X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fanalysis%2FStructureFrequency.java;h=0c9f8308a4d329233f4f195bfbbe2c9daf324ed1;hb=6bd9630607bd38aaf9b42738a0ae90de8fe5c6e8;hp=42e8847fb301940d3c88188fc0c7ec9748b0d38b;hpb=3385d3fe7b3acd45dc5aaa3c7d73f7cce5ea7457;p=jalview.git

diff --git a/src/jalview/analysis/StructureFrequency.java b/src/jalview/analysis/StructureFrequency.java
index 42e8847..0c9f830 100644
--- a/src/jalview/analysis/StructureFrequency.java
+++ b/src/jalview/analysis/StructureFrequency.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.
  * 
@@ -15,6 +15,7 @@
  * 
  * 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;
 
 import java.util.*;
@@ -121,6 +122,9 @@ public class StructureFrequency
       }
       else
       {
+        bpEnd = findPair(rna, i);
+        if (bpEnd>-1)
+        {
         for (j = 0; j < jSize; j++) // foreach row
         {
           if (sequences[j] == null)
@@ -129,11 +133,8 @@ public class StructureFrequency
                     .println("WARNING: Consensus skipping null sequence - possible race condition.");
             continue;
           }
-          seq = sequences[j].getSequence();
-
-          if (seq.length > i)
+          c = sequences[j].getCharAt(i);
           {
-            c = seq[i];
 
             // standard representation for gaps in sequence and structure
             if (c == '.' || c == ' ')
@@ -146,8 +147,7 @@ public class StructureFrequency
               values['-']++;
               continue;
             }
-            bpEnd = findPair(rna, i);
-            cEnd = seq[bpEnd];
+            cEnd = sequences[j].getCharAt(bpEnd);
             if (checkBpType(c, cEnd))
             {
               values['(']++; // H means it's a helix (structured)
@@ -157,6 +157,7 @@ public class StructureFrequency
             maxResidue = "(";
           }
         }
+        }
         // nonGap++;
       }
       // UPDATE this for new values
@@ -405,7 +406,7 @@ public class StructureFrequency
   public static int[] extractProfile(Hashtable hconsensus,
           boolean ignoreGapsInConsensusCalculation)
   {
-    int[] rtnval = new int[51]; // 2*(5*5)+1
+    int[] rtnval = new int[52]; // 2*(5*5)+2
     int[][] profile = (int[][]) hconsensus.get(StructureFrequency.PROFILE);
     int[][] pairs = (int[][]) hconsensus
             .get(StructureFrequency.PAIRPROFILE);
@@ -429,15 +430,17 @@ public class StructureFrequency
     }
     jalview.util.QuickSort.sort(vl, ca);
 
-    rtnval[0] = 1;
+    rtnval[0] = 2;
+    rtnval[1] = 0;
     for (int c = 624; c > 0; c--)
     {
       if (vl[c] > 0)
       {
         rtnval[rtnval[0]++] = ((int[]) ca[c])[0];
         rtnval[rtnval[0]++] = ((int[]) ca[c])[1];
-        rtnval[rtnval[0]++] = (int) ((float) vl[c] * 100f / (float) profile[1][ignoreGapsInConsensusCalculation ? 1
+        rtnval[rtnval[0]] = (int) ((float) vl[c] * 100f / (float) profile[1][ignoreGapsInConsensusCalculation ? 1
                 : 0]);
+        rtnval[1]+=rtnval[rtnval[0]++];
       }
     }