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SequenceGroup parsing added to annotation file
[jalview.git]
/
src
/
jalview
/
schemes
/
UserColourScheme.java
diff --git
a/src/jalview/schemes/UserColourScheme.java
b/src/jalview/schemes/UserColourScheme.java
index
9d61279
..
00f8f6f
100755
(executable)
--- a/
src/jalview/schemes/UserColourScheme.java
+++ b/
src/jalview/schemes/UserColourScheme.java
@@
-186,14
+186,14
@@
public class UserColourScheme
\r
\r
\r
\r
\r
\r
- public Color findColour(String s, int j)
\r
+ public Color findColour(char c, int j)
\r
{
\r
Color currentColour;
\r
{
\r
Color currentColour;
\r
- int index = ResidueProperties.aaIndex[s.charAt(0)];
\r
+ int index = ResidueProperties.aaIndex[c];
\r
\r
\r
- if ((threshold == 0) || aboveThreshold(ResidueProperties.aa[index], j))
\r
+ if ((threshold == 0) || aboveThreshold(c, j))
\r
{
\r
{
\r
- if(lowerCaseColours!=null && 'a' <= s.charAt(0) && s.charAt(0) <= 'z')
\r
+ if(lowerCaseColours!=null && 'a' <= c && c <= 'z')
\r
currentColour = lowerCaseColours[index];
\r
else
\r
currentColour = colors[index];
\r
currentColour = lowerCaseColours[index];
\r
else
\r
currentColour = colors[index];
\r
@@
-204,7
+204,7
@@
public class UserColourScheme
}
\r
\r
if(conservationColouring)
\r
}
\r
\r
if(conservationColouring)
\r
- applyConservation(currentColour, j);
\r
+ currentColour = applyConservation(currentColour, j);
\r
\r
\r
return currentColour;
\r
\r
\r
return currentColour;
\r