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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
9bc76c2
..
eaf2a5f
100755
(executable)
--- a/
src/jalview/schemes/ClustalxColourScheme.java
+++ b/
src/jalview/schemes/ClustalxColourScheme.java
@@
-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
@@
-241,24
+240,22
@@
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
-
\r
- if(cons2.length<=j)
\r
- return currentColour;
\r
+ Color currentColour;
\r
\r
\r
\r
\r
- if ( (threshold != 0) && !aboveThreshold(s, j))
\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
currentColour = Color.white;
\r
\r
\r
currentColour = Color.white;
\r
\r
@@
-284,7
+281,7
@@
public class ClustalxColourScheme
}
\r
\r
if(conservationColouring)
\r
}
\r
\r
if(conservationColouring)
\r
- applyConservation(j);
\r
+ currentColour = applyConservation(currentColour, j);
\r
\r
return currentColour;
\r
}
\r
\r
return currentColour;
\r
}
\r