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[jalview.git]
/
src
/
jalview
/
schemes
/
Blosum62ColourScheme.java
diff --git
a/src/jalview/schemes/Blosum62ColourScheme.java
b/src/jalview/schemes/Blosum62ColourScheme.java
index
356e3fe
..
ec5d4f1
100755
(executable)
--- a/
src/jalview/schemes/Blosum62ColourScheme.java
+++ b/
src/jalview/schemes/Blosum62ColourScheme.java
@@
-1,6
+1,6
@@
/*
\r
* Jalview - A Sequence Alignment Editor and Viewer
\r
/*
\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
*
\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
@@
-20,6
+20,7
@@
package jalview.schemes;
\r
\r
import java.awt.*;
\r
\r
\r
import java.awt.*;
\r
+import jalview.analysis.AAFrequency;
\r
\r
public class Blosum62ColourScheme
\r
extends ResidueColourScheme
\r
\r
public class Blosum62ColourScheme
\r
extends ResidueColourScheme
\r
@@
-31,19
+32,28
@@
public class Blosum62ColourScheme
\r
public Color findColour(String s, int j)
\r
{
\r
\r
public Color findColour(String s, int j)
\r
{
\r
- if ( (threshold != 0) && !aboveThreshold(s, j))
\r
+ char res = s.charAt(0);
\r
+ if ('a' <= res && res <= 'z' )
\r
{
\r
{
\r
- return Color.white;
\r
+ // TO UPPERCASE !!!
\r
+ s = String.valueOf( res -= ('a' - 'A') );
\r
}
\r
\r
}
\r
\r
+ if (consensus == null ||
\r
+ j >= consensus.length ||
\r
+ consensus[j] == null ||
\r
+ (threshold != 0 && !aboveThreshold(s, j)))
\r
+ {
\r
+ return Color.white;
\r
+ }
\r
\r
\r
- if (!jalview.util.Comparison.isGap( (s.charAt(0))))
\r
+ if (!jalview.util.Comparison.isGap( res ))
\r
{
\r
{
\r
- String max = (String) consensus[j].get("maxResidue");
\r
+ String max = (String) consensus[j].get(AAFrequency.MAXRESIDUE);
\r
\r
if (max.indexOf(s) > -1)
\r
{
\r
\r
if (max.indexOf(s) > -1)
\r
{
\r
- return new Color(154, 154, 255);
\r
+ currentColour = new Color(154, 154, 255);
\r
}
\r
else
\r
{
\r
}
\r
else
\r
{
\r
@@
-60,17
+70,22
@@
public class Blosum62ColourScheme
\r
if (c > 0)
\r
{
\r
\r
if (c > 0)
\r
{
\r
- return new Color(204, 204, 255);
\r
+ currentColour = new Color(204, 204, 255);
\r
}
\r
else
\r
{
\r
}
\r
else
\r
{
\r
- return Color.white;
\r
+ currentColour = Color.white;
\r
}
\r
}
\r
}
\r
}
\r
+
\r
+ if(conservationColouring)
\r
+ applyConservation(j);
\r
}
\r
else
\r
{
\r
return Color.white;
\r
}
\r
}
\r
else
\r
{
\r
return Color.white;
\r
}
\r
+
\r
+ return currentColour;
\r
}
\r
}
\r
}
\r
}
\r