+
+ /**
+ * Returns a hashCode derived from the hashcodes of the mappings and fromSeq
+ *
+ * @see SequenceToSequenceMapping#hashCode()
+ */
+ @Override
+ public int hashCode()
+ {
+ return (fromSeq == null ? 0 : fromSeq.hashCode() * 31)
+ + mapping.hashCode();
+ }
+
+ /**
+ * Answers true if the objects hold the same mapping between the same two
+ * sequences
+ *
+ * @see Mapping#equals
+ */
+ @Override
+ public boolean equals(Object obj)
+ {
+ if (!(obj instanceof SequenceToSequenceMapping))
+ {
+ return false;
+ }
+ SequenceToSequenceMapping that = (SequenceToSequenceMapping) obj;
+ if (this.mapping == null)
+ {
+ return that.mapping == null;
+ }
+ // TODO: can simplify by asserting fromSeq is a dataset sequence
+ return (this.fromSeq == that.fromSeq
+ || (this.fromSeq != null && that.fromSeq != null
+ && this.fromSeq.getDatasetSequence() != null
+ && this.fromSeq.getDatasetSequence() == that.fromSeq
+ .getDatasetSequence()))
+ && this.mapping.equals(that.mapping);
+ }
+
+ public SequenceI getFromSeq()
+ {
+ return fromSeq;
+ }
+
+ public Mapping getMapping()
+ {
+ return mapping;
+ }
+
+ /**
+ * Returns true if the mapping covers the full length of the given sequence.
+ * This allows us to distinguish the CDS that codes for a protein from
+ * another overlapping CDS in the parent dna sequence.
+ *
+ * @param seq
+ * @return
+ */
+ public boolean covers(SequenceI seq)
+ {
+ return covers(seq,false);
+ }
+ /**
+ *
+ * @param seq
+ * @param localCover - when true - compare extent of seq's dataset sequence rather than the local extent
+ * @return true if mapping covers full length of given sequence
+ */
+ public boolean covers(SequenceI seq, boolean localCover)
+ {
+ List<int[]> mappedRanges = null;
+ MapList mapList = mapping.getMap();
+ int mstart=seq.getStart(),mend=seq.getEnd()
+ ;
+ if (fromSeq == seq || fromSeq == seq.getDatasetSequence())
+ {
+ if (localCover && fromSeq !=seq)
+ {
+ mstart=fromSeq.getStart();
+ mend=fromSeq.getEnd();
+ }
+ mappedRanges = mapList.getFromRanges();
+ }
+ else if (mapping.to == seq || mapping.to == seq.getDatasetSequence())
+ {
+ if (localCover && mapping.to !=seq)
+ {
+ mstart=mapping.to.getStart();
+ mend=mapping.to.getEnd();
+ }
+ mappedRanges = mapList.getToRanges();
+ }
+ else
+ {
+ return false;
+ }
+
+ /*
+ * check that each mapped range lieS with the sequence range
+ * (necessary for circular CDS - example EMBL:J03321:AAA91567)
+ * and mapped length covers (at least) sequence length
+ */
+ int length = 0;
+ for (int[] range : mappedRanges)
+ {
+ int from = Math.min(range[0], range[1]);
+ int to = Math.max(range[0], range[1]);
+ if (from < mstart || to > mend)
+ {
+ return false;
+ }
+ length += (to - from + 1);
+ }
+ // add 1 to mapped length to allow for a mapped stop codon
+ if (length + 1 < (mend - mstart + 1))
+ {
+ return false;
+ }
+ return true;
+ }