all can threshold

diff --git a/src/jalview/schemes/Blosum62ColourScheme.java b/src/jalview/schemes/Blosum62ColourScheme.java
index 7798672..566d7ed 100755 (executable)
--- a/src/jalview/schemes/Blosum62ColourScheme.java
+++ b/src/jalview/schemes/Blosum62ColourScheme.java
@@ -32,6 +32,9 @@ public class Blosum62ColourScheme extends ResidueColourScheme
 \r
   public Color findColour(String s, int j)\r
   {\r
+    if( threshold!=0 && !aboveThreshold(s,j))\r
+      return Color.white;\r
+\r
     Hashtable hash = (Hashtable)consensus.elementAt(j);\r
 \r
     if (!jalview.util.Comparison.isGap((s.charAt(0))))\r
@@ -60,9 +63,5 @@ public class Blosum62ColourScheme extends ResidueColourScheme
 \r
   }\r
 \r
-  public boolean canThreshold()\r
-  {\r
-    return true;\r
-  }\r
 \r
 }\r

diff --git a/src/jalview/schemes/ClustalxColourScheme.java b/src/jalview/schemes/ClustalxColourScheme.java
index 1bf8567..c6b63dd 100755 (executable)
--- a/src/jalview/schemes/ClustalxColourScheme.java
+++ b/src/jalview/schemes/ClustalxColourScheme.java
@@ -22,7 +22,7 @@ import jalview.datamodel.*;
 import java.util.*;\r
 import java.awt.*;\r
 \r
-public class ClustalxColourScheme implements ColourSchemeI\r
+public class ClustalxColourScheme extends ResidueColourScheme\r
 {\r
   Hashtable[] cons;\r
   int[][] cons2;\r
@@ -227,6 +227,10 @@ public class ClustalxColourScheme implements ColourSchemeI
 \r
   public Color findColour(String s, int j)\r
    {\r
+     if( threshold!=0 && !aboveThreshold(s,j))\r
+      return Color.white;\r
+\r
+\r
      int i = ((Integer)ResidueProperties.aaHash.get(s)).intValue();\r
 \r
      Color c = Color.white;\r
@@ -248,23 +252,6 @@ public class ClustalxColourScheme implements ColourSchemeI
      return c;\r
 \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
-    return false;\r
-  }\r
-\r
-  public boolean isUserDefinable()\r
-  {\r
-    return false;\r
-  }\r
-\r
-\r
 }\r
 \r
 class ConsensusColour {\r

diff --git a/src/jalview/schemes/ColourSchemeI.java b/src/jalview/schemes/ColourSchemeI.java
index c400251..495947a 100755 (executable)
--- a/src/jalview/schemes/ColourSchemeI.java
+++ b/src/jalview/schemes/ColourSchemeI.java
@@ -7,7 +7,5 @@ public interface ColourSchemeI
 {\r
   public Color   findColour(String 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/ColourSchemeProperty.java b/src/jalview/schemes/ColourSchemeProperty.java
index 4343b54..8317bd7 100755 (executable)
--- a/src/jalview/schemes/ColourSchemeProperty.java
+++ b/src/jalview/schemes/ColourSchemeProperty.java
@@ -118,11 +118,7 @@ public class ColourSchemeProperty
       case TURN: cs = new TurnColourScheme(); break;\r
       case BURIED: cs = new BuriedColourScheme(); break;\r
       case NUCLEOTIDE: cs = new NucleotideColourScheme(); break;\r
-      case USER_DEFINED:\r
-       // if(jalview.bin.Cache.getProperty("USER_DEFINED_COLOUR")!=null)\r
-        {\r
-       //   cs = jalview.gui.UserDefinedColours.loadDefaultColours(jalview.bin.Cache.getProperty("USER_DEFINED_COLOUR"));\r
-        }\r
+      case USER_DEFINED: cs = new UserColourScheme(null);\r
         break;\r
 \r
       default: break;\r

diff --git a/src/jalview/schemes/PIDColourScheme.java b/src/jalview/schemes/PIDColourScheme.java
index 916887e..eadf09b 100755 (executable)
--- a/src/jalview/schemes/PIDColourScheme.java
+++ b/src/jalview/schemes/PIDColourScheme.java
@@ -16,8 +16,13 @@ public class PIDColourScheme extends ResidueColourScheme {
     }\r
 \r
 \r
+\r
   public Color findColour(String s, int j) {\r
-      Color     c    = Color.white;\r
+\r
+    if( threshold!=0 && !aboveThreshold(s,j))\r
+      return Color.white;\r
+\r
+    Color     c    = Color.white;\r
       Hashtable hash =  (Hashtable)consensus.elementAt(j);\r
 \r
       double sc = 0;\r

diff --git a/src/jalview/schemes/ResidueColourScheme.java b/src/jalview/schemes/ResidueColourScheme.java
index ac00389..3bd9bca 100755 (executable)
--- a/src/jalview/schemes/ResidueColourScheme.java
+++ b/src/jalview/schemes/ResidueColourScheme.java
@@ -59,11 +59,4 @@ public class ResidueColourScheme implements ColourSchemeI{
 \r
        return false;\r
     }\r
-\r
-    public boolean canThreshold() {\r
-       return true;\r
-    }\r
-    public boolean isUserDefinable() {\r
-       return false;\r
-    }\r
 }\r

diff --git a/src/jalview/schemes/UserColourScheme.java b/src/jalview/schemes/UserColourScheme.java
index bc5e8ea..e6f6c9f 100755 (executable)
--- a/src/jalview/schemes/UserColourScheme.java
+++ b/src/jalview/schemes/UserColourScheme.java
@@ -22,8 +22,13 @@ import java.awt.*;
 \r
 public class UserColourScheme extends ResidueColourScheme\r
 {\r
-  public void setColourScheme(Color [] newColors)\r
+  public UserColourScheme(Color [] newColors)\r
   {\r
     colors = newColors;\r
   }\r
+\r
+  public Color[] getColours()\r
+  {\r
+    return colors;\r
+  }\r
 }\r

diff --git a/src/jalview/schemes/ZappoColourScheme.java b/src/jalview/schemes/ZappoColourScheme.java
index 482a5c0..7cb2327 100755 (executable)
--- a/src/jalview/schemes/ZappoColourScheme.java
+++ b/src/jalview/schemes/ZappoColourScheme.java
@@ -5,9 +5,4 @@ public class ZappoColourScheme extends ResidueColourScheme {
   public ZappoColourScheme() {\r
     super(ResidueProperties.color,0);\r
   }\r
-\r
-  public boolean isUserDefinable() {\r
-    return true;\r
-  }\r
-\r
 }\r