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JAL-2316 Added GUI checks for duplicate link ids
[jalview.git]
/
src
/
jalview
/
schemes
/
Blosum62ColourScheme.java
diff --git
a/src/jalview/schemes/Blosum62ColourScheme.java
b/src/jalview/schemes/Blosum62ColourScheme.java
index
d914168
..
37c31f9
100755
(executable)
--- a/
src/jalview/schemes/Blosum62ColourScheme.java
+++ b/
src/jalview/schemes/Blosum62ColourScheme.java
@@
-1,6
+1,6
@@
/*
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
*
* This file is part of Jalview.
*
@@
-20,17
+20,19
@@
*/
package jalview.schemes;
*/
package jalview.schemes;
-import jalview.analysis.AAFrequency;
-
-import java.awt.Color;
-import java.util.Map;
-
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.Map;
public class Blosum62ColourScheme extends ResidueColourScheme
{
public class Blosum62ColourScheme extends ResidueColourScheme
{
+ private static final Color LIGHT_BLUE = new Color(204, 204, 255);
+ private static final Color DARK_BLUE = new Color(154, 154, 255);
+
public Blosum62ColourScheme()
{
super();
public Blosum62ColourScheme()
{
super();
@@
-53,13
+55,16
@@
public class Blosum62ColourScheme extends ResidueColourScheme
Color currentColour;
Color currentColour;
- if (!jalview.util.Comparison.isGap(res))
+ if (!Comparison.isGap(res))
{
{
- String max = (String) consensus[j].get(AAFrequency.MAXRESIDUE);
+ /*
+ * test if this is the consensus (or joint consensus) residue
+ */
+ String max = consensus[j].getModalResidue();
if (max.indexOf(res) > -1)
{
if (max.indexOf(res) > -1)
{
- currentColour = new Color(154, 154, 255);
+ currentColour = DARK_BLUE;
}
else
{
}
else
{
@@
-74,7
+79,7
@@
public class Blosum62ColourScheme extends ResidueColourScheme
if (c > 0)
{
if (c > 0)
{
- currentColour = new Color(204, 204, 255);
+ currentColour = LIGHT_BLUE;
}
else
{
}
else
{
@@
-94,10
+99,11
@@
public class Blosum62ColourScheme extends ResidueColourScheme
return currentColour;
}
return currentColour;
}
+
@Override
public ColourSchemeI applyTo(AnnotatedCollectionI sg,
Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
@Override
public ColourSchemeI applyTo(AnnotatedCollectionI sg,
Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
- {
+ {
ColourSchemeI newcs = super.applyTo(sg, hiddenRepSequences);
return newcs;
}
ColourSchemeI newcs = super.applyTo(sg, hiddenRepSequences);
return newcs;
}