public PeakTransitionGroupFeatureSet GetFeatureScores(SrmDocument document, IPeakScoringModel scoringModel,
IProgressMonitor progressMonitor)
{
if (!ReferenceEquals(document, _document) ||
!ArrayUtil.EqualsDeep(_cacheCalculators, scoringModel.PeakFeatureCalculators))
{
_document = document;
_cacheCalculators = scoringModel.PeakFeatureCalculators;
_cachedFeatureScores = document.GetPeakFeatures(_cacheCalculators, progressMonitor);
}
return(_cachedFeatureScores);
}
} // Not L10N
public MProphetResultsHandler(SrmDocument document, PeakScoringModelSpec scoringModel,
PeakTransitionGroupFeatureSet features = null)
{
Document = document;
ScoringModel = scoringModel;
_calcs = ScoringModel != null
? ScoringModel.PeakFeatureCalculators
: PeakFeatureCalculator.Calculators.ToArray();
_features = features;
_featureDictionary = new Dictionary <PeakTransitionGroupIdKey, PeakFeatureStatistics>();
// Legacy defaults
QValueCutoff = double.MaxValue;
OverrideManual = true;
IncludeDecoys = true;
}
public void ScoreFeatures(IProgressMonitor progressMonitor = null, bool releaseRawFeatures = false, TextWriter output = null)
{
if (_features == null)
{
_features = Document.GetPeakFeatures(_calcs, progressMonitor);
}
if (ScoringModel == null)
{
return;
}
var bestTargetPvalues = new List <double>(_features.TargetCount);
var targetIds = new List <PeakTransitionGroupIdKey>(_features.TargetCount);
foreach (var transitionGroupFeatures in _features.Features)
{
int bestIndex = 0;
float bestScore = float.MinValue;
float bestPvalue = float.NaN;
var peakGroupFeatures = transitionGroupFeatures.PeakGroupFeatures;
IList <float> mProphetScoresGroup = null, pvalues = null;
if (!releaseRawFeatures)
{
mProphetScoresGroup = new float[peakGroupFeatures.Count];
}
if (!releaseRawFeatures)
{
pvalues = new float[peakGroupFeatures.Count];
}
for (int i = 0; i < peakGroupFeatures.Count; i++)
{
double score = ScoringModel.Score(peakGroupFeatures[i].Features);
if (double.IsNaN(bestScore) || score > bestScore)
{
bestIndex = i;
bestScore = (float)score;
bestPvalue = (float)(1 - Statistics.PNorm(score));
}
if (mProphetScoresGroup != null)
{
mProphetScoresGroup[i] = (float)score;
}
if (pvalues != null)
{
pvalues[i] = (float)(1 - Statistics.PNorm(score));
}
}
if (bestScore == float.MinValue)
{
bestScore = float.NaN;
}
var featureStats = new PeakFeatureStatistics(transitionGroupFeatures,
mProphetScoresGroup, pvalues, bestIndex, bestScore, null);
_featureDictionary.Add(transitionGroupFeatures.Key, featureStats);
if (!transitionGroupFeatures.IsDecoy)
{
bestTargetPvalues.Add(bestPvalue);
targetIds.Add(transitionGroupFeatures.Key);
}
}
_qValues = new Statistics(bestTargetPvalues).Qvalues(MProphetPeakScoringModel.DEFAULT_R_LAMBDA, MProphetPeakScoringModel.PI_ZERO_MIN);
for (int i = 0; i < _qValues.Length; ++i)
{
_featureDictionary[targetIds[i]].QValue = (float)_qValues[i];
}
if (releaseRawFeatures)
{
_features = null; // Done with this memory
}
}
public void OkDialog()
{
var helper = new MessageBoxHelper(this);
double qCutoff = double.MaxValue;
if (reintegrateQCutoff.Checked)
{
if (!helper.ValidateDecimalTextBox(textBoxCutoff, 0.0, 1.0, out qCutoff))
{
return;
}
}
using (var longWaitDlg = new LongWaitDlg
{
Text = Resources.ReintegrateDlg_OkDialog_Reintegrating,
})
{
try
{
var scoringModel = _driverPeakScoringModel.SelectedItem;
if (Equals(scoringModel, LegacyScoringModel.DEFAULT_UNTRAINED_MODEL))
{
scoringModel = LegacyScoringModel.DEFAULT_MODEL;
}
if (scoringModel == null || !scoringModel.IsTrained)
{
throw new InvalidDataException(Resources.ReintegrateDlg_OkDialog_You_must_train_and_select_a_model_in_order_to_reintegrate_peaks_);
}
PeakTransitionGroupFeatureSet featureScores = null;
if (ArrayUtil.EqualsDeep(_cacheCalculators, scoringModel.PeakFeatureCalculators))
{
featureScores = _cachedFeatureScores;
}
var resultsHandler = new MProphetResultsHandler(Document, scoringModel, featureScores)
{
QValueCutoff = qCutoff,
OverrideManual = checkBoxOverwrite.Checked,
};
longWaitDlg.PerformWork(this, 1000, pm =>
{
resultsHandler.ScoreFeatures(pm);
if (resultsHandler.IsMissingScores())
{
throw new InvalidDataException(Resources.ReintegrateDlg_OkDialog_The_current_peak_scoring_model_is_incompatible_with_one_or_more_peptides_in_the_document___Please_train_a_new_model_);
}
Document = resultsHandler.ChangePeaks(pm);
});
if (longWaitDlg.IsCanceled)
{
return;
}
}
catch (Exception x)
{
var message = TextUtil.LineSeparate(string.Format(Resources.ReintegrateDlg_OkDialog_Failed_attempting_to_reintegrate_peaks_),
x.Message);
MessageDlg.ShowWithException(this, message, x);
return;
}
}
var newPeakScoringModel = _driverPeakScoringModel.SelectedItem;
if (!Equals(newPeakScoringModel, Document.Settings.PeptideSettings.Integration.PeakScoringModel))
{
Document = Document.ChangeSettings(Document.Settings.ChangePeptideIntegration(
i => i.ChangePeakScoringModel(newPeakScoringModel)));
}
DialogResult = DialogResult.OK;
}
