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JAL-1684 example uncommented on 2.9.0b1 branch
[jalview.git]
/
src
/
jalview
/
schemes
/
TCoffeeColourScheme.java
diff --git
a/src/jalview/schemes/TCoffeeColourScheme.java
b/src/jalview/schemes/TCoffeeColourScheme.java
index
7caa735
..
bc56281
100644
(file)
--- a/
src/jalview/schemes/TCoffeeColourScheme.java
+++ b/
src/jalview/schemes/TCoffeeColourScheme.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 2.9)
+ * Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
*
*
* This file is part of Jalview.
*
@@
-20,7
+20,6
@@
*/
package jalview.schemes;
*/
package jalview.schemes;
-import jalview.analysis.SequenceIdMatcher;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AnnotatedCollectionI;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AnnotatedCollectionI;
@@
-33,7
+32,6
@@
import java.awt.Color;
import java.util.ArrayList;
import java.util.IdentityHashMap;
import java.util.Map;
import java.util.ArrayList;
import java.util.IdentityHashMap;
import java.util.Map;
-import java.util.TreeMap;
/**
* Defines the color score for T-Coffee MSA
/**
* Defines the color score for T-Coffee MSA
@@
-47,8
+45,7
@@
import java.util.TreeMap;
public class TCoffeeColourScheme extends ResidueColourScheme
{
public class TCoffeeColourScheme extends ResidueColourScheme
{
- static final Color[] colors =
- { new Color(102, 102, 255), // #6666FF
+ static final Color[] colors = { new Color(102, 102, 255), // #6666FF
new Color(0, 255, 0), // #00FF00
new Color(102, 255, 0), // #66FF00
new Color(204, 255, 0), // #CCFF00
new Color(0, 255, 0), // #00FF00
new Color(102, 255, 0), // #66FF00
new Color(204, 255, 0), // #CCFF00
@@
-87,7
+84,8
@@
public class TCoffeeColourScheme extends ResidueColourScheme
// Search alignment to get all tcoffee annotation and pick one set of
// annotation to use to colour seqs.
seqMap = new IdentityHashMap<SequenceI, Color[]>();
// Search alignment to get all tcoffee annotation and pick one set of
// annotation to use to colour seqs.
seqMap = new IdentityHashMap<SequenceI, Color[]>();
- AnnotatedCollectionI alcontext = alignment instanceof AlignmentI ? alignment : alignment.getContext();
+ AnnotatedCollectionI alcontext = alignment instanceof AlignmentI ? alignment
+ : alignment.getContext();
int w = 0;
for (AlignmentAnnotation al : alcontext
.findAnnotation(TCoffeeScoreFile.TCOFFEE_SCORE))
int w = 0;
for (AlignmentAnnotation al : alcontext
.findAnnotation(TCoffeeScoreFile.TCOFFEE_SCORE))
@@
-132,7
+130,7
@@
public class TCoffeeColourScheme extends ResidueColourScheme
}
return cols[j];
}
}
return cols[j];
}
-
+
@Override
public ColourSchemeI applyTo(AnnotatedCollectionI sg,
Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
@Override
public ColourSchemeI applyTo(AnnotatedCollectionI sg,
Map<SequenceI, SequenceCollectionI> hiddenRepSequences)