- getAlignment().addSequence(toAdd.getSequenceAt(i));
- }
-
- setEndSeq(getAlignment().getHeight());
- firePropertyChange("alignment", null, getAlignment().getSequences());
- }
-
- /**
- * Check if any added sequence could be the object of a mapping or
- * cross-reference; if so, make the mapping explicit. Returns the count of
- * mappings updated.
- *
- * @param al
- * @param toAdd
- */
- protected int realiseMappings(AlignmentI al, AlignmentI toAdd)
- {
- // TODO this is proof of concept
- // we might want to give the user some choice here
- int count = 0;
- for (SequenceI seq : toAdd.getSequences())
- {
- count += realiseMappingsTo(al, seq);
- }
- return count;
- }
-
- /**
- * If the alignment holds any mappings to a virtual (placeholder) sequence
- * that matches all or part of the given sequence, then update the mapping to
- * point to the sequence. Returns the number of mappings updated.
- *
- * @param al
- * @param seq
- * @return
- */
- protected int realiseMappingsTo(AlignmentI al, SequenceI seq)
- {
- int count = 0;
- Set<AlignedCodonFrame> mappings = al.getCodonFrames();
- for (AlignedCodonFrame mapping : mappings)
- {