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Works out exisiting colur of a group
[jalview.git]
/
src
/
jalview
/
schemes
/
ConservationColourScheme.java
diff --git
a/src/jalview/schemes/ConservationColourScheme.java
b/src/jalview/schemes/ConservationColourScheme.java
index
1cbc0d4
..
ab5a808
100755
(executable)
--- a/
src/jalview/schemes/ConservationColourScheme.java
+++ b/
src/jalview/schemes/ConservationColourScheme.java
@@
-29,12
+29,11
@@
public class ConservationColourScheme extends ResidueColourScheme {
public int inc = 30;
\r
int colourThreshold = 7;
\r
\r
public int inc = 30;
\r
int colourThreshold = 7;
\r
\r
- public ConservationColourScheme(SequenceGroup sg)
\r
+ public ConservationColourScheme(Conservation cons, ColourSchemeI oldcs)
\r
{
\r
super();
\r
{
\r
super();
\r
- this.conserve = sg.getConservation();
\r
- colourThreshold = 7;
\r
- this.cs = sg.cs;
\r
+ conserve = cons;
\r
+ cs = oldcs;
\r
}
\r
\r
public void setColours(DrawableSequence seq, int j) {
\r
}
\r
\r
public void setColours(DrawableSequence seq, int j) {
\r
@@
-68,7
+67,7
@@
public class ConservationColourScheme extends ResidueColourScheme {
\r
seq.setColor(c);
\r
}
\r
\r
seq.setColor(c);
\r
}
\r
- public Color findColour(SequenceI seq, String s, int i, java.util.Vector whatever)
\r
+ public Color findColour(String s, int i, java.util.Vector whatever)
\r
{
\r
Color c = null;
\r
if (colourThreshold > 0 && conserve.getConsSequence() != null)
\r
{
\r
Color c = null;
\r
if (colourThreshold > 0 && conserve.getConsSequence() != null)
\r
@@
-106,7
+105,7
@@
public class ConservationColourScheme extends ResidueColourScheme {
}
\r
\r
public Color findColour(DrawableSequence seq, String s, int j) {
\r
}
\r
\r
public Color findColour(DrawableSequence seq, String s, int j) {
\r
- return cs.findColour(null, s, -1, null);
\r
+ return cs.findColour( s, -1, null);
\r
}
\r
public boolean fullConservation(int j) {
\r
String tmp = conserve.getConsSequence().getSequence().substring(j,j+1);
\r
}
\r
public boolean fullConservation(int j) {
\r
String tmp = conserve.getConsSequence().getSequence().substring(j,j+1);
\r