Refactored alignment viewport to use common base, extended viewport API with getters...

[jalview.git] / src / jalview / analysis / AAFrequency.java

diff --git a/src/jalview/analysis/AAFrequency.java b/src/jalview/analysis/AAFrequency.java
index 11e7a3d..d56fb01 100755 (executable)
--- a/src/jalview/analysis/AAFrequency.java
+++ b/src/jalview/analysis/AAFrequency.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
@@ -105,6 +105,11 @@ public class AAFrequency
 
       for (j = 0; j < jSize; j++)
       {
+        if (sequences[j]==null)
+        {
+          System.err.println("WARNING: Consensus skipping null sequence - possible race condition.");
+          continue;
+        }
         seq = sequences[j].getSequence();
         if (seq.length > i)
         {
@@ -204,16 +209,20 @@ public class AAFrequency
           boolean includeAllConsSymbols, char[] alphabet)
   {
     float tval, value;
-    if (consensus==null || consensus.annotations==null || consensus.annotations.length<width)
+    if (consensus == null || consensus.annotations == null
+            || consensus.annotations.length < width)
     {
-      // called with a bad alignment annotation row - wait for it to be initialised properly
+      // called with a bad alignment annotation row - wait for it to be
+      // initialised properly
       return;
     }
     for (int i = iStart; i < width; i++)
     {
-      if (i>=hconsensus.length) {
-        // happens if sequences calculated over were shorter than alignment width
-        consensus.annotations[i]=null;
+      if (i >= hconsensus.length)
+      {
+        // happens if sequences calculated over were shorter than alignment
+        // width
+        consensus.annotations[i] = null;
         continue;
       }
       value = 0;
@@ -312,14 +321,16 @@ public class AAFrequency
     }
     ;
     jalview.util.QuickSort.sort(vl, ca);
-    rtnval[0] = 1;
+    rtnval[0] = 2;
+    rtnval[1]=0;
     for (int c = ca.length - 1; profile[0][((char[]) ca[c])[0]] > 0; c--)
     {
       if (((char[]) ca[c])[0] != '-')
       {
         rtnval[rtnval[0]++] = ((char[]) ca[c])[0];
-        rtnval[rtnval[0]++] = (int) (((float) profile[0][((char[]) ca[c])[0]]) * 100f / (float) profile[1][ignoreGapsInConsensusCalculation ? 1
+        rtnval[rtnval[0]] = (int) (((float) profile[0][((char[]) ca[c])[0]]) * 100f / (float) profile[1][ignoreGapsInConsensusCalculation ? 1
                 : 0]);
+        rtnval[1]+=rtnval[rtnval[0]++];
       }
     }
     return rtnval;