public void compressMS2(List <TempIndex> tempIndexList, BlockIndex index)
{
if (converter.jobInfo.jobParams.threadAccelerate)
{
Hashtable table = Hashtable.Synchronized(new Hashtable());
//使用多线程处理数据提取与压缩
Parallel.For(0, tempIndexList.Count, (i, ParallelLoopState) =>
{
TempIndex tempIndex = tempIndexList[i];
TempScan ts = new TempScan(tempIndex.num, tempIndex.rt, tempIndex.tic);
if (converter.jobInfo.jobParams.includeCV)
{
ts.cvs = tempIndex.cvList;
}
converter.compress(converter.spectrumList.spectrum(tempIndex.num, true), ts);
table.Add(i, ts);
});
converter.outputWithOrder(table, index);
}
else
{
foreach (TempIndex tempIndex in tempIndexList)
{
TempScan ts = new TempScan(tempIndex.num, tempIndex.rt, tempIndex.tic);
if (converter.jobInfo.jobParams.includeCV)
{
ts.cvs = tempIndex.cvList;
}
converter.compress(converter.spectrumList.spectrum(tempIndex.num, true), ts);
converter.addToIndex(index, ts);
}
}
}
//建立Ms1Scan的索引
new private TempIndex parseMS1(Spectrum spectrum, int index)
{
TempIndex ms1 = new TempIndex();
ms1.level = 1;
ms1.num = index;
if (spectrum.scanList.scans.Count != 1)
{
return(ms1);
}
Scan scan = spectrum.scanList.scans[0];
if (jobInfo.jobParams.includeCV)
{
ms1.cvList = CV.trans(spectrum);
if (scan.cvParams != null)
{
ms1.cvList.AddRange(CV.trans(scan.cvParams));
}
}
ms1.rt = parseRT(scan);
ms1.tic = parseTIC(spectrum);
if (msType == null)
{
parseMsType(spectrum);
}
if (polarity == null)
{
parsePolarity(spectrum);
}
return(ms1);
}
protected TempIndex parseMS2(Spectrum spectrum, int index, int parentIndex)
{
TempIndex ms2 = new TempIndex();
ms2.level = 2;
ms2.pNum = parentIndex;
ms2.num = index;
try
{
double mz = getPrecursorIsolationWindowParams(spectrum, CVID.MS_isolation_window_target_m_z);
double lowerOffset = getPrecursorIsolationWindowParams(spectrum, CVID.MS_isolation_window_lower_offset);
double upperOffset = getPrecursorIsolationWindowParams(spectrum, CVID.MS_isolation_window_upper_offset);
int charge = getPrecursorCharge(spectrum);
ms2.charge = charge;
ms2.mz = mz;
ms2.mzStart = mz - lowerOffset;
ms2.mzEnd = mz + upperOffset;
ms2.wid = lowerOffset + upperOffset;
}
catch (Exception e)
{
jobInfo.log("ERROR:SpectrumIndex:" + spectrum.index)
.log("ERROR:SpectrumId:" + spectrum.id)
.log("ERROR: mz:" + spectrum.precursors[0].isolationWindow
.cvParamChild(CVID.MS_isolation_window_target_m_z).value)
.log("ERROR: lowerOffset:" + spectrum.precursors[0].isolationWindow
.cvParamChild(CVID.MS_isolation_window_lower_offset).value)
.log("ERROR: upperOffset:" + spectrum.precursors[0].isolationWindow
.cvParamChild(CVID.MS_isolation_window_upper_offset).value);
throw e;
}
if (activator == null)
{
parseActivator(spectrum.precursors[0].activation);
}
if (spectrum.scanList.scans.Count != 1)
{
return(ms2);
}
Scan scan = spectrum.scanList.scans[0];
if (jobInfo.jobParams.includeCV)
{
ms2.cvList = CV.trans(spectrum);
if (scan.cvParams != null)
{
ms2.cvList.AddRange(CV.trans(scan.cvParams));
}
}
ms2.rt = parseRT(scan);
ms2.tic = parseTIC(spectrum);
return(ms2);
}
new private void addToMS2Map(TempIndex ms2Index)
{
if (ms2Table.Contains(ms2Index.pNum))
{
(ms2Table[ms2Index.pNum] as List <TempIndex>).Add(ms2Index);
}
else
{
List <TempIndex> indexList = new List <TempIndex>();
indexList.Add(ms2Index);
ms2Table.Add(ms2Index.pNum, indexList);
}
}
protected void addToMS2Map(TempIndex ms2Index)
{
if (ms2Table.Contains(ms2Index.mz))
{
(ms2Table[ms2Index.mz] as List <TempIndex>).Add(ms2Index);
}
else
{
List <TempIndex> indexList = new List <TempIndex>();
indexList.Add(ms2Index);
ms2Table.Add(ms2Index.mz, indexList);
}
}
private void parseAndStoreMS2Block()
{
jobInfo.log("Start Processing MS2 List");
foreach (double key in ms2Table.Keys)
{
List <TempIndex> tempIndexList = ms2Table[key] as List <TempIndex>;
//为每一个key组创建一个SwathBlock
BlockIndex swathIndex = new BlockIndex();
swathIndex.level = 2;
swathIndex.startPtr = startPosition;
//顺便创建一个WindowRanges,用以让Propro服务端快速获取全局的窗口数目和mz区间
WindowRange range = new WindowRange(tempIndexList[0].mzStart, tempIndexList[0].mzEnd, key);
swathIndex.setWindowRange(range);
ranges.Add(range);
jobInfo.log(null, "MS2:" + progress + "/" + ms2Table.Keys.Count);
progress++;
if (jobInfo.jobParams.threadAccelerate)
{
Hashtable table = Hashtable.Synchronized(new Hashtable());
//使用多线程处理数据提取与压缩
Parallel.For(0, tempIndexList.Count, (i, ParallelLoopState) =>
{
TempIndex index = tempIndexList[i];
TempScan ts = new TempScan(index.num, index.rt, index.tic);
compress(spectrumList.spectrum(index.num, true), ts);
table.Add(i, ts);
});
outputWithOrder(table, swathIndex);
}
else
{
foreach (TempIndex index in tempIndexList)
{
TempScan ts = new TempScan(index.pNum, index.rt, index.tic);
compress(spectrumList.spectrum(index.num, true), ts);
addToIndex(swathIndex, ts);
}
}
swathIndex.endPtr = startPosition;
indexList.Add(swathIndex);
jobInfo.log("MS2 Group Finished:" + progress + "/" + ms2Table.Keys.Count);
}
}
private static string GetDeleteRootSql(DataTable table)
{
List <string> sqls = new List <string>();
using (var temp = TempIndex.Borrow())
{
var index = temp.Item;
FillDeleteByRootIdSql(table, sqls, index);
}
StringBuilder code = new StringBuilder();
foreach (var sql in sqls)
{
code.AppendLine(sql);
}
return(code.ToString().Trim());
}
public void compressMS1(BlockIndex index)
{
if (converter.jobInfo.jobParams.threadAccelerate)
{
Hashtable table = Hashtable.Synchronized(new Hashtable());
//使用多线程处理数据提取与压缩
Parallel.For(0, converter.ms1List.Count, (i, ParallelLoopState) =>
{
converter.jobInfo.log(null, "MS1:" + i + "/" + converter.ms1List.Count);
TempIndex scanIndex = converter.ms1List[i];
TempScan ts = new TempScan(scanIndex.num, scanIndex.rt, scanIndex.tic);
if (converter.jobInfo.jobParams.includeCV)
{
ts.cvs = scanIndex.cvList;
}
converter.compress(converter.spectrumList.spectrum(scanIndex.num, true), ts);
table.Add(i, ts);
});
converter.outputWithOrder(table, index);
}
else
{
for (int i = 0; i < converter.ms1List.Count; i++)
{
converter.jobInfo.log(null, "MS1:" + i + "/" + converter.ms1List.Count);
TempIndex scanIndex = converter.ms1List[i];
TempScan ts = new TempScan(scanIndex.num, scanIndex.rt, scanIndex.tic);
if (converter.jobInfo.jobParams.includeCV)
{
ts.cvs = scanIndex.cvList;
}
converter.compress(converter.spectrumList.spectrum(scanIndex.num, true), ts);
converter.addToIndex(index, ts);
}
}
}
private static void FillDeleteByRootIdSql(DataTable table, List <string> sqls, TempIndex index)
{
foreach (var child in table.BuildtimeChilds)
{
if (!index.TryAdd(child))
{
continue; //已处理过
}
if (child.Type == DataTableType.AggregateRoot)
{
continue; //不删除引用的外部根表
}
FillDeleteByRootIdSql(child, sqls, index);
if (child.Middle != null)
{
FillDeleteByRootIdSql(child.Middle, sqls, index);
}
}
var selfSql = GetDeleteByRootIdSql(table);
if (!sqls.Contains(selfSql))
{
sqls.Add(selfSql);
}
}
//建立Ms2Scan的索引
new private TempIndex parseMS2(Spectrum spectrum, int index, int parentIndex)
{
TempIndex ms2 = new TempIndex();
ms2.level = 2;
ms2.pNum = parentIndex;
ms2.num = index;
try
{
float mz = (float)double.Parse(spectrum.precursors[0].isolationWindow
.cvParamChild(CVID.MS_isolation_window_target_m_z).value.ToString());
//兼容Agilent的DDA数据格式中可能出现的lower offset和upper offset为空的情况
string lowerOffsetStr = spectrum.precursors[0].isolationWindow
.cvParamChild(CVID.MS_isolation_window_lower_offset).value.ToString();
string upperOffsetStr = spectrum.precursors[0].isolationWindow
.cvParamChild(CVID.MS_isolation_window_upper_offset).value.ToString();
float lowerOffset = 0f;
if (!lowerOffsetStr.IsNullOrEmpty())
{
lowerOffset = (float)double.Parse(lowerOffsetStr);
}
float upperOffset = 0f;
if (!upperOffsetStr.IsNullOrEmpty())
{
upperOffset = (float)double.Parse(upperOffsetStr);
}
ms2.charge = getPrecursorCharge(spectrum);
ms2.mz = mz;
ms2.mzStart = mz - lowerOffset;
ms2.mzEnd = mz + upperOffset;
ms2.wid = lowerOffset + upperOffset;
}
catch (Exception e)
{
jobInfo.log("ERROR:SpectrumIndex:" + spectrum.index)
.log("ERROR:SpectrumId:" + spectrum.id)
.log("ERROR: mz:" + spectrum.precursors[0].isolationWindow
.cvParamChild(CVID.MS_isolation_window_target_m_z).value)
.log("ERROR: lowerOffset:" + spectrum.precursors[0].isolationWindow
.cvParamChild(CVID.MS_isolation_window_lower_offset).value)
.log("ERROR: upperOffset:" + spectrum.precursors[0].isolationWindow
.cvParamChild(CVID.MS_isolation_window_upper_offset).value);
throw e;
}
if (spectrum.scanList.scans.Count != 1)
{
return(ms2);
}
Scan scan = spectrum.scanList.scans[0];
if (jobInfo.jobParams.includeCV)
{
ms2.cvList = CV.trans(spectrum);
if (scan.cvParams != null)
{
ms2.cvList.AddRange(CV.trans(scan.cvParams));
}
}
ms2.rt = parseRT(scan);
ms2.tic = parseTIC(spectrum);
if (activator == null)
{
parseActivator(spectrum.precursors[0].activation);
}
return(ms2);
}
public void compressMS1(BlockIndex index)
{
int layers = (int)Math.Pow(2, converter.jobInfo.jobParams.digit); //计算堆叠层数
int iter = converter.ms1List.Count % layers == 0 ? (converter.ms1List.Count / layers) : (converter.ms1List.Count / layers + 1); //计算循环周期
if (converter.jobInfo.jobParams.threadAccelerate)
{
Hashtable table = Hashtable.Synchronized(new Hashtable());
//使用多线程处理数据提取与压缩
Parallel.For(0, iter, (i, ParallelLoopState) =>
{
converter.jobInfo.log(null, "MS1:" + i + "/" + iter);
List <float> rts = new List <float>();
List <int> nums = new List <int>();
List <long> tics = new List <long>();
List <List <CV> > cvs = new List <List <CV> >();
List <Spectrum> spectrumGroup = new List <Spectrum>();
for (int k = 0; k < layers; k++)
{
int realNum = i * layers + k;
if (realNum >= converter.ms1List.Count)
{
break;
}
TempIndex scanIndex = converter.ms1List[realNum];
rts.Add(scanIndex.rt);
nums.Add(scanIndex.num);
tics.Add(scanIndex.tic);
if (converter.jobInfo.jobParams.includeCV)
{
cvs.Add(scanIndex.cvList);
}
spectrumGroup.Add(converter.spectrumList.spectrum(scanIndex.num, true));
}
TempScanSZDPD ts = new TempScanSZDPD(nums, rts, tics);
if (converter.jobInfo.jobParams.includeCV)
{
ts.cvs = cvs;
}
converter.compress(spectrumGroup, ts);
table.Add(i, ts);
});
converter.outputWithOrder(table, index);
}
else
{
for (int i = 0; i < iter; i++)
{
converter.jobInfo.log(null, "MS1:" + i + "/" + iter);
List <float> rts = new List <float>();
List <int> nums = new List <int>();
List <long> tics = new List <long>();
List <List <CV> > cvs = new List <List <CV> >();
List <Spectrum> spectrumGroup = new List <Spectrum>();
for (int k = 0; k < layers; k++)
{
int realNum = i * layers + k;
if (realNum >= converter.ms1List.Count)
{
break;
}
TempIndex scanIndex = converter.ms1List[realNum];
rts.Add(scanIndex.rt);
nums.Add(scanIndex.num);
tics.Add(scanIndex.tic);
if (converter.jobInfo.jobParams.includeCV)
{
cvs.Add(scanIndex.cvList);
}
spectrumGroup.Add(converter.spectrumList.spectrum(scanIndex.num, true));
}
TempScanSZDPD ts = new TempScanSZDPD(nums, rts, tics);
if (converter.jobInfo.jobParams.includeCV)
{
ts.cvs = cvs;
}
converter.compress(spectrumGroup, ts);
converter.addToIndex(index, ts);
}
}
}
