static void MPU_InitData(MSData data)
{
byte i;
for (i = 0; i < 4; i++)
{
data.forLoopCounters[i] = 0xFFFF;
}
for (i = 0; i < NUM_CHANS; i++)
{
data.chanMaps[i] = i;
}
for (i = 0; i < data.controls.Length; i++)
{
data.controls[i].SetMembersTo(0xFF); //memset(data->controls, 0xFF, sizeof(data->controls));
}
Array.Fill <byte>(data.noteOnChans, 0xFF); //memset(data->noteOnChans, 0xFF, sizeof(data->noteOnChans));
data.delay = 0;
data.noteOnCount = 0;
data.globalVolume = 0x5A; /* 90% */
data.globalVolumeTarget = 0x5A; /* 90% */
data.tempoError = 0;
data.tempoPercent = 0x64; /* = 100 */
data.tempoTarget = 0x64; /* = 100 */
data.beatCount = 0;
data.measureCount = 0;
data.timeNumerator = 4;
data.timeFraction = 0x208D5; /* 133333 */
data.beatFraction = 0x208D5; /* 133333 */
data.timePerBeat = 0x7A1200; /* 8000000 */
}
/*
* XMIDI.ASM - reset_sequence
*/
static void MPU_ResetSequence(MSData data)
{
byte chan;
for (chan = 0; chan < NUM_CHANS; chan++)
{
if (data.controls[chan].sustain is not 0xFF and >= 64)
{
s_mpu_controls[chan].sustain = 0;
/* Sustain Off */
MPU_Send((byte)(0xB0 | chan), 64, 0);
}
if (data.controls[chan].chan_lock is not 0xFF and >= 64)
{
MPU_FlushChannel(chan);
MPU_ReleaseChannel(data.chanMaps[chan]); /* release_channel */
data.chanMaps[chan] = chan;
}
if (data.controls[chan].chan_protect is not 0xFF and >= 64)
{
s_mpu_lockStatus[chan] &= 0xBF;
}
if (data.controls[chan].voice_protect is not 0xFF and >= 64)
{
MPU_Send((byte)(0xB0 | chan), 112, 0); /* 112 = VOICE_PROTECT */
}
}
}
public SpectrumSource(string filepath)
{
MSDataList msdList = new MSDataList();
if (!File.Exists(filepath) && !Directory.Exists(filepath)) // Some mass spec "files" are really directory structures
{
throw new FileNotFoundException("Filepath not found: " + filepath, filepath);
}
ReaderList.FullReaderList.read(filepath, msdList, GetReaderConfig());
msDataFile = msdList[0];
//msDataFile = new MSDataFile(filepath);
sourceFilepath = filepath;
// create dummy spectrum/chromatogram list to simplify logic
msDataFile.run.spectrumList = msDataFile.run.spectrumList ?? new SpectrumListSimple();
msDataFile.run.chromatogramList = msDataFile.run.chromatogramList ?? new ChromatogramListSimple();
setInputFileWaitHandle = new EventWaitHandle(false, EventResetMode.ManualReset);
/*setInputFileDelegate = new ParameterizedThreadStart( startSetInputFile );
* Thread setInputFileThread = new Thread( setInputFileDelegate );
*
* setInputFileThread.Start( (object) filepath );*/
}
public SpectrumSource(string filepath)
{
MSDataList msdList = new MSDataList();
var readerConfig = new ReaderConfig
{
simAsSpectra = Program.SimAsSpectra,
srmAsSpectra = Program.SrmAsSpectra
};
ReaderList.FullReaderList.read(filepath, msdList, readerConfig);
msDataFile = msdList[0];
//msDataFile = new MSDataFile(filepath);
sourceFilepath = filepath;
// create dummy spectrum/chromatogram list to simplify logic
msDataFile.run.spectrumList = msDataFile.run.spectrumList ?? new SpectrumListSimple();
msDataFile.run.chromatogramList = msDataFile.run.chromatogramList ?? new ChromatogramListSimple();
setInputFileWaitHandle = new EventWaitHandle(false, EventResetMode.ManualReset);
/*setInputFileDelegate = new ParameterizedThreadStart( startSetInputFile );
* Thread setInputFileThread = new Thread( setInputFileDelegate );
*
* setInputFileThread.Start( (object) filepath );*/
}
public string outputFilename(string inputFilename, MSData inputMsData)
{
string runId = inputMsData.run.id;
// if necessary, adjust runId so it makes a suitable filename
if (String.IsNullOrEmpty(runId))
runId = Path.GetFileNameWithoutExtension(inputFilename) ?? string.Empty;
else
{
string tempExtension = (Path.GetExtension(runId) ?? string.Empty).ToLower();
if (tempExtension == ".mzml" ||
tempExtension == ".mzxml" ||
tempExtension == ".xml" ||
tempExtension == ".mgf" ||
tempExtension == ".ms2" ||
tempExtension == ".cms2")
runId = Path.GetFileNameWithoutExtension(runId) ?? string.Empty;
}
// this list is for Windows; it's a superset of the POSIX list
const string illegalFilename = "\\/*:?<>|\"";
foreach (var t in illegalFilename)
if (runId.Contains(t))
runId = runId.Replace(t, '_');
var newFilename = runId + Extension;
var fullPath = Path.Combine(OutputPath, newFilename);
return fullPath;
}
static void MPU_StopAllNotes(MSData data)
{
byte i;
for (i = 0; i < MAX_NOTES; i++)
{
byte note;
byte chan;
chan = data.noteOnChans[i];
if (chan == 0xFF)
{
continue;
}
data.noteOnChans[i] = 0xFF;
note = data.noteOnNotes[i];
chan = data.chanMaps[chan];
/* Note Off */
MPU_Send((byte)(0x80 | chan), note, 0);
}
data.noteOnCount = 0;
}
public SpectrumSource(string filepath)
{
MSDataList msdList = new MSDataList();
ReaderList.FullReaderList.read(filepath, msdList);
msDataFile = msdList[0];
//msDataFile = new MSDataFile(filepath);
sourceFilepath = filepath;
}
private static Task <DocumentWrapper <T> > PlatformReadAsync <T>(string documentId, string partition, ReadOptions readOptions)
{
var taskCompletionSource = new TaskCompletionSource <DocumentWrapper <T> >();
var msReadOptions = readOptions.ToMSReadOptions();
MSData.Read(documentId, new Class(typeof(MSDictionaryDocument)), partition, msReadOptions, resultDoc =>
{
ProcessResult(resultDoc, taskCompletionSource);
});
return(taskCompletionSource.Task);
}
private static Task <DocumentWrapper <T> > PlatformReplaceAsync <T>(string documentId, T document, string partition, WriteOptions writeOptions)
{
var taskCompletionSource = new TaskCompletionSource <DocumentWrapper <T> >();
var msWriteOptions = writeOptions.ToMSWriteOptions();
MSData.Replace(documentId, document.ToMSDocument(), partition, msWriteOptions, resultDoc =>
{
ProcessResult(resultDoc, taskCompletionSource);
});
return(taskCompletionSource.Task);
}
internal static ushort MPU_SetData(/*byte[]*/ Span <byte> file, ushort index, MSData msdata)
{
var data = msdata;
uint header;
uint size;
ushort i;
var pointer = 0;
if (file == null)
{
return(0xFFFF);
}
for (i = 0; i < 8; i++)
{
if (s_mpu_msdata[i] == null)
{
break;
}
}
if (i == 8)
{
return(0xFFFF);
}
file = MPU_FindSoundStart(file, index);
if (file == null)
{
return(0xFFFF);
}
s_mpu_msdata[i] = data;
data.EVNT = null;
header = Read_BE_UInt32(file.Slice(pointer));
size = 12;
while (header != SharpDune.MultiChar[FourCC.EVNT])
{
pointer += (int)size;
header = Read_BE_UInt32(file.Slice(pointer));
size = Read_BE_UInt32(file.Slice(pointer + 4)) + 8;
}
data.EVNT = file.Slice(pointer).ToArray();
data.playing = 0;
data.delayedClear = false;
s_mpu_msdataSize++;
MPU_InitData(data);
return(i);
}
static Data()
{
_remoteOperationDelegate.OnDataDidCompleteRemoteOperationAction = (operation, documentMetadata, error) =>
{
RemoteOperationCompleted?.Invoke(null, new RemoteOperationCompletedEventArgs
{
Operation = operation,
DocumentMetadata = documentMetadata.ToDocumentMetadata(),
Error = error?.ToDataException()
});
};
MSData.SetRemoteOperationDelegate(_remoteOperationDelegate);
}
protected void readVendorFile()
{
jobInfo.log("Prepare to Parse Vendor File", "Prepare");
msd = new MSDataFile(jobInfo.inputFilePath);
jobInfo.log("Adapting Vendor File API", "Adapting");
List <string> filter = new List <string>();
SpectrumListFactory.wrap(msd, filter); //这一步操作可以帮助加快Wiff文件的初始化速度
spectrumList = msd.run.spectrumList;
if (spectrumList == null || spectrumList.empty())
{
jobInfo.logError("No Spectrums Found");
}
else
{
jobInfo.log("Adapting Finished");
}
if (jobInfo.format.Equals("WIFF"))
{
FileInfo file1 = new FileInfo(jobInfo.inputFilePath);
if (file1.Exists)
{
fileSize += file1.Length;
}
FileInfo file2 = new FileInfo(jobInfo.inputFilePath + ".mtd");
if (file2.Exists)
{
fileSize += file2.Length;
}
FileInfo file3 = new FileInfo(jobInfo.inputFilePath + ".scan");
if (file3.Exists)
{
fileSize += file3.Length;
}
}
if (jobInfo.format.Equals("RAW"))
{
FileInfo file1 = new FileInfo(jobInfo.inputFilePath);
if (file1.Exists)
{
fileSize += file1.Length;
}
}
}
public void MzMLIndexedReadTest(string inputFileRelativePath, int expectedSpectra)
{
if (!TestPath.FindInputFile(inputFileRelativePath, out var sourceFile))
{
Console.WriteLine("File not found: " + inputFileRelativePath);
return;
}
var reader = new MzMLReader(Path.Combine(TestPath.ExtTestDataDirectory, sourceFile.FullName));
//mzMLType mzMLData = reader.Read();
var mzMLData = new MSData(reader.Read());
Console.WriteLine("Spectrum count: " + mzMLData.Run.SpectrumList.Spectra.Count);
Assert.AreEqual(expectedSpectra, mzMLData.Run.SpectrumList.Spectra.Count, "Spectrum count");
}
public SpectrumSource(string filepath)
{
MSDataList msdList = new MSDataList();
ReaderList.FullReaderList.read(filepath, msdList);
msDataFile = msdList[0];
//msDataFile = new MSDataFile(filepath);
sourceFilepath = filepath;
setInputFileWaitHandle = new EventWaitHandle(false, EventResetMode.ManualReset);
/*setInputFileDelegate = new ParameterizedThreadStart( startSetInputFile );
* Thread setInputFileThread = new Thread( setInputFileDelegate );
*
* setInputFileThread.Start( (object) filepath );*/
}
public string outputFilename(string inputFilename, MSData inputMsData)
{
string runId = inputMsData.run.id;
try
{
// if necessary, adjust runId so it makes a suitable filename
if (String.IsNullOrEmpty(runId))
{
runId = Path.GetFileNameWithoutExtension(inputFilename) ?? string.Empty;
}
else
{
string extension = (Path.GetExtension(runId) ?? string.Empty).ToLower();
if (extension == ".mzml" ||
extension == ".mzxml" ||
extension == ".xml" ||
extension == ".mgf" ||
extension == ".ms1" ||
extension == ".cms1" ||
extension == ".ms2" ||
extension == ".cms2" ||
extension == ".mz5")
{
runId = Path.GetFileNameWithoutExtension(runId) ?? string.Empty;
}
}
// this list is for Windows; it's a superset of the POSIX list
const string illegalFilename = "\\/*:?<>|\"";
foreach (var t in illegalFilename)
{
if (runId.Contains(t))
{
runId = runId.Replace(t, '_');
}
}
var newFilename = runId + Extension;
var fullPath = Path.Combine(OutputPath, newFilename);
return(fullPath);
}
catch (ArgumentException e)
{
throw new ArgumentException(String.Format("error generating output filename for input file '{0}' and output run id '{1}'", inputFilename, runId), e);
}
}
public void MzMLIndexedReadTest(string path, int expectedSpectra)
{
var sourceFile = new FileInfo(Path.Combine(TestPath.ExtTestDataDirectory, path));
if (!sourceFile.Exists)
{
Console.WriteLine("File not found: " + sourceFile.FullName);
return;
}
var reader = new MzMLReader(Path.Combine(TestPath.ExtTestDataDirectory, sourceFile.FullName));
//mzMLType mzMLData = reader.Read();
var mzMLData = new MSData(reader.Read());
Console.WriteLine("Spectrum count: " + mzMLData.Run.SpectrumList.Spectra.Count);
Assert.AreEqual(expectedSpectra, mzMLData.Run.SpectrumList.Spectra.Count, "Spectrum count");
}
private static Task <PaginatedDocuments <T> > PlatformListAsync <T>(string partition, ReadOptions readOptions)
{
var taskCompletionSource = new TaskCompletionSource <PaginatedDocuments <T> >();
MSData.List(new Class(typeof(MSDictionaryDocument)), partition, readOptions.ToMSReadOptions(), resultPages =>
{
if (resultPages.CurrentPage().Error == null)
{
taskCompletionSource.SetResult(resultPages.ToPaginatedDocuments <T>());
}
else
{
taskCompletionSource.SetException(resultPages.CurrentPage().Error.ToDataException());
}
});
return(taskCompletionSource.Task);
}
private static Task <DocumentWrapper <T> > PlatformCreateAsync <T>(string documentId, T document, string partition, WriteOptions writeOptions)
{
var taskCompletionSource = new TaskCompletionSource <DocumentWrapper <T> >();
var msWriteOptions = writeOptions.ToMSWriteOptions();
try
{
var msDictionaryDocument = document.ToMSDocument();
MSData.Create(documentId, msDictionaryDocument, partition, msWriteOptions, resultDoc =>
{
ProcessResult(resultDoc, taskCompletionSource);
});
}
catch (NSErrorException e)
{
taskCompletionSource.SetException(e);
}
return(taskCompletionSource.Task);
}
//-------------------------------------------
/// <summary>
/// Just a plain simple way to join peaks that are very close together.
/// This method is recomended to be used after deconvolution
/// </summary>
/// <param name="tolerance"></param>
public void ClusterMSIons(double tolerance)
{
MSData.Sort((a, b) => a.MZ.CompareTo(b.MZ));
bool needsToCluster = true;
int externalCounter = 0;
while (needsToCluster)
{
needsToCluster = false;
List <Ion> ionsToExclude = new List <Ion>(MSData.Count);
for (int i = externalCounter; i < MSData.Count; i++)
{
double upperbound = MSData[i].MZ + tolerance;
for (int k = i; k < MSData.Count; k++)
{
if (i == k)
{
continue;
}
if (MSData[k].MZ > upperbound)
{
break;
}
externalCounter = i;
if (MSData[k].MZ <= upperbound)
{
ionsToExclude.Add(MSData[k]);
}
}
}
if (ionsToExclude.Count > 0)
{
needsToCluster = true;
foreach (Ion i in ionsToExclude)
{
MSData.Remove(i);
}
}
}
}
public string outputFilename(string inputFilename, MSData inputMsData)
{
string runId = inputMsData.run.id;
// if necessary, adjust runId so it makes a suitable filename
if (String.IsNullOrEmpty(runId))
{
runId = Path.GetFileNameWithoutExtension(inputFilename) ?? string.Empty;
}
else
{
string tempExtension = (Path.GetExtension(runId) ?? string.Empty).ToLower();
if (tempExtension == ".mzml" ||
tempExtension == ".mzxml" ||
tempExtension == ".xml" ||
tempExtension == ".mgf" ||
tempExtension == ".ms2" ||
tempExtension == ".cms2")
{
runId = Path.GetFileNameWithoutExtension(runId) ?? string.Empty;
}
}
// this list is for Windows; it's a superset of the POSIX list
const string illegalFilename = "\\/*:?<>|\"";
foreach (var t in illegalFilename)
{
if (runId.Contains(t))
{
runId = runId.Replace(t, '_');
}
}
var newFilename = runId + Extension;
var fullPath = Path.Combine(OutputPath, newFilename);
return(fullPath);
}
public SpectrumSource(OpenDataSourceDialog.MSDataRunPath filepath)
{
if (!File.Exists(filepath.Filepath) && !Directory.Exists(filepath.Filepath)) // Some mass spec "files" are really directory structures
{
throw new FileNotFoundException("Filepath not found: " + filepath, filepath.Filepath);
}
MSDataFile = new MSData();
ReaderList.FullReaderList.read(filepath.Filepath, MSDataFile, filepath.RunIndex, GetReaderConfig());
sourceFilepath = filepath.ToString();
// create dummy spectrum/chromatogram list to simplify logic
MSDataFile.run.spectrumList = MSDataFile.run.spectrumList ?? new SpectrumListSimple();
MSDataFile.run.chromatogramList = MSDataFile.run.chromatogramList ?? new ChromatogramListSimple();
setInputFileWaitHandle = new EventWaitHandle(false, EventResetMode.ManualReset);
/*setInputFileDelegate = new ParameterizedThreadStart( startSetInputFile );
* Thread setInputFileThread = new Thread( setInputFileDelegate );
*
* setInputFileThread.Start( (object) filepath );*/
}
public void MzMLWriteTest(string inPath, string outFolderName, int expectedSpectra)
{
var sourceFile = new FileInfo(Path.Combine(TestPath.ExtTestDataDirectory, inPath));
if (!sourceFile.Exists)
{
Console.WriteLine("File not found: " + sourceFile.FullName);
return;
}
if (sourceFile.DirectoryName == null)
{
throw new DirectoryNotFoundException("Cannot determine the parent folder of " + sourceFile.FullName);
}
var outFolder = new DirectoryInfo(Path.Combine(sourceFile.DirectoryName, outFolderName));
if (!outFolder.Exists)
{
outFolder.Create();
}
var outFile = new FileInfo(Path.Combine(outFolder.FullName, sourceFile.Name));
var reader = new MzMLReader(Path.Combine(TestPath.ExtTestDataDirectory, inPath));
var mzMLData = new MSData(reader.Read());
Console.WriteLine("Array length: " + mzMLData.Run.SpectrumList.Spectra.Count);
Assert.AreEqual(expectedSpectra, mzMLData.Run.SpectrumList.Spectra.Count, "Array length");
var writer = new MzMLWriter(Path.Combine(TestPath.ExtTestDataDirectory, outFile.FullName))
{
MzMLType = MzMLSchemaType.MzML
};
writer.Write(new mzMLType(mzMLData));
}
private static Task <PaginatedDocuments <T> > PlatformListAsync <T>(string partition)
{
var taskCompletionSource = new TaskCompletionSource <PaginatedDocuments <T> >();
try
{
MSData.List(new Class(typeof(MSDictionaryDocument)), partition, resultPages =>
{
if (resultPages.CurrentPage().Error == null)
{
taskCompletionSource.SetResult(resultPages.ToPaginatedDocuments <T>());
}
else
{
taskCompletionSource.SetException(resultPages.CurrentPage().Error.ToDataException());
}
});
}
catch (JsonException e)
{
taskCompletionSource.SetException(new DataException("Failed to list data object(s)", e));
}
return(taskCompletionSource.Task);
}
public SpectrumSource( string filepath )
{
MSDataList msdList = new MSDataList();
var readerConfig = new ReaderConfig
{
simAsSpectra = Program.SimAsSpectra,
srmAsSpectra = Program.SrmAsSpectra
};
ReaderList.FullReaderList.read(filepath, msdList, readerConfig);
msDataFile = msdList[0];
//msDataFile = new MSDataFile(filepath);
sourceFilepath = filepath;
// create dummy spectrum/chromatogram list to simplify logic
msDataFile.run.spectrumList = msDataFile.run.spectrumList ?? new SpectrumListSimple();
msDataFile.run.chromatogramList = msDataFile.run.chromatogramList ?? new ChromatogramListSimple();
setInputFileWaitHandle = new EventWaitHandle( false, EventResetMode.ManualReset );
/*setInputFileDelegate = new ParameterizedThreadStart( startSetInputFile );
Thread setInputFileThread = new Thread( setInputFileDelegate );
setInputFileThread.Start( (object) filepath );*/
}
internal MSDataInternalTypeAbstract()
{
_msData = new MSData(false);
}
public MsDataFileImpl(string path, int sampleIndex = 0, LockMassParameters lockmassParameters = null, bool simAsSpectra = false, bool srmAsSpectra = false, bool acceptZeroLengthSpectra = true, bool requireVendorCentroidedMS1 = false, bool requireVendorCentroidedMS2 = false)
{
// see note above on enabling performance measurement
_perf = PerfUtilFactory.CreatePerfUtil("MsDataFileImpl " + // Not L10N
string.Format("{0},sampleIndex:{1},lockmassCorrection:{2},simAsSpectra:{3},srmAsSpectra:{4},acceptZeroLengthSpectra:{5},requireVendorCentroidedMS1:{6},requireVendorCentroidedMS2:{7}", // Not L10N
path, sampleIndex, !(lockmassParameters == null || lockmassParameters.IsEmpty), simAsSpectra, srmAsSpectra, acceptZeroLengthSpectra, requireVendorCentroidedMS1, requireVendorCentroidedMS2));
using (_perf.CreateTimer("open")) // Not L10N
{
FilePath = path;
_msDataFile = new MSData();
_config = new ReaderConfig {simAsSpectra = simAsSpectra, srmAsSpectra = srmAsSpectra, acceptZeroLengthSpectra = acceptZeroLengthSpectra};
_lockmassParameters = lockmassParameters;
FULL_READER_LIST.read(path, _msDataFile, sampleIndex, _config);
_requireVendorCentroidedMS1 = requireVendorCentroidedMS1;
_requireVendorCentroidedMS2 = requireVendorCentroidedMS2;
}
}
public void Open(string fileName, int sampleIndex)
{
if (_currentSampleIndex != sampleIndex || _currentFileName != fileName)
{
MSDataList msdList = new MSDataList();
ReaderList.FullReaderList.read(fileName, msdList);
_dataFile = msdList[0];
_run = _dataFile.run;
_currentFileName = fileName;
_currentSampleIndex = sampleIndex;
spectrumCache = new SpectrumCache();
ticGenerator = new TicGenerator(_run, spectrumCache);
xicGenerator = new XicGenerator(_run, spectrumCache);
spectrumExtractor = new SpectrumExtractor(_run, spectrumCache);
averagedSpectrumExtractor = new AveragedSpectrumExtractor(_run, spectrumCache);
}
}
public void populateFromMSData( MSData msInfo )
{
hasDetails = true;
spectra = msInfo.run.spectrumList == null ? 0 : msInfo.run.spectrumList.size();
ionSource = analyzer = detector = "";
foreach( InstrumentConfiguration ic in msInfo.instrumentConfigurationList )
{
SortedDictionary<int, string> ionSources = new SortedDictionary<int, string>();
SortedDictionary<int, string> analyzers = new SortedDictionary<int, string>();
SortedDictionary<int, string> detectors = new SortedDictionary<int, string>();
foreach( pwiz.CLI.msdata.Component c in ic.componentList )
{
CVParam term;
switch( c.type )
{
case ComponentType.ComponentType_Source:
term = c.cvParamChild( CVID.MS_ionization_type );
if( !term.empty() )
ionSources.Add( c.order, term.name );
break;
case ComponentType.ComponentType_Analyzer:
term = c.cvParamChild( CVID.MS_mass_analyzer_type );
if( !term.empty() )
analyzers.Add( c.order, term.name );
break;
case ComponentType.ComponentType_Detector:
term = c.cvParamChild( CVID.MS_detector_type );
if( !term.empty() )
detectors.Add( c.order, term.name );
break;
}
}
if( ionSource.Length > 0 )
ionSource += ", ";
ionSource += String.Join( "/", new List<string>( ionSources.Values ).ToArray() );
if( analyzer.Length > 0 )
analyzer += ", ";
analyzer += String.Join( "/", new List<string>( analyzers.Values ).ToArray() );
if( detector.Length > 0 )
detector += ", ";
detector += String.Join( "/", new List<string>( detectors.Values ).ToArray() );
}
System.Collections.Generic.Set<string> contentTypes = new System.Collections.Generic.Set<string>();
CVParamList cvParams = msInfo.fileDescription.fileContent.cvParams;
if( cvParams.Count > 0 )
{
foreach( CVParam term in msInfo.fileDescription.fileContent.cvParams )
contentTypes.Add( term.name );
contentType = String.Join( ", ", new List<string>( contentTypes.Keys ).ToArray() );
}
}
private void listView_ItemSelectionChanged(object sender, ListViewItemSelectionChangedEventArgs e)
{
if (listView.SelectedItems.Count > 1)
{
List <string> dataSourceList = new List <string>();
foreach (ListViewItem item in listView.SelectedItems)
{
if (item.SubItems[1].Text != "File Folder")
{
dataSourceList.Add(String.Format("\"{0}\"", item.SubItems[0].Text));
}
}
sourcePathTextBox.Text = String.Join(" ", dataSourceList.ToArray());
ticGraphControl.GraphPane.GraphObjList.Clear();
ticGraphControl.GraphPane.CurveList.Clear();
ticGraphControl.Visible = false;
}
else if (listView.SelectedItems.Count > 0)
{
sourcePathTextBox.Text = listView.SelectedItems[0].SubItems[0].Text;
ticGraphControl.GraphPane.GraphObjList.Clear();
ticGraphControl.GraphPane.CurveList.Clear();
string sourcePath = Path.Combine(CurrentDirectory, sourcePathTextBox.Text);
string sourceType = getSourceType(sourcePath);
if (!String.IsNullOrEmpty(sourceType) &&
sourceType != "File Folder")
{
using (MSData msd = new MSData())
{
ReaderList.FullReaderList.read(sourcePath, msd, 0, SpectrumSource.GetReaderConfig());
using (ChromatogramList cl = msd.run.chromatogramList)
{
if (cl != null && !cl.empty() && cl.find("TIC") != cl.size())
{
ticGraphControl.Visible = true;
pwiz.CLI.msdata.Chromatogram tic = cl.chromatogram(cl.find("TIC"), true);
Map <double, double> sortedFullPointList = new Map <double, double>();
IList <double> timeList = tic.binaryDataArrays[0].data;
IList <double> intensityList = tic.binaryDataArrays[1].data;
int arrayLength = timeList.Count;
for (int i = 0; i < arrayLength; ++i)
{
sortedFullPointList[timeList[i]] = intensityList[i];
}
ZedGraph.PointPairList points = new ZedGraph.PointPairList(
new List <double>(sortedFullPointList.Keys).ToArray(),
new List <double>(sortedFullPointList.Values).ToArray());
ZedGraph.LineItem item = ticGraphControl.GraphPane.AddCurve("TIC", points, Color.Black, ZedGraph.SymbolType.None);
item.Line.IsAntiAlias = true;
ticGraphControl.AxisChange();
ticGraphControl.Refresh();
}
else
{
ticGraphControl.Visible = false;
}
}
}
}
else
{
ticGraphControl.Visible = false;
}
}
else
{
sourcePathTextBox.Text = "";
}
}
internal MSDataInternalTypeAbstract(MSData instance)
{
MsData = instance;
}
public void Dispose()
{
if (_dataFile != null)
{
_dataFile.Dispose();
_dataFile = null;
GC.SuppressFinalize(this);
}
}
public override void DataDidCompleteRemoteOperation(MSData data, string operation, MSDocumentMetadata documentMetadata, MSDataError error)
{
OnDataDidCompleteRemoteOperationAction.Invoke(operation, documentMetadata, error);
}
private static Task <bool> PlatformIsEnabledAsync()
{
return(Task.FromResult(MSData.IsEnabled()));
}
public SpectrumSource( string filepath )
{
MSDataList msdList = new MSDataList();
ReaderList.FullReaderList.read( filepath, msdList );
msDataFile = msdList[0];
//msDataFile = new MSDataFile(filepath);
sourceFilepath = filepath;
setInputFileWaitHandle = new EventWaitHandle( false, EventResetMode.ManualReset );
/*setInputFileDelegate = new ParameterizedThreadStart( startSetInputFile );
Thread setInputFileThread = new Thread( setInputFileDelegate );
setInputFileThread.Start( (object) filepath );*/
}
private static Task PlatformSetEnabledAsync(bool enabled)
{
MSData.SetEnabled(enabled);
return(Task.CompletedTask);
}
private static void PlatformSetTokenExchangeUrl(string tokenExchangeUrl)
{
MSData.SetTokenExchangeUrl(tokenExchangeUrl);
}
public void populateFromMSData(MSData msInfo)
{
hasDetails = true;
spectra = msInfo.run.spectrumList == null ? 0 : msInfo.run.spectrumList.size();
ionSource = analyzer = detector = "";
foreach (InstrumentConfiguration ic in msInfo.instrumentConfigurationList)
{
SortedDictionary <int, string> ionSources = new SortedDictionary <int, string>();
SortedDictionary <int, string> analyzers = new SortedDictionary <int, string>();
SortedDictionary <int, string> detectors = new SortedDictionary <int, string>();
foreach (pwiz.CLI.msdata.Component c in ic.componentList)
{
CVParam term;
switch (c.type)
{
case ComponentType.ComponentType_Source:
term = c.cvParamChild(CVID.MS_ionization_type);
if (!term.empty())
{
ionSources.Add(c.order, term.name);
}
break;
case ComponentType.ComponentType_Analyzer:
term = c.cvParamChild(CVID.MS_mass_analyzer_type);
if (!term.empty())
{
analyzers.Add(c.order, term.name);
}
break;
case ComponentType.ComponentType_Detector:
term = c.cvParamChild(CVID.MS_detector_type);
if (!term.empty())
{
detectors.Add(c.order, term.name);
}
break;
}
}
if (ionSource.Length > 0)
{
ionSource += ", ";
}
ionSource += String.Join("/", new List <string>(ionSources.Values).ToArray());
if (analyzer.Length > 0)
{
analyzer += ", ";
}
analyzer += String.Join("/", new List <string>(analyzers.Values).ToArray());
if (detector.Length > 0)
{
detector += ", ";
}
detector += String.Join("/", new List <string>(detectors.Values).ToArray());
}
System.Collections.Generic.Set <string> contentTypes = new System.Collections.Generic.Set <string>();
CVParamList cvParams = msInfo.fileDescription.fileContent.cvParams;
if (cvParams.Count > 0)
{
foreach (CVParam term in msInfo.fileDescription.fileContent.cvParams)
{
contentTypes.Add(term.name);
}
contentType = String.Join(", ", new List <string>(contentTypes.Keys).ToArray());
}
}
public void Dispose()
{
if (_spectrumList != null)
_spectrumList.Dispose();
_spectrumList = null;
if (_chromatogramList != null)
_chromatogramList.Dispose();
_chromatogramList = null;
if (_msDataFile != null)
_msDataFile.Dispose();
_msDataFile = null;
}
