git://source.jalview.org
/
jalview.git
/ blobdiff
commit
grep
author
committer
pickaxe
?
search:
re
summary
|
shortlog
|
log
|
commit
|
commitdiff
|
tree
raw
|
inline
| side by side
TreePanel takes viewport
[jalview.git]
/
src
/
jalview
/
schemes
/
Blosum62ColourScheme.java
diff --git
a/src/jalview/schemes/Blosum62ColourScheme.java
b/src/jalview/schemes/Blosum62ColourScheme.java
index
5e86263
..
6e91e0b
100755
(executable)
--- a/
src/jalview/schemes/Blosum62ColourScheme.java
+++ b/
src/jalview/schemes/Blosum62ColourScheme.java
@@
-34,6
+34,7
@@
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
+ // TO UPPERCASE !!!
\r
s = String.valueOf( res -= ('a' - 'A') );
\r
}
\r
\r
s = String.valueOf( res -= ('a' - 'A') );
\r
}
\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