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Merge branch 'Jalview-BH/JAL-3026-JAL-3063-JAXB' of https://source.jalview.org/git...
[jalview.git]
/
src
/
jalview
/
schemes
/
ClustalxColourScheme.java
diff --git
a/src/jalview/schemes/ClustalxColourScheme.java
b/src/jalview/schemes/ClustalxColourScheme.java
index
f13a90c
..
ec13343
100755
(executable)
--- a/
src/jalview/schemes/ClustalxColourScheme.java
+++ b/
src/jalview/schemes/ClustalxColourScheme.java
@@
-43,8
+43,8
@@
public class ClustalxColourScheme extends ResidueColourScheme
{
RED(0.9f, 0.2f, 0.1f), BLUE(0.5f, 0.7f, 0.9f), GREEN(0.1f, 0.8f, 0.1f),
ORANGE(0.9f, 0.6f, 0.3f), CYAN(0.1f, 0.7f, 0.7f),
{
RED(0.9f, 0.2f, 0.1f), BLUE(0.5f, 0.7f, 0.9f), GREEN(0.1f, 0.8f, 0.1f),
ORANGE(0.9f, 0.6f, 0.3f), CYAN(0.1f, 0.7f, 0.7f),
- PINK(0.9f, 0.5f, 0.5f), MAGENTA(0.8f, 0.3f, 0.8f), YELLOW(0.8f, 0.8f,
- 0.0f);
+ PINK(0.9f, 0.5f, 0.5f), MAGENTA(0.8f, 0.3f, 0.8f),
+ YELLOW(0.8f, 0.8f, 0.0f);
final Color colour;
final Color colour;
@@
-53,6
+53,7
@@
public class ClustalxColourScheme extends ResidueColourScheme
colour = new Color(r, g, b);
}
}
colour = new Color(r, g, b);
}
}
+
private class ConsensusColour
{
Consensus[] cons;
private class ConsensusColour
{
Consensus[] cons;
@@
-106,19
+107,18
@@
public class ClustalxColourScheme extends ResidueColourScheme
for (SequenceI sq : seqs)
{
for (SequenceI sq : seqs)
{
- char[] seq = sq.getSequence();
-
- int end_j = seq.length - 1;
+ int end_j = sq.getLength() - 1;
+ int length = sq.getLength();
for (int i = 0; i <= end_j; i++)
{
for (int i = 0; i <= end_j; i++)
{
- if ((seq.length - 1) < i)
+ if (length - 1 < i)
{
res = 23;
}
else
{
{
res = 23;
}
else
{
- res = ResidueProperties.aaIndex[seq[i]];
+ res = ResidueProperties.aaIndex[sq.getCharAt(i)];
}
cons2[i][res]++;
}
}
cons2[i][res]++;
}
@@
-297,8
+297,7
@@
public class ClustalxColourScheme extends ResidueColourScheme
for (int k = 0; k < residueColour[i].cons.length; k++)
{
for (int k = 0; k < residueColour[i].cons.length; k++)
{
- if (residueColour[i].cons[k].isConserved(cons2, j, size,
- includeGaps))
+ if (residueColour[i].cons[k].isConserved(cons2, j, size, includeGaps))
{
colour = residueColour[i].c;
}
{
colour = residueColour[i].c;
}