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;
}
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) {
}
}
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;
}
