private bool ReintegratePeaks(CommandArgs commandArgs)
{
if (!_doc.Settings.HasResults)
{
_out.WriteLine(Resources.CommandLine_ReintegratePeaks_Error__You_must_first_import_results_into_the_document_before_reintegrating_);
return false;
}
else
{
ModelAndFeatures modelAndFeatures;
if (commandArgs.IsCreateScoringModel)
{
modelAndFeatures = CreateScoringModel(commandArgs.ReintegratModelName,
commandArgs.IsDecoyModel, commandArgs.IsSecondBestModel);
if (modelAndFeatures == null)
return false;
}
else
{
PeakScoringModelSpec scoringModel;
if (!Settings.Default.PeakScoringModelList.TryGetValue(commandArgs.ReintegratModelName, out scoringModel))
{
_out.WriteLine(Resources.CommandLine_ReintegratePeaks_Error__Unknown_peak_scoring_model___0__);
return false;
}
modelAndFeatures = new ModelAndFeatures(scoringModel, null);
}
if (!Reintegrate(modelAndFeatures, commandArgs.IsAnnotateScoring, commandArgs.IsOverwritePeaks))
return false;
}
return true;
}
private bool Reintegrate(ModelAndFeatures modelAndFeatures, bool isAnnotateScoring, bool isOverwritePeaks)
{
try
{
var resultsHandler = new MProphetResultsHandler(_doc, modelAndFeatures.ScoringModel, modelAndFeatures.Features)
{
OverrideManual = isOverwritePeaks,
AddAnnotation = isAnnotateScoring,
AddMAnnotation = isAnnotateScoring
};
var progressMonitor = new CommandProgressMonitor(_out, new ProgressStatus(string.Empty));
resultsHandler.ScoreFeatures(progressMonitor);
if (resultsHandler.IsMissingScores())
{
_out.WriteLine(Resources.CommandLine_Reintegrate_Error__The_current_peak_scoring_model_is_incompatible_with_one_or_more_peptides_in_the_document__Please_train_a_new_model_);
return false;
}
_doc = resultsHandler.ChangePeaks(progressMonitor);
return true;
}
catch (Exception x)
{
_out.WriteLine(Resources.CommandLine_Reintegrate_Error__Failed_to_reintegrate_peaks_successfully_);
_out.WriteLine(x.Message);
return false;
}
}