X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fschemes%2FClustalxColourScheme.java;h=d363764857a9c85e105f3f6f2970993e13d4a921;hb=945834b53cf725501cfccb5ca9945c9fb42c0a29;hp=273efb864386df9d2b86d2a89560e6ce62d4aed1;hpb=a79f9e113c51c032070c670e45ce3eb464691166;p=jalview.git

diff --git a/src/jalview/schemes/ClustalxColourScheme.java b/src/jalview/schemes/ClustalxColourScheme.java
index 273efb8..d363764 100755
--- a/src/jalview/schemes/ClustalxColourScheme.java
+++ b/src/jalview/schemes/ClustalxColourScheme.java
@@ -17,10 +17,14 @@
  */
 package jalview.schemes;
 
+import jalview.datamodel.AnnotatedCollectionI;
+import jalview.datamodel.SequenceCollectionI;
 import jalview.datamodel.SequenceI;
 
 import java.awt.Color;
 import java.util.Hashtable;
+import java.util.List;
+import java.util.Map;
 import java.util.Vector;
 
 public class ClustalxColourScheme extends ResidueColourScheme // implements
@@ -55,13 +59,13 @@ public class ClustalxColourScheme extends ResidueColourScheme // implements
     colhash.put("YELLOW", new Color((float) 0.8, (float) 0.8, (float) 0.0));
   }
 
-  public ClustalxColourScheme(Vector seqs, int maxWidth)
+  public ClustalxColourScheme(AnnotatedCollectionI alignment, Map<SequenceI, SequenceCollectionI> hiddenReps)
   {
-    resetClustalX(seqs, maxWidth);
+    alignmentChanged(alignment,hiddenReps);
   }
-
-  public void resetClustalX(Vector seqs, int maxWidth)
-  {
+  public void alignmentChanged(AnnotatedCollectionI alignment, Map<SequenceI, SequenceCollectionI> hiddenReps) {
+    int maxWidth=alignment.getWidth();
+    List<SequenceI> seqs=alignment.getSequences(hiddenReps);
     cons2 = new int[maxWidth][24];
     includeGaps = isIncludeGaps(); // does nothing - TODO replace with call to
     // get the current setting of the
@@ -82,9 +86,9 @@ public class ClustalxColourScheme extends ResidueColourScheme // implements
     int j = 0;
     char[] seq;
 
-    while (j < seqs.size())
+    for (SequenceI sq: seqs)
     {
-      seq = ((SequenceI) seqs.elementAt(j)).getSequence();
+      seq = sq.getSequence();
 
       int end_j = seq.length - 1;