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TreePanel takes viewport
[jalview.git]
/
src
/
jalview
/
schemes
/
PIDColourScheme.java
diff --git
a/src/jalview/schemes/PIDColourScheme.java
b/src/jalview/schemes/PIDColourScheme.java
index
8cea507
..
66f180b
100755
(executable)
--- a/
src/jalview/schemes/PIDColourScheme.java
+++ b/
src/jalview/schemes/PIDColourScheme.java
@@
-37,12
+37,19
@@
public class PIDColourScheme
\r
public Color findColour(String s, int j)
\r
{
\r
\r
public Color findColour(String s, int j)
\r
{
\r
+ char res = s.charAt(0);
\r
+ if ('a' <= res && res <= 'z')
\r
+ {
\r
+ s = String.valueOf(res -= ('a' - 'A'));
\r
+ }
\r
+
\r
+
\r
if ( (threshold != 0) && !aboveThreshold(s, j))
\r
{
\r
return Color.white;
\r
}
\r
\r
if ( (threshold != 0) && !aboveThreshold(s, j))
\r
{
\r
return Color.white;
\r
}
\r
\r
- Color c = Color.white;
\r
+ currentColour = Color.white;
\r
\r
double sc = 0;
\r
\r
\r
double sc = 0;
\r
\r
@@
-51,13
+58,13
@@
public class PIDColourScheme
{
\r
sc = ((Float)consensus[j].get(ignoreGaps)).floatValue();
\r
\r
{
\r
sc = ((Float)consensus[j].get(ignoreGaps)).floatValue();
\r
\r
- if (!jalview.util.Comparison.isGap( (s.charAt(0))))
\r
+ if (!jalview.util.Comparison.isGap( res ))
\r
{
\r
for (int i = 0; i < thresholds.length; i++)
\r
{
\r
if (sc > thresholds[i])
\r
{
\r
{
\r
for (int i = 0; i < thresholds.length; i++)
\r
{
\r
if (sc > thresholds[i])
\r
{
\r
- c = pidColours[i];
\r
+ currentColour = pidColours[i];
\r
\r
break;
\r
}
\r
\r
break;
\r
}
\r
@@
-65,6
+72,9
@@
public class PIDColourScheme
}
\r
}
\r
\r
}
\r
}
\r
\r
- return c;
\r
+ if(conservationColouring)
\r
+ applyConservation(j);
\r
+
\r
+ return currentColour;
\r
}
\r
}
\r
}
\r
}
\r