X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FConservationColourScheme.java;h=6394124a422e7f0c7cef214ed53e174c48e430ae;hb=e542a2b9968ee6a7def19e79e84c27684ee686e3;hp=1cbc0d4ea6ee37faba342ea7c06df0f864a03afc;hpb=4960c54cb378f2fb063cc36336ab3ac22eda660b;p=jalview.git

diff --git a/src/jalview/schemes/ConservationColourScheme.java b/src/jalview/schemes/ConservationColourScheme.java
index 1cbc0d4..6394124 100755
--- a/src/jalview/schemes/ConservationColourScheme.java
+++ b/src/jalview/schemes/ConservationColourScheme.java
@@ -18,109 +18,59 @@
 
 package jalview.schemes;
 import java.awt.*;
-import jalview.gui.*;
-import jalview.datamodel.*;
 import jalview.analysis.*;
+import java.util.Vector;
 
 public class ConservationColourScheme extends ResidueColourScheme {
   public Conservation conserve;
-  boolean byResidue = true;
   public ColourSchemeI cs;
   public int inc = 30;
-  int colourThreshold =  7;
 
-  public ConservationColourScheme(SequenceGroup sg)
+  public ConservationColourScheme(Conservation cons, ColourSchemeI oldcs)
   {
     super();
-    this.conserve = sg.getConservation();
-    colourThreshold = 7;
-    this.cs = sg.cs;
+    conserve = cons;
+    cs = oldcs;
   }
 
-  public void setColours(DrawableSequence seq, int j) {
-    Color c = Color.white;
-    String s = seq.getSequence().substring(j,j+1);
-
-      if (colourThreshold > 0 && conserve.getConsSequence() != null) {
-        if (fullConservation(j)) {
-          if (byResidue) {
-            c = findColour(seq,s,j);
-           } else {
-             c = Color.red;
-           }
-        } else {
-          if (byResidue) {
-
-            int tmp = 10;
-            int t = Integer.parseInt(conserve.getConsSequence().getSequence().substring(j,j+1));
-            c = findColour(seq,s,j);
-
-             while (tmp >= t) {
-              //      c = c.darker();
-              c = lighter(c,inc);
-               tmp--;
-             }
-          } else {
-          c = Color.yellow;
-          }
-        }
-      }
-
-      seq.setColor(c);
+  public void setConsensus(Vector consensus)
+  {
+    this.consensus = consensus;
+    if(cs!=null)
+      cs.setConsensus(consensus);
   }
-   public Color findColour(SequenceI seq, String s, int i, java.util.Vector whatever)
+
+   public Color findColour(String s, int i)
    {
-     Color c = null;
-     if (colourThreshold > 0 && conserve.getConsSequence() != null)
+     Color c = Color.white;
+     if (cs == null)
+       return c;
+
+     char ch = conserve.getConsSequence().getSequence().charAt(i);
+     if (ch == '*' || ch == '+')
      {
-       if (fullConservation(i)) {
-         if (byResidue) {
-           c = findColour(null,s,i);
-          } else {
-            c = Color.red;
-          }
-       } else {
-         if (byResidue) {
+       c = cs.findColour(s, i);
+     }
+     else
+     {
+       int tmp = 10;
+       int t = 0;
+       if (!jalview.util.Comparison.isGap(ch))
+         t = Integer.parseInt(ch + "");
 
-           int tmp = 10;
-           int t = 0;
-           try
-             {t=Integer.parseInt(conserve.getConsSequence().getSequence().substring(i,i+1));}
-             catch(NumberFormatException ex){
-               System.out.println("fix this bug, conserveColourScheme");
-               t=0;
-             }
-           c = findColour(null,s,i);
+       c = cs.findColour(s, i);
 
-            while (tmp >= t) {
-             //      c = c.darker();
-             c = lighter(c,inc);
-              tmp--;
-            }
-         } else {
-         c = Color.yellow;
-         }
+       while (tmp >= t)
+       {
+         c = lighter(c, inc);
+         tmp--;
        }
+
      }
-     return c;
-   }
 
-  public Color findColour(DrawableSequence seq, String s, int j) {
-    return cs.findColour(null, s, -1, null);
-  }
-  public boolean fullConservation(int j) {
-    String tmp = conserve.getConsSequence().getSequence().substring(j,j+1);
-    if (tmp.equals("*")) return true; else return false;
-  }
-  public boolean aboveThreshold(DrawableSequence seq, int j, int threshold) {
-    String tmp = conserve.getConsSequence().getSequence().substring(j,j+1);
+   return c;
+   }
 
-    if (Integer.parseInt(tmp) >= threshold || tmp.equals("*")) {
-      return true;
-    } else {
-      return false;
-    }
-  }
 
   public Color lighter(Color c, int inc) {
     int red = c.getRed();