private Map<String, List<String>> processSamplesGT(Map<String, String> options) {
    Map<String, List<String>> samplesGenotypes = new LinkedHashMap<>(10);
    List<String> genotypesList;

    String key, val;
    for (Map.Entry<String, String> entry : options.entrySet()) {
      key = entry.getKey();
      val = entry.getValue();

      if (key.startsWith("sampleGT_")) {
        String sampleName = key.replace("sampleGT_", "").replace("[]", "");
        String[] genotypes = val.split(",");

        if (samplesGenotypes.containsKey(sampleName)) {
          genotypesList = samplesGenotypes.get(sampleName);
        } else {

          genotypesList = new ArrayList<>();
          samplesGenotypes.put(sampleName, genotypesList);
        }

        for (int i = 0; i < genotypes.length; i++) {

          genotypesList.add(genotypes[i]);
        }
      }
    }
    return samplesGenotypes;
  }
Beispiel #2
0
    public TaskWrite(Map map1, Map m_max, Map m_min, DBCollection coll, ModbusSlaveSet slave) {

      try {
        synchronized (slave) {
          Calendar calener = Calendar.getInstance();
          Date d1 = calener.getTime();
          Date d2 = new Date(calener.getTime().getTime() - 5000);
          BasicDBObject b2 = new BasicDBObject();
          b2.put("$gte", d2);
          b2.put("$lte", d1);
          DBCursor cursor =
              coll.find(new BasicDBObject("_id", b2)).sort(new BasicDBObject("_id", -1)).limit(1);
          while (cursor.hasNext()) {
            DBObject dbo = cursor.next();
            Set set1 = map1.entrySet();
            Iterator it1 = set1.iterator();
            while (it1.hasNext()) {
              Map.Entry<String, Map<String, String>> entry =
                  (Map.Entry<String, Map<String, String>>) it1.next();
              Map<String, String> map2 = entry.getValue();
              for (Iterator it2 = map2.entrySet().iterator(); it2.hasNext(); ) {
                Map.Entry<String, String> entry2 = (Map.Entry<String, String>) it2.next();
                String name = entry2.getKey().toString();
                String paramAddr = entry2.getValue().toString();
                int fun = (int) (Double.parseDouble(paramAddr));
                if (paramAddr.substring(0, 1).equals("4")) {
                  double value = Double.parseDouble(dbo.get(name).toString());
                  double dmax = (Double) m_max.get(name);
                  double dmin = (Double) m_min.get(name);
                  double dValue = 0;
                  if (value > dmax || value < dmin) {
                    if (value >= 0) {
                      dValue = 32000 * (int) (value / dmax);
                    }
                    if (value < 0) {
                      dValue = -32000 * (int) (value / dmin);
                    }
                    // slave.getProcessImage(3).setInputRegister(fun % 10000, (short) dValue);
                  } else { /// 参数超限报警
                    JOptionPane.showMessageDialog(null, "参数超限");
                    slave.stop();
                  }
                }
                if (paramAddr.substring(0, 1).equals("3")) {
                  double value = Double.parseDouble(dbo.get(name).toString());
                  double dmax = (Double) m_max.get(name);
                  double dmin = (Double) m_min.get(name);
                  double dValue = 0;
                  if (value > dmax || value < dmin) {
                    if (value >= 0) {
                      dValue = 32000 * (int) (value / dmax);
                    }
                    if (value < 0) {
                      dValue = -32000 * (int) (value / dmin);
                    }
                    // slave.getProcessImage(3).setHoldingRegister(fun % 10000, (short) dValue);
                  } else { /// 参数超限报警
                    JOptionPane.showMessageDialog(null, "参数超限");
                    slave.stop();
                  }
                  ;
                }
                if (paramAddr.substring(0, 1).equals("2")) {
                  String value = dbo.get(name).toString();
                  /// slave.getProcessImage(4).setInput(fun % 10000, Boolean.valueOf(value));
                }
                if (paramAddr.substring(0, 1).equals("1")) {
                  String value = dbo.get(name).toString();
                  // slave.getProcessImage(4).setCoil(fun % 10000, Boolean.valueOf(value));
                }
              }
            }
          }
        }
      } catch (Exception ex) {
      }
    }
Beispiel #3
0
    public TaskRead(Map map1, Map m_max, Map m_min, DBCollection coll, ModbusSlaveSet slave) {
      try {
        //// 此处只要点击开始就能保存数据
        /// 方案:利用数据源发送单个布尔型变量(1,0)交替,链接成功,先判断是否链接成功,然后在保存数据
        synchronized (slave) {
          Map map = new HashMap();
          Set set1 = map1.entrySet();
          Iterator it1 = set1.iterator();
          while (it1.hasNext()) {
            Map.Entry<String, Map<String, String>> entry =
                (Map.Entry<String, Map<String, String>>) it1.next();
            Map<String, String> map2 = entry.getValue();
            for (Iterator it2 = map2.entrySet().iterator(); it2.hasNext(); ) {
              Map.Entry<String, String> entry2 = (Map.Entry<String, String>) it2.next();
              String name = entry2.getKey().toString();
              String paramAddr = entry2.getValue().toString();
              int fun = (int) (Double.parseDouble(paramAddr));
              if (paramAddr.substring(0, 1).equals("4")) {
                Short d4 = slave.getProcessImage(1).getInputRegister(fun % 10000);
                double dmax = (Double) m_max.get(name);
                double dmin = (Double) m_min.get(name);
                double dValue = 0;
                if (d4 >= 0) {
                  dValue = dmax * d4 / 32000;
                } else {
                  dValue = dmin * d4 / (-32000);
                }
                map.put(name, dValue);
              }
              if (paramAddr.substring(0, 1).equals("3")) {
                Short d3 = slave.getProcessImage(1).getHoldingRegister(fun % 10000);
                double dmax = (Double) m_max.get(name);
                double dmin = (Double) m_min.get(name);
                double dValue = 0;

                if (d3 >= 0) {
                  dValue = dmax * d3 / 32000;
                } else {
                  dValue = dmin * d3 / (-32000);
                }
                map.put(name, dValue);
              }
              if (paramAddr.substring(0, 1).equals("2")) {
                map.put(name, slave.getProcessImage(2).getInput(fun % 10000));
              }
              if (paramAddr.substring(0, 1).equals("1")) {
                Boolean a = slave.getProcessImage(2).getCoil(fun % 10000 - 1);
                map.put(name, a);
              }
            }
          }

          Calendar calendar = Calendar.getInstance();
          Date dd = calendar.getTime();

          BasicDBObject doc = new BasicDBObject();
          doc.put("_id", dd);

          Set set = map.entrySet();
          Iterator it = set.iterator();
          while (it.hasNext()) {
            Map.Entry<String, String> entry1 = (Map.Entry<String, String>) it.next();
            doc.put(entry1.getKey(), entry1.getValue());
          }
          coll.insert(doc);
        }
      } catch (Exception ex) {
      }
    }
  public QueryResult getSimpleVariantsByRegion(
      Region region, String sourceId, QueryOptions options) {
    Long start, end, dbstart, dbend;
    start = System.currentTimeMillis();
    boolean includeStats;
    boolean includeEffects;
    if (!options.containsKey("stats") && !options.containsKey("effects")) {
      includeStats = true;
      includeEffects = true;
    } else {
      includeStats = options.containsKey("stats") && options.getBoolean("stats");
      includeEffects = options.containsKey("effects") && options.getBoolean("effects");
    }

    QueryResult<Variant> queryResult =
        new QueryResult<>(
            String.format("%s:%d-%d", region.getChromosome(), region.getStart(), region.getEnd()));
    List<Variant> results = new ArrayList<>();
    String startRow = buildRowkey(region.getChromosome(), Long.toString(region.getStart()));
    String stopRow = buildRowkey(region.getChromosome(), Long.toString(region.getEnd()));
    BasicDBObject query =
        new BasicDBObject("position", new BasicDBObject("$gte", startRow).append("$lte", stopRow))
            .append("sources.sourceId", sourceId);
    DBCollection collection = db.getCollection("variants");
    dbstart = System.currentTimeMillis();
    DBCursor variantInStudies = collection.find(query);
    dbend = System.currentTimeMillis();
    queryResult.setDbTime(dbend - dbstart);

    for (DBObject result : variantInStudies) {
      String[] rowkeyParts = result.get("position").toString().split("_");
      String chromosome = rowkeyParts[0].replaceFirst("^0+(?!$)", "");
      int position = Integer.parseInt(rowkeyParts[1]);
      BasicDBList studies = (BasicDBList) result.get("sources");
      BasicDBObject st = (BasicDBObject) studies.get(0);
      String ref = (String) st.get("ref");
      String alt = StringUtils.join((ArrayList<String>) st.get("alt"), ",");

      // TODO Needs rework
      Variant variant = new Variant(chromosome, position, position, ref, alt);

      // Set stats informations
      if (includeStats) {
        VariantStats stats = new VariantStats();
        BasicDBObject mongoStats = (BasicDBObject) st.get("stats");
        stats.setMaf((float) (double) mongoStats.get("maf"));
        stats.setMafAllele((String) mongoStats.get("alleleMaf"));
        stats.setMissingGenotypes((int) mongoStats.get("missing"));
        List<Genotype> genotypeCount = new ArrayList<>();
        for (BasicDBObject s : (List<BasicDBObject>) mongoStats.get("genotypeCount")) {
          for (Map.Entry<String, Object> entry : s.entrySet()) {
            Genotype genotype = new Genotype(entry.getKey());
            genotype.setCount((Integer) entry.getValue());
            genotypeCount.add(genotype);
          }
        }
        stats.setGenotypes(genotypeCount);
        variant.setStats(stats);
      }

      // TODO Set consequence type names
      if (includeEffects) {
        BasicDBList mongoEffects = (BasicDBList) st.get("effects");
        if (mongoEffects != null) {
          for (Object e : mongoEffects) {
            String effectObo = e.toString();
            VariantEffect effect = new VariantEffect();
            effect.setConsequenceTypeObo(effectObo);
            variant.addEffect(effect);
          }
        }
      }

      results.add(variant);
    }

    queryResult.setResult(results);
    queryResult.setNumResults(results.size());
    end = System.currentTimeMillis();
    queryResult.setTime(end - start);
    return queryResult;
  }