X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FNucleotideColourScheme.java;h=4977107e656012563ff66ac51672c2997ea0f378;hb=a7169b1c72607f3c9357195b4999869650a2a891;hp=6b1ac51913ca007211bb8e43776acae16a884f8e;hpb=b2f9a8d7bce642ff4011bc6d49e02bb0569fbb11;p=jalview.git
diff --git a/src/jalview/schemes/NucleotideColourScheme.java b/src/jalview/schemes/NucleotideColourScheme.java
index 6b1ac51..4977107 100755
--- a/src/jalview/schemes/NucleotideColourScheme.java
+++ b/src/jalview/schemes/NucleotideColourScheme.java
@@ -1,26 +1,27 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
- * 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.SequenceI;
-
-import java.awt.Color;
+import jalview.api.AlignViewportI;
+import jalview.datamodel.AnnotatedCollectionI;
/**
* DOCUMENT ME!
@@ -35,59 +36,29 @@ public class NucleotideColourScheme extends ResidueColourScheme
*/
public NucleotideColourScheme()
{
- super(ResidueProperties.nucleotideIndex, ResidueProperties.nucleotide,
- 0);
+ super(ResidueProperties.nucleotideIndex, ResidueProperties.nucleotide);
}
- /**
- * DOCUMENT ME!
- *
- * @param n
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
@Override
- public Color findColour(char c)
+ public boolean isNucleotideSpecific()
{
- // System.out.println("called"); log.debug
- return colors[ResidueProperties.nucleotideIndex[c]];
+ return true;
+ }
+
+ @Override
+ public String getSchemeName()
+ {
+ 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(AlignViewportI view,
+ AnnotatedCollectionI coll)
{
- 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();
}
}