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consensus held in residueColour
[jalview.git]
/
src
/
jalview
/
schemes
/
ResidueColourScheme.java
diff --git
a/src/jalview/schemes/ResidueColourScheme.java
b/src/jalview/schemes/ResidueColourScheme.java
index
b0a5caa
..
7eab3dd
100755
(executable)
--- a/
src/jalview/schemes/ResidueColourScheme.java
+++ b/
src/jalview/schemes/ResidueColourScheme.java
@@
-7,13
+7,19
@@
import java.awt.*;
public class ResidueColourScheme implements ColourSchemeI{
\r
Color [] colors;
\r
int threshold = 0;
\r
public class ResidueColourScheme implements ColourSchemeI{
\r
Color [] colors;
\r
int threshold = 0;
\r
+ public Vector consensus;
\r
\r
public ResidueColourScheme(Color[] colors, int threshold) {
\r
\r
public ResidueColourScheme(Color[] colors, int threshold) {
\r
- this.colors = colors;
\r
+ this.colors = colors;
\r
this.threshold = threshold;
\r
}
\r
\r
this.threshold = threshold;
\r
}
\r
\r
- public ResidueColourScheme() {
\r
+ public ResidueColourScheme()
\r
+ { }
\r
+
\r
+ public void setConsensus(Vector consensus)
\r
+ {
\r
+ this.consensus = consensus;
\r
}
\r
\r
public Color findColour(String aa)
\r
}
\r
\r
public Color findColour(String aa)
\r
@@
-21,9
+27,9
@@
public class ResidueColourScheme implements ColourSchemeI{
return colors[((Integer)(ResidueProperties.aaHash.get(aa))).intValue()];
\r
}
\r
\r
return colors[((Integer)(ResidueProperties.aaHash.get(aa))).intValue()];
\r
}
\r
\r
- public Color findColour(String s, int j, Vector aa) {
\r
+ public Color findColour(String s, int j) {
\r
\r
\r
- if( threshold==0 || aboveThreshold(aa,s,j))
\r
+ if( threshold==0 || aboveThreshold(s,j))
\r
return colors[((Integer)(ResidueProperties.aaHash.get(s))).intValue()];
\r
else
\r
return Color.white;
\r
return colors[((Integer)(ResidueProperties.aaHash.get(s))).intValue()];
\r
else
\r
return Color.white;
\r
@@
-38,10
+44,9
@@
public class ResidueColourScheme implements ColourSchemeI{
threshold = ct;
\r
}
\r
\r
threshold = ct;
\r
}
\r
\r
- public boolean aboveThreshold(Vector aa,String s, int j)
\r
+ public boolean aboveThreshold(String s, int j)
\r
{
\r
{
\r
-
\r
- Hashtable hash = (Hashtable)aa.elementAt(j);
\r
+ Hashtable hash = (Hashtable)consensus.elementAt(j);
\r
\r
if ( ( (Integer) hash.get("maxCount")).intValue() != -1 && hash.contains(s))
\r
{
\r
\r
if ( ( (Integer) hash.get("maxCount")).intValue() != -1 && hash.contains(s))
\r
{
\r