From 66b1bf1a6480b320ddaa00d4f5e70b2051041c11 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Wed, 25 May 2005 16:44:11 +0000
Subject: [PATCH] all can threshold

---
 src/jalview/schemes/Blosum62ColourScheme.java |    7 +++----
 src/jalview/schemes/ClustalxColourScheme.java |   23 +++++------------------
 src/jalview/schemes/ColourSchemeI.java        |    2 --
 src/jalview/schemes/ColourSchemeProperty.java |    6 +-----
 src/jalview/schemes/PIDColourScheme.java      |    7 ++++++-
 src/jalview/schemes/ResidueColourScheme.java  |    7 -------
 src/jalview/schemes/UserColourScheme.java     |    7 ++++++-
 src/jalview/schemes/ZappoColourScheme.java    |    5 -----
 8 files changed, 21 insertions(+), 43 deletions(-)

diff --git a/src/jalview/schemes/Blosum62ColourScheme.java b/src/jalview/schemes/Blosum62ColourScheme.java
index 7798672..566d7ed 100755
--- a/src/jalview/schemes/Blosum62ColourScheme.java
+++ b/src/jalview/schemes/Blosum62ColourScheme.java
@@ -32,6 +32,9 @@ public class Blosum62ColourScheme extends ResidueColourScheme
 
   public Color findColour(String s, int j)
   {
+    if( threshold!=0 && !aboveThreshold(s,j))
+      return Color.white;
+
     Hashtable hash = (Hashtable)consensus.elementAt(j);
 
     if (!jalview.util.Comparison.isGap((s.charAt(0))))
@@ -60,9 +63,5 @@ public class Blosum62ColourScheme extends ResidueColourScheme
 
   }
 
-  public boolean canThreshold()
-  {
-    return true;
-  }
 
 }
diff --git a/src/jalview/schemes/ClustalxColourScheme.java b/src/jalview/schemes/ClustalxColourScheme.java
index 1bf8567..c6b63dd 100755
--- a/src/jalview/schemes/ClustalxColourScheme.java
+++ b/src/jalview/schemes/ClustalxColourScheme.java
@@ -22,7 +22,7 @@ import jalview.datamodel.*;
 import java.util.*;
 import java.awt.*;
 
-public class ClustalxColourScheme implements ColourSchemeI
+public class ClustalxColourScheme extends ResidueColourScheme
 {
   Hashtable[] cons;
   int[][] cons2;
@@ -227,6 +227,10 @@ public class ClustalxColourScheme implements ColourSchemeI
 
   public Color findColour(String s, int j)
    {
+     if( threshold!=0 && !aboveThreshold(s,j))
+      return Color.white;
+
+
      int i = ((Integer)ResidueProperties.aaHash.get(s)).intValue();
 
      Color c = Color.white;
@@ -248,23 +252,6 @@ public class ClustalxColourScheme implements ColourSchemeI
      return c;
 
    }
-
-  public void setConsensus(Vector consensus)
-  {
-    // Clustal colouring cannot be coloured by PID
-  }
-
-  public boolean canThreshold()
-  {
-    return false;
-  }
-
-  public boolean isUserDefinable()
-  {
-    return false;
-  }
-
-
 }
 
 class ConsensusColour {
diff --git a/src/jalview/schemes/ColourSchemeI.java b/src/jalview/schemes/ColourSchemeI.java
index c400251..495947a 100755
--- a/src/jalview/schemes/ColourSchemeI.java
+++ b/src/jalview/schemes/ColourSchemeI.java
@@ -7,7 +7,5 @@ public interface ColourSchemeI
 {
   public Color   findColour(String aa);
   public Color   findColour(String s,int j);
-  public boolean canThreshold();
-  public boolean isUserDefinable();
   public void    setConsensus(Vector v);
 }
diff --git a/src/jalview/schemes/ColourSchemeProperty.java b/src/jalview/schemes/ColourSchemeProperty.java
index 4343b54..8317bd7 100755
--- 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;
       case BURIED: cs = new BuriedColourScheme(); break;
       case NUCLEOTIDE: cs = new NucleotideColourScheme(); break;
-      case USER_DEFINED:
-       // if(jalview.bin.Cache.getProperty("USER_DEFINED_COLOUR")!=null)
-        {
-       //   cs = jalview.gui.UserDefinedColours.loadDefaultColours(jalview.bin.Cache.getProperty("USER_DEFINED_COLOUR"));
-        }
+      case USER_DEFINED: cs = new UserColourScheme(null);
         break;
 
       default: break;
diff --git a/src/jalview/schemes/PIDColourScheme.java b/src/jalview/schemes/PIDColourScheme.java
index 916887e..eadf09b 100755
--- a/src/jalview/schemes/PIDColourScheme.java
+++ b/src/jalview/schemes/PIDColourScheme.java
@@ -16,8 +16,13 @@ public class PIDColourScheme extends ResidueColourScheme {
     }
 
 
+
   public Color findColour(String s, int j) {
-      Color     c    = Color.white;
+
+    if( threshold!=0 && !aboveThreshold(s,j))
+      return Color.white;
+
+    Color     c    = Color.white;
       Hashtable hash =  (Hashtable)consensus.elementAt(j);
 
       double sc = 0;
diff --git a/src/jalview/schemes/ResidueColourScheme.java b/src/jalview/schemes/ResidueColourScheme.java
index ac00389..3bd9bca 100755
--- a/src/jalview/schemes/ResidueColourScheme.java
+++ b/src/jalview/schemes/ResidueColourScheme.java
@@ -59,11 +59,4 @@ public class ResidueColourScheme implements ColourSchemeI{
 
 	return false;
     }
-
-    public boolean canThreshold() {
-	return true;
-    }
-    public boolean isUserDefinable() {
-	return false;
-    }
 }
diff --git a/src/jalview/schemes/UserColourScheme.java b/src/jalview/schemes/UserColourScheme.java
index bc5e8ea..e6f6c9f 100755
--- a/src/jalview/schemes/UserColourScheme.java
+++ b/src/jalview/schemes/UserColourScheme.java
@@ -22,8 +22,13 @@ import java.awt.*;
 
 public class UserColourScheme extends ResidueColourScheme
 {
-  public void setColourScheme(Color [] newColors)
+  public UserColourScheme(Color [] newColors)
   {
     colors = newColors;
   }
+
+  public Color[] getColours()
+  {
+    return colors;
+  }
 }
diff --git a/src/jalview/schemes/ZappoColourScheme.java b/src/jalview/schemes/ZappoColourScheme.java
index 482a5c0..7cb2327 100755
--- a/src/jalview/schemes/ZappoColourScheme.java
+++ b/src/jalview/schemes/ZappoColourScheme.java
@@ -5,9 +5,4 @@ public class ZappoColourScheme extends ResidueColourScheme {
   public ZappoColourScheme() {
     super(ResidueProperties.color,0);
   }
-
-  public boolean isUserDefinable() {
-    return true;
-  }
-
 }
-- 
1.7.10.2