/*
- * 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.
*
* 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 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
this.annotation = annotation;
refresh();
}
+
public RNAHelicesColour(AnnotatedCollectionI alignment)
{
super(ResidueProperties.nucleotideIndex);
alignmentChanged(alignment, null);
}
+ /**
+ * clones colour settings and annotation row data
+ *
+ * @param rnaHelicesColour
+ */
+ public RNAHelicesColour(RNAHelicesColour rnaHelicesColour)
+ {
+ super(ResidueProperties.nucleotideIndex);
+ helixcolorhash = rnaHelicesColour.helixcolorhash;
+ 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.
+ // the sequences.
AlignmentAnnotation[] annotations = alignment.getAlignmentAnnotation();
- for (int i = 0; i < annotations.length; i++) {
-
- // is this a sensible way of determining type of annotation?
- if (annotations[i].getRNAStruc() != null) {
- annotation = annotations[i];
- break;
- }
+ for (int i = 0; i < annotations.length; i++)
+ {
+
+ // is this a sensible way of determining type of annotation?
+ if (annotations[i].getRNAStruc() != null)
+ {
+ annotation = annotations[i];
+ break;
+ }
}
refresh();
}
+
private long lastrefresh = -1;
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();
// currentColour);
return currentColour;
}
+
+ @Override
+ public ColourSchemeI applyTo(AnnotatedCollectionI sg,
+ Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
+ {
+ return new RNAHelicesColour(this);
+ }
}