consensus held in residueColour

diff --git a/src/jalview/schemes/Blosum62ColourScheme.java b/src/jalview/schemes/Blosum62ColourScheme.java
index 6c83920..2e18c6a 100755 (executable)
--- a/src/jalview/schemes/Blosum62ColourScheme.java
+++ b/src/jalview/schemes/Blosum62ColourScheme.java
@@ -27,23 +27,14 @@ import jalview.datamodel.*;
 public class Blosum62ColourScheme extends ResidueColourScheme\r
 {\r
 \r
-  // need to keep an eye on the changing visible consensus sequence\r
-  AlignViewport av;\r
-\r
-  public Blosum62ColourScheme(AlignViewport av)\r
+  public Blosum62ColourScheme()\r
   {\r
     super();\r
-    this.av = av;\r
   }\r
 \r
-  public Color findColour(String s, int j, Vector aa)\r
+  public Color findColour(String s, int j)\r
   {\r
-    Hashtable hash;\r
-\r
-    if (aa != null)\r
-      hash = (Hashtable)aa.elementAt(j);\r
-    else\r
-      return Color.white;\r
+    Hashtable hash = (Hashtable)consensus.elementAt(j);\r
 \r
     if (!jalview.util.Comparison.isGap((s.charAt(0))))\r
     {\r
@@ -73,7 +64,7 @@ public class Blosum62ColourScheme extends ResidueColourScheme
 \r
   public boolean canThreshold()\r
   {\r
-    return false;\r
+    return true;\r
   }\r
 \r
 }\r

diff --git a/src/jalview/schemes/ClustalxColourScheme.java b/src/jalview/schemes/ClustalxColourScheme.java
index 2e4678e..06b62c6 100755 (executable)
--- a/src/jalview/schemes/ClustalxColourScheme.java
+++ b/src/jalview/schemes/ClustalxColourScheme.java
@@ -225,7 +225,7 @@ public class ClustalxColourScheme implements ColourSchemeI
    size = i;\r
  }\r
 \r
-  public Color findColour(String s, int j, Vector seqs)\r
+  public Color findColour(String s, int j)\r
    {\r
      int i = ((Integer)ResidueProperties.aaHash.get(s)).intValue();\r
 \r
@@ -249,6 +249,10 @@ public class ClustalxColourScheme implements ColourSchemeI
 \r
    }\r
 \r
+  public void setConsensus(Vector consensus)\r
+  {\r
+    // Clustal colouring cannot be coloured by PID\r
+  }\r
 \r
   public boolean canThreshold()\r
   {\r

diff --git a/src/jalview/schemes/ColourSchemeI.java b/src/jalview/schemes/ColourSchemeI.java
index d82e5f5..fcdaa45 100755 (executable)
--- a/src/jalview/schemes/ColourSchemeI.java
+++ b/src/jalview/schemes/ColourSchemeI.java
@@ -7,7 +7,8 @@ import java.util.*;
 public interface ColourSchemeI\r
 {\r
   public Color   findColour(String aa);\r
-  public Color   findColour(String s,int j, Vector aa);\r
+  public Color   findColour(String s,int j);\r
   public boolean canThreshold();\r
   public boolean isUserDefinable();\r
+  public void    setConsensus(Vector v);\r
 }\r

diff --git a/src/jalview/schemes/ConservationColourScheme.java b/src/jalview/schemes/ConservationColourScheme.java
index cef65c2..d418b4f 100755 (executable)
--- a/src/jalview/schemes/ConservationColourScheme.java
+++ b/src/jalview/schemes/ConservationColourScheme.java
@@ -26,48 +26,44 @@ public class ConservationColourScheme extends ResidueColourScheme {
   public Conservation conserve;\r
   public ColourSchemeI cs;\r
   public int inc = 30;\r
-  int colourThreshold =  7;\r
 \r
   public ConservationColourScheme(Conservation cons, ColourSchemeI oldcs)\r
   {\r
     super();\r
     conserve = cons;\r
     cs = oldcs;\r
-\r
   }\r
 \r
 \r
-   public Color findColour(String s, int i, java.util.Vector v)\r
+   public Color findColour(String s, int i)\r
    {\r
      Color c = Color.white;\r
-     if(cs == null)\r
+     if (cs == null)\r
        return c;\r
 \r
-     if (colourThreshold > 0 && conserve.getConsSequence() != null)\r
+     char ch = conserve.getConsSequence().getSequence().charAt(i);\r
+     if (ch == '*' || ch == '+')\r
+     {\r
+       c = cs.findColour(s, i);\r
+     }\r
+     else\r
      {\r
-       if (conserve.getConsSequence().getSequence().charAt(i) == '*'\r
-           || conserve.getConsSequence().getSequence().charAt(i) == '+')\r
+       int tmp = 10;\r
+       int t = 0;\r
+       if (!jalview.util.Comparison.isGap(ch))\r
+         t = Integer.parseInt(ch + "");\r
+\r
+       c = cs.findColour(s, i);\r
+\r
+       while (tmp >= t)\r
        {\r
-           c = cs.findColour(s, i, v);\r
+         c = lighter(c, inc);\r
+         tmp--;\r
        }\r
-       else\r
-       {\r
-           int tmp = 10;\r
-           int t = 0;\r
-           if (!jalview.util.Comparison.isGap(conserve.getConsSequence().\r
-                                              getSequence().charAt(i)))\r
-             t = Integer.parseInt(conserve.getConsSequence().getSequence().\r
-                                  substring(i, i + 1));\r
 \r
-           c = cs.findColour(s, i, v);\r
-           while (tmp >= t)\r
-           {\r
-             c = lighter(c, inc);\r
-             tmp--;\r
-           }\r
-       }\r
      }\r
-     return c;\r
+\r
+   return c;\r
    }\r
 \r
 \r

diff --git a/src/jalview/schemes/NucleotideColourScheme.java b/src/jalview/schemes/NucleotideColourScheme.java
index caa6998..26aea21 100755 (executable)
--- a/src/jalview/schemes/NucleotideColourScheme.java
+++ b/src/jalview/schemes/NucleotideColourScheme.java
@@ -18,9 +18,9 @@ public class NucleotideColourScheme extends ResidueColourScheme
   }\r
 \r
 \r
-  public Color findColour(String n, int j, Vector aa) {\r
+  public Color findColour(String n, int j) {\r
 \r
-    if (threshold == 0 || aboveThreshold(aa, n, j))\r
+    if (threshold == 0 || aboveThreshold( n, j))\r
       try\r
       {\r
         return colors[ ( (Integer) (ResidueProperties.nucleotideHash.get(n))).intValue()];\r

diff --git a/src/jalview/schemes/PIDColourScheme.java b/src/jalview/schemes/PIDColourScheme.java
index cc050d5..916887e 100755 (executable)
--- a/src/jalview/schemes/PIDColourScheme.java
+++ b/src/jalview/schemes/PIDColourScheme.java
@@ -16,17 +16,9 @@ public class PIDColourScheme extends ResidueColourScheme {
     }\r
 \r
 \r
-  public Color findColour(String s, int j,Vector aa) {\r
+  public Color findColour(String s, int j) {\r
       Color     c    = Color.white;\r
-      Hashtable hash = null;\r
-\r
-\r
-      if (aa != null)\r
-         hash = (Hashtable)aa.elementAt(j);\r
-      else\r
-        return c;\r
-\r
-      String    max  = (String)hash.get("maxResidue");\r
+      Hashtable hash =  (Hashtable)consensus.elementAt(j);\r
 \r
       double sc = 0;\r
       if ( Integer.parseInt( hash.get("maxCount").toString() ) != -1 && hash.contains(s))\r

diff --git a/src/jalview/schemes/ResidueColourScheme.java b/src/jalview/schemes/ResidueColourScheme.java
index b0a5caa..7eab3dd 100755 (executable)
--- a/src/jalview/schemes/ResidueColourScheme.java
+++ b/src/jalview/schemes/ResidueColourScheme.java
@@ -7,13 +7,19 @@ import java.awt.*;
 public class ResidueColourScheme implements ColourSchemeI{\r
     Color    [] colors;\r
     int       threshold = 0;\r
+    public Vector   consensus;\r
 \r
     public ResidueColourScheme(Color[] colors, int threshold) {\r
-       this.colors    = colors;\r
+        this.colors    = colors;\r
        this.threshold = threshold;\r
     }\r
 \r
-    public ResidueColourScheme() {\r
+    public ResidueColourScheme()\r
+    {   }\r
+\r
+    public void setConsensus(Vector consensus)\r
+    {\r
+      this.consensus = consensus;\r
     }\r
 \r
     public Color findColour(String aa)\r
@@ -21,9 +27,9 @@ public class ResidueColourScheme implements ColourSchemeI{
       return colors[((Integer)(ResidueProperties.aaHash.get(aa))).intValue()];\r
     }\r
 \r
-    public Color findColour(String s, int j, Vector aa) {\r
+    public Color findColour(String s, int j) {\r
 \r
-       if( threshold==0 || aboveThreshold(aa,s,j))\r
+       if( threshold==0 || aboveThreshold(s,j))\r
           return colors[((Integer)(ResidueProperties.aaHash.get(s))).intValue()];\r
        else\r
           return Color.white;\r
@@ -38,10 +44,9 @@ public class ResidueColourScheme implements ColourSchemeI{
        threshold = ct;\r
     }\r
 \r
-    public boolean aboveThreshold(Vector aa,String s, int j)\r
+    public boolean aboveThreshold(String s, int j)\r
     {\r
-\r
-       Hashtable hash = (Hashtable)aa.elementAt(j);\r
+       Hashtable hash = (Hashtable)consensus.elementAt(j);\r
 \r
         if ( ( (Integer) hash.get("maxCount")).intValue() != -1 && hash.contains(s))\r
         {\r

diff --git a/src/jalview/schemes/ScoreColourScheme.java b/src/jalview/schemes/ScoreColourScheme.java
index 225f8dd..b62ca18 100755 (executable)
--- a/src/jalview/schemes/ScoreColourScheme.java
+++ b/src/jalview/schemes/ScoreColourScheme.java
@@ -23,12 +23,12 @@ public class ScoreColourScheme extends ResidueColourScheme {
   }\r
 \r
 \r
-    public Color findColour(String s,int j,Vector aa)\r
+    public Color findColour(String s,int j)\r
     {\r
 \r
       if (threshold > 0)\r
       {\r
-         if (!aboveThreshold(aa,s,j))\r
+         if (!aboveThreshold(s,j))\r
              return Color.white;\r
       }\r
 \r