protected override bool LoadBackground(IDocumentContainer container, SrmDocument document,
SrmDocument docCurrent)
{
if (!FastaImporter.HasWebAccess()) // Do we even have web access?
{
EndProcessing(container.Document);
return(false); // Return silently rather than flashing the progress bar
}
SrmDocument docNew, docOrig;
do
{
docOrig = container.Document;
var loadMonitor = new LoadMonitor(this, container, docOrig);
docNew = LookupProteinMetadata(docOrig, loadMonitor);
if (null == docNew)
{
EndProcessing(docOrig);
return(false);
}
} while (!CompleteProcessing(container, docNew, docOrig));
CleanupProcessedNodesDict(docNew); // Drop any completed work, we're done with it
return(true);
}
protected override bool LoadBackground(IDocumentContainer container, SrmDocument document, SrmDocument docCurrent)
{
var loadMonitor = new LoadMonitor(this, container, container.Document);
IPeakScoringModel scoringModel = new MProphetPeakScoringModel(
Path.GetFileNameWithoutExtension(container.DocumentFilePath), null as LinearModelParams,
MProphetPeakScoringModel.GetDefaultCalculators(docCurrent), true);
var targetDecoyGenerator = new TargetDecoyGenerator(docCurrent, scoringModel, this, loadMonitor);
// Get scores for target and decoy groups.
List <IList <float[]> > targetTransitionGroups, decoyTransitionGroups;
targetDecoyGenerator.GetTransitionGroups(out targetTransitionGroups, out decoyTransitionGroups);
if (!decoyTransitionGroups.Any())
{
throw new InvalidDataException();
}
// Set intial weights based on previous model (with NaN's reset to 0)
var initialWeights = new double[scoringModel.PeakFeatureCalculators.Count];
// But then set to NaN the weights that have unknown values for this dataset
for (var i = 0; i < initialWeights.Length; ++i)
{
if (!targetDecoyGenerator.EligibleScores[i])
{
initialWeights[i] = double.NaN;
}
}
var initialParams = new LinearModelParams(initialWeights);
// Train the model.
scoringModel = scoringModel.Train(targetTransitionGroups, decoyTransitionGroups, targetDecoyGenerator, initialParams, null, null, scoringModel.UsesSecondBest, true, loadMonitor);
SrmDocument docNew;
do
{
docCurrent = container.Document;
docNew = docCurrent.ChangeSettings(docCurrent.Settings.ChangePeptideIntegration(i =>
i.ChangeAutoTrain(false).ChangePeakScoringModel((PeakScoringModelSpec)scoringModel)));
// Reintegrate peaks
var resultsHandler = new MProphetResultsHandler(docNew, (PeakScoringModelSpec)scoringModel, _cachedFeatureScores);
resultsHandler.ScoreFeatures(loadMonitor);
if (resultsHandler.IsMissingScores())
{
throw new InvalidDataException(Resources.ImportPeptideSearchManager_LoadBackground_The_current_peak_scoring_model_is_incompatible_with_one_or_more_peptides_in_the_document_);
}
docNew = resultsHandler.ChangePeaks(loadMonitor);
}while (!CompleteProcessing(container, docNew, docCurrent));
return(true);
}
protected override bool LoadBackground(IDocumentContainer container, SrmDocument document, SrmDocument docCurrent)
{
SrmDocument docNew, docOrig;
do
{
docOrig = container.Document;
var loadMonitor = new LoadMonitor(this, container, docOrig);
docNew = DocumentRetentionTimes.RecalculateAlignments(docOrig, loadMonitor);
if (null == docNew)
{
EndProcessing(docOrig);
return false;
}
}
while (!CompleteProcessing(container, docNew, docOrig));
return true;
}
protected override bool LoadBackground(IDocumentContainer container, SrmDocument document, SrmDocument docCurrent)
{
SrmDocument docNew, docOrig;
do
{
docOrig = container.Document;
var loadMonitor = new LoadMonitor(this, container, docOrig);
docNew = DocumentRetentionTimes.RecalculateAlignments(docOrig, loadMonitor);
if (null == docNew)
{
EndProcessing(docOrig);
return(false);
}
}while (!CompleteProcessing(container, docNew, docOrig));
return(true);
}
public void Load()
{
string documentFilePath = _container.DocumentFilePath;
if (documentFilePath == null)
{
return;
}
var results = _docCurrent.Settings.MeasuredResults;
if (results.IsLoaded)
{
return;
}
var loadMonitor = new LoadMonitor(_manager, _container, results)
{
HasUI = _manager.SupportAllGraphs
};
results.Load(_docCurrent, documentFilePath, loadMonitor, FinishLoad);
}
public void Load()
{
string documentFilePath = _container.DocumentFilePath;
if (documentFilePath == null)
return;
var results = _docCurrent.Settings.MeasuredResults;
if (results.IsLoaded)
return;
var loadMonitor = new LoadMonitor(_manager, _container, results) {HasUI = _manager.SupportAllGraphs};
results.Load(_docCurrent, documentFilePath, loadMonitor, FinishLoad);
}
protected override bool LoadBackground(IDocumentContainer container, SrmDocument document,
SrmDocument docCurrent)
{
if (!FastaImporter.HasWebAccess()) // Do we even have web access?
return false; // Return silently rather than flashing the progress bar
SrmDocument docNew, docOrig;
do
{
docOrig = container.Document;
var loadMonitor = new LoadMonitor(this, container, docOrig);
docNew = LookupProteinMetadata(docOrig, loadMonitor);
if (null == docNew)
{
EndProcessing(docOrig);
return false;
}
} while (!CompleteProcessing(container, docNew, docOrig));
CleanupProcessedNodesDict(docNew); // Drop any completed work, we're done with it
return true;
}
