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Format changes
[jalview.git]
/
src
/
jalview
/
schemes
/
NucleotideColourScheme.java
diff --git
a/src/jalview/schemes/NucleotideColourScheme.java
b/src/jalview/schemes/NucleotideColourScheme.java
index
9768d9a
..
4afb321
100755
(executable)
--- a/
src/jalview/schemes/NucleotideColourScheme.java
+++ b/
src/jalview/schemes/NucleotideColourScheme.java
@@
-47,7
+47,7
@@
public class NucleotideColourScheme extends ResidueColourScheme
public Color findColour(String n)
\r
{
\r
// System.out.println("called"); log.debug
\r
public Color findColour(String n)
\r
{
\r
// System.out.println("called"); log.debug
\r
- return colors[((Integer) (ResidueProperties.nucleotideHash.get(n))).intValue()];
\r
+ return colors[ResidueProperties.nucleotideIndex[n.charAt(0)]];
\r
}
\r
\r
/**
\r
}
\r
\r
/**
\r
@@
-60,11
+60,12
@@
public class NucleotideColourScheme extends ResidueColourScheme
*/
\r
public Color findColour(String n, int j)
\r
{
\r
*/
\r
public Color findColour(String n, int j)
\r
{
\r
+ Color currentColour;
\r
if ((threshold == 0) || aboveThreshold(n, j))
\r
{
\r
try
\r
{
\r
if ((threshold == 0) || aboveThreshold(n, j))
\r
{
\r
try
\r
{
\r
- currentColour = colors[((Integer) (ResidueProperties.nucleotideHash.get(n))).intValue()];
\r
+ currentColour = colors[ ResidueProperties.nucleotideIndex[n.charAt(0)]];
\r
}
\r
catch (Exception ex)
\r
{
\r
}
\r
catch (Exception ex)
\r
{
\r
@@
-77,7
+78,7
@@
public class NucleotideColourScheme extends ResidueColourScheme
}
\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