X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fschemes%2FNucleotideColourScheme.java;h=abae7337da966fc1711bebe73d42f5c3e024b5c4;hb=f2a83f0360d406859b80cc798099a9d270461bb3;hp=5844aa2b68f65e25212596edcf71ef73bc94d4d5;hpb=a8f483d04205bb8273ee311c12968b7e86d205fa;p=jalview.git
diff --git a/src/jalview/schemes/NucleotideColourScheme.java b/src/jalview/schemes/NucleotideColourScheme.java
index 5844aa2..abae733 100755
--- a/src/jalview/schemes/NucleotideColourScheme.java
+++ b/src/jalview/schemes/NucleotideColourScheme.java
@@ -1,26 +1,30 @@
/*
- * 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.
*
* 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 jalview.datamodel.AnnotatedCollectionI;
+import jalview.datamodel.SequenceCollectionI;
import jalview.datamodel.SequenceI;
-import java.awt.Color;
+import java.util.Map;
/**
* DOCUMENT ME!
@@ -35,59 +39,29 @@ public class NucleotideColourScheme extends ResidueColourScheme
*/
public NucleotideColourScheme()
{
- super(ResidueProperties.nucleotideIndex, ResidueProperties.nucleotide,
- 0);
+ super(ResidueProperties.nucleotideIndex, ResidueProperties.nucleotide);
+ }
+
+ @Override
+ public boolean isNucleotideSpecific()
+ {
+ return true;
}
- /**
- * DOCUMENT ME!
- *
- * @param n
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
@Override
- public Color findColour(char c)
+ public String getSchemeName()
{
- // System.out.println("called"); log.debug
- return colors[ResidueProperties.nucleotideIndex[c]];
+ return JalviewColourScheme.Nucleotide.toString();
}
/**
- * DOCUMENT ME!
- *
- * @param n
- * DOCUMENT ME!
- * @param j
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
+ * Returns a new instance of this colour scheme with which the given data may
+ * be coloured
*/
@Override
- public Color findColour(char c, int j, SequenceI seq)
+ public ColourSchemeI getInstance(AnnotatedCollectionI coll,
+ Map hrs)
{
- Color currentColour;
- if ((threshold == 0) || aboveThreshold(c, j))
- {
- try
- {
- currentColour = colors[ResidueProperties.nucleotideIndex[c]];
- } catch (Exception ex)
- {
- return Color.white;
- }
- }
- else
- {
- return Color.white;
- }
-
- if (conservationColouring)
- {
- currentColour = applyConservation(currentColour, j);
- }
-
- return currentColour;
+ return new NucleotideColourScheme();
}
}