removed

[jalview.git] / src / jalview / schemes / AnnotationColourGradient.java

diff --git a/src/jalview/schemes/AnnotationColourGradient.java b/src/jalview/schemes/AnnotationColourGradient.java
index 789667e..20b0885 100755 (executable)
--- a/src/jalview/schemes/AnnotationColourGradient.java
+++ b/src/jalview/schemes/AnnotationColourGradient.java
@@ -1,6 +1,6 @@
 /*\r
 * Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
 *\r
 * This program is free software; you can redistribute it and/or\r
 * modify it under the terms of the GNU General Public License\r
@@ -85,6 +85,30 @@ public class AnnotationColourGradient extends ResidueColourScheme
 \r
     }\r
 \r
+\r
+    public String getAnnotation()\r
+    {\r
+      return annotation.label;\r
+    }\r
+\r
+    public int getAboveThreshold()\r
+    {\r
+      return aboveAnnotationThreshold;\r
+    }\r
+\r
+    public float getAnnotationThreshold()\r
+    {\r
+      if(annotationThreshold==null)\r
+        return 0;\r
+      else\r
+        return annotationThreshold.value;\r
+    }\r
+\r
+    public ColourSchemeI getBaseColour()\r
+    {\r
+      return colourScheme;\r
+    }\r
+\r
     public Color getMinColour()\r
     {\r
       return new Color( (int) r1, (int) g1, (int) b1);\r
@@ -102,7 +126,7 @@ public class AnnotationColourGradient extends ResidueColourScheme
      *\r
      * @return DOCUMENT ME!\r
      */\r
-    public Color findColour(String n)\r
+    public Color findColour(char c)\r
     {\r
         return Color.red;\r
     }\r
@@ -115,15 +139,15 @@ public class AnnotationColourGradient extends ResidueColourScheme
      *\r
      * @return DOCUMENT ME!\r
      */\r
-    public Color findColour(String n, int j)\r
+    public Color findColour(char c, int j)\r
     {\r
-        currentColour = Color.white;\r
+        Color currentColour = Color.white;\r
 \r
-        if ((threshold == 0) || aboveThreshold(n, j))\r
+        if ((threshold == 0) || aboveThreshold(c, j))\r
         {\r
           if( j<annotation.annotations.length\r
               && annotation.annotations[j]!=null\r
-              && !jalview.util.Comparison.isGap(n.charAt(0)))\r
+              && !jalview.util.Comparison.isGap(c))\r
           {\r
             if(  aboveAnnotationThreshold==NO_THRESHOLD\r
                || (annotationThreshold!=null && aboveAnnotationThreshold==ABOVE_THRESHOLD && annotation.annotations[j].value>=annotationThreshold.value)\r
@@ -131,7 +155,7 @@ public class AnnotationColourGradient extends ResidueColourScheme
             {\r
               if(colourScheme!=null)\r
               {\r
-                currentColour = colourScheme.findColour(n, j);\r
+                currentColour = colourScheme.findColour(c, j);\r
               }\r
               else if(range!=0)\r
               {\r
@@ -155,7 +179,7 @@ public class AnnotationColourGradient extends ResidueColourScheme
         }\r
 \r
         if(conservationColouring)\r
-         applyConservation(j);\r
+         currentColour = applyConservation(currentColour, j);\r
 \r
        return currentColour;\r
     }\r