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);
}
// 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;
}
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()));
}
}
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 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);
}
protected override bool LoadBackground(IDocumentContainer container, SrmDocument document, SrmDocument docCurrent)
{
// Only allow one background proteome to load at a time. This can
// get tricky, if the user performs an undo and then a redo across
// a change in background proteome.
// Our first priority is doing the digestions, the second is accessing web
// services to add missing protein metadata.
lock (_lockLoadBackgroundProteome)
{
BackgroundProteome originalBackgroundProteome = GetBackgroundProteome(docCurrent);
// Check to see whether the Digestion already exists but has not been queried yet.
BackgroundProteome backgroundProteomeWithDigestions = new BackgroundProteome(originalBackgroundProteome, true);
if (IsNotLoadedExplained(docCurrent, backgroundProteomeWithDigestions, true) == null)
{
// digest is ready, and protein metdata is resolved
CompleteProcessing(container, backgroundProteomeWithDigestions);
return true;
}
// are we here to do the digest, or to resolve the protein metadata?
bool getMetadata = (IsNotLoadedExplained(docCurrent, backgroundProteomeWithDigestions, false) == null) &&
backgroundProteomeWithDigestions.NeedsProteinMetadataSearch;
string name = originalBackgroundProteome.Name;
ProgressStatus progressStatus =
new ProgressStatus(string.Format(getMetadata?Resources.BackgroundProteomeManager_LoadBackground_Resolving_protein_details_for__0__proteome:Resources.BackgroundProteomeManager_LoadBackground_Digesting__0__proteome, name));
try
{
using (FileSaver fs = new FileSaver(originalBackgroundProteome.DatabasePath, StreamManager))
{
File.Copy(originalBackgroundProteome.DatabasePath, fs.SafeName, true);
var digestHelper = new DigestHelper(this, container, docCurrent, name, fs.SafeName, true);
bool success;
if (getMetadata)
success = digestHelper.LookupProteinMetadata(ref progressStatus);
else
success = (digestHelper.Digest(ref progressStatus) != null);
if (!success)
{
// Processing was canceled
EndProcessing(docCurrent);
UpdateProgress(progressStatus.Cancel());
return false;
}
using (var proteomeDb = ProteomeDb.OpenProteomeDb(originalBackgroundProteome.DatabasePath))
{
proteomeDb.DatabaseLock.AcquireWriterLock(int.MaxValue);
try
{
if (!fs.Commit())
{
EndProcessing(docCurrent);
throw new IOException(
string.Format(
Resources
.BackgroundProteomeManager_LoadBackground_Unable_to_rename_temporary_file_to__0__,
fs.RealName));
}
}
finally
{
proteomeDb.DatabaseLock.ReleaseWriterLock();
}
}
CompleteProcessing(container, new BackgroundProteome(originalBackgroundProteome, true));
UpdateProgress(progressStatus.Complete());
return true;
}
}
catch (Exception x)
{
var message = new StringBuilder();
message.AppendLine(
string.Format(Resources.BackgroundProteomeManager_LoadBackground_Failed_updating_background_proteome__0__,
name));
message.Append(x.Message);
UpdateProgress(progressStatus.ChangeErrorException(new IOException(message.ToString(), x)));
return false;
}
}
}
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 void Run(ProcessStartInfo psi, string stdin, IProgressMonitor progress, ref ProgressStatus status)
{
// 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));
}
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()) != null)
{
if (progress == null || line.ToLower().StartsWith("error"))
{
sbError.AppendLine(line);
}
else // if (progress != null)
{
if (progress.IsCanceled)
{
proc.Kill();
progress.UpdateProgress(status = status.Cancel());
return;
}
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 (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.");
}
throw new IOException(sbError.ToString());
}
// Make to complete the status, if the process succeeded, but never
// printed 100% to the console
else if (percentLast < 100)
{
status = status.ChangePercentComplete(100);
if (status.SegmentCount > 0)
{
status = status.NextSegment();
}
if (progress != null)
{
progress.UpdateProgress(status);
}
}
}
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;
}
// ReSharper restore UnusedMember.Local
private bool Load(ILoadMonitor loader)
{
ProgressStatus status =
new ProgressStatus(string.Format(Resources.BiblioSpecLibrary_Load_Loading__0__library,
Path.GetFileName(FilePath)));
loader.UpdateProgress(status);
long lenRead = 0;
// AdlerChecksum checksum = new AdlerChecksum();
try
{
// Use a buffered stream for initial read
BufferedStream stream = new BufferedStream(CreateStream(loader), 32 * 1024);
int countHeader = (int) LibHeaders.count*4;
byte[] libHeader = new byte[countHeader];
if (stream.Read(libHeader, 0, countHeader) != countHeader)
throw new InvalidDataException(Resources.BiblioSpecLibrary_Load_Data_truncation_in_library_header_File_may_be_corrupted);
lenRead += countHeader;
// Check the first byte of the primary version number to determine
// whether the format is little- or big-endian. Little-endian will
// have the version number in this byte, while big-endian will have zero.
if (libHeader[(int) LibHeaders.version1 * 4] == 0)
_bigEndian = true;
int numSpectra = GetInt32(libHeader, (int) LibHeaders.num_spectra);
var dictLibrary = new Dictionary<LibKey, BiblioSpectrumInfo>(numSpectra);
var setSequences = new HashSet<LibSeqKey>();
string revStr = string.Format("{0}.{1}", // Not L10N
GetInt32(libHeader, (int) LibHeaders.version1),
GetInt32(libHeader, (int) LibHeaders.version2));
Revision = float.Parse(revStr, CultureInfo.InvariantCulture);
// checksum.MakeForBuff(libHeader, AdlerChecksum.ADLER_START);
countHeader = (int) SpectrumHeaders.count*4;
byte[] specHeader = new byte[1024];
byte[] specSequence = new byte[1024];
for (int i = 0; i < numSpectra; i++)
{
int percent = i * 100 / numSpectra;
if (status.PercentComplete != percent)
{
// Check for cancellation after each integer change in percent loaded.
if (loader.IsCanceled)
{
loader.UpdateProgress(status.Cancel());
return false;
}
// If not cancelled, update progress.
loader.UpdateProgress(status = status.ChangePercentComplete(percent));
}
// Read spectrum header
int bytesRead = stream.Read(specHeader, 0, countHeader);
if (bytesRead != countHeader)
throw new InvalidDataException(Resources.BiblioSpecLibrary_Load_Data_truncation_in_spectrum_header_File_may_be_corrupted);
// If this is the first header, and the sequence length is zero,
// then this is a Linux format library. Switch to linux format,
// and start over.
if (i == 0 && GetInt32(specHeader, (int)SpectrumHeaders.seq_len) == 0)
{
_linuxFormat = true;
stream.Seek(lenRead, SeekOrigin.Begin);
// Re-ead spectrum header
countHeader = (int)SpectrumHeadersLinux.count * 4;
bytesRead = stream.Read(specHeader, 0, countHeader);
if (bytesRead != countHeader)
throw new InvalidDataException(Resources.BiblioSpecLibrary_Load_Data_truncation_in_spectrum_header_File_may_be_corrupted);
}
lenRead += bytesRead;
// checksum.MakeForBuff(specHeader, checksum.ChecksumValue);
int charge = GetInt32(specHeader, (int)SpectrumHeaders.charge);
if (charge > TransitionGroup.MAX_PRECURSOR_CHARGE)
throw new InvalidDataException(Resources.BiblioSpecLibrary_Load_Invalid_precursor_charge_found_File_may_be_corrupted);
int numPeaks = GetInt32(specHeader, (int)SpectrumHeaders.num_peaks);
int seqLength = GetInt32(specHeader, (_linuxFormat ?
(int)SpectrumHeadersLinux.seq_len : (int)SpectrumHeaders.seq_len));
int copies = GetInt32(specHeader, (_linuxFormat ?
(int)SpectrumHeadersLinux.copies : (int)SpectrumHeaders.copies));
// Read sequence information
int countSeq = (seqLength + 1)*2;
if (stream.Read(specSequence, 0, countSeq) != countSeq)
throw new InvalidDataException(Resources.BiblioSpecLibrary_Load_Data_truncation_in_spectrum_sequence_File_may_be_corrupted);
lenRead += countSeq;
// checksum.MakeForBuff(specSequence, checksum.ChecksumValue);
// Store in dictionary
if (IsUnmodified(specSequence, seqLength + 1, seqLength))
{
// These libraries should not have duplicates, but just in case.
// CONSIDER: Emit error about redundancy?
// These legacy libraries assume [+57.0] modified Cysteine
LibKey key = new LibKey(GetCModified(specSequence, ref seqLength), 0, seqLength, charge);
if (!dictLibrary.ContainsKey(key))
dictLibrary.Add(key, new BiblioSpectrumInfo((short)copies, (short)numPeaks, lenRead));
setSequences.Add(new LibSeqKey(key));
}
// Read over peaks
int countPeaks = 2*sizeof(Single)*numPeaks;
stream.Seek(countPeaks, SeekOrigin.Current); // Skip spectrum
lenRead += countPeaks;
// checksum.MakeForBuff(specPeaks, checksum.ChecksumValue);
}
// Checksum = checksum.ChecksumValue;
_dictLibrary = dictLibrary;
_setSequences = setSequences;
loader.UpdateProgress(status.Complete());
return true;
}
catch (InvalidDataException x)
{
loader.UpdateProgress(status.ChangeErrorException(x));
return false;
}
catch (IOException x)
{
loader.UpdateProgress(status.ChangeErrorException(x));
return false;
}
catch (Exception x)
{
x = new Exception(string.Format(Resources.BiblioSpecLibrary_Load_Failed_loading_library__0__, FilePath), x);
loader.UpdateProgress(status.ChangeErrorException(x));
return false;
}
finally
{
if (ReadStream != null)
{
// Close the read stream to ensure we never leak it.
// This only costs on extra open, the first time the
// active document tries to read.
try { ReadStream.CloseStream(); }
catch(IOException) {}
}
}
}