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new place for sequencefeaturefetcher
[jalview.git]
/
src
/
jalview
/
schemes
/
ClustalxColourScheme.java
diff --git
a/src/jalview/schemes/ClustalxColourScheme.java
b/src/jalview/schemes/ClustalxColourScheme.java
index
7faa9a3
..
1bf8567
100755
(executable)
--- a/
src/jalview/schemes/ClustalxColourScheme.java
+++ b/
src/jalview/schemes/ClustalxColourScheme.java
@@
-60,7
+60,7
@@
public class ClustalxColourScheme implements ColourSchemeI
String seq;
\r
while(j < seqs.size())
\r
{
\r
String seq;
\r
while(j < seqs.size())
\r
{
\r
- seq = ( (SequenceI) seqs.get(j)).getSequence();
\r
+ seq = ( (SequenceI) seqs.elementAt(j)).getSequence();
\r
int end_j = seq.length()-1;
\r
for (i = start; i <= end_j; i++)
\r
{
\r
int end_j = seq.length()-1;
\r
for (i = start; i <= end_j; i++)
\r
{
\r
@@
-225,13
+225,13
@@
public class ClustalxColourScheme implements ColourSchemeI
size = i;
\r
}
\r
\r
size = i;
\r
}
\r
\r
- public Color findColour(String s, int j, Vector seqs)
\r
+ public Color findColour(String s, int j)
\r
{
\r
int i = ((Integer)ResidueProperties.aaHash.get(s)).intValue();
\r
\r
Color c = Color.white;
\r
\r
{
\r
int i = ((Integer)ResidueProperties.aaHash.get(s)).intValue();
\r
\r
Color c = Color.white;
\r
\r
- if(i>20)
\r
+ if(i>19)
\r
return c;
\r
\r
for (int k=0; k < ResidueColour[i].conses.length ; k++)
\r
return c;
\r
\r
for (int k=0; k < ResidueColour[i].conses.length ; k++)
\r
@@
-249,6
+249,10
@@
public class ClustalxColourScheme implements ColourSchemeI
\r
}
\r
\r
\r
}
\r
\r
+ public void setConsensus(Vector consensus)
\r
+ {
\r
+ // Clustal colouring cannot be coloured by PID
\r
+ }
\r
\r
public boolean canThreshold()
\r
{
\r
\r
public boolean canThreshold()
\r
{
\r