/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
+ * Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
*
*/
package jalview.schemes;
-import java.awt.*;
-import java.util.Hashtable;
-import java.util.Map;
-
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AnnotatedCollectionI;
import jalview.datamodel.SequenceCollectionI;
import jalview.datamodel.SequenceI;
+import java.awt.Color;
+import java.util.Hashtable;
+import java.util.Map;
+
/**
* Looks at the information computed from an RNA Stockholm format file on the
* secondary structure of the alignment. Extracts the information on the
{
/**
- * Stores random colors generated for the number of helices
- */
- public Hashtable helixcolorhash = new Hashtable();
-
- /**
* Maps sequence positions to the RNA helix they belong to. Key: position,
- * Value: helix
+ * Value: helix TODO: Revise or drop in favour of annotation position numbers
*/
- public Hashtable positionsToHelix = new Hashtable();
+ public Hashtable<Integer, String> positionsToHelix = new Hashtable<Integer, String>();
/**
* Number of helices in the RNA secondary structure
{
super(ResidueProperties.nucleotideIndex);
this.annotation = annotation;
+ ColourSchemeProperty.resetRnaHelicesShading();
refresh();
}
public RNAHelicesColour(AnnotatedCollectionI alignment)
{
super(ResidueProperties.nucleotideIndex);
+ ColourSchemeProperty.resetRnaHelicesShading();
alignmentChanged(alignment, null);
}
+ /**
+ * clones colour settings and annotation row data
+ *
+ * @param rnaHelicesColour
+ */
+ public RNAHelicesColour(RNAHelicesColour rnaHelicesColour)
+ {
+ super(ResidueProperties.nucleotideIndex);
+ annotation = rnaHelicesColour.annotation;
+ refresh();
+ }
+
@Override
public void alignmentChanged(AnnotatedCollectionI alignment,
Map<SequenceI, SequenceCollectionI> hiddenReps)
{
// is this a sensible way of determining type of annotation?
- if (annotations[i].getRNAStruc() != null)
+ if (annotations[i].visible && annotations[i].isRNA()
+ && annotations[i].isValidStruc())
{
annotation = annotations[i];
break;
annotation.getRNAStruc();
lastrefresh = annotation._rnasecstr.hashCode();
numHelix = 0;
- positionsToHelix = new Hashtable();
+ positionsToHelix = new Hashtable<Integer, String>();
// Figure out number of helices
// Length of rnasecstr is the number of pairs of positions that base pair
}
}
-
- // Generate random colors and store
- for (int j = 0; j <= numHelix; j++)
- {
- if (!helixcolorhash.containsKey(Integer.toString(j)))
- {
- helixcolorhash.put(Integer.toString(j),
- jalview.util.ColorUtils.generateRandomColor(Color.white));
- }
- }
+ ColourSchemeProperty.initRnaHelicesShading(numHelix);
}
}
* @param c
* Character in sequence
* @param j
- * Threshold
+ * position in sequence - used to locate helix
*
* @return Color in RGB
*/
refresh();
Color currentColour = Color.white;
String currentHelix = null;
- currentHelix = (String) positionsToHelix.get(j);
-
+ currentHelix = positionsToHelix.get(j);
if (currentHelix != null)
{
- currentColour = (Color) helixcolorhash.get(currentHelix);
+ currentColour = ColourSchemeProperty.rnaHelices[Integer
+ .parseInt(currentHelix)];
}
-
- // System.out.println(c + " " + j + " helix " + currentHelix + " " +
- // currentColour);
return currentColour;
}
-}
+
+ @Override
+ public ColourSchemeI applyTo(AnnotatedCollectionI sg,
+ Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
+ {
+ return new RNAHelicesColour(this);
+ }
+}
\ No newline at end of file