startup file added

[jalview.git] / src / jalview / schemes / ClustalxColourScheme.java

diff --git a/src/jalview/schemes/ClustalxColourScheme.java b/src/jalview/schemes/ClustalxColourScheme.java
index 2e4678e..1bf8567 100755 (executable)
--- a/src/jalview/schemes/ClustalxColourScheme.java
+++ b/src/jalview/schemes/ClustalxColourScheme.java
@@ -60,7 +60,7 @@ public class ClustalxColourScheme implements ColourSchemeI
       String seq;\r
       while(j < seqs.size())\r
       {\r
-        seq = ( (SequenceI) seqs.get(j)).getSequence();\r
+        seq = ( (SequenceI) seqs.elementAt(j)).getSequence();\r
         int end_j = seq.length()-1;\r
         for (i = start; i <= end_j; i++)\r
         {\r
@@ -225,7 +225,7 @@ public class ClustalxColourScheme implements ColourSchemeI
    size = i;\r
  }\r
 \r
-  public Color findColour(String s, int j, Vector seqs)\r
+  public Color findColour(String s, int j)\r
    {\r
      int i = ((Integer)ResidueProperties.aaHash.get(s)).intValue();\r
 \r
@@ -249,6 +249,10 @@ public class ClustalxColourScheme implements ColourSchemeI
 \r
    }\r
 \r
+  public void setConsensus(Vector consensus)\r
+  {\r
+    // Clustal colouring cannot be coloured by PID\r
+  }\r
 \r
   public boolean canThreshold()\r
   {\r