+ if (!related.contains(mapping.to))
+ {
+ result.add(mapping);
+ related.add(mapping.to);
+ }
+ }
+ }
+ return result;
+ }
+
+ /**
+ * Test whether the given sequence is substitutable for one or more dummy
+ * sequences in this mapping
+ *
+ * @param map
+ * @param seq
+ * @return
+ */
+ public boolean isRealisableWith(SequenceI seq)
+ {
+ return realiseWith(seq, false) > 0;
+ }
+
+ /**
+ * Replace any matchable mapped dummy sequences with the given real one.
+ * Returns the count of sequence mappings instantiated.
+ *
+ * @param seq
+ * @return
+ */
+ public int realiseWith(SequenceI seq)
+ {
+ return realiseWith(seq, true);
+ }
+
+ /**
+ * Returns the number of mapped dummy sequences that could be replaced with
+ * the given real sequence.
+ *
+ * @param seq
+ * a dataset sequence
+ * @param doUpdate
+ * if true, performs replacements, else only counts
+ * @return
+ */
+ protected int realiseWith(SequenceI seq, boolean doUpdate)
+ {
+ SequenceI ds = seq.getDatasetSequence() != null ? seq
+ .getDatasetSequence() : seq;
+ int count = 0;
+
+ /*
+ * check for replaceable DNA ('map from') sequences
+ */
+ for (SequenceToSequenceMapping ssm : mappings)
+ {
+ SequenceI dna = ssm.fromSeq;
+ if (dna instanceof SequenceDummy
+ && dna.getName().equals(ds.getName()))
+ {
+ Mapping mapping = ssm.mapping;
+ int mapStart = mapping.getMap().getFromLowest();
+ int mapEnd = mapping.getMap().getFromHighest();
+ boolean mappable = couldRealiseSequence(dna, ds, mapStart, mapEnd);
+ if (mappable)
+ {
+ count++;
+ if (doUpdate)
+ {
+ // TODO: new method ? ds.realise(dna);
+ // might want to copy database refs as well
+ ds.setSequenceFeatures(dna.getSequenceFeatures());
+ // dnaSeqs[i] = ds;
+ ssm.fromSeq = ds;
+ System.out.println("Realised mapped sequence " + ds.getName());
+ }
+ }
+ }
+
+ /*
+ * check for replaceable protein ('map to') sequences
+ */
+ Mapping mapping = ssm.mapping;
+ SequenceI prot = mapping.getTo();
+ int mapStart = mapping.getMap().getToLowest();
+ int mapEnd = mapping.getMap().getToHighest();
+ boolean mappable = couldRealiseSequence(prot, ds, mapStart, mapEnd);
+ if (mappable)
+ {
+ count++;
+ if (doUpdate)
+ {
+ // TODO: new method ? ds.realise(dna);
+ // might want to copy database refs as well
+ ds.setSequenceFeatures(dna.getSequenceFeatures());
+ ssm.mapping.setTo(ds);
+ }