Пример #1
0
  private Pair<Region, Region> findProbePair(
      String primerName, Map<String, Set<Region>> primerHits) {
    String leftName = String.format("%s_left", primerName);
    String rightName = String.format("%s_right", primerName);

    if (!primerHits.containsKey(leftName) || !primerHits.containsKey(rightName)) {
      return null;
    }
    if (primerHits.get(leftName).size() != 1 || primerHits.get(rightName).size() != 1) {
      return null;
    }

    Iterator<Region> leftitr = primerHits.get(leftName).iterator();
    Iterator<Region> rightitr = primerHits.get(rightName).iterator();
    Region left = leftitr.next();
    Region right = rightitr.next();

    if (!left.getChrom().equals(right.getChrom())) {
      return null;
    }

    return new Pair<Region, Region>(left, right);
  }
  /** Fetches any styles that match the passed into arguments into <code>matches</code>. */
  private void getMatchingStyles(java.util.List matches, JComponent c, Region id) {
    String idName = id.getLowerCaseName();
    String cName = c.getName();

    if (cName == null) {
      cName = "";
    }
    for (int counter = _styles.size() - 1; counter >= 0; counter--) {
      StyleAssociation sa = _styles.get(counter);
      String path;

      if (sa.getID() == NAME) {
        path = cName;
      } else {
        path = idName;
      }

      if (sa.matches(path) && matches.indexOf(sa.getStyle()) == -1) {
        matches.add(sa.getStyle());
      }
    }
  }
Пример #3
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;
  }