}
/**
- * DOCUMENT ME!
+ * Sets the sequence description, and also parses out any special formats of
+ * interest
*
* @param desc
- * DOCUMENT ME!
*/
@Override
public void setDescription(String desc)
this.description = desc;
}
+ @Override
+ public void setGeneLoci(String speciesId, String assemblyId,
+ String chromosomeId, MapList map)
+ {
+ addDBRef(new DBRefEntry(speciesId, assemblyId, DBRefEntry.CHROMOSOME
+ + ":" + chromosomeId, new Mapping(map)));
+ }
+
/**
- * DOCUMENT ME!
+ * Returns the gene loci mapping for the sequence (may be null)
*
- * @return DOCUMENT ME!
+ * @return
+ */
+ @Override
+ public GeneLociI getGeneLoci()
+ {
+ DBRefEntry[] refs = getDBRefs();
+ if (refs != null)
+ {
+ for (final DBRefEntry ref : refs)
+ {
+ if (ref.isChromosome())
+ {
+ return new GeneLociI()
+ {
+ @Override
+ public String getSpeciesId()
+ {
+ return ref.getSource();
+ }
+
+ @Override
+ public String getAssemblyId()
+ {
+ return ref.getVersion();
+ }
+
+ @Override
+ public String getChromosomeId()
+ {
+ // strip off "chromosome:" prefix to chrId
+ return ref.getAccessionId().substring(
+ DBRefEntry.CHROMOSOME.length() + 1);
+ }
+
+ @Override
+ public MapList getMap()
+ {
+ return ref.getMap().getMap();
+ }
+ };
+ }
+ }
+ }
+ return null;
+ }
+
+ /**
+ * Answers the description
+ *
+ * @return
*/
@Override
public String getDescription()
return newSequence.toString();
}
+
+ @Override
+ public int firstResidueOutsideIterator(Iterator<int[]> regions)
+ {
+ int start = 0;
+
+ if (!regions.hasNext())
+ {
+ return findIndex(getStart()) - 1;
+ }
+
+ // Simply walk along the sequence whilst watching for region
+ // boundaries
+ int hideStart = getLength();
+ int hideEnd = -1;
+ boolean foundStart = false;
+
+ // step through the non-gapped positions of the sequence
+ for (int i = getStart(); i <= getEnd() && (!foundStart); i++)
+ {
+ // get alignment position of this residue in the sequence
+ int p = findIndex(i) - 1;
+
+ // update region start/end
+ while (hideEnd < p && regions.hasNext())
+ {
+ int[] region = regions.next();
+ hideStart = region[0];
+ hideEnd = region[1];
+ }
+ if (hideEnd < p)
+ {
+ hideStart = getLength();
+ }
+ // update boundary for sequence
+ if (p < hideStart)
+ {
+ start = p;
+ foundStart = true;
+ }
+ }
+
+ if (foundStart)
+ {
+ return start;
+ }
+ // otherwise, sequence was completely hidden
+ return 0;
+ }
}