X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FBlosum62ColourScheme.java;h=9d092599860175227545083e840dbf595350b41a;hb=3bff70075d04a89d91e6b317a4a3bdb007f32d5f;hp=e9ac579d1febe3b0c5e75c6da7e0f4e0b07ca023;hpb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;p=jalview.git
diff --git a/src/jalview/schemes/Blosum62ColourScheme.java b/src/jalview/schemes/Blosum62ColourScheme.java
index e9ac579..9d09259 100755
--- a/src/jalview/schemes/Blosum62ColourScheme.java
+++ b/src/jalview/schemes/Blosum62ColourScheme.java
@@ -1,25 +1,32 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see .
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemes;
-import java.awt.*;
+import jalview.analysis.AAFrequency;
+import jalview.datamodel.AnnotatedCollectionI;
+import jalview.datamodel.SequenceCollectionI;
+import jalview.datamodel.SequenceI;
-import jalview.analysis.*;
+import java.awt.Color;
+import java.util.Map;
public class Blosum62ColourScheme extends ResidueColourScheme
{
@@ -28,7 +35,8 @@ public class Blosum62ColourScheme extends ResidueColourScheme
super();
}
- public Color findColour(char res, int j)
+ @Override
+ public Color findColour(char res, int j, SequenceI seq)
{
if ('a' <= res && res <= 'z')
{
@@ -50,6 +58,7 @@ public class Blosum62ColourScheme extends ResidueColourScheme
if (max.indexOf(res) > -1)
{
+ // TODO use a constant here?
currentColour = new Color(154, 154, 255);
}
else
@@ -65,6 +74,7 @@ public class Blosum62ColourScheme extends ResidueColourScheme
if (c > 0)
{
+ // TODO use a constant here?
currentColour = new Color(204, 204, 255);
}
else
@@ -85,4 +95,12 @@ public class Blosum62ColourScheme extends ResidueColourScheme
return currentColour;
}
+
+ @Override
+ public ColourSchemeI applyTo(AnnotatedCollectionI sg,
+ Map hiddenRepSequences)
+ {
+ ColourSchemeI newcs = super.applyTo(sg, hiddenRepSequences);
+ return newcs;
+ }
}