Merge branch 'develop' into features/JAL-2446NCList

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

diff --git a/src/jalview/analysis/Conservation.java b/src/jalview/analysis/Conservation.java
index ba4f705..131b39c 100755 (executable)
--- a/src/jalview/analysis/Conservation.java
+++ b/src/jalview/analysis/Conservation.java
@@ -736,28 +736,23 @@ public class Conservation
   public void completeAnnotations(AlignmentAnnotation conservation,
           AlignmentAnnotation quality2, int istart, int alWidth)
   {
-    char[] sequence = getConsSequence().getSequence();
-    float minR;
-    float minG;
-    float minB;
-    float maxR;
-    float maxG;
-    float maxB;
-    minR = 0.3f;
-    minG = 0.0f;
-    minB = 0f;
-    maxR = 1.0f - minR;
-    maxG = 0.9f - minG;
-    maxB = 0f - minB; // scalable range for colouring both Conservation and
-    // Quality
+    SequenceI cons = getConsSequence();
+
+    /*
+     * colour scale for Conservation and Quality;
+     */
+    float minR = 0.3f;
+    float minG = 0.0f;
+    float minB = 0f;
+    float maxR = 1.0f - minR;
+    float maxG = 0.9f - minG;
+    float maxB = 0f - minB;
 
     float min = 0f;
     float max = 11f;
     float qmin = 0f;
     float qmax = 0f;
 
-    char c;
-
     if (conservation != null && conservation.annotations != null
             && conservation.annotations.length < alWidth)
     {
@@ -780,7 +775,7 @@ public class Conservation
     {
       float value = 0;
 
-      c = sequence[i];
+      char c = cons.getCharAt(i);
 
       if (Character.isDigit(c))
       {
@@ -866,8 +861,8 @@ public class Conservation
    */
   String getTooltip(int column)
   {
-    char[] sequence = getConsSequence().getSequence();
-    char val = column < sequence.length ? sequence[column] : '-';
+    SequenceI cons = getConsSequence();
+    char val = column < cons.getLength() ? cons.getCharAt(column) : '-';
     boolean hasConservation = val != '-' && val != '0';
     int consp = column - start;
     String tip = (hasConservation && consp > -1 && consp < consSymbs.length)