+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
+ * 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.
+ *
+ * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.schemes;
import jalview.analysis.SequenceIdMatcher;
// Search alignment to get all tcoffee annotation and pick one set of
// annotation to use to colour seqs.
seqMap = new IdentityHashMap<SequenceI, Color[]>();
+ AnnotatedCollectionI alcontext = alignment instanceof AlignmentI ? alignment
+ : alignment.getContext();
int w = 0;
- for (AlignmentAnnotation al : alignment
+ for (AlignmentAnnotation al : alcontext
.findAnnotation(TCoffeeScoreFile.TCOFFEE_SCORE))
{
if (al.sequenceRef != null && !al.belowAlignment)
}
return cols[j];
}
+
+ @Override
+ public ColourSchemeI applyTo(AnnotatedCollectionI sg,
+ Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
+ {
+ return new TCoffeeColourScheme(sg);
+ }
}