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
Alignment editing columns 0 and 1 fixed
[jalview.git]
/
src
/
jalview
/
schemes
/
ClustalxColourScheme.java
diff --git
a/src/jalview/schemes/ClustalxColourScheme.java
b/src/jalview/schemes/ClustalxColourScheme.java
index
addf00f
..
eaf2a5f
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) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
\r
+ * Copyright (C) 2006 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
@@
-70,24
+70,23
@@
public class ClustalxColourScheme
int res;
\r
int i;
\r
int j = 0;
\r
int res;
\r
int i;
\r
int j = 0;
\r
- String seq;
\r
+ char [] seq;
\r
\r
while (j < seqs.size())
\r
{
\r
seq = ( (SequenceI) seqs.elementAt(j)).getSequence();
\r
\r
\r
while (j < seqs.size())
\r
{
\r
seq = ( (SequenceI) seqs.elementAt(j)).getSequence();
\r
\r
- int end_j = seq.length() - 1;
\r
+ int end_j = seq.length - 1;
\r
\r
for (i = start; i <= end_j; i++)
\r
{
\r
\r
for (i = start; i <= end_j; i++)
\r
{
\r
- if ( (seq.length() - 1) < i)
\r
+ if ( (seq.length - 1) < i)
\r
{
\r
res = 23;
\r
}
\r
else
\r
{
\r
{
\r
res = 23;
\r
}
\r
else
\r
{
\r
- res = ( (Integer) ResidueProperties.aaHash.get(seq.charAt(i) +
\r
- "")).intValue();
\r
+ res = ResidueProperties.aaIndex[seq[i]];
\r
}
\r
\r
cons2[i][res]++;
\r
}
\r
\r
cons2[i][res]++;
\r
@@
-241,44
+240,50
@@
public class ClustalxColourScheme
ResidueColour[19] = colours[0]; // V
\r
}
\r
\r
ResidueColour[19] = colours[0]; // V
\r
}
\r
\r
- public Color findColour(String s)
\r
+ public Color findColour(char c)
\r
{
\r
return Color.pink;
\r
}
\r
\r
{
\r
return Color.pink;
\r
}
\r
\r
- public Color findColour(String s, int j)
\r
+ public Color findColour(char c, int j)
\r
{
\r
{
\r
- if ( (threshold != 0) && !aboveThreshold(s, j))
\r
+ Color currentColour;
\r
+
\r
+
\r
+ if ( cons2.length<=j || (threshold != 0 && !aboveThreshold(c, j)))
\r
{
\r
return Color.white;
\r
}
\r
\r
{
\r
return Color.white;
\r
}
\r
\r
- int i = ( (Integer) ResidueProperties.aaHash.get(s)).intValue();
\r
+ int i = ResidueProperties.aaIndex[c];
\r
\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
+ currentColour = applyConservation(currentColour, j);
\r
+
\r
+ return currentColour;
\r
}
\r
}
\r
\r
}
\r
}
\r
\r