-/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
-*\r
-* This program is free software; you can redistribute it and/or\r
-* modify it under the terms of the GNU General Public License\r
-* as published by the Free Software Foundation; either version 2\r
-* of the License, or (at your option) any later version.\r
-*\r
-* This program is distributed in the hope that it will be useful,\r
-* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
-* GNU General Public License for more details.\r
-*\r
-* You should have received a copy of the GNU General Public License\r
-* along with this program; if not, write to the Free Software\r
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
-*/\r
-package jalview.schemes;\r
-\r
-import java.awt.*;\r
-\r
-\r
-/**\r
- * DOCUMENT ME!\r
- *\r
- * @author $author$\r
- * @version $Revision$\r
- */\r
-public class NucleotideColourScheme extends ResidueColourScheme\r
-{\r
- /**\r
- * Creates a new NucleotideColourScheme object.\r
- */\r
- public NucleotideColourScheme()\r
- {\r
- super(ResidueProperties.nucleotide, 0);\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param n DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public Color findColour(String n)\r
- {\r
- // System.out.println("called"); log.debug\r
- return colors[((Integer) (ResidueProperties.nucleotideHash.get(n))).intValue()];\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param n DOCUMENT ME!\r
- * @param j DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public Color findColour(String n, int j)\r
- {\r
- if ((threshold == 0) || aboveThreshold(n, j))\r
- {\r
- try\r
- {\r
- currentColour = colors[((Integer) (ResidueProperties.nucleotideHash.get(n))).intValue()];\r
- }\r
- catch (Exception ex)\r
- {\r
- return Color.white;\r
- }\r
- }\r
- else\r
- {\r
- return Color.white;\r
- }\r
-\r
- if(conservationColouring)\r
- applyConservation(j);\r
-\r
- return currentColour;\r
- }\r
-}\r
+/*
+ * 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 <http://www.gnu.org/licenses/>.
+ * 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<SequenceI, SequenceCollectionI> hrs)
+ {
+ return new NucleotideColourScheme();
+ }
+}