From 0f530039f8c0ac9c6613063a576c3a13c8644fcd Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Tue, 1 Feb 2005 18:58:40 +0000
Subject: [PATCH] Clustal colours now work

---
 src/jalview/schemes/ClustalxColourScheme.java |   77 ++++++++++++++++++++-----
 src/jalview/schemes/Consensus.java            |   30 +++++-----
 2 files changed, 80 insertions(+), 27 deletions(-)

diff --git a/src/jalview/schemes/ClustalxColourScheme.java b/src/jalview/schemes/ClustalxColourScheme.java
index 128929c..b28ac76 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 +44,32 @@ 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.get(j)).getSequence();
+        for (i = start; i <= end; i++)
+        {
+          res = ( (Integer) ResidueProperties.aaHash.get(seq.charAt(i) + "")).intValue();
+          cons2[i][res]++;
+        }
+        j++;
+      }
+
+    this.size = seqs.size();
     makeColours();
   }
   public void makeColours() {
@@ -196,16 +216,35 @@ public class ClustalxColourScheme implements ColourSchemeI
     return Color.pink;
   }
 
+ public void setGroupSizeChanged(int i)
+ {
+   size = i;
+ }
+
   public Color findColour(String s, int j, Vector seqs)
-  {
+   {
+     int i = ((Integer)ResidueProperties.aaHash.get(s)).intValue();
 
-    int i = Integer.parseInt( ResidueProperties.aaHash.get(s).toString() );
+     Color c = Color.white;
 
-    if(i>22) // ie -, ., or space
-      return Color.white;
+     if(i>20)
+       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;
+
+   }
 
-    return ResidueColour[i].c;
-  }
 
   public boolean canThreshold()
   {
@@ -217,6 +256,7 @@ public class ClustalxColourScheme implements ColourSchemeI
     return false;
   }
 
+
 }
 
 class ConsensusColour {
@@ -236,3 +276,12 @@ class ConsensusColour {
 
 
 
+
+
+
+
+
+
+
+
+
diff --git a/src/jalview/schemes/Consensus.java b/src/jalview/schemes/Consensus.java
index 7b0dbbb..17cb789 100755
--- a/src/jalview/schemes/Consensus.java
+++ b/src/jalview/schemes/Consensus.java
@@ -18,8 +18,6 @@
 
 package jalview.schemes;
 
-import jalview.datamodel.*;
-import java.util.*;
 ////////////////////////////////////////////
 // This does nothing at all at the moment!!!!!!!!!!
 // AW 15th Dec 2004
@@ -28,25 +26,29 @@ public class Consensus {
 
   int[] mask;
   double threshold;
+   String maskstr;
 
-  public Consensus(String m, double threshold)
-  {
-    mask = setNums(m);
+  public Consensus(String mask, double threshold) {
+    // this.id = id;
+    //    this.mask = mask;
+        this.maskstr = mask;
+    setMask(mask);
     this.threshold = threshold;
   }
 
+  public void setMask(String s) {
+    this.mask = setNums(s);
+    //   for (int i=0; i < mask.length; i++) {
+    //  System.out.println(mask[i] + " " + ResidueProperties.aa[mask[i]]);
+    // }
+  }
 
-  public boolean isConserved(int[][] cons2,int col, int res,int size)
-  {
+  public boolean isConserved(int[][] cons2,int col ,int size) {
     int tot = 0;
-
-try{
-    for (int i=0; i < mask.length; i++)
+    for (int i = 0; i < mask.length; i++)
       tot += cons2[col][mask[i]];
-}catch(Exception ex)
-{ return true; }
 
-    if ((double)tot > threshold*size/100)
+    if ( (double) tot > threshold * size / 100)
       return true;
 
     return false;
@@ -60,7 +62,9 @@ try{
     {
       out[i] = ( (Integer) ResidueProperties.aaHash.get(s.substring(i, i + 1))).intValue();
       i++;
+
     }
+
     return out;
   }
 
-- 
1.7.10.2