private static void CheckNumberResults(ComparePeakPickingDlg comparePeakPickingDlg, int numResults)
{
foreach (var comparer in comparePeakPickingDlg.ComparePeakBoundariesList)
{
Assert.AreEqual(comparer.Matches.Count, numResults);
}
}
private static void CheckNumberComparisons(ComparePeakPickingDlg comparePeakPickingDlg,
int rocCurves,
int qCurves,
int detailsChoices,
int compareChoices)
{
TryWaitForConditionUI(() => Equals(rocCurves, Math.Max(comparePeakPickingDlg.CountRocCurves - 1, 0))); // Use WaitForCondition instead of Assert.AreEqual to avoid race conditions
int actualRocCurves = Math.Max(comparePeakPickingDlg.CountRocCurves - 1, 0);
if (!Equals(rocCurves, actualRocCurves))
{
var alertDlg = FindOpenForm <AlertDlg>();
if (alertDlg != null)
{
Assert.Fail("Unexpected alert found: {0}", alertDlg.Message);
}
Assert.Fail(TextUtil.LineSeparate(string.Format("Expecting {0} ROC curves - 1, found {1}", rocCurves, actualRocCurves),
TextUtil.LineSeparate(comparePeakPickingDlg.ZedGraphRoc.GraphPane.CurveList.Select(c => c.Label.Text))));
}
Assert.AreEqual(Math.Max(comparePeakPickingDlg.CountQCurves - 2, 0), qCurves);
Assert.AreEqual(comparePeakPickingDlg.CountDetailsItems, detailsChoices);
Assert.AreEqual(comparePeakPickingDlg.CountCompare1Items, compareChoices);
Assert.AreEqual(comparePeakPickingDlg.CountCompare2Items, compareChoices);
}
private static void AddFile(ComparePeakPickingDlg dlg, string fileName, string filePath, int dialogSkip = 0)
{
var addPeakCompareDlg = ShowDialog <AddPeakCompareDlg>(dlg.Add);
RunUI(() =>
{
addPeakCompareDlg.IsModel = false;
addPeakCompareDlg.FileName = fileName;
addPeakCompareDlg.FilePath = filePath;
});
if (dialogSkip == 0)
{
RunUI(addPeakCompareDlg.OkDialog);
}
else
{
var messageDlg = ShowDialog <MultiButtonMsgDlg>(addPeakCompareDlg.OkDialog);
for (int i = 0; i < dialogSkip; ++i)
{
if (i > 0)
{
messageDlg = WaitForOpenForm <MultiButtonMsgDlg>();
}
RunUI(messageDlg.Btn1Click);
WaitForClosedForm <MultiButtonMsgDlg>();
}
}
WaitForClosedForm <AddPeakCompareDlg>();
}
public static void RemoveComparer(ComparePeakPickingDlg dlg, string comparerName)
{
var editListDlgRemove = ShowDialog <EditListDlg <ComparePeakBoundariesList, ComparePeakBoundaries> >(dlg.EditList);
RunUI(() =>
{
editListDlgRemove.SelectItem(comparerName);
editListDlgRemove.RemoveItem();
});
OkDialog(editListDlgRemove, editListDlgRemove.OkDialog);
}
private static void AddModel(ComparePeakPickingDlg dlg, string modelName)
{
var addPeakCompareDlg = ShowDialog <AddPeakCompareDlg>(dlg.Add);
RunUI(() =>
{
addPeakCompareDlg.IsModel = true;
addPeakCompareDlg.PeakScoringModelSelected = modelName;
});
OkDialog(addPeakCompareDlg, addPeakCompareDlg.OkDialog);
}
private static void AddFile(ComparePeakPickingDlg dlg, string fileName, string filePath)
{
var addPeakCompareDlg = ShowDialog <AddPeakCompareDlg>(dlg.Add);
RunUI(() =>
{
addPeakCompareDlg.IsModel = false;
addPeakCompareDlg.FileName = fileName;
addPeakCompareDlg.FilePath = filePath;
});
OkDialog(addPeakCompareDlg, addPeakCompareDlg.OkDialog);
}
private static void CheckNumberComparisons(ComparePeakPickingDlg comparePeakPickingDlg,
int rocCurves,
int qCurves,
int detailsChoices,
int compareChoices)
{
WaitForConditionUI(() => Equals(Math.Max(comparePeakPickingDlg.CountRocCurves - 1, 0), rocCurves), "unexpected rocCurves count"); // Use WaitForCondition instead of Assert.AreEqual to avoid race conditions
Assert.AreEqual(Math.Max(comparePeakPickingDlg.CountQCurves - 2, 0), qCurves);
Assert.AreEqual(comparePeakPickingDlg.CountDetailsItems, detailsChoices);
Assert.AreEqual(comparePeakPickingDlg.CountCompare1Items, compareChoices);
Assert.AreEqual(comparePeakPickingDlg.CountCompare2Items, compareChoices);
}
private static void AddFile(ComparePeakPickingDlg dlg, string fileName, string filePath, string outDir, int dialogSkip = 0)
{
string intlPath = Path.Combine(outDir, fileName + "Intl" + Path.GetExtension(filePath));
if (TextUtil.WriteDsvToCsvLocal(filePath, intlPath, true))
{
filePath = intlPath;
}
var addPeakCompareDlg = ShowDialog <AddPeakCompareDlg>(dlg.Add);
RunUI(() =>
{
addPeakCompareDlg.IsModel = false;
addPeakCompareDlg.FileName = fileName;
addPeakCompareDlg.FilePath = filePath;
});
if (dialogSkip == 0)
{
RunUI(addPeakCompareDlg.OkDialog);
}
else
{
var messageDlg = ShowDialog <MultiButtonMsgDlg>(addPeakCompareDlg.OkDialog);
for (int i = 0; i < dialogSkip; ++i)
{
if (i > 0)
{
messageDlg = WaitForOpenForm <MultiButtonMsgDlg>();
}
OkDialog(messageDlg, messageDlg.Btn1Click);
}
}
var messageDlgExtra = TryWaitForOpenForm <MultiButtonMsgDlg>(100);
if (messageDlgExtra != null)
{
string message = messageDlgExtra.Message;
OkDialog(messageDlgExtra, messageDlgExtra.BtnCancelClick);
Assert.Fail("Unexpected message dialog after {0}: {1}", dialogSkip, message);
}
WaitForClosedForm <AddPeakCompareDlg>();
}
public void ShowCompareModelsDlg()
{
var document = DocumentUI;
if (!document.Settings.HasResults)
{
MessageDlg.Show(SkylineWindow, Resources.SkylineWindow_ShowReintegrateDialog_The_document_must_have_imported_results_);
return;
}
if (document.MoleculeCount == 0)
{
MessageDlg.Show(SkylineWindow, Resources.SkylineWindow_ShowCompareModelsDlg_The_document_must_have_targets_in_order_to_compare_model_peak_picking_);
return;
}
if (!document.IsLoaded)
{
MessageDlg.Show(SkylineWindow, Resources.SkylineWindow_ShowCompareModelsDlg_The_document_must_be_fully_loaded_in_order_to_compare_model_peak_picking_);
return;
}
var dlg = new ComparePeakPickingDlg(document);
dlg.Show(SkylineWindow);
}
public DataSetAnalyzer(string skylineDocument,
IList <string> modelNames,
IEnumerable <string> filePaths,
string outDir,
IList <int> dialogSkips,
TextWriter resultsWriter,
bool rescorePeaks)
{
OutDir = outDir;
Settings.Default.PeakScoringModelList.Clear();
RunUI(() => SkylineWindow.OpenFile(skylineDocument));
WaitForDocumentLoaded();
if (rescorePeaks)
{
RescorePeaks();
}
CreateModels();
foreach (var modelName in modelNames)
{
TrainModel(modelName);
}
var comparePeakPickingDlg = ShowDialog <ComparePeakPickingDlg>(SkylineWindow.ShowCompareModelsDlg);
foreach (var modelName in modelNames)
{
AddModel(comparePeakPickingDlg, modelName);
}
int i = 0;
foreach (var filePath in filePaths)
{
var fileName = Path.GetFileNameWithoutExtension(filePath);
Assert.IsNotNull(fileName);
AddFile(comparePeakPickingDlg, fileName, filePath, dialogSkips[i]);
++i;
}
comparePeakPickingDlg.ComboYAxis = Resources.ComparePeakPickingDlg_ComparePeakPickingDlg_Fraction_of_Manual_ID_s;
var trimmedDoc = Path.GetFileNameWithoutExtension(skylineDocument);
foreach (var comparePeakBoundaries in comparePeakPickingDlg.ComparePeakBoundariesList)
{
PointPairList rocPoints;
PointPairList qqPoints;
ComparePeakPickingDlg.MakeRocLists(comparePeakBoundaries, ComparePeakPickingDlg.NormalizeType.frac_manual, out rocPoints);
ComparePeakPickingDlg.MakeQValueLists(comparePeakBoundaries, out qqPoints);
double peptides01 = GetCurveThreshold(rocPoints, LOW_SIG);
double peptides05 = GetCurveThreshold(rocPoints, HIGH_SIG);
double peptidesAll = GetCurveThreshold(rocPoints, Double.MaxValue);
double qValue01 = GetCurveThreshold(qqPoints, LOW_SIG);
double qValue05 = GetCurveThreshold(qqPoints, HIGH_SIG);
WriteLine(resultsWriter, trimmedDoc, comparePeakBoundaries.Name, peptides01, peptides05, peptidesAll, qValue01, qValue05);
}
var sbRoc = new StringBuilder(trimmedDoc);
sbRoc.Append("-roc.bmp");
comparePeakPickingDlg.ZedGraphRoc.MasterPane.GetImage().Save(Path.Combine(outDir, sbRoc.ToString()));
var sbQq = new StringBuilder(trimmedDoc);
sbQq.Append("-qq.bmp");
comparePeakPickingDlg.ZedGraphQq.MasterPane.GetImage().Save(Path.Combine(outDir, sbQq.ToString()));
var sbFiles = new StringBuilder(trimmedDoc);
sbFiles.Append("-files.bmp");
comparePeakPickingDlg.ZedGraphFile.MasterPane.GetImage().Save(Path.Combine(outDir, sbFiles.ToString()));
// TODO: How can I copy the data using commands?
OkDialog(comparePeakPickingDlg, comparePeakPickingDlg.OkDialog);
}
