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ensure lastSeq is refreshed if new feature added
[jalview.git]
/
src
/
jalview
/
schemes
/
Blosum62ColourScheme.java
diff --git
a/src/jalview/schemes/Blosum62ColourScheme.java
b/src/jalview/schemes/Blosum62ColourScheme.java
index
d3b93bf
..
02545a3
100755
(executable)
--- a/
src/jalview/schemes/Blosum62ColourScheme.java
+++ b/
src/jalview/schemes/Blosum62ColourScheme.java
@@
-30,20
+30,18
@@
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
-
\r
- char res = s.charAt(0);
\r
if ('a' <= res && res <= 'z' )
\r
{
\r
// TO UPPERCASE !!!
\r
if ('a' <= res && res <= 'z' )
\r
{
\r
// TO UPPERCASE !!!
\r
- s = String.valueOf( res -= ('a' - 'A') );
\r
+ res -= ('a' - 'A');
\r
}
\r
\r
if (consensus == null ||
\r
j >= consensus.length ||
\r
consensus[j] == null ||
\r
}
\r
\r
if (consensus == null ||
\r
j >= consensus.length ||
\r
consensus[j] == null ||
\r
- (threshold != 0 && !aboveThreshold(s, j)))
\r
+ (threshold != 0 && !aboveThreshold(res, j)))
\r
{
\r
return Color.white;
\r
}
\r
{
\r
return Color.white;
\r
}
\r
@@
-54,7
+52,7
@@
public class Blosum62ColourScheme
{
\r
String max = (String) consensus[j].get(AAFrequency.MAXRESIDUE);
\r
\r
{
\r
String max = (String) consensus[j].get(AAFrequency.MAXRESIDUE);
\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
@@
-66,8
+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
@@
-82,7
+80,7
@@
public class Blosum62ColourScheme
}
\r
\r
if(conservationColouring)
\r
}
\r
\r
if(conservationColouring)
\r
- applyConservation(currentColour, j);
\r
+ currentColour = applyConservation(currentColour, j);
\r
}
\r
else
\r
{
\r
}
\r
else
\r
{
\r