X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FRNAInteractionColourScheme.java;h=d23680373986212d94875a38748c9f61f3710648;hb=7047b076a62df177047ceb16c3611efe020bdd76;hp=42f4feb37cca6f6ddcc4ac85dc7809581e3a33d5;hpb=3e7ebcfda0bc54b3b91905e21835142bfd1fe8a0;p=jalview.git
diff --git a/src/jalview/schemes/RNAInteractionColourScheme.java b/src/jalview/schemes/RNAInteractionColourScheme.java
index 42f4feb..d236803 100644
--- a/src/jalview/schemes/RNAInteractionColourScheme.java
+++ b/src/jalview/schemes/RNAInteractionColourScheme.java
@@ -1,82 +1,81 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * 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;
+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();
- }
+ @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 hrs)
+ {
+ return new RNAInteractionColourScheme();
+ }
+}