -116,63 +116,69 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
 \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
-                pid = Comparison.PID( seqi,\r
-                                     seqj,\r
-                                     sg.getStartRes(), sg.getEndRes());\r
+              if(omitHidden==null)\r
+              {\r
+                seqi = originalSequences[i].getSequence(start, end);\r
+                seqj = originalSequences[j].getSequence(start, end);\r
+              }\r
               else\r
-                pid = Comparison.PID( seqi,  seqj );\r
+              {\r
+                seqi = omitHidden[i];\r
+                seqj = omitHidden[j];\r
+              }\r
 \r
+              pid = 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
@@ -180,7 +186,6 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
             }\r
         }\r
 \r
-\r
         progress.setIndeterminate(false);\r
         progress.setVisible(false);\r
         progress = null;\r
@@ -191,7 +196,7 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
         valueField.setVisible(true);\r
 \r
         validate();\r
-       // System.out.println("blob done "+ (System.currentTimeMillis()-start));\r
+       // System.out.println((System.currentTimeMillis()-start));\r
     }\r
 \r
     void sliderValueChanged()\r
@@ -204,9 +209,9 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
       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
@@ -241,7 +246,7 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
         {\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.add(seq);\r
             if (sg != null)\r
@@ -269,9 +274,9 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
 \r
     void resetColours()\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