X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fschemes%2FBuriedColourScheme.java;h=a3b85b98130e7dd8f6c92bdfe92da930fe9381fb;hb=a42904684c75b2729d763af933e5a991a3424f67;hp=c973035e0a2f6641782cfc6905fb97288dbe1808;hpb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3;p=jalview.git
diff --git a/src/jalview/schemes/BuriedColourScheme.java b/src/jalview/schemes/BuriedColourScheme.java
index c973035..a3b85b9 100755
--- a/src/jalview/schemes/BuriedColourScheme.java
+++ b/src/jalview/schemes/BuriedColourScheme.java
@@ -1,52 +1,83 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program 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 2
- * of the License, or (at your option) any later version.
- *
- * This program 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
- */
-package jalview.schemes;
-
-import java.awt.*;
-
-/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
- */
-public class BuriedColourScheme
- extends ScoreColourScheme
-{
- /**
- * Creates a new BuriedColourScheme object.
- */
- public BuriedColourScheme()
- {
- super(ResidueProperties.buried, ResidueProperties.buriedmin,
- ResidueProperties.buriedmax);
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param c DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public Color makeColour(float c)
- {
- return new Color(0, (float) (1.0 - c), c);
- }
-}
+/*
+ * 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.
+ *
+ * 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 .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.schemes;
+
+import jalview.datamodel.AnnotatedCollectionI;
+import jalview.datamodel.SequenceCollectionI;
+import jalview.datamodel.SequenceI;
+
+import java.awt.Color;
+import java.util.Map;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class BuriedColourScheme extends ScoreColourScheme
+{
+ /**
+ * Creates a new BuriedColourScheme object.
+ */
+ public BuriedColourScheme()
+ {
+ super(ResidueProperties.aaIndex, ResidueProperties.buried,
+ ResidueProperties.buriedmin, ResidueProperties.buriedmax);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param c
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ @Override
+ public Color makeColour(float c)
+ {
+ return new Color(0, (float) (1.0 - c), c);
+ }
+
+ @Override
+ public boolean isPeptideSpecific()
+ {
+ return true;
+ }
+
+ @Override
+ public String getSchemeName()
+ {
+ return JalviewColourScheme.Buried.toString();
+ }
+
+ /**
+ * Returns a new instance of this colour scheme with which the given data may
+ * be coloured
+ */
+ @Override
+ public ColourSchemeI getInstance(AnnotatedCollectionI coll,
+ Map hrs)
+ {
+ return new BuriedColourScheme();
+ }
+}