colours are right, but not the conservation bit!!

diff --git a/src/jalview/schemes/ClustalxColourScheme.java b/src/jalview/schemes/ClustalxColourScheme.java
index 0479e5c..3a91018 100755 (executable)
--- a/src/jalview/schemes/ClustalxColourScheme.java
+++ b/src/jalview/schemes/ClustalxColourScheme.java
@@ -15,7 +15,7 @@
  * along with this program; if not, write to the Free Software\r
  * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.\r
  */\r
-/*\r
+\r
 package jalview.schemes;\r
 import java.util.*;\r
 import java.awt.*;\r
@@ -191,55 +191,43 @@ public class ClustalxColourScheme implements ColourSchemeI
     ResidueColour[19] = colours[0]; // V\r
   }\r
 \r
-  public Color findColour(DrawableSequence seq, String s, int j) {\r
-    // System.out.println("Finding colour for " + s + " " + j);\r
-    int i = seq.num[j];\r
-    Color c = Color.white;\r
-    for (int k=0; k < ResidueColour[i].conses.length ; k++) {\r
-      if (ResidueColour[i].conses[k].isConserved(cons2,j,seq.num[j],size)) {\r
-        c =  ResidueColour[i].c;\r
-      }\r
-    }\r
-    if (i ==4) {\r
-      if (conses[27].isConserved(cons2,j,seq.num[j],size)) {\r
-        c = (Color)colhash.get("PINK");\r
-      }\r
-    }\r
-    return c;\r
+  public Color findColour(String s)\r
+  {\r
+    return Color.pink;\r
   }\r
 \r
-  public void setColours(DrawableSequence seq, int j) {\r
-    Color c = Color.white;\r
+  public Color findColour(String s, int j, Vector seqs)\r
+  {\r
 \r
-    String s = seq.getSequence().substring(j,j+1);\r
-    try {\r
-      c = findColour(seq,s,j);\r
-      seq.setResidueBoxColour(j,c);\r
-    } catch (Exception e) {\r
-      seq.setResidueBoxColour(j,Color.white);\r
-    }\r
-  }\r
+    int i = Integer.parseInt( ResidueProperties.aaHash.get(s).toString() );\r
 \r
-  public void setColours(DrawableSequence s) {\r
-    for (int j = 0; j < s.sequence.length(); j++) {\r
-      setColours(s,j);\r
-    }\r
+    return ResidueColour[i].c;\r
   }\r
 \r
-  public void setColours(SequenceGroup sg) {\r
-    for (int j = 0; j < sg.sequences.size(); j++) {\r
+  public boolean canThreshold()\r
+  {\r
+    return false;\r
+  }\r
 \r
-      DrawableSequence s = (DrawableSequence)sg.sequences.elementAt(j);\r
-      for (int i = 0; i < s.getSequence().length();i++) {\r
-        setColours(s,i);\r
-      }\r
-    }\r
+  public boolean isUserDefinable()\r
+  {\r
+    return false;\r
   }\r
 \r
+}\r
+\r
+class ConsensusColour {\r
+\r
+  Consensus[] conses;\r
+  Color c;\r
 \r
+  public ConsensusColour(Color c,Consensus[] conses) {\r
+    this.conses = conses;\r
+    //    this.list = list;\r
+    this.c = c;\r
+  }\r
 }\r
 \r
-*/\r
 \r
 \r
 \r