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minor change to output of main method for testing file IO
[jalview.git]
/
src
/
jalview
/
schemes
/
Blosum62ColourScheme.java
diff --git
a/src/jalview/schemes/Blosum62ColourScheme.java
b/src/jalview/schemes/Blosum62ColourScheme.java
index
2c0836d
..
0db55c0
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) 2007 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
@@
-18,9
+18,10
@@
*/
\r
package jalview.schemes;
\r
\r
*/
\r
package jalview.schemes;
\r
\r
-
\r
import java.awt.*;
\r
\r
import java.awt.*;
\r
\r
+import jalview.analysis.*;
\r
+
\r
public class Blosum62ColourScheme
\r
extends ResidueColourScheme
\r
{
\r
public class Blosum62ColourScheme
\r
extends ResidueColourScheme
\r
{
\r
@@
-29,26
+30,29
@@
public class Blosum62ColourScheme
super();
\r
}
\r
\r
super();
\r
}
\r
\r
- public Color findColour(String s, int j)
\r
+ public Color findColour(char res, int j)
\r
{
\r
{
\r
- char res = s.charAt(0);
\r
- if ('a' <= res && res <= 'z' )
\r
+ if ('a' <= res && res <= 'z')
\r
{
\r
{
\r
- // TO UPPERCASE !!!
\r
- s = String.valueOf( res -= ('a' - 'A') );
\r
+ // TO UPPERCASE !!!
\r
+ res -= ('a' - 'A');
\r
}
\r
\r
}
\r
\r
-
\r
- if ( j>=consensus.length || (threshold != 0 && !aboveThreshold(s, j) ))
\r
+ if (consensus == null ||
\r
+ j >= consensus.length ||
\r
+ consensus[j] == null ||
\r
+ (threshold != 0 && !aboveThreshold(res, j)))
\r
{
\r
return Color.white;
\r
}
\r
\r
{
\r
return Color.white;
\r
}
\r
\r
- if (!jalview.util.Comparison.isGap( res ))
\r
+ Color currentColour;
\r
+
\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
\r
- if (max.indexOf(s) > -1)
\r
+ if (max.indexOf(res) > -1)
\r
{
\r
currentColour = new Color(154, 154, 255);
\r
}
\r
{
\r
currentColour = new Color(154, 154, 255);
\r
}
\r
@@
-60,8
+64,8
@@
public class Blosum62ColourScheme
\r
do
\r
{
\r
\r
do
\r
{
\r
- c += ResidueProperties.getBLOSUM62(max.substring(max_aa,
\r
- max_aa + 1), s);
\r
+ c += ResidueProperties.getBLOSUM62(
\r
+ max.charAt(max_aa), res);
\r
}
\r
while (++max_aa < n);
\r
\r
}
\r
while (++max_aa < n);
\r
\r
@@
-75,8
+79,10
@@
public class Blosum62ColourScheme
}
\r
}
\r
\r
}
\r
}
\r
\r
- if(conservationColouring)
\r
- applyConservation(j);
\r
+ if (conservationColouring)
\r
+ {
\r
+ currentColour = applyConservation(currentColour, j);
\r
+ }
\r
}
\r
else
\r
{
\r
}
\r
else
\r
{
\r