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various loadTree bits for loading and saving trees.
[jalview.git]
/
src
/
jalview
/
schemes
/
PIDColourScheme.java
diff --git
a/src/jalview/schemes/PIDColourScheme.java
b/src/jalview/schemes/PIDColourScheme.java
index
e587fee
..
cc050d5
100755
(executable)
--- a/
src/jalview/schemes/PIDColourScheme.java
+++ b/
src/jalview/schemes/PIDColourScheme.java
@@
-16,7
+16,7
@@
public class PIDColourScheme extends ResidueColourScheme {
}
\r
\r
\r
}
\r
\r
\r
- public Color findColour(SequenceI seq,String s, int j,Vector aa) {
\r
+ public Color findColour(String s, int j,Vector aa) {
\r
Color c = Color.white;
\r
Hashtable hash = null;
\r
\r
Color c = Color.white;
\r
Hashtable hash = null;
\r
\r
@@
-31,10
+31,9
@@
public class PIDColourScheme extends ResidueColourScheme {
double sc = 0;
\r
if ( Integer.parseInt( hash.get("maxCount").toString() ) != -1 && hash.contains(s))
\r
{
\r
double sc = 0;
\r
if ( Integer.parseInt( hash.get("maxCount").toString() ) != -1 && hash.contains(s))
\r
{
\r
-
\r
sc = ( (Integer) hash.get(s)).intValue() * 100.0 / ((Integer)hash.get("size")).intValue() ;
\r
// MC Should be isGap
\r
sc = ( (Integer) hash.get(s)).intValue() * 100.0 / ((Integer)hash.get("size")).intValue() ;
\r
// MC Should be isGap
\r
- if (!s.equals("-") && !s.equals(".") && !s.equals(" "))
\r
+ if (!jalview.util.Comparison.isGap((s.charAt(0))))
\r
{
\r
for (int i = 0; i < thresholds.length; i++)
\r
{
\r
{
\r
for (int i = 0; i < thresholds.length; i++)
\r
{
\r
@@
-45,8
+44,7
@@
public class PIDColourScheme extends ResidueColourScheme {
}
\r
}
\r
}
\r
}
\r
}
\r
}
\r
- else
\r
- c = Color.white;
\r
+
\r
}
\r
return c;
\r
}
\r
}
\r
return c;
\r
}
\r