X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fschemes%2FRNAInteractionColourScheme.java;h=d23680373986212d94875a38748c9f61f3710648;hb=903aec15b7d5462d5637662b3f02d84de1b8a67b;hp=2738f229aeb6f2a89a04c455e320d9d4570200fe;hpb=47168f025aefdaa044802bd5f8f510ffe43a4808;p=jalview.git
diff --git a/src/jalview/schemes/RNAInteractionColourScheme.java b/src/jalview/schemes/RNAInteractionColourScheme.java
index 2738f22..d236803 100644
--- a/src/jalview/schemes/RNAInteractionColourScheme.java
+++ b/src/jalview/schemes/RNAInteractionColourScheme.java
@@ -1,6 +1,6 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * 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.
*
@@ -18,68 +18,64 @@
* 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();
+ }
+}