public static void GetLibIrtProviders(Library lib, IrtStandard standard, IProgressMonitor monitor,
out IRetentionTimeProvider[] irtProviders, out List <IrtStandard> autoStandards, out DbIrtPeptide[] cirtPeptides)
{
monitor?.UpdateProgress(new ProgressStatus().ChangePercentComplete(-1));
irtProviders = lib.RetentionTimeProvidersIrt.ToArray();
if (!irtProviders.Any())
{
irtProviders = lib.RetentionTimeProviders.ToArray();
}
var isAuto = ReferenceEquals(standard, IrtStandard.AUTO);
autoStandards = isAuto
? IrtStandard.BestMatch(irtProviders.SelectMany(provider => provider.PeptideRetentionTimes).Select(rt => rt.PeptideSequence))
: null;
if (ReferenceEquals(standard, IrtStandard.CIRT_SHORT) || isAuto && autoStandards.Count == 0)
{
var libPeptides = new TargetMap <bool>(irtProviders
.SelectMany(provider => provider.PeptideRetentionTimes)
.Select(rt => new KeyValuePair <Target, bool>(rt.PeptideSequence, true)));
cirtPeptides = IrtStandard.CIRT.Peptides.Where(pep => libPeptides.ContainsKey(pep.ModifiedTarget)).ToArray();
}
else
{
cirtPeptides = new DbIrtPeptide[0];
}
}
/// <summary>
/// Creates bitmaps for the texture
/// </summary>
private static Bitmap[] CreateTextureBitmaps( IProgressMonitor progressMonitor, ISpherePlanet planet )
{
Bitmap[] faceBitmaps = new Bitmap[ 6 ];
int width = 256;
int height = 256;
progressMonitor.UpdateProgress( 0 );
ISpherePlanetTerrainRenderer renderer = planet.Renderer.GetRenderer<ISpherePlanetTerrainRenderer>( );
if ( renderer == null )
{
throw new InvalidOperationException( "Expected a valid ISpherePlanetTerrainRenderer to be available" );
}
faceBitmaps[ ( int )CubeMapFace.PositiveX ] = renderer.CreateMarbleTextureFace( CubeMapFace.PositiveX, width, height ); progressMonitor.UpdateProgress( 1 / 6.0f );
faceBitmaps[ ( int )CubeMapFace.NegativeX ] = renderer.CreateMarbleTextureFace( CubeMapFace.NegativeX, width, height ); progressMonitor.UpdateProgress( 2 / 6.0f );
faceBitmaps[ ( int )CubeMapFace.PositiveY ] = renderer.CreateMarbleTextureFace( CubeMapFace.PositiveY, width, height ); progressMonitor.UpdateProgress( 3 / 6.0f );
faceBitmaps[ ( int )CubeMapFace.NegativeY ] = renderer.CreateMarbleTextureFace( CubeMapFace.NegativeY, width, height ); progressMonitor.UpdateProgress( 4 / 6.0f );
faceBitmaps[ ( int )CubeMapFace.PositiveZ ] = renderer.CreateMarbleTextureFace( CubeMapFace.PositiveZ, width, height ); progressMonitor.UpdateProgress( 5 / 6.0f );
faceBitmaps[ ( int )CubeMapFace.NegativeZ ] = renderer.CreateMarbleTextureFace( CubeMapFace.NegativeZ, width, height );
progressMonitor.UpdateProgress( 1 );
foreach ( object cubeMapFace in Enum.GetValues( typeof( CubeMapFace ) ) )
{
faceBitmaps[ ( int )cubeMapFace ].Save( "PlanetCubeMap" + cubeMapFace + ".png" );
}
return faceBitmaps;
}
private OptimizationDb Load(IProgressMonitor loadMonitor, ProgressStatus status)
{
var result = ChangeProp(ImClone(this), im => im.LoadOptimizations(im.GetOptimizations()));
// Not really possible to show progress, unless we switch to raw reading
if (loadMonitor != null)
{
loadMonitor.UpdateProgress(status.ChangePercentComplete(100));
}
return(result);
}
public bool Export(CancellationToken cancellationToken, IProgressMonitor progressMonitor, ref IProgressStatus status, ViewInfo viewInfo, TextWriter writer, DsvWriter dsvWriter)
{
progressMonitor = progressMonitor ?? new SilentProgressMonitor();
using (var bindingListSource = new BindingListSource(cancellationToken))
{
bindingListSource.SetViewContext(this, viewInfo);
progressMonitor.UpdateProgress(status = status.ChangePercentComplete(5)
.ChangeMessage(Resources.ExportReportDlg_ExportReport_Writing_report));
WriteDataWithStatus(progressMonitor, ref status, writer, bindingListSource, dsvWriter);
if (progressMonitor.IsCanceled)
{
return(false);
}
writer.Flush();
progressMonitor.UpdateProgress(status = status.Complete());
}
return(true);
}
private IrtDb Load(IProgressMonitor loadMonitor, ProgressStatus status, out IList <DbIrtPeptide> dbPeptides)
{
var rawPeptides = dbPeptides = GetPeptides();
var result = ChangeProp(ImClone(this), im => im.LoadPeptides(rawPeptides));
// Not really possible to show progress, unless we switch to raw reading
if (loadMonitor != null)
{
loadMonitor.UpdateProgress(status.ChangePercentComplete(100));
}
return(result);
}
private bool UpdateProgressAndCheckForCancellation(IProgressMonitor progressMonitor, ref IProgressStatus status, string message, int pctComplete)
{
if (progressMonitor.IsCanceled)
{
return(false);
}
if (pctComplete != status.PercentComplete)
{
progressMonitor.UpdateProgress(status = status.ChangeMessage(message).ChangePercentComplete(pctComplete));
}
return(true);
}
public void Extract(IProgressMonitor progressMonitor)
{
ProgressMonitor = progressMonitor;
ProgressMonitor.UpdateProgress(_progressStatus = new ProgressStatus(DefaultMessage));
var extractDir = ExtractDir(SharedPath);
using (ZipFile zip = ZipFile.Read(SharedPath))
{
CountEntries = zip.Entries.Count;
ExpectedSize = zip.Entries.Select(entry => entry.UncompressedSize).Sum();
zip.ExtractProgress += SrmDocumentSharing_ExtractProgress;
string documentName = FindSharedSkylineFile(zip);
string parentDir = Path.GetDirectoryName(SharedPath);
if (!string.IsNullOrEmpty(parentDir))
{
extractDir = Path.Combine(parentDir, extractDir);
}
extractDir = GetNonExistentDir(extractDir);
DocumentPath = Path.Combine(extractDir, documentName);
foreach (var entry in zip.Entries)
{
if (ProgressMonitor.IsCanceled)
{
break;
}
try
{
entry.Extract(extractDir);
ExtractedSize += entry.UncompressedSize;
}
catch (Exception)
{
if (!ProgressMonitor.IsCanceled)
{
throw;
}
}
}
}
if (ProgressMonitor.IsCanceled)
{
DirectoryEx.SafeDelete(extractDir);
}
}
public void webClient_UploadProgressChanged(object sender, UploadProgressChangedEventArgs e)
{
var message = string.Format(FileSize.FormatProvider,
Resources.WebPanoramaPublishClient_webClient_UploadProgressChanged_Uploaded__0_fs__of__1_fs_,
e.BytesSent, e.TotalBytesToSend);
_progressStatus = _progressStatus.ChangeMessage(message).ChangePercentComplete(e.ProgressPercentage);
_progressMonitor.UpdateProgress(_progressStatus);
if (_progressMonitor.IsCanceled)
{
_webClient.CancelAsync();
}
}
private void Download(SkypFile skyp, IProgressMonitor progressMonitor, FormEx parentWindow = null)
{
var progressStatus =
new ProgressStatus(string.Format(Resources.SkypSupport_Download_Downloading__0_, skyp.SkylineDocUri));
progressMonitor.UpdateProgress(progressStatus);
if (DownloadClient == null)
{
DownloadClient = new WebDownloadClient(progressMonitor, progressStatus);
}
DownloadClient.Download(skyp.SkylineDocUri, skyp.DownloadPath, skyp.Server?.Username, skyp.Server?.Password);
if (progressMonitor.IsCanceled || DownloadClient.IsError)
{
FileEx.SafeDelete(skyp.DownloadPath, true);
}
if (DownloadClient.IsError)
{
var message =
string.Format(
Resources
.SkypSupport_Download_There_was_an_error_downloading_the_Skyline_document_specified_in_the_skyp_file___0__,
skyp.SkylineDocUri);
if (DownloadClient.Error != null)
{
var exceptionMsg = DownloadClient.Error.Message;
message = TextUtil.LineSeparate(message, exceptionMsg);
if (exceptionMsg.Contains(ERROR401))
{
message = TextUtil.LineSeparate(message,
string.Format(
Resources
.SkypSupport_Download_You_may_have_to_add__0__as_a_Panorama_server_from_the_Tools___Options_menu_in_Skyline_,
skyp.SkylineDocUri.Host));
}
else if (exceptionMsg.Contains(ERROR403))
{
message = TextUtil.LineSeparate(message,
string.Format(
Resources.SkypSupport_Download_You_do_not_have_permissions_to_download_this_file_from__0__,
skyp.SkylineDocUri.Host));
}
}
throw new Exception(message, DownloadClient.Error);
}
}
private void RunExecutable(SrmDocument document, IToolMacroProvider toolMacroProvider, TextWriter textWriter, IProgressMonitor progressMonitor, Control parent)
{
ActionUtil.RunAsync(() =>
{
try
{
RunExecutableBackground(document, toolMacroProvider, textWriter, progressMonitor, parent);
}
catch (Exception e)
{
progressMonitor.UpdateProgress(new ProgressStatus(string.Empty).ChangeErrorException(e));
}
}, @"Run Executable");
}
private void PostToLink(string url, SrmDocument doc, IProgressMonitor progressMonitor, IWebHelpers webHelpers)
{
ActionUtil.RunAsync(() =>
{
try
{
PostToLinkBackground(url, doc, progressMonitor, webHelpers);
}
catch (Exception exception)
{
progressMonitor.UpdateProgress(new ProgressStatus(string.Empty).ChangeErrorException(exception));
}
}, @"Post To Link");
}
public static ProcessedIrtAverages ProcessRetentionTimes(IProgressMonitor monitor,
IEnumerable <IRetentionTimeProvider> providers, int countProviders,
DbIrtPeptide[] standardPeptideList, DbIrtPeptide[] items)
{
IProgressStatus status = new ProgressStatus(Resources.LibraryGridViewDriver_ProcessRetentionTimes_Adding_retention_times);
var dictProviderData = new List <KeyValuePair <string, RetentionTimeProviderData> >();
var dictPeptideAverages = new Dictionary <Target, IrtPeptideAverages>();
var runCount = 0;
foreach (var retentionTimeProvider in providers)
{
if (monitor.IsCanceled)
{
return(null);
}
var message = string.Format(Resources.LibraryGridViewDriver_ProcessRetentionTimes_Converting_retention_times_from__0__, retentionTimeProvider.Name);
monitor.UpdateProgress(status = status.ChangeMessage(message));
runCount++;
var data = new RetentionTimeProviderData(retentionTimeProvider, standardPeptideList.OrderBy(peptide => peptide.Irt));
if (data.RegressionSuccess || data.CalcRegressionWith(retentionTimeProvider, standardPeptideList, items))
{
// Trace.WriteLine(string.Format("slope = {0}, intercept = {1}", data.RegressionRefined.Slope, data.RegressionRefined.Intercept));
AddRetentionTimesToDict(retentionTimeProvider, data.RegressionRefined, dictPeptideAverages, standardPeptideList);
}
dictProviderData.Add(new KeyValuePair <string, RetentionTimeProviderData>(retentionTimeProvider.Name, data));
monitor.UpdateProgress(status = status.ChangePercentComplete(runCount * 100 / countProviders));
}
monitor.UpdateProgress(status.Complete());
return(new ProcessedIrtAverages(dictPeptideAverages, dictProviderData));
}
public static SrmDocument UpdateAnnotations(SrmDocument document, IProgressMonitor progressMonitor, IProgressStatus status)
{
if (document.Settings.DataSettings.AnnotationDefs.All(def => def.Expression == null))
{
return(document);
}
if (progressMonitor != null)
{
progressMonitor.UpdateProgress(status.ChangeMessage(Resources.DocumentAnnotationUpdater_UpdateAnnotations_Updating_calculated_annotations));
}
DocumentAnnotationUpdater updater = new DocumentAnnotationUpdater(document, progressMonitor);
return(updater.UpdateDocument(document));
}
public static void CreateIrtDb(string path, ProcessedIrtAverages processed, DbIrtPeptide[] standardPeptides, bool recalibrate, IrtRegressionType regressionType, IProgressMonitor monitor)
{
DbIrtPeptide[] newStandards = null;
if (recalibrate)
{
monitor.UpdateProgress(new ProgressStatus().ChangeSegments(0, 2));
newStandards = processed.RecalibrateStandards(standardPeptides).ToArray();
processed = RCalcIrt.ProcessRetentionTimes(monitor,
processed.ProviderData.Select(data => data.RetentionTimeProvider).ToArray(),
newStandards.ToArray(), new DbIrtPeptide[0], regressionType);
}
var irtDb = IrtDb.CreateIrtDb(path);
irtDb.AddPeptides(monitor, (newStandards ?? standardPeptides).Concat(processed.DbIrtPeptides).ToList());
}
private void PostToLink(string url, SrmDocument doc, IProgressMonitor progressMonitor, IWebHelpers webHelpers)
{
var thread = new Thread(() =>
{
try
{
PostToLinkBackground(url, doc, progressMonitor, webHelpers);
}
catch (Exception exception)
{
progressMonitor.UpdateProgress(new ProgressStatus(string.Empty).ChangeErrorException(exception));
}
});
thread.Start();
}
private void RunExecutable(SrmDocument document, IToolMacroProvider toolMacroProvider, TextWriter textWriter, IProgressMonitor progressMonitor, Control parent)
{
var thread = new Thread(() =>
{
try
{
RunExecutableBackground(document, toolMacroProvider, textWriter, progressMonitor, parent);
}
catch (Exception e)
{
progressMonitor.UpdateProgress(new ProgressStatus(string.Empty).ChangeErrorException(e));
}
});
LocalizationHelper.InitThread(thread);
thread.Start();
}
public void Share(IProgressMonitor progressMonitor)
{
ProgressMonitor = progressMonitor;
ProgressMonitor.UpdateProgress(_progressStatus = new ProgressStatus(DefaultMessage));
using (var zip = new ZipFileShare())
{
if (ShareType.Complete)
{
ShareComplete(zip);
}
else
{
ShareMinimal(zip);
}
}
}
public ProgressStatus UpdatePercentCompleteProgress(IProgressMonitor progressMonitor,
long currentCount, long totalCount)
{
if (progressMonitor.IsCanceled)
{
throw new OperationCanceledException();
}
int percentComplete = (int)(100 * currentCount / totalCount);
if (percentComplete == PercentComplete)
{
return(this);
}
var statusNew = ChangePercentComplete(percentComplete);
progressMonitor.UpdateProgress(statusNew);
return(statusNew);
}
/// <summary>
/// Initialize isolation scheme export.
/// </summary>
protected bool InitExport(string fileName, IProgressMonitor progressMonitor)
{
if (progressMonitor.IsCanceled)
{
return(false);
}
// First export transition lists to map in memory
Export(null, progressMonitor);
// If filename is null, then no more work needs to be done.
if (fileName == null)
{
progressMonitor.UpdateProgress(new ProgressStatus(string.Empty).Complete());
return(false);
}
return(true);
}
public void Share(IProgressMonitor progressMonitor)
{
ProgressMonitor = progressMonitor;
ProgressMonitor.UpdateProgress(_progressStatus = new ProgressStatus(DefaultMessage));
using (var zip = new ZipFile())
{
// Make sure large files don't cause this to fail.
zip.UseZip64WhenSaving = Zip64Option.AsNecessary;
if (CompleteSharing)
{
ShareComplete(zip);
}
else
{
ShareMinimal(zip);
}
}
}
public void ExportSpectralLibrary(string path, IProgressMonitor progressMonitor)
{
const string name = "exported";
var spectra = new Dictionary <LibKey, SpectrumMzInfo>();
foreach (var nodePepGroup in Document.MoleculeGroups)
{
foreach (var nodePep in nodePepGroup.Molecules)
{
foreach (var nodeTranGroup in nodePep.TransitionGroups)
{
for (var i = 0; i < Document.Settings.MeasuredResults.Chromatograms.Count; i++)
{
ProcessTransitionGroup(spectra, nodePepGroup, nodePep, nodeTranGroup, i);
}
}
}
}
var rCalcIrt = Document.Settings.HasRTPrediction
? Document.Settings.PeptideSettings.Prediction.RetentionTime.Calculator as RCalcIrt
: null;
IProgressStatus status = new ProgressStatus();
if (rCalcIrt != null && progressMonitor != null)
{
progressMonitor.UpdateProgress(status = status.ChangeSegments(0, 2));
}
using (var blibDb = BlibDb.CreateBlibDb(path))
{
var libSpec = new BiblioSpecLiteSpec(name, path);
blibDb.CreateLibraryFromSpectra(libSpec, spectra.Values.ToList(), name, progressMonitor, ref status);
}
if (rCalcIrt != null)
{
IrtDb.CreateIrtDb(path).AddPeptides(progressMonitor, rCalcIrt.GetDbIrtPeptides().ToList(), ref status);
}
}
public static ProcessedIrtAverages ProcessRetentionTimes(IProgressMonitor monitor,
IRetentionTimeProvider[] providers, DbIrtPeptide[] standardPeptideList, DbIrtPeptide[] items)
{
var matchedStandard = IrtStandard.WhichStandard(standardPeptideList.Select(pep => pep.ModifiedTarget));
if (matchedStandard != null)
{
var dummyDoc = new SrmDocument(SrmSettingsList.GetDefault());
using (var reader = matchedStandard.GetDocumentReader())
{
if (reader != null)
{
dummyDoc = dummyDoc.ImportDocumentXml(reader,
string.Empty,
MeasuredResults.MergeAction.remove,
false,
null,
Settings.Default.StaticModList,
Settings.Default.HeavyModList,
null,
out _,
out _,
false);
standardPeptideList = standardPeptideList.Select(pep => new DbIrtPeptide(pep)).ToArray();
foreach (var dummyPep in dummyDoc.Molecules.Where(pep => pep.HasExplicitMods))
{
var standardPepIdx = standardPeptideList.IndexOf(pep => dummyPep.ModifiedTarget.Equals(pep.ModifiedTarget));
standardPeptideList[standardPepIdx] = new DbIrtPeptide(standardPeptideList[standardPepIdx])
{
ModifiedTarget = dummyDoc.Settings.GetModifiedSequence(dummyPep.ModifiedTarget, IsotopeLabelType.heavy, dummyPep.ExplicitMods)
};
}
}
}
}
IProgressStatus status = new ProgressStatus(Resources.LibraryGridViewDriver_ProcessRetentionTimes_Adding_retention_times);
var dictPeptideAverages = new Dictionary <Target, IrtPeptideAverages>();
var providerData = new List <RetentionTimeProviderData>();
var runCount = 0;
foreach (var retentionTimeProvider in providers)
{
if (monitor.IsCanceled)
{
return(null);
}
monitor.UpdateProgress(status = status.ChangeMessage(string.Format(
Resources.LibraryGridViewDriver_ProcessRetentionTimes_Converting_retention_times_from__0__,
retentionTimeProvider.Name)));
runCount++;
var data = new RetentionTimeProviderData(retentionTimeProvider, standardPeptideList);
if (data.RegressionSuccess || data.CalcRegressionWith(retentionTimeProvider, standardPeptideList, items))
{
AddRetentionTimesToDict(retentionTimeProvider, data.RegressionRefined, dictPeptideAverages, standardPeptideList);
}
providerData.Add(data);
monitor.UpdateProgress(status = status.ChangePercentComplete(runCount * 100 / providers.Length));
}
monitor.UpdateProgress(status.Complete());
return(new ProcessedIrtAverages(dictPeptideAverages, providerData));
}
//Throws DatabaseOpeningException
public static IrtDb GetIrtDb(string path, IProgressMonitor loadMonitor)
{
var status = new ProgressStatus(string.Format(Resources.IrtDb_GetIrtDb_Loading_iRT_database__0_, path));
if (loadMonitor != null)
loadMonitor.UpdateProgress(status);
try
{
if (path == null)
throw new DatabaseOpeningException(Resources.IrtDb_GetIrtDb_Database_path_cannot_be_null);
if (!File.Exists(path))
throw new DatabaseOpeningException(String.Format(Resources.IrtDb_GetIrtDb_The_file__0__does_not_exist_, path));
string message;
Exception xInner = null;
try
{
//Check for a valid SQLite file and that it has our schema
//Allow only one thread at a time to read from the same path
using (var sessionFactory = GetSessionFactory(path))
{
lock (sessionFactory)
{
return new IrtDb(path, sessionFactory).Load(loadMonitor, status);
}
}
}
catch (UnauthorizedAccessException x)
{
message = string.Format(Resources.IrtDb_GetIrtDb_You_do_not_have_privileges_to_access_the_file__0_, path);
xInner = x;
}
catch (DirectoryNotFoundException x)
{
message = string.Format(Resources.IrtDb_GetIrtDb_The_path_containing__0__does_not_exist, path);
xInner = x;
}
catch (FileNotFoundException x)
{
message = string.Format(Resources.IrtDb_GetIrtDb_The_file__0__could_not_be_created_Perhaps_you_do_not_have_sufficient_privileges, path);
xInner = x;
}
catch (SQLiteException x)
{
message = string.Format(Resources.IrtDb_GetIrtDb_The_file__0__is_not_a_valid_iRT_database_file, path);
xInner = x;
}
catch (Exception x)
{
message = string.Format(Resources.IrtDb_GetIrtDb_The_file__0__could_not_be_opened, path);
xInner = x;
}
throw new DatabaseOpeningException(message, xInner);
}
catch (DatabaseOpeningException x)
{
if (loadMonitor == null)
throw;
loadMonitor.UpdateProgress(status.ChangeErrorException(x));
return null;
}
}
private IrtDb Load(IProgressMonitor loadMonitor, ProgressStatus status)
{
var result = ChangeProp(ImClone(this), im => im.LoadPeptides(im.GetPeptides()));
// Not really possible to show progress, unless we switch to raw reading
if (loadMonitor != null)
loadMonitor.UpdateProgress(status.ChangePercentComplete(100));
return result;
}
public bool BuildLibrary(IProgressMonitor progress)
{
_ambiguousMatches = null;
ProgressStatus status = new ProgressStatus(Resources.BiblioSpecLiteBuilder_BuildLibrary_Preparing_to_build_library);
progress.UpdateProgress(status);
if (InputFiles.Any(f => f.EndsWith(EXT_PILOT)))
{
try
{
InputFiles = VendorIssueHelper.ConvertPilotFiles(InputFiles, progress, status);
if (progress.IsCanceled)
return false;
}
catch (Exception x)
{
progress.UpdateProgress(status.ChangeErrorException(x));
return false;
}
}
string message = string.Format(Resources.BiblioSpecLiteBuilder_BuildLibrary_Building__0__library,
Path.GetFileName(OutputPath));
progress.UpdateProgress(status = status.ChangeMessage(message));
string redundantLibrary = BiblioSpecLiteSpec.GetRedundantName(OutputPath);
var blibBuilder = new BlibBuild(redundantLibrary, InputFiles, TargetSequences)
{
Authority = Authority,
IncludeAmbiguousMatches = IncludeAmbiguousMatches,
CutOffScore = CutOffScore,
Id = Id,
};
try
{
if (!blibBuilder.BuildLibrary(Action, progress, ref status, out _ambiguousMatches))
{
return false;
}
}
catch (IOException x)
{
progress.UpdateProgress(status.ChangeErrorException(x));
return false;
}
catch (Exception x)
{
Console.WriteLine(x.Message);
progress.UpdateProgress(status.ChangeErrorException(
new Exception(string.Format(Resources.BiblioSpecLiteBuilder_BuildLibrary_Failed_trying_to_build_the_redundant_library__0__,
redundantLibrary))));
return false;
}
var blibFilter = new BlibFilter();
status = new ProgressStatus(message);
progress.UpdateProgress(status);
// Write the non-redundant library to a temporary file first
try
{
using (var saver = new FileSaver(OutputPath))
{
if (!blibFilter.Filter(redundantLibrary, saver.SafeName, progress, ref status))
{
return false;
}
saver.Commit();
}
}
catch (IOException x)
{
progress.UpdateProgress(status.ChangeErrorException(x));
return false;
}
catch
{
progress.UpdateProgress(status.ChangeErrorException(
new Exception(string.Format(Resources.BiblioSpecLiteBuilder_BuildLibrary_Failed_trying_to_build_the_library__0__,
OutputPath))));
return false;
}
finally
{
if (!KeepRedundant)
FileEx.SafeDelete(redundantLibrary, true);
}
return true;
}
public void Extract(IProgressMonitor progressMonitor)
{
ProgressMonitor = progressMonitor;
ProgressMonitor.UpdateProgress(_progressStatus = new ProgressStatus(DefaultMessage));
string extractDir = Path.GetFileName(SharedPath) ?? string.Empty;
if (PathEx.HasExtension(extractDir, EXT_SKY_ZIP))
extractDir = extractDir.Substring(0, extractDir.Length - EXT_SKY_ZIP.Length);
else if (PathEx.HasExtension(extractDir, EXT))
extractDir = extractDir.Substring(0, extractDir.Length - EXT.Length);
using (ZipFile zip = ZipFile.Read(SharedPath))
{
CountEntries = zip.Entries.Count;
ExpectedSize = zip.Entries.Select(entry => entry.UncompressedSize).Sum();
zip.ExtractProgress += SrmDocumentSharing_ExtractProgress;
string documentName = FindSharedSkylineFile(zip);
string parentDir = Path.GetDirectoryName(SharedPath);
if (!string.IsNullOrEmpty(parentDir))
extractDir = Path.Combine(parentDir, extractDir);
extractDir = GetNonExistantDir(extractDir);
DocumentPath = Path.Combine(extractDir, documentName);
foreach (var entry in zip.Entries)
{
if (ProgressMonitor.IsCanceled)
break;
try
{
entry.Extract(extractDir);
ExtractedSize += entry.UncompressedSize;
}
catch (Exception)
{
if (!ProgressMonitor.IsCanceled)
throw;
}
}
}
if (ProgressMonitor.IsCanceled)
{
DirectoryEx.SafeDelete(extractDir);
}
}
private SrmDocument LookupProteinMetadata(SrmDocument docOrig, IProgressMonitor progressMonitor)
{
lock (_processedNodes)
{
// Check to make sure this operation was not canceled while this thread was
// waiting to acquire the lock. This also cleans up pending work.
if (progressMonitor.IsCanceled)
return null;
var progressStatus = new ProgressStatus(Resources.ProteinMetadataManager_LookupProteinMetadata_resolving_protein_details);
int nResolved = 0;
int nUnresolved = docOrig.PeptideGroups.Select(pg => pg.ProteinMetadata.NeedsSearch()).Count();
if ((nUnresolved > 0) && !docOrig.Settings.PeptideSettings.BackgroundProteome.IsNone)
{
// Do a quick check to see if background proteome already has the info
if (!docOrig.Settings.PeptideSettings.BackgroundProteome.NeedsProteinMetadataSearch)
{
try
{
using (var proteomeDb = docOrig.Settings.PeptideSettings.BackgroundProteome.OpenProteomeDb())
{
foreach (PeptideGroupDocNode nodePepGroup in docOrig.PeptideGroups)
{
if (_processedNodes.ContainsKey(nodePepGroup.Id.GlobalIndex))
{
// We did this before we were interrupted
progressMonitor.UpdateProgress(progressStatus = progressStatus.ChangePercentComplete(100 * nResolved++ / nUnresolved));
}
else if (nodePepGroup.ProteinMetadata.NeedsSearch())
{
var proteinMetadata = proteomeDb.GetProteinMetadataByName(nodePepGroup.Name);
if ((proteinMetadata == null) && !Equals(nodePepGroup.Name, nodePepGroup.OriginalName))
proteinMetadata = proteomeDb.GetProteinMetadataByName(nodePepGroup.OriginalName); // Original name might hit
if ((proteinMetadata == null) && !String.IsNullOrEmpty(nodePepGroup.ProteinMetadata.Accession))
proteinMetadata = proteomeDb.GetProteinMetadataByName(nodePepGroup.ProteinMetadata.Accession); // Parsed accession might hit
if ((proteinMetadata != null) && !proteinMetadata.NeedsSearch())
{
// Background proteome has already resolved this
_processedNodes.Add(nodePepGroup.Id.GlobalIndex, proteinMetadata);
progressMonitor.UpdateProgress(
progressStatus =
progressStatus.ChangePercentComplete(100*nResolved++/nUnresolved));
}
}
if (progressMonitor.IsCanceled)
{
progressMonitor.UpdateProgress(progressStatus.Cancel());
return null;
}
}
}
}
// ReSharper disable once EmptyGeneralCatchClause
catch
{
// The protDB file is busy, or some other issue - just go directly to web
}
}
}
if (nResolved != nUnresolved)
{
try
{
// Now go to the web for more protein metadata (or pretend to, depending on WebEnabledFastaImporter.DefaultWebAccessMode)
var docNodesWithUnresolvedProteinMetadata = new Dictionary<ProteinSearchInfo,PeptideGroupDocNode>();
var proteinsToSearch = new List<ProteinSearchInfo>();
foreach (PeptideGroupDocNode node in docOrig.PeptideGroups)
{
if (node.ProteinMetadata.NeedsSearch() && !_processedNodes.ContainsKey(node.Id.GlobalIndex)) // Did we already process this?
{
var proteinMetadata = node.ProteinMetadata;
if (proteinMetadata.WebSearchInfo.IsEmpty()) // Never even been hit with regex
{
// Use Regexes to get some metadata, and a search term
var parsedProteinMetaData = FastaImporter.ParseProteinMetaData(proteinMetadata);
if ((parsedProteinMetaData == null) || Equals(parsedProteinMetaData.Merge(proteinMetadata),proteinMetadata.SetWebSearchCompleted()))
{
// That didn't parse well enough to make a search term, or didn't add any new info - just set it as searched so we don't keep trying
_processedNodes.Add(node.Id.GlobalIndex, proteinMetadata.SetWebSearchCompleted());
progressMonitor.UpdateProgress(progressStatus = progressStatus.ChangePercentComplete(100 * nResolved++ / nUnresolved));
proteinMetadata = null; // No search to be done
}
else
{
proteinMetadata = proteinMetadata.Merge(parsedProteinMetaData); // Fill in any gaps with parsed info
}
}
if (proteinMetadata != null)
{
// We note the sequence length because it's useful in disambiguating search results
proteinsToSearch.Add(new ProteinSearchInfo(new DbProteinName(null, proteinMetadata),
node.PeptideGroup.Sequence == null ? 0 : node.PeptideGroup.Sequence.Length));
docNodesWithUnresolvedProteinMetadata.Add(proteinsToSearch.Last(), node);
}
}
}
if (progressMonitor.IsCanceled)
{
progressMonitor.UpdateProgress(progressStatus.Cancel());
return null;
}
progressMonitor.UpdateProgress(progressStatus = progressStatus.ChangePercentComplete(100 * nResolved / nUnresolved));
// Now we actually hit the internet
if (proteinsToSearch.Any())
{
foreach (var result in FastaImporter.DoWebserviceLookup(proteinsToSearch, progressMonitor, false)) // Resolve them all, now
{
Debug.Assert(!result.GetProteinMetadata().NeedsSearch());
_processedNodes.Add(docNodesWithUnresolvedProteinMetadata[result].Id.GlobalIndex, result.GetProteinMetadata());
progressMonitor.UpdateProgress(progressStatus = progressStatus.ChangePercentComplete(100 * nResolved++ / nUnresolved));
}
}
}
catch (OperationCanceledException)
{
progressMonitor.UpdateProgress(progressStatus.Cancel());
return null;
}
}
// And finally write back to the document
var listProteins = new List<PeptideGroupDocNode>();
foreach (PeptideGroupDocNode node in docOrig.MoleculeGroups)
{
if (_processedNodes.ContainsKey(node.Id.GlobalIndex))
{
listProteins.Add(node.ChangeProteinMetadata(_processedNodes[node.Id.GlobalIndex]));
}
else
{
listProteins.Add(node);
}
}
var docNew = docOrig.ChangeChildrenChecked(listProteins.Cast<DocNode>().ToArray());
progressMonitor.UpdateProgress(progressStatus.Complete());
return (SrmDocument)docNew;
}
}
public IEnumerable<PeptideGroupDocNode> Import(TextReader reader, IProgressMonitor progressMonitor, long lineCount)
{
// Set starting values for limit counters
_countPeptides = Document.PeptideCount;
_countIons = Document.PeptideTransitionCount;
// Store set of existing FASTA sequences to keep from duplicating
HashSet<FastaSequence> set = new HashSet<FastaSequence>();
foreach (PeptideGroupDocNode nodeGroup in Document.Children)
{
FastaSequence fastaSeq = nodeGroup.Id as FastaSequence;
if (fastaSeq != null)
set.Add(fastaSeq);
}
var peptideGroupsNew = new List<PeptideGroupDocNode>();
PeptideGroupBuilder seqBuilder = null;
long linesRead = 0;
int progressPercent = -1;
string line;
var status = new ProgressStatus(string.Empty);
while ((line = reader.ReadLine()) != null)
{
linesRead++;
if (progressMonitor != null)
{
// TODO when changing from ILongWaitBroker to IProgressMonitor, the old code was:
// if (progressMonitor.IsCanceled || progressMonitor.IsDocumentChanged(Document))
// IProgressMonitor does not have IsDocumentChangesd.
if (progressMonitor.IsCanceled)
return new PeptideGroupDocNode[0];
int progressNew = (int) (linesRead*100/lineCount);
if (progressPercent != progressNew)
progressMonitor.UpdateProgress(status = status.ChangePercentComplete(progressPercent = progressNew));
}
if (line.StartsWith(">")) // Not L10N
{
if (_countIons > SrmDocument.MAX_TRANSITION_COUNT ||
_countPeptides > SrmDocument.MAX_PEPTIDE_COUNT)
throw new InvalidDataException(Resources.FastaImporter_Import_Document_size_limit_exceeded);
if (seqBuilder != null)
AddPeptideGroup(peptideGroupsNew, set, seqBuilder);
seqBuilder = _modMatcher == null
? new PeptideGroupBuilder(line, PeptideList, Document.Settings)
: new PeptideGroupBuilder(line, _modMatcher, Document.Settings);
if (progressMonitor != null)
progressMonitor.UpdateProgress(status = status.ChangeMessage(string.Format(Resources.FastaImporter_Import_Adding_protein__0__, seqBuilder.Name)));
}
else if (seqBuilder == null)
{
if (line.Trim().Length == 0)
continue;
break;
}
else
{
seqBuilder.AppendSequence(line);
}
}
// Add last sequence.
if (seqBuilder != null)
AddPeptideGroup(peptideGroupsNew, set, seqBuilder);
return peptideGroupsNew;
}
public void Run(ProcessStartInfo psi, string stdin, IProgressMonitor progress, ref ProgressStatus status, TextWriter writer)
{
if (shouldCancel)
{
status.Cancel();
progress.UpdateProgress(status = status.Cancel());
return;
}
if (!string.IsNullOrEmpty(stringToWriteToWriter))
writer.WriteLine(stringToWriteToWriter);
status.ChangePercentComplete(100);
progress.UpdateProgress(status);
}
/// <summary>
/// Called to generate cloud bitmaps
/// </summary>
private void GenerateBitmaps( IProgressMonitor progress )
{
GameProfiles.Game.CloudGeneration.Begin( );
m_XOffset = Utils.Wrap( m_XOffset + 0.002f, 0, Constants.TwoPi );
m_ZOffset = Utils.Wrap( m_ZOffset + 0.0025f, 0, Constants.TwoPi );
// Simple cloud coverage cycle
m_CloudCoverage = Utils.Wrap( m_CloudCoverage + 0.01f, 0, Constants.TwoPi );
progress.UpdateProgress( 0 );
BuildFaceBitmap( CubeMapFace.PositiveX ); progress.UpdateProgress( 1 / 6.0f );
BuildFaceBitmap( CubeMapFace.NegativeX ); progress.UpdateProgress( 2 / 6.0f );
BuildFaceBitmap( CubeMapFace.PositiveY ); progress.UpdateProgress( 3 / 6.0f );
BuildFaceBitmap( CubeMapFace.NegativeY ); progress.UpdateProgress( 4 / 6.0f );
BuildFaceBitmap( CubeMapFace.PositiveZ ); progress.UpdateProgress( 5 / 6.0f );
BuildFaceBitmap( CubeMapFace.NegativeZ );
progress.UpdateProgress( 1 );
GameProfiles.Game.CloudGeneration.End( );
GameProfiles.Game.CloudGeneration.Reset( );
}
private Bitmap GenerateNormalMap( WaveAnimationParameters parameters, float t, float maxT, IProgressMonitor progress, float curProgress, float progressPerFrame )
{
int width = parameters.Width;
int height = parameters.Height;
ComplexF[] frequencyMap = GetFrequencyMap( parameters );
ComplexF[] invFrequencyMap = GetInvFrequencyMap( parameters );
Bitmap bmp = new Bitmap( width, height, PixelFormat.Format24bppRgb );
ComplexF[] resMap = Generate( frequencyMap, invFrequencyMap, width, height, t, maxT, true );
Fourier.FFT2( resMap, width, height, FourierDirection.Backward );
for ( int y = 0; y < height; ++y)
{
for ( int x = 0; x < width; ++x )
{
byte nX = ( byte )( Math.Max( 0, Math.Min( 256, 128 + resMap[ x + y * width ].Re * 8 ) ) );
byte nY = ( byte )( Math.Max( 0, Math.Min( 256, 128 + resMap[ x + y * width ].Im * 8 ) ) );
bmp.SetPixel( x, y, Color.FromArgb( nX, 0, nY ) );
}
progress.UpdateProgress( curProgress + progressPerFrame * ( y / ( float )( height - 1 ) ) );
}
return bmp;
}
/// <summary>
/// Generate an isolation list containing multiplexed windows, attempting to minimize the number
/// and frequency of repeated window pairings within each scan.
/// </summary>
/// <param name="writer">writer to write results</param>
/// <param name="windowsPerScan">how many windows are contained in each scan</param>
/// <param name="progressMonitor">progress monitor</param>
private void WriteMultiplexedWindows(TextWriter writer, int windowsPerScan, IProgressMonitor progressMonitor)
{
int maxInstrumentWindows = Assume.Value(_maxInstrumentWindows);
int windowCount = IsolationScheme.PrespecifiedIsolationWindows.Count;
int cycleCount = maxInstrumentWindows / windowCount;
double totalScore = 0.0;
// Prepare to generate the best isolation list possible within the given time limit.
var startTime = DateTime.Now;
var cycle = new Cycle(windowCount, windowsPerScan);
int cyclesGenerated = 0;
ProgressStatus status = new ProgressStatus(Resources.AbstractDiaExporter_WriteMultiplexedWindows_Exporting_Isolation_List);
progressMonitor.UpdateProgress(status);
// Generate each cycle.
for (int cycleNumber = 1; cycleNumber <= cycleCount; cycleNumber++)
{
// Update status.
if (progressMonitor.IsCanceled)
return;
progressMonitor.UpdateProgress(status.ChangePercentComplete(
(int) (DateTime.Now - startTime).TotalSeconds*100/CalculationTime).ChangeMessage(
string.Format(Resources.AbstractDiaExporter_WriteMultiplexedWindows_Exporting_Isolation_List__0__cycles_out_of__1__,
cycleNumber - 1, cycleCount)));
double secondsRemaining = CalculationTime - (DateTime.Now - startTime).TotalSeconds;
double secondsPerCycle = secondsRemaining / (cycleCount - cycleNumber + 1);
var endTime = DateTime.Now.AddSeconds(secondsPerCycle);
Cycle bestCycle = null;
do
{
// Generate a bunch of cycles, looking for one with the lowest score.
const int attemptCount = 50;
for (int i = 0; i < attemptCount; i++)
{
cycle.Generate(cycleNumber);
if (bestCycle == null || bestCycle.CycleScore > cycle.CycleScore)
{
bestCycle = new Cycle(cycle);
if (bestCycle.CycleScore == 0.0)
{
cyclesGenerated += i + 1 - attemptCount;
endTime = DateTime.Now; // Break outer loop.
break;
}
}
}
cyclesGenerated += attemptCount;
} while (DateTime.Now < endTime);
// ReSharper disable PossibleNullReferenceException
totalScore += bestCycle.CycleScore;
WriteCycle(writer, bestCycle, cycleNumber);
WriteCycleInfo(bestCycle, cycleNumber, cyclesGenerated, startTime);
// ReSharper restore PossibleNullReferenceException
}
WriteTotalScore(totalScore);
// Show 100% in the wait dialog.
progressMonitor.UpdateProgress(status.ChangePercentComplete(100).ChangeMessage(
string.Format(Resources.AbstractDiaExporter_WriteMultiplexedWindows_Exporting_Isolation_List__0__cycles_out_of__0__,
cycleCount)));
}
/// <summary>
/// Train the model by iterative calculating weights to separate target and decoy transition groups.
/// </summary>
/// <param name="targets">Target transition groups.</param>
/// <param name="decoys">Decoy transition groups.</param>
/// <param name="initParameters">Initial model parameters (weights and bias)</param>
/// <param name="includeSecondBest"> Include the second best peaks in the targets as decoys?</param>
/// <param name="preTrain">Use a pre-trained model to bootstrap the learning.</param>
/// <param name="progressMonitor"></param>
/// <returns>Immutable model with new weights.</returns>
public override IPeakScoringModel Train(IList <IList <float[]> > targets, IList <IList <float[]> > decoys, LinearModelParams initParameters,
bool includeSecondBest = false, bool preTrain = true, IProgressMonitor progressMonitor = null)
{
if (initParameters == null)
{
initParameters = new LinearModelParams(_peakFeatureCalculators.Count);
}
return(ChangeProp(ImClone(this), im =>
{
targets = targets.Where(list => list.Count > 0).ToList();
decoys = decoys.Where(list => list.Count > 0).ToList();
var targetTransitionGroups = new ScoredGroupPeaksSet(targets);
var decoyTransitionGroups = new ScoredGroupPeaksSet(decoys);
// Bootstrap from the pre-trained legacy model
if (preTrain)
{
var preTrainedWeights = new double[initParameters.Weights.Count];
for (int i = 0; i < preTrainedWeights.Length; ++i)
{
if (double.IsNaN(initParameters.Weights[i]))
{
preTrainedWeights[i] = double.NaN;
}
}
int standardEnabledCount = GetEnabledCount(LegacyScoringModel.StandardFeatureCalculators, initParameters.Weights);
int analyteEnabledCount = GetEnabledCount(LegacyScoringModel.AnalyteFeatureCalculators, initParameters.Weights);
bool hasStandards = standardEnabledCount >= analyteEnabledCount;
var calculators = hasStandards ? LegacyScoringModel.StandardFeatureCalculators : LegacyScoringModel.AnalyteFeatureCalculators;
for (int i = 0; i < calculators.Length; ++i)
{
if (calculators[i].GetType() == typeof(MQuestRetentionTimePredictionCalc))
{
continue;
}
SetCalculatorValue(calculators[i].GetType(), LegacyScoringModel.DEFAULT_WEIGHTS[i], preTrainedWeights);
}
targetTransitionGroups.ScorePeaks(preTrainedWeights);
decoyTransitionGroups.ScorePeaks(preTrainedWeights);
}
// Iteratively refine the weights through multiple iterations.
var calcWeights = new double[initParameters.Weights.Count];
Array.Copy(initParameters.Weights.ToArray(), calcWeights, initParameters.Weights.Count);
double decoyMean = 0;
double decoyStdev = 0;
bool colinearWarning = false;
// This may take a long time between progress updates, but just measure progress by cycles through the training
IProgressStatus status = new ProgressStatus(Resources.MProphetPeakScoringModel_Train_Training_peak_scoring_model);
if (progressMonitor != null)
{
progressMonitor.UpdateProgress(status);
}
for (int iteration = 0; iteration < MAX_ITERATIONS; iteration++)
{
if (progressMonitor != null)
{
if (progressMonitor.IsCanceled)
{
throw new OperationCanceledException();
}
progressMonitor.UpdateProgress(status =
status.ChangeMessage(string.Format(Resources.MProphetPeakScoringModel_Train_Training_peak_scoring_model__iteration__0__of__1__, iteration + 1, MAX_ITERATIONS))
.ChangePercentComplete((iteration + 1) * 100 / (MAX_ITERATIONS + 1)));
}
im.CalculateWeights(iteration, targetTransitionGroups, decoyTransitionGroups,
includeSecondBest, calcWeights, out decoyMean, out decoyStdev, ref colinearWarning);
GC.Collect(); // Each loop generates a number of large objects. GC helps to keep private bytes under control
}
if (progressMonitor != null)
{
progressMonitor.UpdateProgress(status.ChangePercentComplete(100));
}
var parameters = new LinearModelParams(calcWeights);
parameters = parameters.RescaleParameters(decoyMean, decoyStdev);
im.Parameters = parameters;
im.ColinearWarning = colinearWarning;
im.UsesSecondBest = includeSecondBest;
im.UsesDecoys = decoys.Count > 0;
}));
}
private static void ConvertBrukerToMzml(string filePathBruker,
string outputPath, IProgressMonitor monitor, ProgressStatus status)
{
// We use CompassXport, if it is installed, to convert a Bruker raw file to mzML. This solves two
// issues: the Bruker reader can't be called on any thread other than the main thread, and there
// is no 64-bit version of the reader. So we start CompassXport in its own 32-bit process,
// and use it to convert the raw data to mzML in a temporary file, which we read back afterwards.
var key = Registry.LocalMachine.OpenSubKey(KEY_COMPASSXPORT, false);
string compassXportExe = (key != null) ? (string)key.GetValue(string.Empty) : null;
if (compassXportExe == null)
throw new IOException(Resources.VendorIssueHelper_ConvertBrukerToMzml_CompassXport_software_must_be_installed_to_import_Bruker_raw_data_files_);
// CompassXport arguments
// ReSharper disable NonLocalizedString
var argv = new[]
{
"-a \"" + filePathBruker + "\"", // input file (directory)
"-o \"" + outputPath + "\"", // output file (directory)
"-mode 2", // mode 2 (mzML)
"-raw 0" // export line spectra (profile data is HUGE and SLOW!)
};
// ReSharper restore NonLocalizedString
// Start CompassXport in its own process.
var psi = new ProcessStartInfo(compassXportExe)
{
CreateNoWindow = true,
UseShellExecute = false,
// Common directory includes the directory separator
WorkingDirectory = Path.GetDirectoryName(Assembly.GetExecutingAssembly().Location) ?? string.Empty,
Arguments = string.Join(" ", argv), // Not L10N
RedirectStandardError = true,
RedirectStandardOutput = true,
};
var proc = new Process { StartInfo = psi };
proc.Start();
// CompassXport starts by calculating a hash of the input file. This takes a long time, and there is
// no intermediate output during this time. So we set the progress bar some fraction of the way and
// let it sit there and animate while we wait for the start of spectra processing.
const int hashPercent = 25; // percentage of import time allocated to calculating the input file hash
int spectrumCount = 0;
var sbOut = new StringBuilder();
var reader = new ProcessStreamReader(proc);
string line;
while ((line = reader.ReadLine()) != null)
{
if (monitor.IsCanceled)
{
proc.Kill();
throw new LoadCanceledException(status.Cancel());
}
sbOut.AppendLine(line);
line = line.Trim();
// The main part of conversion starts with the hash calculation.
if (line.StartsWith("Calculating hash")) // Not L10N
{
status = status.ChangeMessage(Resources.VendorIssueHelper_ConvertBrukerToMzml_Calculating_hash_of_input_file)
.ChangePercentComplete(hashPercent);
monitor.UpdateProgress(status);
continue;
}
// Determine how many spectra will be converted so we can track progress.
var match = Regex.Match(line, @"Converting (\d+) spectra"); // Not L10N
if (match.Success)
{
spectrumCount = int.Parse(match.Groups[1].Value);
continue;
}
// Update progress as each spectra batch is converted.
match = Regex.Match(line, @"Spectrum \d+ - (\d+)"); // Not L10N
if (match.Success)
{
var spectrumEnd = int.Parse(match.Groups[1].Value);
var percentComplete = hashPercent + (100-hashPercent)*spectrumEnd/spectrumCount;
status = status.ChangeMessage(line).ChangePercentComplete(percentComplete);
monitor.UpdateProgress(status);
}
}
while (!proc.WaitForExit(200))
{
if (monitor.IsCanceled)
{
proc.Kill();
throw new LoadCanceledException(status.Cancel());
}
}
if (proc.ExitCode != 0)
{
throw new IOException(TextUtil.LineSeparate(string.Format(Resources.VendorIssueHelper_ConvertBrukerToMzml_Failure_attempting_to_convert__0__to_mzML_using_CompassXport_,
filePathBruker), string.Empty, sbOut.ToString()));
}
}
/// <summary>
/// Make a BiblioSpec SQLite library from a list of spectra and their intensities.
/// </summary>
/// <param name="librarySpec">Library spec for which the new library is created</param>
/// <param name="listSpectra">List of existing spectra, by LibKey</param>
/// <param name="libraryName">Name of the library to be created</param>
/// <param name="progressMonitor">Progress monitor to display progress in creating library</param>
/// <returns>A library of type <see cref="BiblioSpecLiteLibrary"/></returns>
public BiblioSpecLiteLibrary CreateLibraryFromSpectra(BiblioSpecLiteSpec librarySpec,
List<SpectrumMzInfo> listSpectra,
string libraryName,
IProgressMonitor progressMonitor)
{
const string libAuthority = BiblioSpecLiteLibrary.DEFAULT_AUTHORITY;
const int majorVer = 1;
const int minorVer = 0;
string libId = libraryName;
// Use a very specific LSID, since it really only matches this document.
string libLsid = string.Format("urn:lsid:{0}:spectral_libary:bibliospec:nr:minimal:{1}:{2}:{3}.{4}", // Not L10N
libAuthority, libId, Guid.NewGuid(), majorVer, minorVer);
var dictLibrary = new Dictionary<LibKey, BiblioLiteSpectrumInfo>();
using (ISession session = OpenWriteSession())
using (ITransaction transaction = session.BeginTransaction())
{
int progressPercent = 0;
int i = 0;
var status = new ProgressStatus(Resources.BlibDb_CreateLibraryFromSpectra_Creating_spectral_library_for_imported_transition_list);
foreach (var spectrum in listSpectra)
{
++i;
var dbRefSpectrum = RefSpectrumFromPeaks(spectrum);
session.Save(dbRefSpectrum);
dictLibrary.Add(spectrum.Key,
new BiblioLiteSpectrumInfo(spectrum.Key, dbRefSpectrum.Copies,
dbRefSpectrum.NumPeaks,
(int)(dbRefSpectrum.Id ?? 0),
default(IndexedRetentionTimes),
default(IndexedIonMobilities)));
if (progressMonitor != null)
{
if (progressMonitor.IsCanceled)
return null;
int progressNew = (i * 100 / listSpectra.Count);
if (progressPercent != progressNew)
{
progressMonitor.UpdateProgress(status = status.ChangePercentComplete(progressNew));
progressPercent = progressNew;
}
}
}
session.Flush();
session.Clear();
// Simulate ctime(d), which is what BlibBuild uses.
string createTime = string.Format("{0:ddd MMM dd HH:mm:ss yyyy}", DateTime.Now); // Not L10N? different date/time format in different countries
DbLibInfo libInfo = new DbLibInfo
{
LibLSID = libLsid,
CreateTime = createTime,
NumSpecs = dictLibrary.Count,
MajorVersion = majorVer,
MinorVersion = minorVer
};
session.Save(libInfo);
session.Flush();
session.Clear();
transaction.Commit();
}
var libraryEntries = dictLibrary.Values.ToArray();
return new BiblioSpecLiteLibrary(librarySpec, libLsid, majorVer, minorVer,
libraryEntries, FileStreamManager.Default);
}
public UpdateProgressResponse UpdateProgress(IProgressStatus status)
{
return(_monitor.UpdateProgress(status));
}
/// <summary>
/// Train the model by iterative calculating weights to separate target and decoy transition groups.
/// </summary>
/// <param name="targets">Target transition groups.</param>
/// <param name="decoys">Decoy transition groups.</param>
/// <param name="initParameters">Initial model parameters (weights and bias)</param>
/// <param name="includeSecondBest"> Include the second best peaks in the targets as decoys?</param>
/// <param name="preTrain">Use a pre-trained model to bootstrap the learning.</param>
/// <param name="progressMonitor"></param>
/// <returns>Immutable model with new weights.</returns>
public override IPeakScoringModel Train(IList<IList<float[]>> targets, IList<IList<float[]>> decoys, LinearModelParams initParameters,
bool includeSecondBest = false, bool preTrain = true, IProgressMonitor progressMonitor = null)
{
if(initParameters == null)
initParameters = new LinearModelParams(_peakFeatureCalculators.Count);
return ChangeProp(ImClone(this), im =>
{
targets = targets.Where(list => list.Count > 0).ToList();
decoys = decoys.Where(list => list.Count > 0).ToList();
var targetTransitionGroups = new ScoredGroupPeaksSet(targets);
var decoyTransitionGroups = new ScoredGroupPeaksSet(decoys);
// Bootstrap from the pre-trained legacy model
if (preTrain)
{
var preTrainedWeights = new double[initParameters.Weights.Count];
for (int i = 0; i < preTrainedWeights.Length; ++i)
{
if (double.IsNaN(initParameters.Weights[i]))
{
preTrainedWeights[i] = double.NaN;
}
}
int standardEnabledCount = GetEnabledCount(LegacyScoringModel.StandardFeatureCalculators, initParameters.Weights);
int analyteEnabledCount = GetEnabledCount(LegacyScoringModel.AnalyteFeatureCalculators, initParameters.Weights);
bool hasStandards = standardEnabledCount >= analyteEnabledCount;
var calculators = hasStandards ? LegacyScoringModel.StandardFeatureCalculators : LegacyScoringModel.AnalyteFeatureCalculators;
for (int i = 0; i < calculators.Length; ++i)
{
if (calculators[i].GetType() == typeof (MQuestRetentionTimePredictionCalc))
continue;
SetCalculatorValue(calculators[i].GetType(), LegacyScoringModel.DEFAULT_WEIGHTS[i], preTrainedWeights);
}
targetTransitionGroups.ScorePeaks(preTrainedWeights);
decoyTransitionGroups.ScorePeaks(preTrainedWeights);
}
// Iteratively refine the weights through multiple iterations.
var calcWeights = new double[initParameters.Weights.Count];
Array.Copy(initParameters.Weights.ToArray(), calcWeights, initParameters.Weights.Count);
double decoyMean = 0;
double decoyStdev = 0;
bool colinearWarning = false;
// This may take a long time between progress updates, but just measure progress by cycles through the training
var status = new ProgressStatus(Resources.MProphetPeakScoringModel_Train_Training_peak_scoring_model);
if (progressMonitor != null)
progressMonitor.UpdateProgress(status);
for (int iteration = 0; iteration < MAX_ITERATIONS; iteration++)
{
if (progressMonitor != null)
{
if (progressMonitor.IsCanceled)
throw new OperationCanceledException();
progressMonitor.UpdateProgress(status =
status.ChangeMessage(string.Format(Resources.MProphetPeakScoringModel_Train_Training_peak_scoring_model__iteration__0__of__1__, iteration + 1, MAX_ITERATIONS))
.ChangePercentComplete((iteration + 1) * 100 / (MAX_ITERATIONS + 1)));
}
im.CalculateWeights(iteration, targetTransitionGroups, decoyTransitionGroups,
includeSecondBest, calcWeights, out decoyMean, out decoyStdev, ref colinearWarning);
GC.Collect(); // Each loop generates a number of large objects. GC helps to keep private bytes under control
}
if (progressMonitor != null)
progressMonitor.UpdateProgress(status.ChangePercentComplete(100));
var parameters = new LinearModelParams(calcWeights);
parameters = parameters.RescaleParameters(decoyMean, decoyStdev);
im.Parameters = parameters;
im.ColinearWarning = colinearWarning;
im.UsesSecondBest = includeSecondBest;
im.UsesDecoys = decoys.Count > 0;
});
}
// ReSharper restore NonLocalizedString
/// <summary>
/// Executes an export for all chromatograms in the document
/// with file names matching one of the files in filesToExport
/// writer = location to write the chromatogram data to
/// longWaitBroker = progress bar (can be null)
/// filesToExport = file names for which to write chromatograms
/// cultureInfo = local culture
/// chromExtractors = list of special chromatogram types to include (base peak, etc)
/// chromSources = type of ions to include (precursor, product)
/// </summary>
public void Export(TextWriter writer,
IProgressMonitor longWaitBroker,
IList<string> filesToExport,
CultureInfo cultureInfo,
IList<ChromExtractor> chromExtractors,
IList<ChromSource> chromSources)
{
int currentReplicates = 0;
int totalReplicates = _chromatogramSets.Count;
var status = new ProgressStatus(string.Empty);
FormatHeader(writer, FIELD_NAMES);
foreach (var chromatograms in _chromatogramSets)
{
if (longWaitBroker != null)
{
int percentComplete = currentReplicates++ * 100 / totalReplicates;
if (percentComplete < 100)
{
longWaitBroker.UpdateProgress(status = status.ChangeMessage(string.Format(Resources.ChromatogramExporter_Export_Exporting_Chromatograms_for__0_,
chromatograms.Name)).ChangePercentComplete(percentComplete));
}
}
foreach (var extractor in chromExtractors)
{
ChromatogramGroupInfo[] arrayChromSpecial;
if (!_measuredResults.TryLoadAllIonsChromatogram(chromatograms, extractor, true, out arrayChromSpecial))
{
// TODO: need error determination here
continue;
}
foreach (var chromInfo in arrayChromSpecial)
{
string fileName = chromInfo.FilePath.GetFileName();
// Skip the files that have not been selected for export
if (!filesToExport.Contains(fileName))
continue;
IList<float> times = chromInfo.Times;
IList<float> intensities = chromInfo.IntensityArray[0];
float tic = CalculateTic(times, intensities);
string extractorName = GetExtractorName(extractor);
string[] fieldArray =
{
fileName,
TextUtil.EXCEL_NA,
TextUtil.EXCEL_NA,
TextUtil.EXCEL_NA,
extractorName,
TextUtil.EXCEL_NA,
TextUtil.EXCEL_NA,
System.Convert.ToString(tic, cultureInfo)
};
FormatChromLine(writer, fieldArray, times, intensities, cultureInfo);
}
}
foreach (var peptideNode in Document.Molecules)
{
foreach (TransitionGroupDocNode groupNode in peptideNode.Children)
ExportGroupNode(peptideNode, groupNode, chromatograms, filesToExport, chromSources, writer, cultureInfo);
}
}
}
// Throws DatabaseOpeningException
public static IonMobilityDb GetIonMobilityDb(string path, IProgressMonitor loadMonitor)
{
var status = new ProgressStatus(string.Format(Resources.IonMobilityDb_GetIonMobilityDb_Loading_ion_mobility_library__0_, path));
if (loadMonitor != null)
loadMonitor.UpdateProgress(status);
try
{
if (String.IsNullOrEmpty(path))
throw new DatabaseOpeningException(Resources.IonMobilityDb_GetIonMobilityDb_Please_provide_a_path_to_an_existing_ion_mobility_library_);
if (!File.Exists(path))
throw new DatabaseOpeningException(
string.Format(
Resources.IonMobilityDb_GetIonMobilityDb_The_ion_mobility_library_file__0__could_not_be_found__Perhaps_you_did_not_have_sufficient_privileges_to_create_it_,
path));
string message;
try
{
//Check for a valid SQLite file and that it has our schema
//Allow only one thread at a time to read from the same path
using (var sessionFactory = GetSessionFactory(path))
{
lock (sessionFactory)
{
return new IonMobilityDb(path, sessionFactory).Load(loadMonitor, status);
}
}
}
catch (UnauthorizedAccessException)
{
message = string.Format(Resources.IonMobilityDb_GetIonMobilityDb_You_do_not_have_privileges_to_access_the_ion_mobility_library_file__0_, path);
}
catch (DirectoryNotFoundException)
{
message = string.Format(Resources.IonMobilityDb_GetIonMobilityDb_The_path_containing_ion_mobility_library__0__does_not_exist_, path);
}
catch (FileNotFoundException)
{
message = string.Format(Resources.IonMobilityDb_GetIonMobilityDb_The_ion_mobility_library_file__0__could_not_be_found__Perhaps_you_did_not_have_sufficient_privileges_to_create_it_, path);
}
catch (Exception) // SQLiteException is already something of a catch-all, just lump it with the others here
{
message = string.Format(Resources.IonMobilityDb_GetIonMobilityDb_The_file__0__is_not_a_valid_ion_mobility_library_file_, path);
}
throw new DatabaseOpeningException(message);
}
catch (DatabaseOpeningException x)
{
if (loadMonitor == null)
throw;
loadMonitor.UpdateProgress(status.ChangeErrorException(x));
return null;
}
}
public void Run(ProcessStartInfo psi, string stdin, IProgressMonitor progress, ref ProgressStatus status, TextWriter writer)
{
// Make sure required streams are redirected.
psi.RedirectStandardOutput = true;
psi.RedirectStandardError = true;
var proc = Process.Start(psi);
if (proc == null)
throw new IOException(string.Format("Failure starting {0} command.", psi.FileName)); // Not L10N
if (stdin != null)
{
try
{
proc.StandardInput.Write(stdin);
}
finally
{
proc.StandardInput.Close();
}
}
var reader = new ProcessStreamReader(proc);
StringBuilder sbError = new StringBuilder();
int percentLast = 0;
string line;
while ((line = reader.ReadLine(progress)) != null)
{
if (writer != null && !line.StartsWith(HideLinePrefix))
writer.WriteLine(line);
if (progress == null || line.ToLowerInvariant().StartsWith("error")) // Not L10N
{
sbError.AppendLine(line);
}
else // if (progress != null)
{
if (progress.IsCanceled)
{
proc.Kill();
progress.UpdateProgress(status = status.Cancel());
return;
}
if (line.EndsWith("%")) // Not L10N
{
double percent;
string[] parts = line.Split(' ');
string percentPart = parts[parts.Length - 1];
if (double.TryParse(percentPart.Substring(0, percentPart.Length - 1), out percent))
{
percentLast = (int) percent;
status = status.ChangePercentComplete(percentLast);
if (percent >= 100 && status.SegmentCount > 0)
status = status.NextSegment();
progress.UpdateProgress(status);
}
}
else if (MessagePrefix == null || line.StartsWith(MessagePrefix))
{
// Remove prefix, if there is one.
if (MessagePrefix != null)
line = line.Substring(MessagePrefix.Length);
status = status.ChangeMessage(line);
progress.UpdateProgress(status);
}
}
}
proc.WaitForExit();
int exit = proc.ExitCode;
if (exit != 0)
{
line = proc.StandardError.ReadLine();
if (line != null)
sbError.AppendLine(line);
if (sbError.Length == 0)
throw new IOException("Error occurred running process."); // Not L10N
throw new IOException(sbError.ToString());
}
// Make to complete the status, if the process succeeded, but never
// printed 100% to the console
if (percentLast < 100)
{
status = status.ChangePercentComplete(100);
if (status.SegmentCount > 0)
status = status.NextSegment();
if (progress != null)
progress.UpdateProgress(status);
}
}
public bool BuildLibrary(IProgressMonitor progress)
{
_ambiguousMatches = null;
IProgressStatus status = new ProgressStatus(Resources.BiblioSpecLiteBuilder_BuildLibrary_Preparing_to_build_library);
progress.UpdateProgress(status);
if (InputFiles.Any(f => f.EndsWith(EXT_PILOT)))
{
try
{
InputFiles = VendorIssueHelper.ConvertPilotFiles(InputFiles, progress, status);
if (progress.IsCanceled)
{
return(false);
}
}
catch (Exception x)
{
progress.UpdateProgress(status.ChangeErrorException(x));
return(false);
}
}
string message = string.Format(Resources.BiblioSpecLiteBuilder_BuildLibrary_Building__0__library,
Path.GetFileName(OutputPath));
progress.UpdateProgress(status = status.ChangeMessage(message));
string redundantLibrary = BiblioSpecLiteSpec.GetRedundantName(OutputPath);
var blibBuilder = new BlibBuild(redundantLibrary, InputFiles, TargetSequences)
{
IncludeAmbiguousMatches = IncludeAmbiguousMatches,
CutOffScore = CutOffScore,
Id = Id,
};
try
{
if (!blibBuilder.BuildLibrary(Action, progress, ref status, out _ambiguousMatches))
{
return(false);
}
}
catch (IOException x)
{
progress.UpdateProgress(status.ChangeErrorException(x));
return(false);
}
catch (Exception x)
{
Console.WriteLine(x.Message);
progress.UpdateProgress(status.ChangeErrorException(
new Exception(string.Format(Resources.BiblioSpecLiteBuilder_BuildLibrary_Failed_trying_to_build_the_redundant_library__0__,
redundantLibrary))));
return(false);
}
var blibFilter = new BlibFilter();
status = new ProgressStatus(message);
progress.UpdateProgress(status);
// Write the non-redundant library to a temporary file first
try
{
using (var saver = new FileSaver(OutputPath))
{
if (!blibFilter.Filter(redundantLibrary, saver.SafeName, progress, ref status))
{
return(false);
}
saver.Commit();
}
}
catch (IOException x)
{
progress.UpdateProgress(status.ChangeErrorException(x));
return(false);
}
catch
{
progress.UpdateProgress(status.ChangeErrorException(
new Exception(string.Format(Resources.BiblioSpecLiteBuilder_BuildLibrary_Failed_trying_to_build_the_library__0__,
OutputPath))));
return(false);
}
finally
{
if (!KeepRedundant)
{
FileEx.SafeDelete(redundantLibrary, true);
}
}
return(true);
}
// Throws DatabaseOpeningException
public static IonMobilityDb GetIonMobilityDb(string path, IProgressMonitor loadMonitor)
{
var status = new ProgressStatus(string.Format(Resources.IonMobilityDb_GetIonMobilityDb_Loading_ion_mobility_library__0_, path));
if (loadMonitor != null)
{
loadMonitor.UpdateProgress(status);
}
try
{
if (String.IsNullOrEmpty(path))
{
throw new DatabaseOpeningException(Resources.IonMobilityDb_GetIonMobilityDb_Please_provide_a_path_to_an_existing_ion_mobility_library_);
}
if (!File.Exists(path))
{
throw new DatabaseOpeningException(
string.Format(
Resources.IonMobilityDb_GetIonMobilityDb_The_ion_mobility_library_file__0__could_not_be_found__Perhaps_you_did_not_have_sufficient_privileges_to_create_it_,
path));
}
string message;
Exception xInner = null;
try
{
//Check for a valid SQLite file and that it has our schema
//Allow only one thread at a time to read from the same path
using (var sessionFactory = GetSessionFactory(path))
{
lock (sessionFactory)
{
return(new IonMobilityDb(path, sessionFactory).Load(loadMonitor, status));
}
}
}
catch (UnauthorizedAccessException x)
{
message = string.Format(Resources.IonMobilityDb_GetIonMobilityDb_You_do_not_have_privileges_to_access_the_ion_mobility_library_file__0_, path);
xInner = x;
}
catch (DirectoryNotFoundException x)
{
message = string.Format(Resources.IonMobilityDb_GetIonMobilityDb_The_path_containing_ion_mobility_library__0__does_not_exist_, path);
xInner = x;
}
catch (FileNotFoundException x)
{
message = string.Format(Resources.IonMobilityDb_GetIonMobilityDb_The_ion_mobility_library_file__0__could_not_be_found__Perhaps_you_did_not_have_sufficient_privileges_to_create_it_, path);
xInner = x;
}
catch (Exception x) // SQLiteException is already something of a catch-all, just lump it with the others here
{
message = string.Format(Resources.IonMobilityDb_GetIonMobilityDb_The_file__0__is_not_a_valid_ion_mobility_library_file_, path);
xInner = x;
}
throw new DatabaseOpeningException(message, xInner);
}
catch (DatabaseOpeningException x)
{
if (loadMonitor == null)
{
throw;
}
loadMonitor.UpdateProgress(status.ChangeErrorException(x));
return(null);
}
}
public ProgressStatus UpdatePercentCompleteProgress(IProgressMonitor progressMonitor,
long currentCount, long totalCount)
{
if (progressMonitor.IsCanceled)
throw new OperationCanceledException();
int percentComplete = (int) (100 * currentCount / totalCount);
if (percentComplete == PercentComplete)
return this;
var statusNew = ChangePercentComplete(percentComplete);
progressMonitor.UpdateProgress(statusNew);
return statusNew;
}
public static SrmDocument RecalculateAlignments(SrmDocument document, IProgressMonitor progressMonitor)
{
var newSources = ListAvailableRetentionTimeSources(document.Settings);
var newResultsSources = ListSourcesForResults(document.Settings.MeasuredResults, newSources);
var allLibraryRetentionTimes = ReadAllRetentionTimes(document, newSources);
var newFileAlignments = new List<FileRetentionTimeAlignments>();
var progressStatus = new ProgressStatus("Aligning retention times"); // Not L10N? Will users see this?
foreach (var retentionTimeSource in newResultsSources.Values)
{
progressStatus = progressStatus.ChangePercentComplete(100*newFileAlignments.Count/newResultsSources.Count);
progressMonitor.UpdateProgress(progressStatus);
try
{
var fileAlignments = CalculateFileRetentionTimeAlignments(retentionTimeSource.Name, allLibraryRetentionTimes, progressMonitor);
newFileAlignments.Add(fileAlignments);
}
catch (OperationCanceledException)
{
progressMonitor.UpdateProgress(progressStatus.Cancel());
return null;
}
}
var newDocRt = new DocumentRetentionTimes(newSources.Values, newFileAlignments);
var newDocument = document.ChangeSettings(document.Settings.ChangeDocumentRetentionTimes(newDocRt));
Debug.Assert(IsLoaded(newDocument));
progressMonitor.UpdateProgress(progressStatus.Complete());
return newDocument;
}
public SrmDocument Import(TextReader reader, IProgressMonitor progressMonitor, long lineCount, bool isMinutes, bool removeMissing = false, bool changePeaks = true)
{
var status = new ProgressStatus(Resources.PeakBoundaryImporter_Import_Importing_Peak_Boundaries);
double timeConversionFactor = isMinutes ? 1.0 : 60.0;
int linesRead = 0;
int progressPercent = 0;
var docNew = (SrmDocument) Document.ChangeIgnoreChangingChildren(true);
var docReference = docNew;
var sequenceToNode = new Dictionary<Tuple<string, bool>, IList<IdentityPath>>();
var fileNameToFileMatch = new Dictionary<string, ChromSetFileMatch>();
var trackAdjustedResults = new HashSet<ResultsKey>();
var modMatcher = new ModificationMatcher();
// Make the dictionary of modified peptide strings to doc nodes and paths
for (int i = 0; i < Document.MoleculeCount; ++i)
{
IdentityPath peptidePath = Document.GetPathTo((int) SrmDocument.Level.Molecules, i);
PeptideDocNode peptideNode = (PeptideDocNode) Document.FindNode(peptidePath);
var peptidePair = new Tuple<string, bool>(peptideNode.RawTextId, peptideNode.IsDecoy);
IList<IdentityPath> idPathList;
// Each (sequence, isDecoy) pair can be associated with more than one peptide,
// to handle the case of duplicate peptides in the doucment.
if (sequenceToNode.TryGetValue(peptidePair, out idPathList))
{
idPathList.Add(peptidePath);
sequenceToNode[peptidePair] = idPathList;
}
else
{
idPathList = new List<IdentityPath> { peptidePath };
sequenceToNode.Add(peptidePair, idPathList);
}
}
// Add annotations as possible columns
var allFieldNames = new List<string[]>(FIELD_NAMES);
allFieldNames.AddRange(from def in Document.Settings.DataSettings.AnnotationDefs
where def.AnnotationTargets.Contains(AnnotationDef.AnnotationTarget.precursor_result)
select new[] { def.Name });
string line = reader.ReadLine();
linesRead++;
int[] fieldIndices;
int fieldsTotal;
// If we aren't changing peaks, allow start and end time to be missing
var requiredFields = changePeaks ? REQUIRED_FIELDS : REQUIRED_NO_CHROM;
char correctSeparator = ReadFirstLine(line, allFieldNames, requiredFields, out fieldIndices, out fieldsTotal);
while ((line = reader.ReadLine()) != null)
{
linesRead++;
if (progressMonitor != null)
{
if (progressMonitor.IsCanceled)
return Document;
int progressNew = (int) (linesRead*100/lineCount);
if (progressPercent != progressNew)
{
progressMonitor.UpdateProgress(status = status.ChangePercentComplete(progressNew));
progressPercent = progressNew;
}
}
var dataFields = new DataFields(fieldIndices, line.ParseDsvFields(correctSeparator), allFieldNames);
if (dataFields.Length != fieldsTotal)
{
throw new IOException(string.Format(Resources.PeakBoundaryImporter_Import_Line__0__field_count__1__differs_from_the_first_line__which_has__2_,
linesRead, dataFields.Length, fieldsTotal));
}
string modifiedPeptideString = dataFields.GetField(Field.modified_peptide);
modMatcher.CreateMatches(Document.Settings,
new List<string> {modifiedPeptideString},
Settings.Default.StaticModList,
Settings.Default.HeavyModList);
// Convert the modified peptide string into a standardized form that
// converts unimod, names, etc, into masses, eg [+57.0]
var nodeForModPep = modMatcher.GetModifiedNode(modifiedPeptideString);
if (nodeForModPep == null)
{
throw new IOException(string.Format(Resources.PeakBoundaryImporter_Import_Peptide_has_unrecognized_modifications__0__at_line__1_, modifiedPeptideString, linesRead));
}
nodeForModPep = nodeForModPep.ChangeSettings(Document.Settings, SrmSettingsDiff.ALL);
modifiedPeptideString = nodeForModPep.RawTextId; // Modified sequence, or custom ion name
string fileName = dataFields.GetField(Field.filename);
bool isDecoy = dataFields.IsDecoy(linesRead);
var peptideIdentifier = new Tuple<string, bool>(modifiedPeptideString, isDecoy);
int charge;
bool chargeSpecified = dataFields.TryGetCharge(linesRead, out charge);
string sampleName = dataFields.GetField(Field.sample_name);
double? startTime = null;
double? endTime = null;
if (changePeaks)
{
startTime = dataFields.GetTime(Field.start_time, Resources.PeakBoundaryImporter_Import_The_value___0___on_line__1__is_not_a_valid_start_time_, linesRead);
if (startTime.HasValue)
startTime = startTime / timeConversionFactor;
endTime = dataFields.GetTime(Field.end_time, Resources.PeakBoundaryImporter_Import_The_value___0___on_line__1__is_not_a_valid_end_time_, linesRead);
if (endTime.HasValue)
endTime = endTime / timeConversionFactor;
}
// Error if only one of startTime and endTime is null
if (startTime == null && endTime != null)
throw new IOException(string.Format(Resources.PeakBoundaryImporter_Import_Missing_start_time_on_line__0_, linesRead));
if (startTime != null && endTime == null)
throw new IOException(string.Format(Resources.PeakBoundaryImporter_Import_Missing_end_time_on_line__0_, linesRead));
// Add filename to second dictionary if not yet encountered
ChromSetFileMatch fileMatch;
if (!fileNameToFileMatch.TryGetValue(fileName, out fileMatch))
{
fileMatch = Document.Settings.MeasuredResults.FindMatchingMSDataFile(MsDataFileUri.Parse(fileName));
fileNameToFileMatch.Add(fileName, fileMatch);
}
if (fileMatch == null)
{
UnrecognizedFiles.Add(fileName);
continue;
}
var chromSet = fileMatch.Chromatograms;
string nameSet = chromSet.Name;
ChromFileInfoId[] fileIds;
if (sampleName == null)
{
fileIds = chromSet.MSDataFileInfos.Select(x => x.FileId).ToArray();
}
else
{
var sampleFile = chromSet.MSDataFileInfos.FirstOrDefault(info => Equals(sampleName, info.FilePath.GetSampleName()));
if (sampleFile == null)
{
throw new IOException(string.Format(Resources.PeakBoundaryImporter_Import_Sample__0__on_line__1__does_not_match_the_file__2__, sampleName, linesRead, fileName));
}
fileIds = new[] {sampleFile.FileId};
}
// Look up the IdentityPath of peptide in first dictionary
IList<IdentityPath> pepPaths;
if (!sequenceToNode.TryGetValue(peptideIdentifier, out pepPaths))
{
UnrecognizedPeptides.Add(modifiedPeptideString);
continue;
}
// Define the annotations to be added
var annotations = dataFields.GetAnnotations();
AnnotationsAdded = annotations.Keys.ToList();
// Loop over all the transition groups in that peptide to find matching charge,
// or use all transition groups if charge not specified
bool foundSample = false;
foreach (var pepPath in pepPaths)
{
var nodePep = (PeptideDocNode)docNew.FindNode(pepPath);
for(int i = 0; i < nodePep.Children.Count; ++i)
{
var groupRelPath = nodePep.GetPathTo(i);
var groupNode = (TransitionGroupDocNode) nodePep.FindNode(groupRelPath);
if (!chargeSpecified || charge == groupNode.TransitionGroup.PrecursorCharge)
{
var groupFileIndices =
new HashSet<int>(groupNode.ChromInfos.Select(x => x.FileId.GlobalIndex));
// Loop over the files in this groupNode to find the correct sample
// Change peak boundaries for the transition group
foreach (var fileId in fileIds)
{
if (groupFileIndices.Contains(fileId.GlobalIndex))
{
var groupPath = new IdentityPath(pepPath, groupNode.Id);
// Attach annotations
docNew = docNew.AddPrecursorResultsAnnotations(groupPath, fileId, annotations);
// Change peak
var filePath = chromSet.GetFileInfo(fileId).FilePath;
if (changePeaks)
{
docNew = docNew.ChangePeak(groupPath, nameSet, filePath,
null, startTime, endTime, UserSet.IMPORTED, null, false);
}
// For removing peaks that are not in the file, if removeMissing = true
trackAdjustedResults.Add(new ResultsKey(fileId.GlobalIndex, groupNode.Id));
foundSample = true;
}
}
}
}
}
if (!foundSample)
{
UnrecognizedChargeStates.Add(new UnrecognizedChargeState(charge, fileName, modifiedPeptideString));
}
}
// Remove peaks from the document that weren't in the file.
if (removeMissing)
docNew = RemoveMissing(docNew, trackAdjustedResults, changePeaks);
// If nothing has changed, return the old Document before ChangeIgnoreChangingChildren was turned off
if (!ReferenceEquals(docNew, docReference))
Document = (SrmDocument) Document.ChangeIgnoreChangingChildren(false).ChangeChildrenChecked(docNew.Children);
return Document;
}
public SrmDocument Import(TextReader reader, IProgressMonitor progressMonitor, long lineCount, bool isMinutes, bool removeMissing = false, bool changePeaks = true)
{
IProgressStatus status = new ProgressStatus(Resources.PeakBoundaryImporter_Import_Importing_Peak_Boundaries);
double timeConversionFactor = isMinutes ? 1.0 : 60.0;
int linesRead = 0;
int progressPercent = 0;
var docNew = (SrmDocument)Document.ChangeIgnoreChangingChildren(true);
var docReference = docNew;
var sequenceToNode = MakeSequenceDictionary(Document);
var fileNameToFileMatch = new Dictionary <string, ChromSetFileMatch>();
var trackAdjustedResults = new HashSet <ResultsKey>();
var modMatcher = new ModificationMatcher();
var canonicalSequenceDict = new Dictionary <string, string>();
// Add annotations as possible columns
var allFieldNames = new List <string[]>(FIELD_NAMES);
allFieldNames.AddRange(from def in Document.Settings.DataSettings.AnnotationDefs
where def.AnnotationTargets.Contains(AnnotationDef.AnnotationTarget.precursor_result)
select new[] { def.Name });
string line = reader.ReadLine();
linesRead++;
int[] fieldIndices;
int fieldsTotal;
// If we aren't changing peaks, allow start and end time to be missing
var requiredFields = changePeaks ? REQUIRED_FIELDS : REQUIRED_NO_CHROM;
char correctSeparator = ReadFirstLine(line, allFieldNames, requiredFields, out fieldIndices, out fieldsTotal);
while ((line = reader.ReadLine()) != null)
{
linesRead++;
if (progressMonitor != null)
{
if (progressMonitor.IsCanceled)
{
return(Document);
}
int progressNew = (int)(linesRead * 100 / lineCount);
if (progressPercent != progressNew)
{
progressMonitor.UpdateProgress(status = status.ChangePercentComplete(progressNew));
progressPercent = progressNew;
}
}
var dataFields = new DataFields(fieldIndices, line.ParseDsvFields(correctSeparator), allFieldNames);
if (dataFields.Length != fieldsTotal)
{
throw new IOException(string.Format(Resources.PeakBoundaryImporter_Import_Line__0__field_count__1__differs_from_the_first_line__which_has__2_,
linesRead, dataFields.Length, fieldsTotal));
}
string modifiedPeptideString = dataFields.GetField(Field.modified_peptide);
string fileName = dataFields.GetField(Field.filename);
bool isDecoy = dataFields.IsDecoy(linesRead);
IList <IdentityPath> pepPaths;
if (!sequenceToNode.TryGetValue(Tuple.Create(modifiedPeptideString, isDecoy), out pepPaths))
{
string canonicalSequence;
if (!canonicalSequenceDict.TryGetValue(modifiedPeptideString, out canonicalSequence))
{
if (modifiedPeptideString.Any(c => c < 'A' || c > 'Z'))
{
modMatcher.CreateMatches(Document.Settings,
new List <string> {
modifiedPeptideString
},
Settings.Default.StaticModList,
Settings.Default.HeavyModList);
var nodeForModPep = modMatcher.GetModifiedNode(modifiedPeptideString);
if (nodeForModPep == null)
{
throw new IOException(string.Format(Resources.PeakBoundaryImporter_Import_Peptide_has_unrecognized_modifications__0__at_line__1_, modifiedPeptideString, linesRead));
}
nodeForModPep = nodeForModPep.ChangeSettings(Document.Settings, SrmSettingsDiff.ALL);
// Convert the modified peptide string into a standardized form that
// converts unimod, names, etc, into masses, eg [+57.0]
canonicalSequence = nodeForModPep.ModifiedTarget.Sequence;
canonicalSequenceDict.Add(modifiedPeptideString, canonicalSequence);
}
}
if (null != canonicalSequence)
{
sequenceToNode.TryGetValue(Tuple.Create(canonicalSequence, isDecoy), out pepPaths);
}
}
if (null == pepPaths)
{
UnrecognizedPeptides.Add(modifiedPeptideString);
continue;
}
Adduct charge;
bool chargeSpecified = dataFields.TryGetCharge(linesRead, out charge);
string sampleName = dataFields.GetField(Field.sample_name);
double?apexTime = dataFields.GetTime(Field.apex_time, timeConversionFactor,
Resources.PeakBoundaryImporter_Import_The_value___0___on_line__1__is_not_a_valid_time_, linesRead);
double?startTime = dataFields.GetTime(Field.start_time, timeConversionFactor,
Resources.PeakBoundaryImporter_Import_The_value___0___on_line__1__is_not_a_valid_start_time_, linesRead);
double?endTime = dataFields.GetTime(Field.end_time, timeConversionFactor,
Resources.PeakBoundaryImporter_Import_The_value___0___on_line__1__is_not_a_valid_end_time_, linesRead);
// Error if only one of startTime and endTime is null
if (startTime == null && endTime != null)
{
if (changePeaks)
{
throw new IOException(string.Format(Resources.PeakBoundaryImporter_Import_Missing_start_time_on_line__0_, linesRead));
}
endTime = null;
}
if (startTime != null && endTime == null)
{
if (changePeaks)
{
throw new IOException(string.Format(Resources.PeakBoundaryImporter_Import_Missing_end_time_on_line__0_, linesRead));
}
startTime = null;
}
// Add filename to second dictionary if not yet encountered
ChromSetFileMatch fileMatch;
if (!fileNameToFileMatch.TryGetValue(fileName, out fileMatch))
{
fileMatch = Document.Settings.MeasuredResults.FindMatchingMSDataFile(MsDataFileUri.Parse(fileName));
fileNameToFileMatch.Add(fileName, fileMatch);
}
if (fileMatch == null)
{
UnrecognizedFiles.Add(fileName);
continue;
}
var chromSet = fileMatch.Chromatograms;
string nameSet = chromSet.Name;
ChromFileInfoId[] fileIds;
if (sampleName == null)
{
fileIds = chromSet.MSDataFileInfos.Select(x => x.FileId).ToArray();
}
else
{
var sampleFile = chromSet.MSDataFileInfos.FirstOrDefault(info => Equals(sampleName, info.FilePath.GetSampleName()));
if (sampleFile == null)
{
throw new IOException(string.Format(Resources.PeakBoundaryImporter_Import_Sample__0__on_line__1__does_not_match_the_file__2__, sampleName, linesRead, fileName));
}
fileIds = new[] { sampleFile.FileId };
}
// Define the annotations to be added
var annotations = dataFields.GetAnnotations();
if (!changePeaks)
{
if (apexTime.HasValue)
{
annotations.Add(ComparePeakBoundaries.APEX_ANNOTATION, dataFields.GetField(Field.apex_time));
}
if (startTime.HasValue && endTime.HasValue)
{
annotations.Add(ComparePeakBoundaries.START_TIME_ANNOTATION, dataFields.GetField(Field.start_time));
annotations.Add(ComparePeakBoundaries.END_TIME_ANNOTATION, dataFields.GetField(Field.end_time));
}
}
AnnotationsAdded = annotations.Keys.ToList();
// Loop over all the transition groups in that peptide to find matching charge,
// or use all transition groups if charge not specified
bool foundSample = false;
foreach (var pepPath in pepPaths)
{
var nodePep = (PeptideDocNode)docNew.FindNode(pepPath);
foreach (TransitionGroupDocNode groupNode in nodePep.Children)
{
if (chargeSpecified && charge != groupNode.TransitionGroup.PrecursorAdduct)
{
continue;
}
// Loop over the files in this groupNode to find the correct sample
// Change peak boundaries for the transition group
foreach (var fileId in GetApplicableFiles(fileIds, groupNode))
{
var groupPath = new IdentityPath(pepPath, groupNode.Id);
// Attach annotations
if (annotations.Any())
{
docNew = docNew.AddPrecursorResultsAnnotations(groupPath, fileId, annotations);
}
// Change peak
var filePath = chromSet.GetFileInfo(fileId).FilePath;
if (changePeaks)
{
docNew = docNew.ChangePeak(groupPath, nameSet, filePath,
null, startTime, endTime, UserSet.IMPORTED, null, false);
}
// For removing peaks that are not in the file, if removeMissing = true
trackAdjustedResults.Add(new ResultsKey(fileId.GlobalIndex, groupNode.Id));
foundSample = true;
}
}
}
if (!foundSample)
{
UnrecognizedChargeStates.Add(new UnrecognizedChargeState(charge, fileName, modifiedPeptideString));
}
}
// Remove peaks from the document that weren't in the file.
if (removeMissing)
{
docNew = RemoveMissing(docNew, trackAdjustedResults, changePeaks);
}
// If nothing has changed, return the old Document before ChangeIgnoreChangingChildren was turned off
if (!ReferenceEquals(docNew, docReference))
{
Document = (SrmDocument)Document.ChangeIgnoreChangingChildren(false).ChangeChildrenChecked(docNew.Children);
}
return(Document);
}
public void Run(ProcessStartInfo psi, string stdin, IProgressMonitor progress, ref IProgressStatus status, TextWriter writer)
{
// Make sure required streams are redirected.
psi.RedirectStandardOutput = true;
psi.RedirectStandardError = true;
_messageLog.Clear();
var proc = Process.Start(psi);
if (proc == null)
{
throw new IOException(string.Format(@"Failure starting {0} command.", psi.FileName));
}
if (stdin != null)
{
try
{
proc.StandardInput.Write(stdin);
}
finally
{
proc.StandardInput.Close();
}
}
var reader = new ProcessStreamReader(proc);
StringBuilder sbError = new StringBuilder();
int percentLast = 0;
string line;
while ((line = reader.ReadLine(progress)) != null)
{
if (writer != null && !line.StartsWith(HideLinePrefix))
{
writer.WriteLine(line);
}
if (progress == null || line.ToLowerInvariant().StartsWith(@"error"))
{
sbError.AppendLine(line);
}
else // if (progress != null)
{
if (progress.IsCanceled)
{
proc.Kill();
progress.UpdateProgress(status = status.Cancel());
return;
}
if (!string.IsNullOrEmpty(MessagePrefix) && line.StartsWith(MessagePrefix))
{
_messageLog.Add(line.Substring(MessagePrefix.Length));
}
else if (line.EndsWith(@"%"))
{
double percent;
string[] parts = line.Split(' ');
string percentPart = parts[parts.Length - 1];
if (double.TryParse(percentPart.Substring(0, percentPart.Length - 1), out percent))
{
percentLast = (int)percent;
status = status.ChangePercentComplete(percentLast);
if (percent >= 100 && status.SegmentCount > 0)
{
status = status.NextSegment();
}
progress.UpdateProgress(status);
}
}
else if (StatusPrefix == null || line.StartsWith(StatusPrefix))
{
// Remove prefix, if there is one.
if (StatusPrefix != null)
{
line = line.Substring(StatusPrefix.Length);
}
status = status.ChangeMessage(line);
progress.UpdateProgress(status);
}
}
}
proc.WaitForExit();
int exit = proc.ExitCode;
if (exit != 0)
{
line = proc.StandardError.ReadLine();
if (line != null)
{
sbError.AppendLine(line);
}
if (sbError.Length == 0)
{
sbError.AppendLine(@"Error occurred running process.");
}
string processPath = Path.GetDirectoryName(psi.FileName)?.Length == 0
? Path.Combine(Environment.CurrentDirectory, psi.FileName)
: psi.FileName;
// ReSharper disable LocalizableElement
sbError.AppendFormat("\r\nCommand-line: {0} {1}\r\nWorking directory: {2}{3}", processPath,
// ReSharper restore LocalizableElement
string.Join(" ", proc.StartInfo.Arguments), psi.WorkingDirectory,
stdin != null ? "\r\nStandard input:\r\n" + stdin : "");
throw new IOException(sbError.ToString());
}
// Make to complete the status, if the process succeeded, but never
// printed 100% to the console
if (percentLast < 100)
{
status = status.ChangePercentComplete(100);
if (status.SegmentCount > 0)
{
status = status.NextSegment();
}
if (progress != null)
{
progress.UpdateProgress(status);
}
}
}
public static IEnumerable <ValidatingIonMobilityPeptide> ConvertDriftTimesToCollisionalCrossSections(IProgressMonitor monitor,
IEnumerable <IIonMobilityInfoProvider> providers,
int countProviders,
IDictionary <int, RegressionLine> regressions)
{
IProgressStatus status = new ProgressStatus(Resources.CollisionalCrossSectionGridViewDriver_ProcessIonMobilityValues_Reading_ion_mobility_information);
var peptideIonMobilities = new List <ValidatingIonMobilityPeptide>();
int runCount = 0;
foreach (var ionMobilityInfoProvider in providers)
{
if ((monitor != null) && monitor.IsCanceled)
{
return(null);
}
runCount++;
string message = string.Format(Resources.CollisionalCrossSectionGridViewDriver_ProcessDriftTimes_Reading_ion_mobility_data_from__0__, ionMobilityInfoProvider.Name);
if (monitor != null)
{
monitor.UpdateProgress(status = status.ChangeMessage(message));
}
foreach (var ionMobilityList in ionMobilityInfoProvider.GetIonMobilityDict())
{
// If there is more than one value, just average them
double totalDrift = 0;
double totalHighEnergyOffset = 0;
int count = 0;
foreach (var ionMobilityInfo in ionMobilityList.Value)
{
totalHighEnergyOffset += ionMobilityInfo.HighEnergyDriftTimeOffsetMsec;
if (ionMobilityInfo.IsCollisionalCrossSection)
{
totalDrift += ionMobilityInfo.Value;
}
else
{
// Convert from a measured drift time
RegressionLine regression;
if ((regressions != null) && regressions.TryGetValue(ionMobilityList.Key.Charge, out regression))
{
totalDrift += regression.GetX(ionMobilityInfo.Value); // x = (y-intercept)/slope
}
else
{
throw new Exception(String.Format(Resources.CollisionalCrossSectionGridViewDriver_ProcessIonMobilityValues_Cannot_import_measured_drift_time_for_sequence__0___no_collisional_cross_section_conversion_parameters_were_provided_for_charge_state__1__,
ionMobilityList.Key.Sequence,
ionMobilityList.Key.Charge));
}
}
count++;
}
if (count > 0)
{
peptideIonMobilities.Add(new ValidatingIonMobilityPeptide(ionMobilityList.Key.Sequence, totalDrift / count, totalHighEnergyOffset / count));
}
}
if (monitor != null)
{
monitor.UpdateProgress(status = status.ChangePercentComplete(runCount * 100 / countProviders));
}
}
if (monitor != null)
{
monitor.UpdateProgress(status.Complete());
}
return(peptideIonMobilities);
}
public void Share(IProgressMonitor progressMonitor)
{
ProgressMonitor = progressMonitor;
ProgressMonitor.UpdateProgress(_progressStatus = new ProgressStatus(DefaultMessage));
using (var zip = new ZipFile())
{
// Make sure large files don't cause this to fail.
zip.UseZip64WhenSaving = Zip64Option.AsNecessary;
if (CompleteSharing)
ShareComplete(zip);
else
ShareMinimal(zip);
}
}
// ReSharper restore NonLocalizedString
public static List<string> ConvertPilotFiles(IList<string> inputFiles, IProgressMonitor progress, ProgressStatus status)
{
string groupConverterExePath = null;
var inputFilesPilotConverted = new List<string>();
for (int index = 0; index < inputFiles.Count; index++)
{
string inputFile = inputFiles[index];
if (!inputFile.EndsWith(BiblioSpecLiteBuilder.EXT_PILOT))
{
inputFilesPilotConverted.Add(inputFile);
continue;
}
string outputFile = Path.ChangeExtension(inputFile, BiblioSpecLiteBuilder.EXT_PILOT_XML);
// Avoid re-converting files that have already been converted
if (File.Exists(outputFile))
{
// Avoid duplication, in case the user accidentally adds both .group and .group.xml files
// for the same results
if (!inputFiles.Contains(outputFile))
inputFilesPilotConverted.Add(outputFile);
continue;
}
string message = string.Format(Resources.VendorIssueHelper_ConvertPilotFiles_Converting__0__to_xml, Path.GetFileName(inputFile));
int percent = index * 100 / inputFiles.Count;
progress.UpdateProgress(status = status.ChangeMessage(message).ChangePercentComplete(percent));
if (groupConverterExePath == null)
{
var key = Registry.LocalMachine.OpenSubKey(KEY_PROTEIN_PILOT, false);
if (key != null)
{
string proteinPilotCommandWithArgs = (string)key.GetValue(string.Empty);
var proteinPilotCommandWithArgsSplit =
proteinPilotCommandWithArgs.Split(new[] { "\" \"" }, StringSplitOptions.RemoveEmptyEntries); // Remove " "%1" // Not L10N
string path = Path.GetDirectoryName(proteinPilotCommandWithArgsSplit[0].Trim(new[] { '\\', '\"' })); // Remove preceding "
if (path != null)
{
var groupFileExtractorPath = Path.Combine(path, EXE_GROUP_FILE_EXTRACTOR);
if (File.Exists(groupFileExtractorPath))
{
groupConverterExePath = groupFileExtractorPath;
}
else
{
var group2XmlPath = Path.Combine(path, EXE_GROUP2_XML);
if (File.Exists(group2XmlPath))
{
groupConverterExePath = group2XmlPath;
}
else
{
string errorMessage = string.Format(Resources.VendorIssueHelper_ConvertPilotFiles_Unable_to_find__0__or__1__in_directory__2____Please_reinstall_ProteinPilot_software_to_be_able_to_handle__group_files_,
EXE_GROUP_FILE_EXTRACTOR, EXE_GROUP2_XML, path);
throw new IOException(errorMessage);
}
}
}
}
if (groupConverterExePath == null)
{
throw new IOException(Resources.VendorIssueHelper_ConvertPilotFiles_ProteinPilot_software__trial_or_full_version__must_be_installed_to_convert___group__files_to_compatible___group_xml__files_);
}
}
// run group2xml
// ReSharper disable NonLocalizedString
var argv = new[]
{
"XML",
"\"" + inputFile + "\"",
"\"" + outputFile + "\""
};
// ReSharper restore NonLocalizedString
var psi = new ProcessStartInfo(groupConverterExePath)
{
CreateNoWindow = true,
UseShellExecute = false,
// Common directory includes the directory separator
WorkingDirectory = Path.GetDirectoryName(groupConverterExePath) ?? string.Empty,
Arguments = string.Join(" ", argv.ToArray()), // Not L10N
RedirectStandardError = true,
RedirectStandardOutput = true,
};
var sbOut = new StringBuilder();
var proc = new Process {StartInfo = psi};
proc.Start();
var reader = new ProcessStreamReader(proc);
string line;
while ((line = reader.ReadLine()) != null)
{
if (progress.IsCanceled)
{
proc.Kill();
throw new LoadCanceledException(status.Cancel());
}
sbOut.AppendLine(line);
}
while (!proc.WaitForExit(200))
{
if (progress.IsCanceled)
{
proc.Kill();
return inputFilesPilotConverted;
}
}
if (proc.ExitCode != 0)
{
throw new IOException(TextUtil.LineSeparate(string.Format(Resources.VendorIssueHelper_ConvertPilotFiles_Failure_attempting_to_convert_file__0__to__group_xml_,
inputFile), string.Empty, sbOut.ToString()));
}
inputFilesPilotConverted.Add(outputFile);
}
progress.UpdateProgress(status.ChangePercentComplete(100));
return inputFilesPilotConverted;
}
//Throws DatabaseOpeningException
public static OptimizationDb GetOptimizationDb(string path, IProgressMonitor loadMonitor, SrmDocument document)
{
var status = new ProgressStatus(string.Format(Resources.OptimizationDb_GetOptimizationDb_Loading_optimization_library__0_, path));
if (loadMonitor != null)
loadMonitor.UpdateProgress(status);
try
{
if (path == null)
throw new OptimizationsOpeningException(Resources.OptimizationDb_GetOptimizationDb_Library_path_cannot_be_null_);
if (!File.Exists(path))
throw new OptimizationsOpeningException(String.Format(Resources.OptimizationDb_GetOptimizationDb_The_file__0__does_not_exist_, path));
string message;
try
{
//Check for a valid SQLite file and that it has our schema
//Allow only one thread at a time to read from the same path
using (var sessionFactory = GetSessionFactory(path))
{
lock (sessionFactory)
{
return new OptimizationDb(path, sessionFactory).Load(loadMonitor, status);
}
}
}
catch (UnauthorizedAccessException)
{
message = string.Format(Resources.OptimizationDb_GetOptimizationDb_You_do_not_have_privilieges_to_access_the_file__0__, path);
}
catch (DirectoryNotFoundException)
{
message = string.Format(Resources.OptimizationDb_GetOptimizationDb_The_path_containing__0__does_not_exist_, path);
}
catch (FileNotFoundException)
{
message = string.Format(Resources.OptimizationDb_GetOptimizationDb_The_file__0__could_not_be_created__Perhaps_you_do_not_have_sufficient_privileges_, path);
}
catch (SQLiteException)
{
message = string.Format(Resources.OptimizationDb_GetOptimizationDb_The_file__0__is_not_a_valid_optimization_library_file_, path);
}
catch (GenericADOException)
{
try
{
return ConvertFromOldFormat(path, loadMonitor, status, document);
}
catch (Exception e)
{
message = string.Format(Resources.OptimizationDb_GetOptimizationDb_The_file__0__could_not_be_opened__conversion_from_old_format_failed____1_, path, e.Message);
}
}
catch (Exception e)
{
message = string.Format(Resources.OptimizationDb_GetOptimizationDb_The_file__0__could_not_be_opened___1_, path, e.Message);
}
throw new OptimizationsOpeningException(message);
}
catch (OptimizationsOpeningException x)
{
if (loadMonitor == null)
throw;
loadMonitor.UpdateProgress(status.ChangeErrorException(x));
return null;
}
}
// ReSharper restore NonLocalizedString
/// <summary>
/// Executes an export for all chromatograms in the document
/// with file names matching one of the files in filesToExport
/// writer = location to write the chromatogram data to
/// longWaitBroker = progress bar (can be null)
/// filesToExport = file names for which to write chromatograms
/// cultureInfo = local culture
/// chromExtractors = list of special chromatogram types to include (base peak, etc)
/// chromSources = type of ions to include (precursor, product)
/// </summary>
public void Export(TextWriter writer,
IProgressMonitor longWaitBroker,
IList <string> filesToExport,
CultureInfo cultureInfo,
IList <ChromExtractor> chromExtractors,
IList <ChromSource> chromSources)
{
int currentReplicates = 0;
int totalReplicates = _chromatogramSets.Count;
IProgressStatus status = new ProgressStatus(string.Empty);
FormatHeader(writer, FIELD_NAMES);
foreach (var chromatograms in _chromatogramSets)
{
if (longWaitBroker != null)
{
int percentComplete = currentReplicates++ *100 / totalReplicates;
if (percentComplete < 100)
{
longWaitBroker.UpdateProgress(status = status.ChangeMessage(string.Format(Resources.ChromatogramExporter_Export_Exporting_Chromatograms_for__0_,
chromatograms.Name)).ChangePercentComplete(percentComplete));
}
}
foreach (var extractor in chromExtractors)
{
ChromatogramGroupInfo[] arrayChromSpecial;
if (!_measuredResults.TryLoadAllIonsChromatogram(chromatograms, extractor, true, out arrayChromSpecial))
{
// TODO: need error determination here
continue;
}
foreach (var chromInfo in arrayChromSpecial)
{
string fileName = chromInfo.FilePath.GetFileName();
// Skip the files that have not been selected for export
if (!filesToExport.Contains(fileName))
{
continue;
}
var firstChromatogram = chromInfo.TransitionPointSets.First();
IList <float> times = firstChromatogram.Times;
IList <float> intensities = firstChromatogram.Intensities;
float tic = CalculateTic(times, intensities);
string extractorName = GetExtractorName(extractor);
string[] fieldArray =
{
fileName,
TextUtil.EXCEL_NA,
TextUtil.EXCEL_NA,
TextUtil.EXCEL_NA,
extractorName,
TextUtil.EXCEL_NA,
TextUtil.EXCEL_NA,
System.Convert.ToString(tic, cultureInfo)
};
FormatChromLine(writer, fieldArray, times, intensities, cultureInfo);
}
}
var molecules = Document.Molecules.ToArray();
for (int iMolecule = 0; iMolecule < molecules.Length; iMolecule++)
{
if (longWaitBroker != null)
{
if (longWaitBroker.IsCanceled)
{
return;
}
longWaitBroker.UpdateProgress(status = status.ChangePercentComplete(iMolecule * 100 / molecules.Length));
}
var peptideNode = molecules[iMolecule];
foreach (TransitionGroupDocNode groupNode in peptideNode.Children)
{
if (longWaitBroker != null && longWaitBroker.IsCanceled)
{
return;
}
ExportGroupNode(peptideNode, groupNode, chromatograms, filesToExport, chromSources, writer, cultureInfo);
}
}
}
}
public static OptimizationDb ConvertFromOldFormat(string path, IProgressMonitor loadMonitor, ProgressStatus status, SrmDocument document)
{
// Try to open assuming old format (Id, PeptideModSeq, Charge, Mz, Value, Type)
var precursors = new Dictionary<string, HashSet<int>>(); // PeptideModSeq -> charges
var optimizations = new List<Tuple<DbOptimization, double>>(); // DbOptimization, product m/z
int maxCharge = 1;
using (SQLiteConnection connection = new SQLiteConnection("Data Source = " + path)) // Not L10N
using (SQLiteCommand command = new SQLiteCommand(connection))
{
connection.Open();
command.CommandText = "SELECT PeptideModSeq, Charge, Mz, Value, Type FROM OptimizationLibrary"; // Not L10N
using (SQLiteDataReader reader = command.ExecuteReader())
{
while (reader.Read())
{
var type = (OptimizationType)reader["Type"]; // Not L10N
var modifiedSequence = reader["PeptideModSeq"].ToString(); // Not L10N
var charge = (int)reader["Charge"]; // Not L10N
var productMz = (double)reader["Mz"]; // Not L10N
var value = (double)reader["Value"]; // Not L10N
optimizations.Add(new Tuple<DbOptimization, double>(new DbOptimization(type, modifiedSequence, charge, string.Empty, -1, value), productMz));
if (!precursors.ContainsKey(modifiedSequence))
{
precursors[modifiedSequence] = new HashSet<int>();
}
precursors[modifiedSequence].Add(charge);
if (charge > maxCharge)
{
maxCharge = charge;
}
}
}
}
var peptideList = (from precursor in precursors
from charge in precursor.Value
select string.Format("{0}{1}", precursor.Key, Transition.GetChargeIndicator(charge)) // Not L10N
).ToList();
var newDoc = new SrmDocument(document != null ? document.Settings : SrmSettingsList.GetDefault());
newDoc = newDoc.ChangeSettings(newDoc.Settings
.ChangePeptideLibraries(libs => libs.ChangePick(PeptidePick.filter))
.ChangeTransitionFilter(filter =>
filter.ChangeFragmentRangeFirstName("ion 1") // Not L10N
.ChangeFragmentRangeLastName("last ion") // Not L10N
.ChangeProductCharges(Enumerable.Range(1, maxCharge).ToList())
.ChangeIonTypes(new []{ IonType.y, IonType.b }))
.ChangeTransitionLibraries(libs => libs.ChangePick(TransitionLibraryPick.none))
);
var matcher = new ModificationMatcher { FormatProvider = NumberFormatInfo.InvariantInfo };
matcher.CreateMatches(newDoc.Settings, peptideList, Settings.Default.StaticModList, Settings.Default.HeavyModList);
FastaImporter importer = new FastaImporter(newDoc, matcher);
string text = string.Format(">>{0}\r\n{1}", newDoc.GetPeptideGroupId(true), TextUtil.LineSeparate(peptideList)); // Not L10N
PeptideGroupDocNode imported = importer.Import(new StringReader(text), null, Helpers.CountLinesInString(text)).First();
int optimizationsUpdated = 0;
foreach (PeptideDocNode nodePep in imported.Children)
{
string sequence = newDoc.Settings.GetSourceTextId(nodePep);
foreach (var nodeGroup in nodePep.TransitionGroups)
{
int charge = nodeGroup.PrecursorCharge;
foreach (var nodeTran in nodeGroup.Transitions)
{
double productMz = nodeTran.Mz;
foreach (var optimization in optimizations.Where(opt =>
string.IsNullOrEmpty(opt.Item1.FragmentIon) &&
opt.Item1.ProductCharge == -1 &&
opt.Item1.PeptideModSeq == sequence &&
opt.Item1.Charge == charge &&
Math.Abs(opt.Item2 - productMz) < 0.00001))
{
optimization.Item1.FragmentIon = nodeTran.FragmentIonName;
optimization.Item1.ProductCharge = nodeTran.Transition.Charge;
++optimizationsUpdated;
}
}
}
}
if (optimizations.Count > optimizationsUpdated)
{
throw new OptimizationsOpeningException(string.Format(Resources.OptimizationDb_ConvertFromOldFormat_Failed_to_convert__0__optimizations_to_new_format_,
optimizations.Count - optimizationsUpdated));
}
using (var fs = new FileSaver(path))
{
OptimizationDb db = CreateOptimizationDb(fs.SafeName);
db.UpdateOptimizations(optimizations.Select(opt => opt.Item1).ToArray(), new DbOptimization[0]);
fs.Commit();
if (loadMonitor != null)
loadMonitor.UpdateProgress(status.ChangePercentComplete(100));
return GetOptimizationDb(fs.RealName, null, null);
}
}
public static IrtDb GetIrtDb(string path, IProgressMonitor loadMonitor, out IList <DbIrtPeptide> dbPeptides)
{
var status = new ProgressStatus(string.Format(Resources.IrtDb_GetIrtDb_Loading_iRT_database__0_, path));
if (loadMonitor != null)
{
loadMonitor.UpdateProgress(status);
}
try
{
if (path == null)
{
throw new DatabaseOpeningException(Resources.IrtDb_GetIrtDb_Database_path_cannot_be_null);
}
if (!File.Exists(path))
{
throw new DatabaseOpeningException(String.Format(Resources.IrtDb_GetIrtDb_The_file__0__does_not_exist_, path));
}
string message;
Exception xInner = null;
try
{
//Check for a valid SQLite file and that it has our schema
//Allow only one thread at a time to read from the same path
using (var sessionFactory = GetSessionFactory(path))
{
lock (sessionFactory)
{
return(new IrtDb(path, sessionFactory).Load(loadMonitor, status, out dbPeptides));
}
}
}
catch (UnauthorizedAccessException x)
{
message = string.Format(Resources.IrtDb_GetIrtDb_You_do_not_have_privileges_to_access_the_file__0_, path);
xInner = x;
}
catch (DirectoryNotFoundException x)
{
message = string.Format(Resources.IrtDb_GetIrtDb_The_path_containing__0__does_not_exist, path);
xInner = x;
}
catch (FileNotFoundException x)
{
message = string.Format(Resources.IrtDb_GetIrtDb_The_file__0__could_not_be_created_Perhaps_you_do_not_have_sufficient_privileges, path);
xInner = x;
}
catch (SQLiteException x)
{
message = string.Format(Resources.IrtDb_GetIrtDb_The_file__0__is_not_a_valid_iRT_database_file, path);
xInner = x;
}
catch (Exception x)
{
message = string.Format(Resources.IrtDb_GetIrtDb_The_file__0__could_not_be_opened, path);
xInner = x;
}
throw new DatabaseOpeningException(message, xInner);
}
catch (DatabaseOpeningException x)
{
if (loadMonitor == null)
{
throw;
}
loadMonitor.UpdateProgress(status.ChangeErrorException(x));
dbPeptides = new DbIrtPeptide[0];
return(null);
}
}
/// <summary>
/// Initialize isolation scheme export.
/// </summary>
protected bool InitExport(string fileName, IProgressMonitor progressMonitor)
{
if (progressMonitor.IsCanceled)
return false;
// First export transition lists to map in memory
Export(null, progressMonitor);
// If filename is null, then no more work needs to be done.
if (fileName == null)
{
progressMonitor.UpdateProgress(new ProgressStatus(string.Empty).Complete());
return false;
}
return true;
}
