/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 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.datamodel;
+import jalview.util.MessageManager;
+
import java.util.*;
/**
*/
public static AlignmentI createAlignment(CigarArray compactAlignment)
{
- throw new Error("Alignment(CigarArray) not yet implemented");
+ throw new Error(MessageManager.getString("error.alignment_cigararray_not_implemented"));
// this(compactAlignment.refCigars);
}
return;
}
}
-
+ sg.setContext(this);
groups.add(sg);
}
}
{
removeAnnotationForGroup(null);
}
+ for (SequenceGroup sg : groups)
+ {
+ sg.setContext(null);
+ }
groups.clear();
}
}
{
removeAnnotationForGroup(g);
groups.remove(g);
+ g.setContext(null);
}
}
}
SequenceGroup groupRef)
{
assert (name != null);
- for (AlignmentAnnotation annot : getAlignmentAnnotation())
+ if (annotations != null)
{
- if (annot.autoCalculated == autoCalc && (name.equals(annot.label))
- && (calcId == null || annot.getCalcId().equals(calcId))
- && annot.sequenceRef == seqRef && annot.groupRef == groupRef)
+ for (AlignmentAnnotation annot : getAlignmentAnnotation())
{
- return annot;
+ if (annot.autoCalculated == autoCalc && (name.equals(annot.label))
+ && (calcId == null || annot.getCalcId().equals(calcId))
+ && annot.sequenceRef == seqRef
+ && annot.groupRef == groupRef)
+ {
+ return annot;
+ }
}
}
AlignmentAnnotation annot = new AlignmentAnnotation(name, name,
}
}
+ @Override
+ public void validateAnnotation(AlignmentAnnotation alignmentAnnotation)
+ {
+ alignmentAnnotation.validateRangeAndDisplay();
+ if (isNucleotide() && alignmentAnnotation.isValidStruc())
+ {
+ hasRNAStructure = true;
+ }
+ }
+
+ @Override
+ public int getEndRes()
+ {
+ return getWidth() - 1;
+ }
+
+ @Override
+ public int getStartRes()
+ {
+ return 0;
+ }
+
+ /*
+ * In the case of AlignmentI - returns the dataset for the alignment, if set
+ * (non-Javadoc)
+ *
+ * @see jalview.datamodel.AnnotatedCollectionI#getContext()
+ */
+ @Override
+ public AnnotatedCollectionI getContext()
+ {
+ return dataset;
+ }
}