public void doLayout() {
    selections.clear();
    if (points == null) {
      points = new Vector<ExprPoint>();
    }
    points.clear();

    for (Pair<Integer, Double> p : watsonProbes) {
      ExprPoint ep = new ExprPoint(p.getFirst(), p.getLast(), '+');
      points.add(ep);
    }

    for (Pair<Integer, Double> p : crickProbes) {
      ExprPoint ep = new ExprPoint(p.getFirst(), p.getLast(), '-');
      points.add(ep);
    }
  }
Пример #2
0
  public Collection<NamedRegion> parseProbes() throws IOException {
    double ethreshold = 1.0e-3;
    Parser<BlastTabEntry> parser =
        new Parser<BlastTabEntry>(blasttab, new BlastTabEntry.ParsingMapper());
    Iterator<BlastTabEntry> itr =
        new FilterIterator<BlastTabEntry, BlastTabEntry>(
            new BlastTabEntry.ExpectedScoreFilter(ethreshold), parser);

    Map<String, Set<Region>> primerHits = new TreeMap<String, Set<Region>>();
    Set<String> primerNames = new TreeSet<String>();

    while (itr.hasNext()) {
      BlastTabEntry entry = itr.next();
      NamedRegion r = createNamedRegion(entry);
      if (!primerHits.containsKey(entry.getQuery())) {
        primerHits.put(entry.getQuery(), new HashSet<Region>());
      }
      primerHits.get(entry.getQuery()).add(r);
      primerNames.add(removePrimerLR(entry.getQuery()));
    }

    LinkedList<NamedRegion> probes = new LinkedList<NamedRegion>();

    for (String primerName : primerNames) {
      Pair<Region, Region> hits = findProbePair(primerName, primerHits);
      if (hits != null) {
        Region left = hits.getFirst(), right = hits.getLast();
        int start = Math.min(left.getStart(), right.getStart());
        int end = Math.max(left.getEnd(), right.getEnd());

        NamedRegion probe = new NamedRegion(genome, left.getChrom(), start, end, primerName);
        probes.addLast(probe);
      }
    }

    return probes;
  }