/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, 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 <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemes;
-import java.awt.*;
-import java.util.Hashtable;
-
+import jalview.api.AlignViewportI;
import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+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<>();
/**
* 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)
{
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)
+ {
+
+ // 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++)
+ {
+
+ // is this a sensible way of determining type of annotation?
+ if (annotations[i].visible && annotations[i].isRNA()
+ && annotations[i].isValidStruc())
+ {
+ annotation = annotations[i];
+ break;
+ }
+ }
+
refresh();
+
}
private long lastrefresh = -1;
public void refresh()
{
- if (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();
+ positionsToHelix = new Hashtable<>();
// Figure out number of helices
// Length of rnasecstr is the number of pairs of positions that base pair
{
/*
- * System.out.println(this.annotation._rnasecstr[x] + " Begin" +
+ * jalview.bin.Console.outPrintln(this.annotation._rnasecstr[x] + " Begin" +
* this.annotation._rnasecstr[x].getBegin());
*/
- // System.out.println(this.annotation._rnasecstr[x].getFeatureGroup());
+ // jalview.bin.Console.outPrintln(this.annotation._rnasecstr[x].getFeatureGroup());
positionsToHelix.put(this.annotation._rnasecstr[x].getBegin(),
this.annotation._rnasecstr[x].getFeatureGroup());
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());
}
}
-
- // 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 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 false;
+ }
}
git://source.jalview.org / jalview.git / blobdiff