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Merge branch 'features/JAL-2446NCList' into features/JAL-2574findFeaturesByColumn
[jalview.git]
/
src
/
jalview
/
schemes
/
ClustalxColourScheme.java
diff --git
a/src/jalview/schemes/ClustalxColourScheme.java
b/src/jalview/schemes/ClustalxColourScheme.java
index
2bb64fc
..
f13a90c
100755
(executable)
--- a/
src/jalview/schemes/ClustalxColourScheme.java
+++ b/
src/jalview/schemes/ClustalxColourScheme.java
@@
-23,6
+23,7
@@
package jalview.schemes;
import jalview.datamodel.AnnotatedCollectionI;
import jalview.datamodel.SequenceCollectionI;
import jalview.datamodel.SequenceI;
import jalview.datamodel.AnnotatedCollectionI;
import jalview.datamodel.SequenceCollectionI;
import jalview.datamodel.SequenceI;
+import jalview.util.Comparison;
import java.awt.Color;
import java.util.List;
import java.awt.Color;
import java.util.List;
@@
-276,23
+277,22
@@
public class ClustalxColourScheme extends ResidueColourScheme
}
@Override
}
@Override
- public Color findColour(char c, int j, SequenceI seq)
+ protected Color findColour(char c, int j, SequenceI seq)
{
{
- Color currentColour;
-
- if (cons2.length <= j
- || (includeGaps && threshold != 0 && !aboveThreshold(c, j)))
+ // TODO why the test for includeGaps here?
+ if (cons2.length <= j || Comparison.isGap(c)
+ /*|| (includeGaps && threshold != 0 && !aboveThreshold(c, j))*/)
{
return Color.white;
}
int i = ResidueProperties.aaIndex[c];
{
return Color.white;
}
int i = ResidueProperties.aaIndex[c];
- currentColour = Color.white;
+ Color colour = Color.white;
if (i > 19)
{
if (i > 19)
{
- return currentColour;
+ return colour;
}
for (int k = 0; k < residueColour[i].cons.length; k++)
}
for (int k = 0; k < residueColour[i].cons.length; k++)
@@
-300,27
+300,22
@@
public class ClustalxColourScheme extends ResidueColourScheme
if (residueColour[i].cons[k].isConserved(cons2, j, size,
includeGaps))
{
if (residueColour[i].cons[k].isConserved(cons2, j, size,
includeGaps))
{
- currentColour = residueColour[i].c;
+ colour = residueColour[i].c;
}
}
if (i == 4)
{
/*
}
}
if (i == 4)
{
/*
- * override to colour C pink if 100% conserved
+ * override to colour C pink if >85% conserved
*/
if (conses[27].isConserved(cons2, j, size, includeGaps))
{
*/
if (conses[27].isConserved(cons2, j, size, includeGaps))
{
- currentColour = ClustalColour.PINK.colour;
+ colour = ClustalColour.PINK.colour;
}
}
}
}
- if (conservationColouring)
- {
- currentColour = applyConservation(currentColour, j);
- }
-
- return currentColour;
+ return colour;
}
/**
}
/**
@@
-361,4
+356,10
@@
public class ClustalxColourScheme extends ResidueColourScheme
{
return JalviewColourScheme.Clustal.toString();
}
{
return JalviewColourScheme.Clustal.toString();
}
+
+ @Override
+ public boolean isSimple()
+ {
+ return false;
+ }
}
}