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
Formatting
[jalview.git]
/
src
/
jalview
/
schemes
/
ClustalxColourScheme.java
diff --git
a/src/jalview/schemes/ClustalxColourScheme.java
b/src/jalview/schemes/ClustalxColourScheme.java
index
eaf2a5f
..
8dd8994
100755
(executable)
--- a/
src/jalview/schemes/ClustalxColourScheme.java
+++ b/
src/jalview/schemes/ClustalxColourScheme.java
@@
-1,6
+1,6
@@
/*
\r
* Jalview - A Sequence Alignment Editor and Viewer
\r
/*
\r
* Jalview - A Sequence Alignment Editor and Viewer
\r
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
\r
+ * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
\r
*
\r
* This program is free software; you can redistribute it and/or
\r
* modify it under the terms of the GNU General Public License
\r
*
\r
* This program is free software; you can redistribute it and/or
\r
* modify it under the terms of the GNU General Public License
\r
@@
-70,7
+70,7
@@
public class ClustalxColourScheme
int res;
\r
int i;
\r
int j = 0;
\r
int res;
\r
int i;
\r
int j = 0;
\r
- char [] seq;
\r
+ char[] seq;
\r
\r
while (j < seqs.size())
\r
{
\r
\r
while (j < seqs.size())
\r
{
\r
@@
-86,7
+86,7
@@
public class ClustalxColourScheme
}
\r
else
\r
{
\r
}
\r
else
\r
{
\r
- res = ResidueProperties.aaIndex[seq[i]];
\r
+ res = ResidueProperties.aaIndex[seq[i]];
\r
}
\r
\r
cons2[i][res]++;
\r
}
\r
\r
cons2[i][res]++;
\r
@@
-249,8
+249,7
@@
public class ClustalxColourScheme
{
\r
Color currentColour;
\r
\r
{
\r
Color currentColour;
\r
\r
-
\r
- if ( cons2.length<=j || (threshold != 0 && !aboveThreshold(c, j)))
\r
+ if (cons2.length <= j || (threshold != 0 && !aboveThreshold(c, j)))
\r
{
\r
return Color.white;
\r
}
\r
{
\r
return Color.white;
\r
}
\r
@@
-264,13
+263,13
@@
public class ClustalxColourScheme
return currentColour;
\r
}
\r
\r
return currentColour;
\r
}
\r
\r
- for (int k = 0; k < ResidueColour[i].conses.length; k++)
\r
- {
\r
- if (ResidueColour[i].conses[k].isConserved(cons2, j, size))
\r
+ for (int k = 0; k < ResidueColour[i].conses.length; k++)
\r
{
\r
{
\r
- currentColour = ResidueColour[i].c;
\r
+ if (ResidueColour[i].conses[k].isConserved(cons2, j, size))
\r
+ {
\r
+ currentColour = ResidueColour[i].c;
\r
+ }
\r
}
\r
}
\r
- }
\r
\r
if (i == 4)
\r
{
\r
\r
if (i == 4)
\r
{
\r
@@
-280,8
+279,10
@@
public class ClustalxColourScheme
}
\r
}
\r
\r
}
\r
}
\r
\r
- if(conservationColouring)
\r
+ if (conservationColouring)
\r
+ {
\r
currentColour = applyConservation(currentColour, j);
\r
currentColour = applyConservation(currentColour, j);
\r
+ }
\r
\r
return currentColour;
\r
}
\r
\r
return currentColour;
\r
}
\r