Getcolours is not needed ????

diff --git a/src/jalview/schemes/ColourSchemeI.java b/src/jalview/schemes/ColourSchemeI.java
index e3d2bbf..8835680 100755 (executable)
--- a/src/jalview/schemes/ColourSchemeI.java
+++ b/src/jalview/schemes/ColourSchemeI.java
@@ -7,9 +7,6 @@ import java.util.*;
 public interface ColourSchemeI\r
 {\r
   public Color   findColour(String aa);\r
-  public Vector  getColours(SequenceI s, Vector aa);\r
-  public Color   getColour (SequenceI s, int pos, Vector aa);\r
-  public Vector  getColours(SequenceGroup sg, Vector aa);\r
   public Color   findColour(SequenceI seq, String s,int j, Vector aa);\r
 \r
   public boolean canThreshold();\r

diff --git a/src/jalview/schemes/PIDColourScheme.java b/src/jalview/schemes/PIDColourScheme.java
index 69cd269..0a28c33 100755 (executable)
--- a/src/jalview/schemes/PIDColourScheme.java
+++ b/src/jalview/schemes/PIDColourScheme.java
@@ -14,7 +14,7 @@ public class PIDColourScheme extends ResidueColourScheme {
        this.pidColours = ResidueProperties.pidColours;\r
        this.thresholds = ResidueProperties.pidThresholds;\r
     }\r
-  public Color getColour(SequenceI seq, int j,Vector aa) {\r
+ /* public Color getColour(SequenceI seq, int j,Vector aa) {\r
     Color c = Color.white;\r
 \r
     String       s = seq.getSequence(j,j+1);\r
@@ -25,7 +25,7 @@ public class PIDColourScheme extends ResidueColourScheme {
 \r
     return c;\r
   }\r
-\r
+*/\r
   public Color findColour(SequenceI seq,String s, int j,Vector aa) {\r
       Color     c    = Color.white;\r
       Hashtable hash = null;\r

diff --git a/src/jalview/schemes/ResidueColourScheme.java b/src/jalview/schemes/ResidueColourScheme.java
index 48f7c38..f16bcca 100755 (executable)
--- a/src/jalview/schemes/ResidueColourScheme.java
+++ b/src/jalview/schemes/ResidueColourScheme.java
@@ -30,7 +30,7 @@ public class ResidueColourScheme implements ColourSchemeI{
     }\r
 \r
     // aa should maybe be a class\r
-    public Color getColour(SequenceI seq, int j,Vector aa) {\r
+  /*  public Color getColour(SequenceI seq, int j,Vector aa) {\r
 \r
        Color  c       = Color.white;\r
        String s       = seq.getSequence(j,j+1);\r
@@ -45,7 +45,8 @@ public class ResidueColourScheme implements ColourSchemeI{
 \r
 \r
       return c;\r
-    }\r
+    }*/\r
+\r
     public int getThreshold() {\r
        return threshold;\r
     }\r
@@ -54,28 +55,6 @@ public class ResidueColourScheme implements ColourSchemeI{
        threshold = ct;\r
     }\r
 \r
-    public Vector  getColours(SequenceI s, Vector aa) {\r
-       Vector colours = new Vector();\r
-\r
-       for (int j = 0; j < s.getLength(); j++)\r
-           colours.addElement(getColour(s,j,aa));\r
-\r
-       return colours;\r
-    }\r
-\r
-    public Vector getColours(SequenceGroup sg, Vector aa) {\r
-       Vector colours = new Vector();\r
-\r
-       for (int j = 0; j < sg.getSize(); j++) {\r
-           SequenceI s = sg.getSequenceAt(j);\r
-\r
-           for (int i = 0; i < s.getLength();i++) {\r
-               colours.addElement(getColour(s,i,aa));\r
-           }\r
-       }\r
-       return colours;\r
-    }\r
-\r
     public boolean aboveThreshold(Vector aa,SequenceI seq, int j, int threshold) {\r
        String    s    = seq.getSequence(j,j+1);\r
        Hashtable hash = (Hashtable)aa.elementAt(j);\r

diff --git a/src/jalview/schemes/ScoreColourScheme.java b/src/jalview/schemes/ScoreColourScheme.java
index e8d7156..89e94fd 100755 (executable)
--- a/src/jalview/schemes/ScoreColourScheme.java
+++ b/src/jalview/schemes/ScoreColourScheme.java
@@ -22,7 +22,7 @@ public class ScoreColourScheme extends ResidueColourScheme {
     this.max = max;\r
   }\r
 \r
-  public Color getColour(SequenceI seq, int j, Vector aa) {\r
+ /* public Color getColour(SequenceI seq, int j, Vector aa) {\r
       Color c = Color.white;\r
       String s = seq.getSequence(j,j+1);\r
 \r
@@ -37,7 +37,7 @@ public class ScoreColourScheme extends ResidueColourScheme {
        //  c = Color.white;\r
 \r
       return c;\r
-  }\r
+  }*/\r
 \r
     public Color findColour(SequenceI seq,String s,int j,Vector aa)\r
     {\r