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SequenceGroup parsing added to annotation file
[jalview.git]
/
src
/
jalview
/
schemes
/
NucleotideColourScheme.java
diff --git
a/src/jalview/schemes/NucleotideColourScheme.java
b/src/jalview/schemes/NucleotideColourScheme.java
index
8785954
..
899fc60
100755
(executable)
--- a/
src/jalview/schemes/NucleotideColourScheme.java
+++ b/
src/jalview/schemes/NucleotideColourScheme.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
@@
-44,10
+44,10
@@
public class NucleotideColourScheme extends ResidueColourScheme
*
\r
* @return DOCUMENT ME!
\r
*/
\r
*
\r
* @return DOCUMENT ME!
\r
*/
\r
- public Color findColour(String n)
\r
+ public Color findColour(char c)
\r
{
\r
// System.out.println("called"); log.debug
\r
{
\r
// System.out.println("called"); log.debug
\r
- return colors[((Integer) (ResidueProperties.nucleotideHash.get(n))).intValue()];
\r
+ return colors[ResidueProperties.nucleotideIndex[c]];
\r
}
\r
\r
/**
\r
}
\r
\r
/**
\r
@@
-58,13
+58,14
@@
public class NucleotideColourScheme extends ResidueColourScheme
*
\r
* @return DOCUMENT ME!
\r
*/
\r
*
\r
* @return DOCUMENT ME!
\r
*/
\r
- public Color findColour(String n, int j)
\r
+ public Color findColour(char c, int j)
\r
{
\r
{
\r
- if ((threshold == 0) || aboveThreshold(n, j))
\r
+ Color currentColour;
\r
+ if ((threshold == 0) || aboveThreshold(c, j))
\r
{
\r
try
\r
{
\r
{
\r
try
\r
{
\r
- return colors[((Integer) (ResidueProperties.nucleotideHash.get(n))).intValue()];
\r
+ currentColour = colors[ ResidueProperties.nucleotideIndex[c]];
\r
}
\r
catch (Exception ex)
\r
{
\r
}
\r
catch (Exception ex)
\r
{
\r
@@
-75,5
+76,10
@@
public class NucleotideColourScheme extends ResidueColourScheme
{
\r
return Color.white;
\r
}
\r
{
\r
return Color.white;
\r
}
\r
+
\r
+ if(conservationColouring)
\r
+ currentColour = applyConservation(currentColour, j);
\r
+
\r
+ return currentColour;
\r
}
\r
}
\r
}
\r
}
\r