X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fschemes%2FNucleotideColourScheme.java;h=abae7337da966fc1711bebe73d42f5c3e024b5c4;hb=faa3d71f9d120d665870e72b7217ae6b8bd6062d;hp=26aea21416df83754bf284108ef018daceb6b3e3;hpb=ac4bbf6dd2bfccdaae9067fb4765c73600dea729;p=jalview.git
diff --git a/src/jalview/schemes/NucleotideColourScheme.java b/src/jalview/schemes/NucleotideColourScheme.java
index 26aea21..abae733 100755
--- a/src/jalview/schemes/NucleotideColourScheme.java
+++ b/src/jalview/schemes/NucleotideColourScheme.java
@@ -1,37 +1,67 @@
-package jalview.schemes;
-
-import java.awt.*;
-import java.util.*;
-
-
-public class NucleotideColourScheme extends ResidueColourScheme
-{
- public NucleotideColourScheme() {
- super(ResidueProperties.nucleotide,0);
- }
-
-
- public Color findColour(String n)
- {
- System.out.println("called");
- return colors[((Integer)(ResidueProperties.nucleotideHash.get(n))).intValue()];
- }
-
-
- public Color findColour(String n, int j) {
-
- if (threshold == 0 || aboveThreshold( n, j))
- try
- {
- return colors[ ( (Integer) (ResidueProperties.nucleotideHash.get(n))).intValue()];
- }
- catch (Exception ex)
- {
- return Color.white;
- }
- else
- return Color.white;
-
- }
-
-}
+/*
+ * 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.util.Map;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class NucleotideColourScheme extends ResidueColourScheme
+{
+ /**
+ * Creates a new NucleotideColourScheme object.
+ */
+ public NucleotideColourScheme()
+ {
+ super(ResidueProperties.nucleotideIndex, ResidueProperties.nucleotide);
+ }
+
+ @Override
+ public boolean isNucleotideSpecific()
+ {
+ return true;
+ }
+
+ @Override
+ public String getSchemeName()
+ {
+ return JalviewColourScheme.Nucleotide.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 NucleotideColourScheme();
+ }
+}