X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FConservation.java;h=e77a67af4b504b45b17a761910f0e656bc88856a;hb=c19d2a91ca05e052e3408bf5852d88eb5d0608f1;hp=76323bc2285bf81e3be6486b4d051843308c3975;hpb=601a323b3e90e2320c52d8b03aba55b1c535a9d0;p=jalview.git

diff --git a/src/jalview/analysis/Conservation.java b/src/jalview/analysis/Conservation.java
index 76323bc..e77a67a 100755
--- a/src/jalview/analysis/Conservation.java
+++ b/src/jalview/analysis/Conservation.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
+ * Copyright (C) 2015 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -280,8 +280,7 @@ public class Conservation
                 resultHash.put(type, ht.get("-"));
               }
             }
-            else if (((Integer) resultHash.get(type)).equals(ht
-                    .get(res)) == false)
+            else if (((Integer) resultHash.get(type)).equals(ht.get(res)) == false)
             {
               resultHash.put(type, new Integer(-1));
             }
@@ -374,14 +373,14 @@ public class Conservation
     {
       consString.append('-');
     }
-    consSymbs = new String[end-start+1];
+    consSymbs = new String[end - start + 1];
     for (int i = start; i <= end; i++)
     {
       gapcons = countConsNGaps(i);
       totGaps = gapcons[1];
       pgaps = ((float) totGaps * 100) / sequences.length;
-      consSymbs[i-start]=new String();
-      
+      consSymbs[i - start] = new String();
+
       if (percentageGaps > pgaps)
       {
         resultHash = total[i - start];
@@ -398,7 +397,7 @@ public class Conservation
           {
             if (result.intValue() == 1)
             {
-              consSymbs[i-start] = type+" "+consSymbs[i-start];
+              consSymbs[i - start] = type + " " + consSymbs[i - start];
               count++;
             }
           }
@@ -406,14 +405,17 @@ public class Conservation
           {
             if (result.intValue() != -1)
             {
-              { 
-                 if (result.intValue()==0) {
-                   consSymbs[i-start] = consSymbs[i-start]+ " !"+type;
-                 } else {
-                   consSymbs[i-start] = type+" "+consSymbs[i-start];
-                 }
+              {
+                if (result.intValue() == 0)
+                {
+                  consSymbs[i - start] = consSymbs[i - start] + " !" + type;
+                }
+                else
+                {
+                  consSymbs[i - start] = type + " " + consSymbs[i - start];
+                }
               }
-              
+
               count++;
             }
           }
@@ -698,10 +700,12 @@ public class Conservation
 
       float vprop = value - min;
       vprop /= max;
+      int consp = i - start;
+      String conssym = (value > 0 && consp > -1 && consp < consSymbs.length) ? consSymbs[consp]
+              : "";
       conservation.annotations[i] = new Annotation(String.valueOf(c),
-              consSymbs[i-start], ' ', value, new Color(minR
-                      + (maxR * vprop), minG + (maxG * vprop), minB
-                      + (maxB * vprop)));
+              conssym, ' ', value, new Color(minR + (maxR * vprop), minG
+                      + (maxG * vprop), minB + (maxB * vprop)));
 
       // Quality calc
       if (quality2 != null)