X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fschemes%2FConservationColourScheme.java;h=af52bda7994d29be7e77a855f65f0d2a680589c9;hb=09b64bea954c283bde1d21c0a230f51f1ae89373;hp=1cbc0d4ea6ee37faba342ea7c06df0f864a03afc;hpb=4960c54cb378f2fb063cc36336ab3ac22eda660b;p=jalview.git

diff --git a/src/jalview/schemes/ConservationColourScheme.java b/src/jalview/schemes/ConservationColourScheme.java
index 1cbc0d4..af52bda 100755
--- a/src/jalview/schemes/ConservationColourScheme.java
+++ b/src/jalview/schemes/ConservationColourScheme.java
@@ -29,99 +29,64 @@ public class ConservationColourScheme extends ResidueColourScheme {
   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 Color findColour(SequenceI seq, String s, int i, java.util.Vector whatever)
+   public Color findColour(String s, int i, java.util.Vector whatever)
    {
      Color c = null;
      if (colourThreshold > 0 && conserve.getConsSequence() != null)
      {
-       if (fullConservation(i)) {
-         if (byResidue) {
-           c = findColour(null,s,i);
-          } else {
-            c = Color.red;
-          }
-       } else {
-         if (byResidue) {
+       if (conserve.getConsSequence().getSequence().charAt(i)=='*')
+       {
+         if (byResidue)
+           c = findColour(s, i);
+         else
+           c = Color.red;
+       }
+       else
+       {
+         if (byResidue)
+         {
 
            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);
-
-            while (tmp >= t) {
+           if (!jalview.util.Comparison.isGap(conserve.getConsSequence().
+                                              getSequence().charAt(i)))
+             t = Integer.parseInt(conserve.getConsSequence().getSequence().
+                                  substring(i, i + 1));
+
+           c = findColour(s, i);
+
+           while (tmp >= t)
+           {
              //      c = c.darker();
-             c = lighter(c,inc);
-              tmp--;
-            }
-         } else {
-         c = Color.yellow;
+             c = lighter(c, inc);
+             tmp--;
+           }
          }
+         else
+           c = Color.yellow;
        }
      }
      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);
-
-    if (Integer.parseInt(tmp) >= threshold || tmp.equals("*")) {
-      return true;
-    } else {
-      return false;
-    }
+  public Color findColour(String s, int j) {
+    if(cs!=null)
+      return cs.findColour( s, j, null);
+    else
+      return Color.white;
   }
 
+
+
   public Color lighter(Color c, int inc) {
     int red = c.getRed();
     int blue = c.getBlue();