From: amwaterhouse <Andrew Waterhouse>
Date: Wed, 15 Dec 2004 17:29:19 +0000 (+0000)
Subject: colours are right, but not the conservation bit!!
X-Git-Tag: Release_2_0~799
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=88706aa93cd35546349b8ef7f84fb2df64387d8b;p=jalview.git

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
--- 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
  * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
  */
-/*
+
 package jalview.schemes;
 import java.util.*;
 import java.awt.*;
@@ -191,55 +191,43 @@ 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 Color findColour(String s, int j, Vector seqs)
+  {
 
-    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);
-    }
-  }
+    int i = Integer.parseInt( ResidueProperties.aaHash.get(s).toString() );
 
-  public void setColours(DrawableSequence s) {
-    for (int j = 0; j < s.sequence.length(); j++) {
-      setColours(s,j);
-    }
+    return ResidueColour[i].c;
   }
 
-  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;
+  }
 }
 
-*/