AAFrequency optimized

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

diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java
index fc46386..998a4a4 100755 (executable)
--- a/src/jalview/appletgui/AlignViewport.java
+++ b/src/jalview/appletgui/AlignViewport.java
@@ -87,7 +87,7 @@ public class AlignViewport
   boolean showHiddenMarkers = true;\r
 \r
 \r
-  public Vector vconsensus;\r
+  public Hashtable [] hconsensus;\r
   AlignmentAnnotation consensus;\r
   AlignmentAnnotation conservation;\r
   AlignmentAnnotation quality;\r
@@ -179,7 +179,7 @@ public class AlignViewport
         globalColourScheme = ColourSchemeProperty.getColour(alignment, colour);\r
         if (globalColourScheme != null)\r
         {\r
-          globalColourScheme.setConsensus(vconsensus);\r
+          globalColourScheme.setConsensus(hconsensus);\r
         }\r
       }\r
 \r
@@ -305,37 +305,28 @@ public class AlignViewport
 \r
   public void updateConsensus()\r
   {\r
-    Annotation[] annotations = new Annotation[alignment.getWidth()];\r
-\r
     // this routine prevents vconsensus becoming a new object each time\r
     // consenus is calculated. Important for speed of Blosum62\r
     // and PID colouring of alignment\r
-    if (vconsensus == null)\r
-    {\r
-      vconsensus = alignment.getAAFrequency();\r
-    }\r
-    else\r
-    {\r
-      Vector temp = alignment.getAAFrequency();\r
-      vconsensus.removeAllElements();\r
-      Enumeration e = temp.elements();\r
-      while (e.hasMoreElements())\r
-      {\r
-        vconsensus.addElement(e.nextElement());\r
-      }\r
-    }\r
-    Hashtable hash = null;\r
-    for (int i = 0; i < alignment.getWidth(); i++)\r
+    int aWidth = alignment.getWidth();\r
+\r
+    Annotation[] annotations = new Annotation[aWidth];\r
+\r
+    hconsensus = new Hashtable[aWidth];\r
+    AAFrequency.calculate(alignment.getSequencesArray(),\r
+                          0, aWidth,\r
+                          hconsensus);\r
+\r
+    for (int i = 0; i < aWidth; i++)\r
     {\r
-      hash = (Hashtable) vconsensus.elementAt(i);\r
       float value = 0;\r
       if(ignoreGapsInConsensusCalculation)\r
-        value = ((Float)hash.get("pid_nogaps")).floatValue();\r
+        value = ((Float)hconsensus[i].get("pid_nogaps")).floatValue();\r
       else\r
-        value = ((Float)hash.get("pid_gaps")).floatValue();\r
+        value = ((Float)hconsensus[i].get("pid_gaps")).floatValue();\r
 \r
-      String maxRes = hash.get("maxResidue").toString();\r
-      String mouseOver = hash.get("maxResidue") + " ";\r
+      String maxRes = hconsensus[i].get("maxResidue").toString();\r
+      String mouseOver = hconsensus[i].get("maxResidue") + " ";\r
       if (maxRes.length() > 1)\r
       {\r
         mouseOver = "[" + maxRes + "] ";\r
@@ -363,7 +354,7 @@ public class AlignViewport
     }\r
 \r
     if(globalColourScheme!=null)\r
-          globalColourScheme.setConsensus(vconsensus);\r
+          globalColourScheme.setConsensus(hconsensus);\r
 \r
   }\r
   /**\r