/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
- * 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.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
import jalview.datamodel.AnnotatedCollectionI;
import jalview.datamodel.SequenceCollectionI;
import jalview.datamodel.SequenceI;
public AlignmentAnnotation annotation;
/**
+ * Default constructor (required for ColourSchemes cache)
+ */
+ public RNAHelicesColour()
+ {
+
+ }
+
+ /**
* Creates a new RNAHelicesColour object.
*/
public RNAHelicesColour(AlignmentAnnotation annotation)
// This loop will find the first rna structure annotation by which to colour
// the sequences.
AlignmentAnnotation[] annotations = alignment.getAlignmentAnnotation();
+ if (annotations == null)
+ {
+ return;
+ }
for (int i = 0; i < annotations.length; i++)
{
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();
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,
+ public ColourSchemeI getInstance(AnnotatedCollectionI sg,
Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
{
- return new RNAHelicesColour(this);
+ 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 false;
}
-}
\ No newline at end of file
+}