X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fschemes%2FClustalxColourScheme.java;h=1bf8567861579edd333dcd8bd658f1a8bfa26f84;hb=79e0822af333c1c0597d53b0aa679846a590beb3;hp=0479e5c9854d3e584fa0957221f8b59bc6c21e11;hpb=1ecf6419aba86993b3c223bf5ec0fa79427baf85;p=jalview.git

diff --git a/src/jalview/schemes/ClustalxColourScheme.java b/src/jalview/schemes/ClustalxColourScheme.java
index 0479e5c..1bf8567 100755
--- a/src/jalview/schemes/ClustalxColourScheme.java
+++ b/src/jalview/schemes/ClustalxColourScheme.java
@@ -15,8 +15,10 @@
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
  */
-/*
+
 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() {
@@ -191,55 +215,79 @@ public class ClustalxColourScheme implements ColourSchemeI
     ResidueColour[19] = colours[0]; // V
   }
 
-  public Color findColour(DrawableSequence seq, String s, int j) {
-    // System.out.println("Finding colour for " + s + " " + j);
-    int i = seq.num[j];
-    Color c = Color.white;
-    for (int k=0; k < ResidueColour[i].conses.length ; k++) {
-      if (ResidueColour[i].conses[k].isConserved(cons2,j,seq.num[j],size)) {
-        c =  ResidueColour[i].c;
-      }
-    }
-    if (i ==4) {
-      if (conses[27].isConserved(cons2,j,seq.num[j],size)) {
-        c = (Color)colhash.get("PINK");
-      }
-    }
-    return c;
+  public Color findColour(String s)
+  {
+    return Color.pink;
   }
 
-  public void setColours(DrawableSequence seq, int j) {
-    Color c = Color.white;
+ public void setGroupSizeChanged(int i)
+ {
+   size = i;
+ }
 
-    String s = seq.getSequence().substring(j,j+1);
-    try {
-      c = findColour(seq,s,j);
-      seq.setResidueBoxColour(j,c);
-    } catch (Exception e) {
-      seq.setResidueBoxColour(j,Color.white);
-    }
-  }
+  public Color findColour(String s, int j)
+   {
+     int i = ((Integer)ResidueProperties.aaHash.get(s)).intValue();
+
+     Color c = Color.white;
 
-  public void setColours(DrawableSequence s) {
-    for (int j = 0; j < s.sequence.length(); j++) {
-      setColours(s,j);
+     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");
     }
+
+
+     return c;
+
+   }
+
+  public void setConsensus(Vector consensus)
+  {
+    // Clustal colouring cannot be coloured by PID
   }
 
-  public void setColours(SequenceGroup sg) {
-    for (int j = 0; j < sg.sequences.size(); j++) {
+  public boolean canThreshold()
+  {
+    return false;
+  }
 
-      DrawableSequence s = (DrawableSequence)sg.sequences.elementAt(j);
-      for (int i = 0; i < s.getSequence().length();i++) {
-        setColours(s,i);
-      }
-    }
+  public boolean isUserDefinable()
+  {
+    return false;
   }
 
 
 }
 
-*/
+class ConsensusColour {
+
+  Consensus[] conses;
+  Color c;
+
+  public ConsensusColour(Color c,Consensus[] conses) {
+    this.conses = conses;
+    //    this.list = list;
+    this.c = c;
+  }
+}
+
+
+
+
+
+
+
+
+
+