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Comment out start and end refs
[jalview.git]
/
src
/
jalview
/
schemes
/
Blosum62ColourScheme.java
diff --git
a/src/jalview/schemes/Blosum62ColourScheme.java
b/src/jalview/schemes/Blosum62ColourScheme.java
index
4b1bf15
..
2c0836d
100755
(executable)
--- a/
src/jalview/schemes/Blosum62ColourScheme.java
+++ b/
src/jalview/schemes/Blosum62ColourScheme.java
@@
-34,11
+34,12
@@
public class Blosum62ColourScheme
char res = s.charAt(0);
\r
if ('a' <= res && res <= 'z' )
\r
{
\r
char res = s.charAt(0);
\r
if ('a' <= res && res <= 'z' )
\r
{
\r
- s = Character.toString( res -= ('a' - 'A') );
\r
+ // TO UPPERCASE !!!
\r
+ s = String.valueOf( res -= ('a' - 'A') );
\r
}
\r
\r
\r
}
\r
\r
\r
- if ( (threshold != 0) && !aboveThreshold(s, j))
\r
+ if ( j>=consensus.length || (threshold != 0 && !aboveThreshold(s, j) ))
\r
{
\r
return Color.white;
\r
}
\r
{
\r
return Color.white;
\r
}
\r
@@
-49,7
+50,7
@@
public class Blosum62ColourScheme
\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
@@
-66,17
+67,22
@@
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