X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAAFrequency.java;h=50b1b4b3bac0c06def14a0fd471a4fe17c535f6e;hb=7a8bd034d39520a7bc471f09f95ec28e6208275e;hp=375504d8c8c2e9306f0895a92a7bab4f0f9b5885;hpb=c78ae20a67370e2566d204e3f4c55749ad9bad27;p=jalview.git

diff --git a/src/jalview/analysis/AAFrequency.java b/src/jalview/analysis/AAFrequency.java
index 375504d..50b1b4b 100755
--- a/src/jalview/analysis/AAFrequency.java
+++ b/src/jalview/analysis/AAFrequency.java
@@ -1,18 +1,18 @@
 /*
- * 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
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * 
  * This file is part of Jalview.
- *
+ * 
  * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
+ * modify it under the terms of the GNU General Public License 
  * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
  * PURPOSE.  See the GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  */
 package jalview.analysis;
@@ -26,7 +26,7 @@ import jalview.datamodel.*;
  * returns a new Hashtable[] of size maxSeqLength, if Hashtable not supplied.
  * This class is used extensively in calculating alignment colourschemes that
  * depend on the amount of conservation in each alignment column.
- *
+ * 
  * @author $author$
  * @version $Revision$
  */
@@ -44,37 +44,38 @@ public class AAFrequency
 
   public static final String PROFILE = "P";
 
-  public static final Hashtable[] calculate(List<SequenceI> list, int start,
-          int end)
+  public static final Hashtable[] calculate(List<SequenceI> list,
+          int start, int end)
   {
     return calculate(list, start, end, false);
   }
 
-  public static final Hashtable[] calculate(List<SequenceI> sequences, int start,
-          int end, boolean profile)
+  public static final Hashtable[] calculate(List<SequenceI> sequences,
+          int start, int end, boolean profile)
   {
     SequenceI[] seqs = new SequenceI[sequences.size()];
     int width = 0;
-    synchronized (sequences) {
-    for (int i = 0; i < sequences.size(); i++)
+    synchronized (sequences)
     {
-      seqs[i] = sequences.get(i);
-      if (seqs[i].getLength() > width)
+      for (int i = 0; i < sequences.size(); i++)
       {
-        width = seqs[i].getLength();
+        seqs[i] = sequences.get(i);
+        if (seqs[i].getLength() > width)
+        {
+          width = seqs[i].getLength();
+        }
       }
-    }
 
-    Hashtable[] reply = new Hashtable[width];
+      Hashtable[] reply = new Hashtable[width];
 
-    if (end >= width)
-    {
-      end = width;
-    }
+      if (end >= width)
+      {
+        end = width;
+      }
 
-    calculate(seqs, start, end, reply, profile);
-    return reply;
-  }
+      calculate(seqs, start, end, reply, profile);
+      return reply;
+    }
   }
 
   public static final void calculate(SequenceI[] sequences, int start,
@@ -106,9 +107,10 @@ public class AAFrequency
 
       for (j = 0; j < jSize; j++)
       {
-        if (sequences[j]==null)
+        if (sequences[j] == null)
         {
-          System.err.println("WARNING: Consensus skipping null sequence - possible race condition.");
+          System.err
+                  .println("WARNING: Consensus skipping null sequence - possible race condition.");
           continue;
         }
         seq = sequences[j].getSequence();
@@ -184,7 +186,7 @@ public class AAFrequency
   /**
    * Compute all or part of the annotation row from the given consensus
    * hashtable
-   *
+   * 
    * @param consensus
    *          - pre-allocated annotation row
    * @param hconsensus
@@ -219,33 +221,40 @@ public class AAFrequency
     }
     for (int i = iStart; i < width; i++)
     {
-      if (i >= hconsensus.length)
+      Hashtable hci;
+      if (i >= hconsensus.length || ((hci = hconsensus[i]) == null))
       {
         // happens if sequences calculated over were shorter than alignment
         // width
         consensus.annotations[i] = null;
         continue;
       }
+
       value = 0;
+      Float fv;
       if (ignoreGapsInConsensusCalculation)
       {
-        value = ((Float) hconsensus[i].get(AAFrequency.PID_NOGAPS))
-                .floatValue();
+        fv = (Float) hci.get(AAFrequency.PID_NOGAPS);
       }
       else
       {
-        value = ((Float) hconsensus[i].get(AAFrequency.PID_GAPS))
-                .floatValue();
+        fv = (Float) hci.get(AAFrequency.PID_GAPS);
       }
-
-      String maxRes = hconsensus[i].get(AAFrequency.MAXRESIDUE).toString();
-      String mouseOver = hconsensus[i].get(AAFrequency.MAXRESIDUE) + " ";
+      if (fv == null)
+      {
+        consensus.annotations[i] = null;
+        // data has changed below us .. give up and
+        continue;
+      }
+      value = fv.floatValue();
+      String maxRes = hci.get(AAFrequency.MAXRESIDUE).toString();
+      String mouseOver = hci.get(AAFrequency.MAXRESIDUE) + " ";
       if (maxRes.length() > 1)
       {
         mouseOver = "[" + maxRes + "] ";
         maxRes = "+";
       }
-      int[][] profile = (int[][]) hconsensus[i].get(AAFrequency.PROFILE);
+      int[][] profile = (int[][]) hci.get(AAFrequency.PROFILE);
       if (profile != null && includeAllConsSymbols)
       {
         mouseOver = "";
@@ -253,10 +262,8 @@ public class AAFrequency
         {
           for (int c = 0; c < alphabet.length; c++)
           {
-            tval = profile[0][alphabet[c]]
-                    * 100f
-                    / profile[1][ignoreGapsInConsensusCalculation ? 1
-                            : 0];
+            tval = profile[0][alphabet[c]] * 100f
+                    / profile[1][ignoreGapsInConsensusCalculation ? 1 : 0];
             mouseOver += ((c == 0) ? "" : "; ") + alphabet[c] + " "
                     + ((int) tval) + "%";
           }
@@ -279,8 +286,7 @@ public class AAFrequency
             {
               tval = profile[0][((char[]) ca[c])[0]]
                       * 100f
-                      / profile[1][ignoreGapsInConsensusCalculation ? 1
-                              : 0];
+                      / profile[1][ignoreGapsInConsensusCalculation ? 1 : 0];
               mouseOver += ((p == 0) ? "" : "; ") + ((char[]) ca[c])[0]
                       + " " + ((int) tval) + "%";
               p++;
@@ -301,7 +307,7 @@ public class AAFrequency
 
   /**
    * get the sorted profile for the given position of the consensus
-   *
+   * 
    * @param hconsensus
    * @return
    */
@@ -323,7 +329,7 @@ public class AAFrequency
     ;
     jalview.util.QuickSort.sort(vl, ca);
     rtnval[0] = 2;
-    rtnval[1]=0;
+    rtnval[1] = 0;
     for (int c = ca.length - 1; profile[0][((char[]) ca[c])[0]] > 0; c--)
     {
       if (((char[]) ca[c])[0] != '-')
@@ -331,7 +337,7 @@ public class AAFrequency
         rtnval[rtnval[0]++] = ((char[]) ca[c])[0];
         rtnval[rtnval[0]] = (int) (profile[0][((char[]) ca[c])[0]] * 100f / profile[1][ignoreGapsInConsensusCalculation ? 1
                 : 0]);
-        rtnval[1]+=rtnval[rtnval[0]++];
+        rtnval[1] += rtnval[rtnval[0]++];
       }
     }
     return rtnval;