public ImportPeptideSearchDlg(SkylineWindow skylineWindow, LibraryManager libraryManager)
{
SkylineWindow = skylineWindow;
ImportPeptideSearch = new ImportPeptideSearch();
InitializeComponent();
Icon = Resources.Skyline;
CurrentPage = Pages.spectra_page;
btnNext.Text = Resources.ImportPeptideSearchDlg_ImportPeptideSearchDlg_Next;
AcceptButton = btnNext;
btnNext.Enabled = HasUnmatchedLibraryRuns(SkylineWindow.DocumentUI);
// Create and add wizard pages
BuildPepSearchLibControl = new BuildPeptideSearchLibraryControl(SkylineWindow, ImportPeptideSearch, libraryManager)
{
Anchor = (AnchorStyles.Top | AnchorStyles.Bottom | AnchorStyles.Left | AnchorStyles.Right),
Location = new Point(2, 50)
};
BuildPepSearchLibControl.InputFilesChanged += BuildPepSearchLibForm_OnInputFilesChanged;
buildSearchSpecLibPage.Controls.Add(BuildPepSearchLibControl);
ImportFastaControl = new ImportFastaControl(SkylineWindow)
{
Anchor = (AnchorStyles.Top | AnchorStyles.Bottom | AnchorStyles.Left | AnchorStyles.Right),
Location = new Point(2, 60)
};
importFastaPage.Controls.Add(ImportFastaControl);
MatchModificationsControl = new MatchModificationsControl(SkylineWindow, ImportPeptideSearch)
{
Anchor = (AnchorStyles.Top | AnchorStyles.Bottom | AnchorStyles.Left | AnchorStyles.Right),
Location = new Point(2, 60)
};
matchModificationsPage.Controls.Add(MatchModificationsControl);
TransitionSettingsControl = new TransitionSettingsControl(SkylineWindow)
{
Anchor = (AnchorStyles.Top | AnchorStyles.Bottom | AnchorStyles.Left | AnchorStyles.Right),
Location = new Point(18, 60)
};
transitionSettingsUiPage.Controls.Add(TransitionSettingsControl);
FullScanSettingsControl = new FullScanSettingsControl(SkylineWindow)
{
Anchor = (AnchorStyles.Top | AnchorStyles.Bottom | AnchorStyles.Left | AnchorStyles.Right),
Location = new Point(18, 50)
};
ms1FullScanSettingsPage.Controls.Add(FullScanSettingsControl);
ImportResultsControl = new ImportResultsControl(ImportPeptideSearch, SkylineWindow.DocumentFilePath)
{
Anchor = (AnchorStyles.Top | AnchorStyles.Bottom | AnchorStyles.Left | AnchorStyles.Right),
Location = new Point(2, 60)
};
getChromatogramsPage.Controls.Add((Control) ImportResultsControl);
_pagesToSkip = new HashSet<Pages>();
}
public ImportResultsControl(ImportPeptideSearch importPeptideSearch, string documentPath)
{
ImportPeptideSearch = importPeptideSearch;
DocumentDirectory = Path.GetDirectoryName(documentPath);
InitializeComponent();
}
public MatchModificationsControl(SkylineWindow skylineWindow, ImportPeptideSearch importPeptideSearch)
{
SkylineWindow = skylineWindow;
ImportPeptideSearch = importPeptideSearch;
InitializeComponent();
}
public BuildPeptideSearchLibraryControl(SkylineWindow skylineWindow, ImportPeptideSearch importPeptideSearch, LibraryManager libraryManager)
{
SkylineWindow = skylineWindow;
ImportPeptideSearch = importPeptideSearch;
LibraryManager = libraryManager;
InitializeComponent();
textCutoff.Text = ImportPeptideSearch.CutoffScore.ToString(LocalizationHelper.CurrentCulture);
if (SkylineWindow.Document.PeptideCount == 0)
cbFilterForDocumentPeptides.Hide();
}
private bool ImportSearchInternal(CommandArgs commandArgs, ref SrmDocument doc)
{
var progressMonitor = new CommandProgressMonitor(_out, new ProgressStatus(String.Empty));
var import = new ImportPeptideSearch
{
SearchFilenames = commandArgs.SearchResultsFiles.ToArray(),
CutoffScore = commandArgs.CutoffScore.GetValueOrDefault()
};
// Build library
var builder = import.GetLibBuilder(doc, commandArgs.Saving ? commandArgs.SaveFile : commandArgs.SkylineFile, commandArgs.IncludeAmbiguousMatches);
ImportPeptideSearch.ClosePeptideSearchLibraryStreams(doc);
_out.WriteLine(Resources.CommandLine_ImportSearch_Creating_spectral_library_from_files_);
foreach (var file in commandArgs.SearchResultsFiles)
_out.WriteLine(Path.GetFileName(file));
if (!builder.BuildLibrary(progressMonitor))
return false;
if (!string.IsNullOrEmpty(builder.AmbiguousMatchesMessage))
_out.WriteLine(builder.AmbiguousMatchesMessage);
var docLibSpec = builder.LibrarySpec.ChangeDocumentLibrary(true);
_out.WriteLine(Resources.CommandLine_ImportSearch_Loading_library);
var libraryManager = new LibraryManager();
if (!import.LoadPeptideSearchLibrary(libraryManager, docLibSpec, progressMonitor))
return false;
doc = import.AddDocumentSpectralLibrary(doc, docLibSpec);
if (doc == null)
return false;
if (!import.VerifyRetentionTimes(import.GetFoundResultsFiles().Select(f => f.Path)))
{
_out.WriteLine(TextUtil.LineSeparate(
Resources.ImportPeptideSearchDlg_NextPage_The_document_specific_spectral_library_does_not_have_valid_retention_times_,
Resources.ImportPeptideSearchDlg_NextPage_Please_check_your_peptide_search_pipeline_or_contact_Skyline_support_to_ensure_retention_times_appear_in_your_spectral_libraries_));
return false;
}
// Look for results files to import
import.InitializeSpectrumSourceFiles(doc);
import.UpdateSpectrumSourceFilesFromDirs(import.GetDirsToSearch(Path.GetDirectoryName(commandArgs.SkylineFile)), false, null);
var missingResultsFiles = import.GetMissingResultsFiles().ToArray();
if (missingResultsFiles.Any())
{
foreach (var file in missingResultsFiles)
{
if (doc.Settings.HasResults && doc.Settings.MeasuredResults.FindMatchingMSDataFile(new MsDataFilePath(file)) != null)
continue;
_out.WriteLine(Resources.CommandLine_ImportSearch_Warning__Unable_to_locate_results_file___0__, Path.GetFileName(file));
}
}
// Add all modifications, if requested
if (commandArgs.AcceptAllModifications)
{
import.InitializeModifications(doc);
var foundMods = import.GetMatchedMods().Count();
var newModifications = new PeptideModifications(import.MatcherPepMods.StaticModifications,
new[] {new TypedModifications(IsotopeLabelType.heavy, import.MatcherHeavyMods)});
var newSettings = import.AddModifications(doc, newModifications);
if (!ReferenceEquals(doc.Settings, newSettings))
{
if (foundMods != 1)
_out.WriteLine(Resources.CommandLine_ImportSearch_Adding__0__modifications_, foundMods);
else
_out.WriteLine(Resources.CommandLine_ImportSearch_Adding_1_modification_);
doc = doc.ChangeSettings(newSettings);
doc.Settings.UpdateDefaultModifications(false);
}
}
// Import FASTA
if (commandArgs.ImportingFasta)
{
_out.WriteLine(Resources.CommandLine_ImportFasta_Importing_FASTA_file__0____, Path.GetFileName(commandArgs.FastaPath));
doc = ImportPeptideSearch.PrepareImportFasta(doc);
int emptyProteins;
try
{
IdentityPath firstAdded, nextAdd;
doc = ImportPeptideSearch.ImportFasta(doc, commandArgs.FastaPath, progressMonitor, null,
out firstAdded, out nextAdd, out emptyProteins);
}
catch (Exception x)
{
_out.WriteLine(Resources.CommandLine_Run_Error__Failed_importing_the_file__0____1_, commandArgs.FastaPath, x.Message);
_doc = doc;
return true; // So that document will be saved with the new library
}
if (emptyProteins > 0 && !commandArgs.KeepEmptyProteins)
{
doc = ImportPeptideSearch.RemoveEmptyProteins(doc);
}
}
// Import results
_doc = doc;
ImportFoundResultsFiles(commandArgs, import);
return true;
}
private void ImportFoundResultsFiles(CommandArgs commandArgs, ImportPeptideSearch import)
{
foreach (var resultFile in import.GetFoundResultsFiles())
{
var filePath = new MsDataFilePath(resultFile.Path);
if (!_doc.Settings.HasResults || _doc.Settings.MeasuredResults.FindMatchingMSDataFile(filePath) == null)
{
if (!ImportResultsFile(filePath.ChangeParameters(_doc, commandArgs.LockMassParameters), resultFile.Name, null, null, null))
break; // Lots of work completed, still want to save
}
}
}