Added PadGaps and made treeSortMenu dynamic (it gets added when there is a tree order...

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

diff --git a/src/jalview/schemes/ClustalxColourScheme.java b/src/jalview/schemes/ClustalxColourScheme.java
index b28ac76..1bf8567 100755 (executable)
--- a/src/jalview/schemes/ClustalxColourScheme.java
+++ b/src/jalview/schemes/ClustalxColourScheme.java
@@ -60,10 +60,14 @@ public class ClustalxColourScheme implements ColourSchemeI
       String seq;\r
       while(j < seqs.size())\r
       {\r
-        seq = ( (SequenceI) seqs.get(j)).getSequence();\r
-        for (i = start; i <= end; i++)\r
+        seq = ( (SequenceI) seqs.elementAt(j)).getSequence();\r
+        int end_j = seq.length()-1;\r
+        for (i = start; i <= end_j; i++)\r
         {\r
-          res = ( (Integer) ResidueProperties.aaHash.get(seq.charAt(i) + "")).intValue();\r
+          if(seq.length()-1<i)\r
+            res = 23;\r
+          else\r
+            res = ( (Integer) ResidueProperties.aaHash.get(seq.charAt(i) + "")).intValue();\r
           cons2[i][res]++;\r
         }\r
         j++;\r
@@ -221,13 +225,13 @@ 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
      Color c = Color.white;\r
 \r
-     if(i>20)\r
+     if(i>19)\r
        return c;\r
 \r
      for (int k=0; k < ResidueColour[i].conses.length ; k++)\r
@@ -245,6 +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