/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
- * Copyright (C) 2015 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.
*
*/
package jalview.schemes;
+import jalview.api.AlignViewportI;
import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
import jalview.datamodel.AnnotatedCollectionI;
import jalview.datamodel.SequenceCollectionI;
import jalview.datamodel.SequenceI;
* Maps sequence positions to the RNA helix they belong to. Key: position,
* Value: helix TODO: Revise or drop in favour of annotation position numbers
*/
- public Hashtable<Integer, String> positionsToHelix = new Hashtable<Integer, String>();
+ public Hashtable<Integer, String> positionsToHelix = new Hashtable<>();
/**
* Number of helices in the RNA secondary structure
public AlignmentAnnotation annotation;
/**
+ * Default constructor (required for ColourSchemes cache)
+ */
+ public RNAHelicesColour()
+ {
+
+ }
+
+ /**
* Creates a new RNAHelicesColour object.
*/
public RNAHelicesColour(AlignmentAnnotation annotation)
public void refresh()
{
- if (annotation != null
- && ((annotation._rnasecstr == null || lastrefresh != annotation._rnasecstr
- .hashCode()) && annotation.isValidStruc()))
+ if (annotation != null && ((annotation._rnasecstr == null
+ || lastrefresh != annotation._rnasecstr.hashCode())
+ && annotation.isValidStruc()))
{
annotation.getRNAStruc();
lastrefresh = annotation._rnasecstr.hashCode();
numHelix = 0;
- positionsToHelix = new Hashtable<Integer, String>();
+ positionsToHelix = new Hashtable<>();
// Figure out number of helices
// Length of rnasecstr is the number of pairs of positions that base pair
positionsToHelix.put(this.annotation._rnasecstr[x].getEnd(),
this.annotation._rnasecstr[x].getFeatureGroup());
- if (Integer.parseInt(this.annotation._rnasecstr[x]
- .getFeatureGroup()) > numHelix)
+ if (Integer.parseInt(
+ this.annotation._rnasecstr[x].getFeatureGroup()) > numHelix)
{
- numHelix = Integer.parseInt(this.annotation._rnasecstr[x]
- .getFeatureGroup());
+ numHelix = Integer.parseInt(
+ this.annotation._rnasecstr[x].getFeatureGroup());
}
}
}
@Override
- public ColourSchemeI applyTo(AnnotatedCollectionI sg,
- Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
+ public ColourSchemeI getInstance(AlignViewportI view,
+ AnnotatedCollectionI sg)
+ {
+ return new RNAHelicesColour(sg);
+ }
+
+ @Override
+ public boolean isNucleotideSpecific()
+ {
+ return true;
+ }
+
+ /**
+ * Answers true if the data has RNA secondary structure annotation
+ */
+ @Override
+ public boolean isApplicableTo(AnnotatedCollectionI ac)
+ {
+ if (ac instanceof AlignmentI && ((AlignmentI) ac).hasRNAStructure())
+ {
+ return true;
+ }
+
+ /*
+ * not currently supporting this option for group annotation / colouring
+ */
+ return false;
+ }
+
+ @Override
+ public String getSchemeName()
+ {
+ return JalviewColourScheme.RNAHelices.toString();
+ }
+
+ @Override
+ public boolean isSimple()
{
- return new RNAHelicesColour(this);
+ return false;
}
-}
\ No newline at end of file
+}