protected override void DoTest()
{
RunUI(() => SkylineWindow.OpenFile(TestFilesDir.GetTestPath("test.sky")));
var importResultsDlg = ShowDialog <ImportResultsDlg>(SkylineWindow.ImportResults);
var openDataSourceDialog = ShowDialog <OpenDataSourceDialog>(importResultsDlg.OkDialog);
var editAccountDlg = ShowDialog <EditRemoteAccountDlg>(() => openDataSourceDialog.CurrentDirectory = RemoteUrl.EMPTY);
RunUI(() => editAccountDlg.SetRemoteAccount(UnifiTestUtil.GetTestAccount()));
OkDialog(editAccountDlg, editAccountDlg.OkDialog);
OpenFile(openDataSourceDialog, "Company");
OpenFile(openDataSourceDialog, "Test Data");
OpenFile(openDataSourceDialog, "HDMSe");
OpenFile(openDataSourceDialog, "250 fmol Hi3 E coli peptides 3-6 min");
var lockMassDlg = WaitForOpenForm <ImportResultsLockMassDlg>();
OkDialog(lockMassDlg, lockMassDlg.OkDialog);
// It takes a really long time to extract chromatograms, so we let it run for 5 seconds and then open a file where it's already imported
WaitForDocumentLoaded(5000);
RunUI(() => SkylineWindow.OpenFile(TestFilesDir.GetTestPath("test_imported.sky")));
WaitForDocumentLoaded();
RunUI(() => SkylineWindow.SelectElement(ElementRefs.FromObjectReference(ElementLocator.Parse("Molecule:/sp|P0A6A8|ACP_ECOLI/ITTVQAAIDYINGHQA"))));
ClickChromatogram(4.0, 100);
GraphFullScan graphFullScan = FindOpenForm <GraphFullScan>();
Assert.IsNotNull(graphFullScan);
}
/// <summary>
/// Examine the values in the DocumentGrid which is showing the "NormalizedAreas" form,
/// and make sure that all the numbers are correct.
/// </summary>
private void VerifyNormalizedAreaForm()
{
var normalizedAreasGrid = EnsureNormalizedAreasForm();
var dataGridView = normalizedAreasGrid.DataGridView;
WaitForConditionUI(() => normalizedAreasGrid.IsComplete);
var document = SkylineWindow.Document;
Assert.AreSame(document, ((SkylineDataSchema)normalizedAreasGrid.ViewInfo.DataSchema).Document);
RunUI(() =>
{
var colPeptideLocator = FindColumn(dataGridView, "PeptideLocator");
var colResultFileLocator = FindColumn(dataGridView, "ResultFileLocator");
var colRatioLightToGlobalStandard = FindColumn(dataGridView, "RatioLightToGlobalStandards");
var colNormalizedArea = FindColumn(dataGridView, "NormalizedArea");
for (int iRow = 0; iRow < dataGridView.Rows.Count; iRow++)
{
var row = dataGridView.Rows[iRow];
var moleculeRef = (MoleculeRef)
ElementRefs.FromObjectReference(
ElementLocator.Parse((string)row.Cells[colPeptideLocator.Index].Value));
var peptideDocNode = (PeptideDocNode)moleculeRef.FindNode(document);
var resultFileRef = (ResultFileRef)
ElementRefs.FromObjectReference(
ElementLocator.Parse((string)row.Cells[colResultFileLocator.Index].Value));
var chromFileInfo = document.Settings.MeasuredResults.Chromatograms
.SelectMany(c => c.MSDataFileInfos)
.FirstOrDefault(fileInfo => resultFileRef.Matches(fileInfo.FilePath));
Assert.IsNotNull(chromFileInfo);
var peptideChromInfo = FindChromInfo(peptideDocNode.Results, chromFileInfo.FileId);
var ratioToGlobalStandard = (double?)row.Cells[colRatioLightToGlobalStandard.Index].Value;
double?normalizedArea = (double?)row.Cells[colNormalizedArea.Index].Value;
var normalizationMethod = peptideDocNode.NormalizationMethod;
double expectedNormalizedArea = double.NaN;
double totalArea = peptideDocNode.TransitionGroups.Sum(tg =>
FindChromInfo(tg.Results, chromFileInfo.FileId)?.Area ?? 0);
if (normalizationMethod == null)
{
expectedNormalizedArea = totalArea;
}
else if (NormalizationMethod.GLOBAL_STANDARDS.Equals(normalizationMethod))
{
expectedNormalizedArea = ratioToGlobalStandard ?? 0;
}
else if (normalizationMethod is NormalizationMethod.RatioToSurrogate)
{
var ratioToSurrogate = (NormalizationMethod.RatioToSurrogate)normalizationMethod;
double surrogateArea = CalculateStandardArea(document, chromFileInfo.FileId,
peptide => peptide.ModifiedTarget.InvariantName == ratioToSurrogate.SurrogateName);
expectedNormalizedArea = totalArea / surrogateArea;
}
else
{
Assert.Fail("Unexpected normalization method {0}", normalizationMethod);
}
AssertValuesEqual(expectedNormalizedArea, normalizedArea ?? 0);
if (peptideChromInfo == null)
{
Assert.IsNull(ratioToGlobalStandard);
Assert.IsNull(normalizedArea);
}
else
{
var ratioValue = peptideChromInfo.LabelRatios.FirstOrDefault(ratio =>
IsotopeLabelType.light.Equals(ratio.LabelType) && null == ratio.StandardType).Ratio;
if (ratioValue == null)
{
Assert.IsNull(ratioToGlobalStandard);
}
else
{
Assert.IsNotNull(normalizedArea);
AssertValuesEqual(ratioValue.Ratio, ratioToGlobalStandard.Value);
}
}
}
});
}
public void ReadAllAnnotations(CancellationToken cancellationToken, DsvFileReader fileReader)
{
var fieldNames = fileReader.FieldNames;
int locatorColumnIndex = fieldNames.IndexOf(COLUMN_LOCATOR);
if (locatorColumnIndex < 0)
{
throw new InvalidDataException(string.Format(Resources.Columns_Columns_Missing_column___0__,
COLUMN_LOCATOR));
}
string[] row;
while ((row = fileReader.ReadLine()) != null)
{
cancellationToken.ThrowIfCancellationRequested();
ElementLocator elementLocator = ElementLocator.Parse(row[locatorColumnIndex]);
var elementRef = ElementRefs.FromObjectReference(elementLocator);
ElementHandler handler;
if (!_elementHandlers.TryGetValue(elementRef.ElementType, out handler))
{
throw ElementNotSupportedException(elementRef);
}
SkylineObject element = handler.FindElement(elementRef);
if (element == null)
{
throw ElementNotFoundException(elementRef);
}
for (int icol = 0; icol < fieldNames.Count; icol++)
{
if (icol == locatorColumnIndex)
{
continue;
}
string fieldName = fieldNames[icol];
TextColumnWrapper propertyInfo = null;
AnnotationDef annotationDef = null;
if (fieldName.StartsWith(PROPERTY_PREFIX))
{
propertyInfo = handler.FindProperty(fieldName.Substring(PROPERTY_PREFIX.Length));
}
else if (fieldName.StartsWith(ANNOTATION_PREFIX))
{
annotationDef = handler.FindAnnotation(fieldName.Substring(ANNOTATION_PREFIX.Length));
}
if (propertyInfo == null && annotationDef == null)
{
propertyInfo = handler.FindProperty(fieldName);
if (propertyInfo == null)
{
annotationDef = handler.FindAnnotation(fieldName);
}
}
string fieldValue = row[icol];
if (propertyInfo == null && annotationDef == null)
{
if (string.IsNullOrEmpty(fieldValue))
{
continue;
}
throw AnnotationDoesNotApplyException(fieldName, elementRef);
}
if (propertyInfo != null)
{
object value = propertyInfo.ParseTextValue(CultureInfo, fieldValue);
propertyInfo.SetValue(element, value);
}
if (annotationDef != null)
{
SetAnnotationValue(element, annotationDef, fieldValue);
}
}
}
}