+/*
+ * 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.awt.Color;
+import java.util.Map;
+public class RNAInteractionColourScheme extends ResidueColourScheme
+{
+ public RNAInteractionColourScheme()
+ {
+ super();
+ }
-public class RNAInteractionColourScheme extends ResidueColourScheme{
- public RNAInteractionColourScheme()
- {
- super(ResidueProperties.nucleotide, 0);
- }
+ @Override
+ public Color findColour(char c)
+ {
+ // FIXME this is just a copy of NucleotideColourScheme
+ return colors[ResidueProperties.nucleotideIndex[c]];
+ }
- /**
- * DOCUMENT ME!
- *
- * @param n
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- @Override
- public Color findColour(char c)
- {
- // System.out.println("called"); log.debug
- return colors[ResidueProperties.nucleotideIndex[c]];
- }
+ @Override
+ public Color findColour(char c, int j, SequenceI seq)
+ {
+ // FIXME this is just a copy of NucleotideColourScheme
+ Color currentColour = Color.white;
+ try
+ {
+ currentColour = colors[ResidueProperties.nucleotideIndex[c]];
+ } catch (Exception ex)
+ {
+ }
- /**
- * DOCUMENT ME!
- *
- * @param n
- * DOCUMENT ME!
- * @param j
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- @Override
- public Color findColour(char c, int j, SequenceI seq)
- {
- Color currentColour;
- if ((threshold == 0) || aboveThreshold(c, j))
- {
- try
- {
- currentColour = colors[ResidueProperties.nucleotideIndex[c]];
- } catch (Exception ex)
- {
- return Color.white;
- }
- }
- else
- {
- return Color.white;
- }
+ return currentColour;
+ }
- if (conservationColouring)
- {
- currentColour = applyConservation(currentColour, j);
- }
+ @Override
+ public boolean isNucleotideSpecific()
+ {
+ return true;
+ }
- return currentColour;
- }
- }
+ @Override
+ public String getSchemeName()
+ {
+ return "RNA Interaction type";
+ }
+
+ /**
+ * 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 RNAInteractionColourScheme();
+ }
+}