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
Add pdb ref
[jalview.git]
/
src
/
jalview
/
schemes
/
ClustalxColourScheme.java
diff --git
a/src/jalview/schemes/ClustalxColourScheme.java
b/src/jalview/schemes/ClustalxColourScheme.java
index
addf00f
..
1e38a6d
100755
(executable)
--- a/
src/jalview/schemes/ClustalxColourScheme.java
+++ b/
src/jalview/schemes/ClustalxColourScheme.java
@@
-248,6
+248,11
@@
public class ClustalxColourScheme
\r
public Color findColour(String s, int j)
\r
{
\r
\r
public Color findColour(String s, int j)
\r
{
\r
+
\r
+ if(cons2.length<=j)
\r
+ return currentColour;
\r
+
\r
+
\r
if ( (threshold != 0) && !aboveThreshold(s, j))
\r
{
\r
return Color.white;
\r
if ( (threshold != 0) && !aboveThreshold(s, j))
\r
{
\r
return Color.white;
\r
@@
-255,30
+260,33
@@
public class ClustalxColourScheme
\r
int i = ( (Integer) ResidueProperties.aaHash.get(s)).intValue();
\r
\r
\r
int i = ( (Integer) ResidueProperties.aaHash.get(s)).intValue();
\r
\r
- Color c = Color.white;
\r
+ currentColour = Color.white;
\r
\r
if (i > 19)
\r
{
\r
\r
if (i > 19)
\r
{
\r
- return c;
\r
+ return currentColour;
\r
}
\r
\r
}
\r
\r
- for (int k = 0; k < ResidueColour[i].conses.length; k++)
\r
+ for (int k = 0; k < ResidueColour[i].conses.length; k++)
\r
+ {
\r
+ if (ResidueColour[i].conses[k].isConserved(cons2, j, size))
\r
{
\r
{
\r
- if (ResidueColour[i].conses[k].isConserved(cons2, j, size))
\r
- {
\r
- c = ResidueColour[i].c;
\r
- }
\r
+ currentColour = ResidueColour[i].c;
\r
}
\r
}
\r
+ }
\r
\r
if (i == 4)
\r
{
\r
if (conses[27].isConserved(cons2, j, size))
\r
{
\r
\r
if (i == 4)
\r
{
\r
if (conses[27].isConserved(cons2, j, size))
\r
{
\r
- c = (Color) colhash.get("PINK");
\r
+ currentColour = (Color) colhash.get("PINK");
\r
}
\r
}
\r
\r
}
\r
}
\r
\r
- return c;
\r
+ if(conservationColouring)
\r
+ applyConservation(j);
\r
+
\r
+ return currentColour;
\r
}
\r
}
\r
\r
}
\r
}
\r
\r