X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FClustalxColourScheme.java;h=1bf8567861579edd333dcd8bd658f1a8bfa26f84;hb=58ba1562a8a739699ce47a338803b2641f6d7913;hp=128929ccd8d201235a44d9ea8f490f6a9f34f496;hpb=47984e1d3e480c5c8099aeb9481c87936ae12eb4;p=jalview.git

diff --git a/src/jalview/schemes/ClustalxColourScheme.java b/src/jalview/schemes/ClustalxColourScheme.java
index 128929c..1bf8567 100755
--- a/src/jalview/schemes/ClustalxColourScheme.java
+++ b/src/jalview/schemes/ClustalxColourScheme.java
@@ -17,6 +17,8 @@
  */
 
 package jalview.schemes;
+
+import jalview.datamodel.*;
 import java.util.*;
 import java.awt.*;
 
@@ -42,14 +44,36 @@ public class ClustalxColourScheme implements ColourSchemeI
 
     }
   Vector colourTable = new Vector();
-  public ClustalxColourScheme() {
-    this.cons2 = null;
-    this.size = 0;
-    makeColours();
-  }
-  public ClustalxColourScheme(int[][] cons2, int size) {
-    this.cons2 = cons2;
-    this.size = size;
+
+
+  public ClustalxColourScheme(Vector seqs, int maxWidth)
+  {
+    cons2 = new int[maxWidth][24];
+    int start = 0, end = maxWidth-1;
+
+    // Initialize the array
+    for (int j=0;j<24;j++)
+      for (int i=0; i < maxWidth;i++)
+        cons2[i][j] = 0;
+
+      int res,i, j = 0;
+      String seq;
+      while(j < seqs.size())
+      {
+        seq = ( (SequenceI) seqs.elementAt(j)).getSequence();
+        int end_j = seq.length()-1;
+        for (i = start; i <= end_j; i++)
+        {
+          if(seq.length()-1<i)
+            res = 23;
+          else
+            res = ( (Integer) ResidueProperties.aaHash.get(seq.charAt(i) + "")).intValue();
+          cons2[i][res]++;
+        }
+        j++;
+      }
+
+    this.size = seqs.size();
     makeColours();
   }
   public void makeColours() {
@@ -196,15 +220,38 @@ public class ClustalxColourScheme implements ColourSchemeI
     return Color.pink;
   }
 
-  public Color findColour(String s, int j, Vector seqs)
-  {
+ public void setGroupSizeChanged(int i)
+ {
+   size = i;
+ }
+
+  public Color findColour(String s, int j)
+   {
+     int i = ((Integer)ResidueProperties.aaHash.get(s)).intValue();
+
+     Color c = Color.white;
+
+     if(i>19)
+       return c;
+
+     for (int k=0; k < ResidueColour[i].conses.length ; k++)
+       if (ResidueColour[i].conses[k].isConserved(cons2,j,size))
+         c =  ResidueColour[i].c;
+
+     if (i == 4)
+    {
+      if (conses[27].isConserved(cons2, j, size))
+        c = (Color) colhash.get("PINK");
+    }
+
 
-    int i = Integer.parseInt( ResidueProperties.aaHash.get(s).toString() );
+     return c;
 
-    if(i>22) // ie -, ., or space
-      return Color.white;
+   }
 
-    return ResidueColour[i].c;
+  public void setConsensus(Vector consensus)
+  {
+    // Clustal colouring cannot be coloured by PID
   }
 
   public boolean canThreshold()
@@ -217,6 +264,7 @@ public class ClustalxColourScheme implements ColourSchemeI
     return false;
   }
 
+
 }
 
 class ConsensusColour {
@@ -236,3 +284,12 @@ class ConsensusColour {
 
 
 
+
+
+
+
+
+
+
+
+