public void MakeFilesLists(ComparePeakBoundaries comparer, double falsePositiveCutoff, out PointPairList filesPoints, out List <string> filesNames)
{
filesPoints = new PointPairList();
filesNames = new List <string>();
var matches = comparer.Matches;
var matchesByFile = matches.GroupBy(match => match.FileName).OrderBy(group => group.Key);
int i = 1;
foreach (var matchGroup in matchesByFile)
{
PointPairList rocPoints;
var matchesInGroup = matchGroup.ToList();
if (comparer.HasNoScores)
{
matchesInGroup.Sort(PeakBoundsMatch.CompareQValue);
}
else
{
matchesInGroup.Sort(PeakBoundsMatch.CompareScore);
}
RocFromSortedMatches(matchesInGroup, Normalizer, out rocPoints);
double correctPeaks = GetCurveThreshold(rocPoints, falsePositiveCutoff);
filesPoints.Add(i++, correctPeaks);
filesNames.Add(matchGroup.Key);
}
}
public static void MakeQValueLists(ComparePeakBoundaries comparer, out PointPairList qqPoints)
{
qqPoints = new PointPairList();
var matches = comparer.Matches;
matches.Sort(PeakBoundsMatch.CompareQValue);
int truePositives = 0;
int falsePositives = 0;
foreach (var match in matches)
{
if (match.IsFalsePositive)
{
falsePositives++;
}
if (match.IsPickedApexBetweenCuratedBoundaries)
{
truePositives++;
}
// Null qValues get the worst score
double qValue = match.QValue ?? 1.0;
var qqPoint = new PointPair(qValue, falsePositives / (double)(truePositives + falsePositives));
qqPoints.Add(qqPoint);
}
}
public void MakeFilesLists(ComparePeakBoundaries comparer, double falsePositiveCutoff, bool observed, out PointPairList filesPoints, out List <string> filesNames)
{
filesPoints = new PointPairList();
filesNames = new List <string>();
var matches = comparer.Matches;
var matchesByFile = matches.GroupBy(match => match.ReplicateName).OrderBy(group => group.Key);
int i = 1;
foreach (var matchGroup in matchesByFile)
{
PointPairList rocPoints;
var matchesInGroup = matchGroup.ToList();
if (comparer.HasNoScores)
{
matchesInGroup.Sort(PeakBoundsMatch.CompareQValue);
}
else
{
matchesInGroup.Sort(PeakBoundsMatch.CompareScore);
}
RocFromSortedMatches(matchesInGroup, Normalizer, out rocPoints);
var pointThreshold = GetCurveThreshold(rocPoints, falsePositiveCutoff, observed);
// Error is 2x the observed error rate, so that wiskers extend above and below bar item
// by the number of observed false-positives
filesPoints.Add(MeanErrorBarItem.MakePointPair(i++, pointThreshold.Y, pointThreshold.X * pointThreshold.Y * 2));
filesNames.Add(matchGroup.Key);
}
}
public static void MakeRocLists(ComparePeakBoundaries comparer, NormalizeType normalizer, out PointPairList rocPoints)
{
var matches = comparer.Matches;
if (comparer.HasNoScores)
{
matches.Sort(PeakBoundsMatch.CompareQValue);
}
else
{
matches.Sort(PeakBoundsMatch.CompareScore);
}
RocFromSortedMatches(matches, normalizer, out rocPoints);
}
public AddPeakCompareDlg(SrmDocument document, ComparePeakBoundaries current, IEnumerable <ComparePeakBoundaries> existing)
: this(document, existing)
{
// If second argument is null, treat it as if it wasn't there -- for EditListDlg
if (current == null)
{
return;
}
_current = current;
radioButtonModel.Checked = current.IsModel;
radioButtonFile.Checked = !current.IsModel;
textFilePath.Text = current.FilePath;
textName.Text = current.FileName;
var model = current.PeakScoringModel;
_driverPeakScoringModel.LoadList(model != null ? model.Name : null);
}
public void OkDialog()
{
bool isModel = radioButtonModel.Checked;
if (isModel)
{
var model = _driverPeakScoringModel.SelectedItem;
if (model == null)
{
MessageDlg.Show(this, Resources.PeakBoundaryCompareTest_DoTest_Must_select_a_model_for_comparison_);
return;
}
if (!model.IsTrained)
{
MessageDlg.Show(this, Resources.AddPeakCompareDlg_OkDialog_Model_must_be_trained_before_it_can_be_used_for_peak_boundary_comparison_);
return;
}
BoundaryComparer = new ComparePeakBoundaries(model);
}
else
{
string displayName = textName.Text;
if (displayName.Length == 0)
{
MessageDlg.Show(this, Resources.AddPeakCompareDlg_OkDialog_Comparison_name_cannot_be_empty_);
return;
}
string filePath = textFilePath.Text;
if (filePath.Length == 0)
{
MessageDlg.Show(this, Resources.AddPeakCompareDlg_OkDialog_File_path_cannot_be_empty_);
return;
}
if (!File.Exists(filePath))
{
MessageDlg.Show(this, Resources.AddPeakCompareDlg_OkDialog_File_path_field_must_contain_a_path_to_a_valid_file_);
return;
}
BoundaryComparer = new ComparePeakBoundaries(displayName, filePath);
}
var compNames = _existing.Select(comp => comp.Name);
if (compNames.Contains(BoundaryComparer.Name) && (_current == null || _current.Name != BoundaryComparer.Name))
{
var message = isModel
? Resources.AddPeakCompareDlg_OkDialog_The_selected_model_is_already_included_in_the_list_of_comparisons__Please_choose_another_model_
: Resources.AddPeakCompareDlg_OkDialog_There_is_already_an_imported_file_with_the_current_name___Please_choose_another_name;
MessageDlg.Show(this, message);
return;
}
using (var longWaitDlg = new LongWaitDlg
{
Text = isModel ? Resources.AddPeakCompareDlg_OkDialog_Comparing_Models : Resources.AddPeakCompareDlg_OkDialog_Comparing_Imported_Files
})
{
try
{
longWaitDlg.PerformWork(this, 1000, pm => BoundaryComparer.GenerateComparison(Document, pm));
if (BoundaryComparer.Matches.Count == 0)
{
throw new IOException(Resources.AddPeakCompareDlg_OkDialog_Document_has_no_eligible_chromatograms_for_analysis___Valid_chromatograms_must_not_be_decoys_or_iRT_standards_);
}
if (BoundaryComparer.Matches.All(match => match.IsMissingPickedPeak))
{
throw new IOException(Resources.AddPeakCompareDlg_OkDialog_The_selected_file_or_model_does_not_assign_peak_boundaries_to_any_chromatograms_in_the_document___Please_select_a_different_model_or_file_);
}
if (BoundaryComparer.HasNoQValues && BoundaryComparer.HasNoScores)
{
throw new IOException(Resources.AddPeakCompareDlg_OkDialog_The_current_file_or_model_has_no_q_values_or_scores_to_analyze___Either_q_values_or_scores_are_necessary_to_compare_peak_picking_tools_);
}
if (BoundaryComparer.CountMissing > 0)
{
var missingMessage = string.Format(Resources.AddPeakCompareDlg_OkDialog_The_imported_file_does_not_contain_any_peak_boundaries_for__0__transition_group___file_pairs___These_chromatograms_will_be_treated_as_if_no_boundary_was_selected_,
BoundaryComparer.CountMissing);
var dlgMissing = MultiButtonMsgDlg.Show(this, missingMessage, MultiButtonMsgDlg.BUTTON_OK);
if (dlgMissing == DialogResult.Cancel)
{
return;
}
}
// Show a warning message and give a chance to cancel, if there are unrecognized peptides
if (BoundaryComparer.Importer != null && !BoundaryComparer.Importer.UnrecognizedPeptidesCancel(this))
{
return;
}
}
catch (Exception x)
{
string initMessage = isModel
? Resources.AddPeakCompareDlg_OkDialog_Error_comparing_model_peak_boundaries___0_
: Resources.AddPeakCompareDlg_OkDialog_Error_applying_imported_peak_boundaries___0_;
MessageDlg.ShowWithException(this, string.Format(initMessage, x.Message), x);
return;
}
}
DialogResult = DialogResult.OK;
}
