/**
* 循环搜索,直到出现第一个重复的MS窗口停止
* 即便这样,如果在第一轮扫描中没有出现的窗口是无法被初始化的,需要在后续不断的作补充
*
*/
private void buildWindowsRanges()
{
jobInfo.log("Start getting windows", "Getting Windows");
int i = 0;
Spectrum spectrum = spectrumList.spectrum(0);
while (spectrum.cvParamChild(CVID.MS_ms_level).value.ToString().Equals(MsLevel.MS2))
{
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);
if (rangeMap.Contains(mz))
{
break;
}
WindowRange range = new WindowRange(mz - lowerOffset, mz + upperOffset, mz);
BlockIndex swathIndex = new BlockIndex();
swathIndex.setWindowRange(range);
rangeMap.Add(mz, swathIndex);
ms2Map.Add(mz, ArrayList.Synchronized(new ArrayList()));
i++;
spectrum = spectrumList.spectrum(i);
}
jobInfo.log("Finished Getting Windows");
}
private void parseAndStoreMS2Block()
{
jobInfo.log("Start Processing MS2 List");
IZDPD izdpd;
if (jobInfo.jobParams.useStackZDPD())
{
izdpd = new StackZDPD(this);
}
else
{
izdpd = new ZDPD(this);
}
foreach (double key in ms2Table.Keys)
{
List <TempIndex> tempIndexList = ms2Table[key] as List <TempIndex>;
WindowRange range = rangeTable[key] as WindowRange;
//为每一个key组创建一个SwathBlock
BlockIndex index = new BlockIndex();
index.level = 2;
index.startPtr = startPosition;
index.setWindowRange(range);
jobInfo.log(null, "MS2:" + progress + "/" + ms2Table.Keys.Count);
progress++;
izdpd.compressMS2(tempIndexList, index);
index.endPtr = startPosition;
indexList.Add(index);
jobInfo.log("MS2 Group Finished:" + progress + "/" + ms2Table.Keys.Count);
}
}
//计算窗口间的重叠区域的大小
private void computeOverlap()
{
WindowRange range1 = ranges[0];
double range1Right = range1.end;
WindowRange range2 = ranges[1];
double range2Left = range2.start;
overlap = range1Right - range2Left;
featuresMap.Add(Features.overlap, overlap);
}
//提取SWATH 窗口信息
private void buildWindowsRanges()
{
jobInfo.log("Start getting windows", "Getting Windows");
int i = 0;
List <Double> mzList = new List <Double>();
//找到第一张MS1图,如果找不到,则继续往下搜索,如果搜索了500张以上的谱图或者搜索了超过一半的谱图都没有MS1图,则认为数据格式有问题
Spectrum spectrum = spectrumList.spectrum(0);
while (!spectrum.cvParamChild(CVID.MS_ms_level).value.ToString().Equals(MsLevel.MS1))
{
i++;
spectrum = spectrumList.spectrum(i);
if (i > spectrumList.size() / 2 || i > 500)
{
//如果找了一半的spectrum或者找了超过500个spectrum仍然没有找到ms1,那么数据格式有问题,返回空;
jobInfo.logError("Search for more than 500 spectrums and no ms1 was found. File Format Error");
throw new Exception("Search for more than 500 spectrums and no ms1 was found. File Format Error");
}
}
while (true)
{
if (spectrum.cvParamChild(CVID.MS_ms_level).value.ToString().Equals(MsLevel.MS1))
{
ms1Size++;
i++;
spectrum = spectrumList.spectrum(i);
continue;
}
double mz, lowerOffset, upperOffset;
mz = getPrecursorIsolationWindowParams(spectrum, CVID.MS_isolation_window_target_m_z);
if (mzList.Contains(mz))
{
break;
}
mzList.Add(mz);
lowerOffset = getPrecursorIsolationWindowParams(spectrum, CVID.MS_isolation_window_lower_offset);
upperOffset = getPrecursorIsolationWindowParams(spectrum, CVID.MS_isolation_window_upper_offset);
WindowRange range = new WindowRange(mz - lowerOffset, mz + upperOffset, mz);
Hashtable features = new Hashtable();
features.Add(Features.original_width, lowerOffset + upperOffset);
features.Add(Features.original_precursor_mz_start, mz - lowerOffset);
features.Add(Features.original_precursor_mz_end, mz + upperOffset);
range.features = FeaturesUtil.toString(features);
ranges.Add(range);
i++;
spectrum = spectrumList.spectrum(i);
}
jobInfo.log("Finished Getting Windows");
}
//处理MS2,由于每一个MS1只跟随少量的MS2光谱图,因此DDA采集模式下MS2的压缩模式仍然使用Aird ZDPD的压缩算法
private void doWithMS2Block()
{
jobInfo.log("Start Processing MS2 List");
ArrayList keys = new ArrayList(ms2Table.Keys);
keys.Sort();
foreach (int key in keys)
{
List <TempIndex> tempIndexList = ms2Table[key] as List <TempIndex>;
//为每一组key创建一个Block
BlockIndex blockIndex = new BlockIndex();
blockIndex.level = 2;
blockIndex.startPtr = startPosition;
blockIndex.num = key;
//创建这一个block中每一个ms2的窗口序列
List <WindowRange> ms2Ranges = new List <WindowRange>();
jobInfo.log(null, "MS2:" + progress + "/" + ms2Table.Keys.Count);
progress++;
foreach (TempIndex index in tempIndexList)
{
WindowRange range = new WindowRange(index.mzStart, index.mzEnd, index.mz);
if (index.charge != 0)
{
range.charge = index.charge;
}
ms2Ranges.Add(range);
TempScan ts = new TempScan(index.num, index.rt, index.tic);
if (jobInfo.jobParams.includeCV)
{
ts.cvs = index.cvList;
}
compress(spectrumList.spectrum(index.num, true), ts);
blockIndex.nums.Add(ts.num);
blockIndex.rts.Add(ts.rt);
blockIndex.tics.Add(ts.tic);
if (jobInfo.jobParams.includeCV)
{
blockIndex.cvList.Add(ts.cvs);
}
blockIndex.mzs.Add(ts.mzArrayBytes.Length);
blockIndex.ints.Add(ts.intArrayBytes.Length);
startPosition = startPosition + ts.mzArrayBytes.Length + ts.intArrayBytes.Length;
airdStream.Write(ts.mzArrayBytes, 0, ts.mzArrayBytes.Length);
airdStream.Write(ts.intArrayBytes, 0, ts.intArrayBytes.Length);
}
blockIndex.rangeList = ms2Ranges;
blockIndex.endPtr = startPosition;
indexList.Add(blockIndex);
}
}
private void scan(int i)
{
Spectrum spectrum = spectrumList.spectrum(i, true);
//忽略所有MS1的谱图
if (spectrum.cvParamChild(CVID.MS_ms_level).value.ToString().Equals(MsLevel.MS1))
{
return;
}
double targetMz = getPrecursorIsolationWindowParams(spectrum, CVID.MS_isolation_window_target_m_z);
ArrayList ms2List = null;
if (rangeMap.Contains(targetMz))
{
ms2List = (ArrayList)ms2Map[targetMz];
}
else
{
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);
WindowRange range = new WindowRange(mz - lowerOffset, mz + upperOffset, mz);
BlockIndex addIndex = new BlockIndex();
addIndex.setWindowRange(range);
rangeMap.Add(targetMz, addIndex);
ms2Map.Add(targetMz, ArrayList.Synchronized(new ArrayList()));
ms2List = (ArrayList)ms2Map[targetMz];
}
if (spectrum.scanList.scans.Count != 1)
{
return;
}
try
{
TempScan ts = new TempScan(i, parseRT(spectrum.scanList.scans[0]), parseTIC(spectrum));
if (jobInfo.jobParams.includeCV)
{
ts.cvs = CV.trans(spectrum);
}
compress(spectrum, ts);
ms2List.Add(ts);
}
catch (Exception exception)
{
jobInfo.log(exception.Message);
return;
}
}
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);
}
}
