X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FClustalxColourScheme.java;h=19723ca64f67b020e6ba2bcf78852d1c2dd8460d;hb=c5b363c47e896e47fe5b6d3b64abbdf47bd6f94a;hp=3c9f095f0a1626b0918e2e8b2d2a3fb1ae734ef5;hpb=a3fb8ffb6b29504b24717bf1dafc45d8f04abc67;p=jalview.git

diff --git a/src/jalview/schemes/ClustalxColourScheme.java b/src/jalview/schemes/ClustalxColourScheme.java
index 3c9f095..19723ca 100755
--- a/src/jalview/schemes/ClustalxColourScheme.java
+++ b/src/jalview/schemes/ClustalxColourScheme.java
@@ -20,6 +20,7 @@
  */
 package jalview.schemes;
 
+import jalview.api.AlignViewportI;
 import jalview.datamodel.AnnotatedCollectionI;
 import jalview.datamodel.SequenceCollectionI;
 import jalview.datamodel.SequenceI;
@@ -43,8 +44,8 @@ public class ClustalxColourScheme extends ResidueColourScheme
   {
     RED(0.9f, 0.2f, 0.1f), BLUE(0.5f, 0.7f, 0.9f), GREEN(0.1f, 0.8f, 0.1f),
     ORANGE(0.9f, 0.6f, 0.3f), CYAN(0.1f, 0.7f, 0.7f),
-    PINK(0.9f, 0.5f, 0.5f), MAGENTA(0.8f, 0.3f, 0.8f), YELLOW(0.8f, 0.8f,
-            0.0f);
+    PINK(0.9f, 0.5f, 0.5f), MAGENTA(0.8f, 0.3f, 0.8f),
+    YELLOW(0.8f, 0.8f, 0.0f);
 
     final Color colour;
 
@@ -53,6 +54,7 @@ public class ClustalxColourScheme extends ResidueColourScheme
       colour = new Color(r, g, b);
     }
   }
+
   private class ConsensusColour
   {
     Consensus[] cons;
@@ -106,19 +108,18 @@ public class ClustalxColourScheme extends ResidueColourScheme
 
     for (SequenceI sq : seqs)
     {
-      char[] seq = sq.getSequence();
-
-      int end_j = seq.length - 1;
+      int end_j = sq.getLength() - 1;
+      int length = sq.getLength();
 
       for (int i = 0; i <= end_j; i++)
       {
-        if ((seq.length - 1) < i)
+        if (length - 1 < i)
         {
           res = 23;
         }
         else
         {
-          res = ResidueProperties.aaIndex[seq[i]];
+          res = ResidueProperties.aaIndex[sq.getCharAt(i)];
         }
         cons2[i][res]++;
       }
@@ -297,8 +298,7 @@ public class ClustalxColourScheme extends ResidueColourScheme
 
     for (int k = 0; k < residueColour[i].cons.length; k++)
     {
-      if (residueColour[i].cons[k].isConserved(cons2, j, size,
-              includeGaps))
+      if (residueColour[i].cons[k].isConserved(cons2, j, size, includeGaps))
       {
         colour = residueColour[i].c;
       }
@@ -307,7 +307,7 @@ public class ClustalxColourScheme extends ResidueColourScheme
     if (i == 4)
     {
       /*
-       * override to colour C pink if 100% conserved
+       * override to colour C pink if >85% conserved
        */
       if (conses[27].isConserved(cons2, j, size, includeGaps))
       {
@@ -336,11 +336,11 @@ public class ClustalxColourScheme extends ResidueColourScheme
   }
 
   @Override
-  public ColourSchemeI getInstance(AnnotatedCollectionI sg,
-          Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
+  public ColourSchemeI getInstance(AlignViewportI view,
+          AnnotatedCollectionI sg)
   {
     ClustalxColourScheme css = new ClustalxColourScheme(sg,
-            hiddenRepSequences);
+            view == null ? null : view.getHiddenRepSequences());
     css.includeGaps = includeGaps;
     return css;
   }