/// <summary>
/// Use the DocumentGrid to set the PrecursorConcentration values on all of the precursors in the document.
/// </summary>
private void SetPrecursorConcentrations(DocumentGridForm documentGrid)
{
RunUI(() => documentGrid.ChooseView(Resources.SkylineViewContext_GetDocumentGridRowSources_Precursors));
WaitForConditionUI(() => documentGrid.IsComplete);
var viewEditor = ShowDialog <ViewEditor>(documentGrid.DataboundGridControl.NavBar.CustomizeView);
RunUI(() =>
{
viewEditor.ActiveAvailableFieldsTree.SelectColumn(PropertyPath.Root.Property("Proteins")
.LookupAllItems().Property("Peptides").LookupAllItems().Property("Precursors").LookupAllItems()
.Property("PrecursorConcentration"));
viewEditor.ChooseColumnsTab.AddColumn(
PropertyPath.Parse("Proteins!*.Peptides!*.Precursors!*.PrecursorConcentration"));
viewEditor.ViewName = "PrecursorConcentrations";
});
OkDialog(viewEditor, viewEditor.OkDialog);
WaitForConditionUI(() => documentGrid.IsComplete);
var colPrecursorConcentration =
documentGrid.DataboundGridControl.FindColumn(PropertyPath.Root.Property("PrecursorConcentration"));
Assert.IsNotNull(colPrecursorConcentration);
// These are the concentrations of the light, heavy4, heavy3, heavy2, heavy1
double[] concentrations = { 0.125, 200, 20, 2, .5 };
// Set the clipboard text to the list of concentrations repeated twice since there are two peptides
ClipboardEx.SetText(string.Join(Environment.NewLine, concentrations.Concat(concentrations)));
RunUI(() =>
{
documentGrid.DataGridView.CurrentCell =
documentGrid.DataGridView.Rows[0].Cells[colPrecursorConcentration.Index];
documentGrid.DataGridView.SendPaste();
});
}
private void gridStatistics_KeyDown(object sender, KeyEventArgs e)
{
// Handle Ctrl + C for copy
if (e.KeyCode == Keys.V && e.Control)
{
StringBuilder sb = new StringBuilder();
foreach (DataGridViewRow row in gridStatistics.Rows)
{
if (row.IsNewRow)
{
continue;
}
foreach (DataGridViewCell cell in row.Cells)
{
if (sb[sb.Length - 1] != '\n') // Not L10N
{
sb.Append('\t'); // Not L10N
}
sb.Append(cell.Value);
}
sb.Append('\n'); // Not L10N
}
try
{
ClipboardEx.Clear();
ClipboardEx.SetText(sb.ToString());
}
catch (ExternalException)
{
MessageDlg.Show(this, ClipboardHelper.GetOpenClipboardMessage(Resources.RTDetails_gridStatistics_KeyDown_Failed_setting_data_to_clipboard));
}
}
}
/// <summary>
/// 右クリックメニュー「読み筋を表示のままの文字列でクリップボードに貼り付ける(&P)」
/// </summary>
/// <param name="sender"></param>
/// <param name="e"></param>
private void PastePvToClipboard_Click(object sender, EventArgs e)
{
if (pvTextOnClick == null)
{
return;
}
ClipboardEx.SetText(pvTextOnClick);
ResetContextMenu();
}
private void HandleTextBoxCommandPreviewExecuted(object sender, ExecutedRoutedEventArgs e)
{
if (e.Command == ApplicationCommands.Cut)
{
var textBox = (TextBox)sender;
if (textBox.SelectionLength == textBox.Text.Length)
{
ClipboardEx.SetText(textBox.Text);
SetNullText(textBox);
e.Handled = true;
}
}
}
/// <summary>
/// [UI Thread] : クリップボードに文字列を設定する。
///
/// 注意 : Clipboard.SetText() を実行するスレッドは Single Thread Apartment モードに設定されていなければならない
/// UI Threadからこのメソッドを呼び出すこと。
/// </summary>
/// <param name="o"></param>
public static void SetText(string s)
{
try
{
if (s.Empty())
{
return;
}
ClipboardEx.SetText(s);
}
catch (Exception) { }
}
/// <summary>
/// 右クリックメニュー「読み筋をKIF形式でクリップボードに貼り付ける(&K)」
/// </summary>
/// <param name="sender"></param>
/// <param name="e"></param>
private void PasteKifToClipboard_Click(object sender, EventArgs e)
{
// KIF形式で保存する
var kifu = KifuManager.ToStringFromRootSfenAndMoves(KifuFileType.KIF,
boardDataOnRightClick.rootSfen, boardDataOnRightClick.moves);
if (kifu == null)
{
return;
}
ClipboardEx.SetText(kifu);
ResetContextMenu();
}
public CopyColorForm(Color color, Point invocationOrigin, int indexUnderMouse = 1)
{
InitializeComponent();
SuspendLayout();
colorBox.Color = color;
StartPosition = FormStartPosition.Manual;
var lastLabelPosition = new Point(12, 42);
for (int i = 0; i < _formats.Count; ++i)
{
var format = _formats[i];
var formattedColor = format(color);
var l = new CopyCodeLinkLabel()
{
Text = formattedColor,
Location = new Point(
lastLabelPosition.X,
lastLabelPosition.Y + 18 + 3
),
Padding = new Padding(0, 0, 0, 10),
AutoSize = true,
};
l.Click += (s, e) =>
{
ClipboardEx.SetText(formattedColor);
Close();
};
Controls.Add(l);
if (i == indexUnderMouse)
{
Location = new Point(
invocationOrigin.X - (l.Location.X + 20),
invocationOrigin.Y - (l.Location.Y + 20)
);
}
lastLabelPosition = l.Location;
}
ResumeLayout(true);
}
/// <summary>
/// Copy the data from the curves in the ZedGraphControl to the clipboard.
/// </summary>
public static void CopyGraphData(ZedGraphControl zedGraphControl)
{
var graphData = GraphData.GetGraphData(zedGraphControl.MasterPane);
if (graphData.Panes.Count == 0)
{
return;
}
try
{
ClipboardEx.Clear();
ClipboardEx.SetText(graphData.ToString());
}
catch (ExternalException)
{
MessageBox.Show(ClipboardHelper.GetOpenClipboardMessage(Resources.CopyGraphDataToolStripMenuItem_CopyGraphData_Failed_setting_data_to_clipboard), Program.Name);
}
}
/// <summary>
/// Use the DocumentGrid to set the PrecursorConcentration values on all of the precursors in the document.
/// </summary>
private void SetPrecursorConcentrations(DocumentGridForm documentGrid)
{
RunUI(() => documentGrid.ChooseView(PRECURSOR_CONCENTRATIONS_VIEW));
WaitForConditionUI(() => documentGrid.IsComplete);
var colPrecursorConcentration = documentGrid.DataboundGridControl.FindColumn(
PropertyPath.Root.Property(nameof(Precursor.PrecursorConcentration)));
Assert.IsNotNull(colPrecursorConcentration);
// These are the concentrations of the light, heavy4, heavy3, heavy2, heavy1
double[] concentrations = { 0.125, 200, 20, 2, .5 };
// Set the clipboard text to the list of concentrations repeated twice since there are two peptides
ClipboardEx.SetText(string.Join(Environment.NewLine, concentrations.Concat(concentrations)));
RunUI(() =>
{
documentGrid.DataGridView.CurrentCell =
documentGrid.DataGridView.Rows[0].Cells[colPrecursorConcentration.Index];
documentGrid.DataGridView.SendPaste();
});
}
public void CopyMessage()
{
const string separator = "---------------------------"; // Not L10N
List <string> lines = new List <String>();
lines.Add(separator);
lines.Add(Text);
lines.Add(separator);
lines.Add(Message);
lines.Add(separator);
lines.Add(TextUtil.SpaceSeparate(VisibleButtons.Select(btn => btn.Text)));
if (null != DetailMessage)
{
lines.Add(separator);
lines.Add(DetailMessage);
}
lines.Add(separator);
lines.Add(string.Empty);
ClipboardEx.SetText(TextUtil.LineSeparate(lines));
}
public static void InvokeUploadFinishedUI(UploadResult result, HSSettings settingsContext)
{
Debug.Assert(result != null);
Debug.Assert(!string.IsNullOrWhiteSpace(result.Url));
switch (settingsContext.ActionAfterUpload)
{
case UploadHandlingAction.Flyout:
(new UploadResultForm(result, settingsContext)).Show();
break;
case UploadHandlingAction.CopyToClipboard:
{
var success = ClipboardEx.SetText(result.Url);
if (settingsContext.ShowCopyConfirmation)
{
if (success)
{
NotificationManager.ShowCopyConfirmation(result.Url);
}
else
{
NotificationManager.CopyingFailed(result.Url);
}
}
}
break;
case UploadHandlingAction.None:
// Intentionally left empty
break;
default:
// Intentionally left empty
break;
}
}
private void copyButton_Click(object sender, EventArgs e)
{
ClipboardEx.SetText(extraInfoTextBox.Text);
}
private void btnCopyLink_Click(object sender, EventArgs e)
{
ClipboardEx.SetText(LinkUrl);
}
protected override void DoTest()
{
RunUI(() => SetClipboardFileText(@"RenameProteinsTest\Fasta.txt")); // Not L10N
RunUI(() => SkylineWindow.Paste());
WaitForCondition(() => SkylineWindow.SequenceTree.Nodes.Count > 4);
var docOrig = WaitForProteinMetadataBackgroundLoaderCompletedUI();
Assert.AreNotEqual(FIRST_RENAMED_PROTEIN, docOrig.PeptideGroups.ToArray()[1].Name);
RunUI(() =>
{
SkylineWindow.SequenceTree.SelectedNode = SkylineWindow.SequenceTree.Nodes[1];
SkylineWindow.SequenceTree.BeginEdit(false);
SkylineWindow.SequenceTree.StatementCompletionEditBox.TextBox.Text = FIRST_RENAMED_PROTEIN;
SkylineWindow.SequenceTree.CommitEditBox(false);
});
var docEdited = WaitForDocumentChange(docOrig);
Assert.AreEqual(FIRST_RENAMED_PROTEIN, docEdited.PeptideGroups.ToArray()[1].Name);
RunUI(() =>
{
SkylineWindow.SequenceTree.SelectedNode = SkylineWindow.SequenceTree.Nodes[SkylineWindow.SequenceTree.Nodes.Count - 1];
SkylineWindow.SequenceTree.BeginEdit(false);
SkylineWindow.SequenceTree.StatementCompletionEditBox.TextBox.Text = NON_FASTA_PROTEIN;
SkylineWindow.SequenceTree.CommitEditBox(false);
});
// Choose valid proteins to rename
{
ClipboardEx.SetText(string.Format("YAL001C\n{0}\nYAL003W\t{1}\nYAL035W\n{2}\t{3}\n", FIRST_RENAMED_PROTEIN,
SECOND_RENAMED_PROTEIN, NON_FASTA_PROTEIN, NON_FASTA_PROTEIN_RENAMED));
RunDlg <RenameProteinsDlg>(SkylineWindow.ShowRenameProteinsDlg,
renameProteinsDlg =>
{
renameProteinsDlg.Paste();
Assert.IsTrue(Equals(renameProteinsDlg.NameCount, 5));
renameProteinsDlg.OkDialog();
});
RunUI(() =>
{
SkylineWindow.SequenceTree.SelectedNode = SkylineWindow.SequenceTree.Nodes[2];
Assert.IsTrue(Equals(SkylineWindow.SequenceTree.SelectedNode.Text, SECOND_RENAMED_PROTEIN));
SkylineWindow.SequenceTree.SelectedNode =
SkylineWindow.SequenceTree.Nodes[SkylineWindow.SequenceTree.Nodes.Count - (TestSmallMolecules ? 3 : 2)];
Assert.IsTrue(Equals(SkylineWindow.SequenceTree.SelectedNode.Text, NON_FASTA_PROTEIN_RENAMED));
});
}
// Choose invalid proteins to rename
{
ClipboardEx.SetText(string.Format("Random\tHello\n{0}\n{1}\nYAL035W\n", FIRST_RENAMED_PROTEIN, SECOND_RENAMED_PROTEIN));
var renameProteinsDlg = ShowDialog <RenameProteinsDlg>(SkylineWindow.ShowRenameProteinsDlg);
RunUI(renameProteinsDlg.Paste);
RunDlg <MessageDlg>(renameProteinsDlg.OkDialog,
messageDlg =>
{
AssertEx.AreComparableStrings(Resources.RenameProteinsDlg_OkDialog__0__is_not_a_current_protein, messageDlg.Message, 1);
messageDlg.OkDialog();
});
RunUI(renameProteinsDlg.Clear);
// Try to rename a protein twice
ClipboardEx.SetText(string.Format("YAL001C\tTest2\n{0}\n{1}\nYAL001C\tTest3\n", FIRST_RENAMED_PROTEIN, SECOND_RENAMED_PROTEIN));
RunUI(renameProteinsDlg.Paste);
RunDlg <MessageDlg>(renameProteinsDlg.OkDialog,
messageDlg =>
{
AssertEx.AreComparableStrings(
Resources.
RenameProteinsDlg_OkDialog_Cannot_rename__0__more_than_once__Please_remove_either__1__or__2__,
messageDlg.Message, 3);
messageDlg.OkDialog();
});
// Populate grid test
RunUI(() =>
{
renameProteinsDlg.PopulateGrid();
Assert.IsTrue(Equals(renameProteinsDlg.NameCount, SkylineWindow.Document.MoleculeGroupCount));
renameProteinsDlg.CancelButton.PerformClick();
});
WaitForClosedForm(renameProteinsDlg);
}
// Use FASTA File
{
Assert.AreNotSame(docOrig, SkylineWindow.Document);
RunUI(() =>
{
SkylineWindow.Undo(); // Rename
SkylineWindow.Undo(); // Add nonFASTA protein
SkylineWindow.Undo(); // Direct edit
});
WaitForCondition(() => !Equals(SkylineWindow.Document.PeptideGroups.ToArray()[1].Name, FIRST_RENAMED_PROTEIN));
WaitForProteinMetadataBackgroundLoaderCompletedUI();
Assert.AreSame(docOrig, SkylineWindow.Document);
Assert.AreNotEqual(FIRST_RENAMED_PROTEIN, docOrig.PeptideGroups.ToArray()[1].Name);
WaitForCondition(() => !Equals(SkylineWindow.SequenceTree.Nodes[2].Text, SECOND_RENAMED_PROTEIN));
WaitForProteinMetadataBackgroundLoaderCompletedUI();
RunUI(() =>
{
SkylineWindow.SequenceTree.SelectedNode = SkylineWindow.SequenceTree.Nodes[2];
Assert.IsTrue(!Equals(SkylineWindow.SequenceTree.SelectedNode.Text, SECOND_RENAMED_PROTEIN));
});
// Use FASTA file where only two names differ
RunDlg <RenameProteinsDlg>(SkylineWindow.ShowRenameProteinsDlg,
renameProteinsDlg =>
{
renameProteinsDlg.UseFastaFile(TestFilesDir.GetTestPath(@"RenameProteinsTest\FastaPartialRenamed.txt"));
Assert.IsTrue(Equals(renameProteinsDlg.NameCount, 2));
renameProteinsDlg.CancelButton.PerformClick();
});
// Use FASTA file where all names differ
RunDlg <RenameProteinsDlg>(SkylineWindow.ShowRenameProteinsDlg,
renameProteinsDlg =>
{
renameProteinsDlg.UseFastaFile(TestFilesDir.GetTestPath(@"RenameProteinsTest\FastaRenamed.txt"));
Assert.IsTrue(Equals(renameProteinsDlg.NameCount, SkylineWindow.Document.PeptideGroupCount));
renameProteinsDlg.OkDialog();
});
var docFastaRename = WaitForDocumentChange(docOrig);
var peptideGroups = docFastaRename.PeptideGroups.ToArray();
for (int i = 0; i < peptideGroups.Length; i++)
{
Assert.AreEqual(string.Format("Test{0}", i + 1), peptideGroups[i].Name);
}
}
// Reopen file
{
RunUI(() =>
{
SkylineWindow.SaveDocument(TestContext.GetTestPath("test.sky"));
SkylineWindow.NewDocument();
SkylineWindow.OpenFile(TestContext.GetTestPath("test.sky"));
});
var docFastaRename = WaitForDocumentChange(docOrig);
var peptideGroups = docFastaRename.PeptideGroups.ToArray();
for (int i = 0; i < peptideGroups.Length; i++)
{
Assert.AreEqual(string.Format("Test{0}", i + 1), peptideGroups[i].Name);
}
}
// Name repetition
{
RunUI(() =>
{
SkylineWindow.SequenceTree.SelectedNode = SkylineWindow.SequenceTree.Nodes[0];
SkylineWindow.SequenceTree.BeginEdit(false);
SkylineWindow.SequenceTree.StatementCompletionEditBox.TextBox.Text = FIRST_RENAMED_PROTEIN;
SkylineWindow.SequenceTree.CommitEditBox(false);
SkylineWindow.SequenceTree.SelectedNode = SkylineWindow.SequenceTree.Nodes[1];
SkylineWindow.SequenceTree.BeginEdit(false);
SkylineWindow.SequenceTree.StatementCompletionEditBox.TextBox.Text = FIRST_RENAMED_PROTEIN;
SkylineWindow.SequenceTree.CommitEditBox(false);
});
var renameProteinsDlg = ShowDialog <RenameProteinsDlg>(SkylineWindow.ShowRenameProteinsDlg);
RunDlg <MessageDlg>(() => renameProteinsDlg.UseFastaFile(TestFilesDir.GetTestPath(@"RenameProteinsTest\Fasta.txt")),
messageDlg =>
{
AssertEx.AreComparableStrings(Resources.RenameProteinsDlg_UseFastaFile_The_document_contains_a_naming_conflict_The_name__0__is_currently_used_by_multiple_protein_sequences, messageDlg.Message, 1);
messageDlg.OkDialog();
});
RunUI(() => renameProteinsDlg.CancelButton.PerformClick());
WaitForClosedForm(renameProteinsDlg);
}
}
static async Task InvokeAfterCaptureAction(ScreenRecording recording, HSSettings settingsContext)
{
switch (settingsContext.ActionAfterVideoCapture)
{
case VideoCaptureHandlingAction.Upload:
try
{
var payload = new VideoUploadPayload(recording);
var result = await UploadDispatcher.InitiateUploadToDefaultUploader(payload, settingsContext, HolzShotsApplication.Instance.Uploaders, null).ConfigureAwait(true);
UploadHelper.InvokeUploadFinishedUI(result, settingsContext);
}
catch (UploadCanceledException)
{
NotificationManager.ShowOperationCanceled();
}
catch (UploadException ex)
{
await NotificationManager.UploadFailed(ex);
}
return;
case VideoCaptureHandlingAction.CopyFile:
{
var success = ClipboardEx.SetFiles(recording.FilePath);
if (settingsContext.ShowCopyConfirmation)
{
if (success)
{
NotificationManager.ShowFileCopyConfirmation();
}
else
{
NotificationManager.CopyingFileFailed();
}
}
}
break;
case VideoCaptureHandlingAction.CopyFilePath:
{
var success = ClipboardEx.SetText(recording.FilePath);
if (settingsContext.ShowCopyConfirmation)
{
if (success)
{
NotificationManager.ShowFilePathCopyConfirmation();
}
else
{
NotificationManager.CopyingFilePathFailed();
}
}
}
break;
case VideoCaptureHandlingAction.ShowInExplorer:
IO.HolzShotsPaths.OpenSelectedFileInExplorer(recording.FilePath);
return;
case VideoCaptureHandlingAction.OpenInDefaultApp:
Process.Start(recording.FilePath);
return;
case VideoCaptureHandlingAction.None: return;
default: throw new ArgumentException("Unhandled VideoCaptureHandlingAction: " + settingsContext.ActionAfterVideoCapture);
}
}
/// <summary>
/// Use the document grid to change the StandardType and NormalizationMethod values for
/// several peptides in the document.
/// </summary>
private void SetNormalizationMethodsInDocumentGrid()
{
RunUI(() => SkylineWindow.ShowDocumentGrid(true));
var documentGrid = FormUtil.OpenForms.OfType <DocumentGridForm>()
.FirstOrDefault(form => form.ShowViewsMenu);
Assert.IsNotNull(documentGrid);
RunUI(() => documentGrid.ChooseView("NormalizationMethods"));
WaitForConditionUI(() => documentGrid.IsComplete);
var colModifiedSequence =
documentGrid.FindColumn(PropertyPath.Root.Property("ModifiedSequence").Property("MonoisotopicMasses"));
Assert.IsNotNull(colModifiedSequence);
string[] modifiedSequences = null;
RunUI(() =>
{
modifiedSequences = documentGrid.DataGridView.Rows.OfType <DataGridViewRow>()
.Select(row => row.Cells[colModifiedSequence.Index].Value.ToString()).ToArray();
});
string[] expectedPeptides =
{
"GNPTVEVELTTEK",
"SIVPSGASTGVHEALEMR",
"NVNDVIAPAFVK",
"AVDDFLISLDGTANK",
"LGANAILGVSLAASR",
"TSPYVLPVPFLNVLNGGSHAGGALALQEFMIAPTGAK",
"IGSEVYHNLK",
"YGASAGNVGDEGGVAPNIQTAEEALDLIVDAIK",
"IGLDC[+57.021464]ASSEFFK",
"WLTGPQLADLYHSLMK",
"YPIVSIEDPFAEDDWEAWSHFFK",
"TAGIQIVADDLTVTNPK",
"VNQIGTLSESIK",
"SGETEDTFIADLVVGLR",
"IEEELGDNAVFAGENFHHGDK",
};
CollectionAssert.AreEqual(expectedPeptides, modifiedSequences);
StandardType[] newStandardTypes =
{
null,
null,
StandardType.GLOBAL_STANDARD, // NVNDVIAPAFVK
StandardType.SURROGATE_STANDARD, // AVDDFLISLDGTANK
null,
null,
null,
null,
StandardType.SURROGATE_STANDARD, // IGLDC[+57.021464]ASSEFFK
null,
null,
StandardType.GLOBAL_STANDARD, // TAGIQIVADDLTVTNPK
null,
null,
null
};
Assert.AreEqual(expectedPeptides.Length, newStandardTypes.Length);
var colStandardType = documentGrid.FindColumn(PropertyPath.Root.Property("StandardType"));
Assert.IsNotNull(colStandardType);
RunUI(() =>
{
documentGrid.DataGridView.CurrentCell =
documentGrid.DataGridView.Rows[0].Cells[colStandardType.Index];
string strStandardTypes = string.Join(Environment.NewLine, newStandardTypes.Cast <object>()
.Select(standardType => (standardType ?? string.Empty).ToString()));
ClipboardEx.SetText(strStandardTypes);
documentGrid.DataGridView.SendPaste();
});
VerifyCalculatedAreas();
WaitForConditionUI(() => documentGrid.IsComplete);
NormalizationMethod[] normalizationMethods =
{
new NormalizationMethod.RatioToSurrogate("IGLDC[+57.021464]ASSEFFK"),
NormalizationMethod.GLOBAL_STANDARDS,
null,
null,
new NormalizationMethod.RatioToSurrogate("AVDDFLISLDGTANK")
};
var colNormalizationMethod = documentGrid.FindColumn(PropertyPath.Root.Property("NormalizationMethod"));
Assert.IsNotNull(colNormalizationMethod);
RunUI(() =>
{
documentGrid.DataGridView.CurrentCell =
documentGrid.DataGridView.Rows[0].Cells[colNormalizationMethod.Index];
string strNormalizationMethods = string.Join(Environment.NewLine, normalizationMethods.Cast <object>()
.Select(normalizationMethod => (normalizationMethod ?? string.Empty).ToString()));
ClipboardEx.SetText(strNormalizationMethods);
documentGrid.DataGridView.SendPaste();
});
var actualNormalizationMethods = SkylineWindow.Document.Molecules.Select(mol => mol.NormalizationMethod)
.ToArray();
var expectedNormalizationMethods = normalizationMethods.Concat(Enumerable.Repeat((NormalizationMethod)null,
actualNormalizationMethods.Length - normalizationMethods.Length)).ToArray();
CollectionAssert.AreEqual(expectedNormalizationMethods, actualNormalizationMethods);
VerifyCalculatedAreas();
}
protected override void DoTest()
{
RunUI(() =>
{
SkylineWindow.ResetDefaultSettings();
SkylineWindow.NewDocument();
});
ShowAndPositionAuditLog(false);
PauseForScreenShot <AuditLogForm>("Empty Audit Log form.", 2);
// Configuring Settings for Inserting a New Peptide, p. 3
{
var doc = SkylineWindow.Document;
var transitionSettingsUI = ShowDialog <TransitionSettingsUI>(SkylineWindow.ShowTransitionSettingsUI);
RunUI(() =>
{
// Filter Settings
transitionSettingsUI.SelectedTab = TransitionSettingsUI.TABS.Filter;
transitionSettingsUI.RangeFrom = Resources.TransitionFilter_FragmentStartFinders_ion_3;
transitionSettingsUI.RangeTo = Resources.TransitionFilter_FragmentEndFinders_last_ion_minus_1;
});
OkDialog(transitionSettingsUI, transitionSettingsUI.OkDialog);
WaitForDocumentChange(doc);
}
PeptideSettingsUI peptideSettingsUi = ShowDialog <PeptideSettingsUI>(SkylineWindow.ShowPeptideSettingsUI);
RunUI(() => peptideSettingsUi.SelectedTab = PeptideSettingsUI.TABS.Modifications);
var modHeavyK = new StaticMod("Label:13C(6)15N(2) (C-term K)", "K", ModTerminus.C, false, null, LabelAtoms.C13 | LabelAtoms.N15,
RelativeRT.Matching, null, null, null);
AddHeavyMod(modHeavyK, peptideSettingsUi);
RunUI(() => peptideSettingsUi.PickedHeavyMods = new[] { modHeavyK.Name });
OkDialog(peptideSettingsUi, peptideSettingsUi.OkDialog);
PauseForScreenShot <AuditLogForm>("Audit Log form with settings modifications.", 4);
RunUI(() =>
{
SkylineWindow.AuditLogForm.Close();
SkylineWindow.Width = 1010;
});
PauseForScreenShot("Undo list expanded. (manual)", 4);
RunUI(SkylineWindow.Undo);
PauseForScreenShot("Redo list expanded. (manual)", 5);
RunUI(SkylineWindow.Redo);
// Inserting a peptide sequence p. 5
using (new CheckDocumentState(1, 1, 2, 10))
{
WaitForProteinMetadataBackgroundLoaderCompletedUI();
var pasteDlg = ShowDialog <PasteDlg>(SkylineWindow.ShowPastePeptidesDlg);
RunUI(() => SetClipboardText("IEAIPQIDK\tGST-tag"));
RunUI(pasteDlg.PastePeptides);
RunUI(() =>
{
pasteDlg.Size = new Size(700, 210);
pasteDlg.Top = SkylineWindow.Bottom + 20;
});
PauseForScreenShot <PasteDlg.PeptideListTab>("Insert Peptide List", 6);
using (new WaitDocumentChange())
{
OkDialog(pasteDlg, pasteDlg.OkDialog);
}
WaitForConditionUI(() => SkylineWindow.SequenceTree.Nodes.Count > 0);
}
RunUI(() =>
{
SkylineWindow.ExpandPrecursors();
SkylineWindow.Height = 390;
});
PauseForScreenShot("Main window with Targets view", 6);
ShowAndPositionAuditLog(true);
PauseForScreenShot <AuditLogForm>("Audit Log form with inserted peptide.", 7);
ShowLastExtraInfo("Extra info form with inserted peptide info.", 7);
string documentPath = GetTestPath("AuditLogTutorial" + SrmDocument.EXT);
RunUI(() => SkylineWindow.SaveDocument(documentPath));
WaitForCondition(() => File.Exists(documentPath));
// Importing RAW files into Skyline p. 7
var importResultsDlg = ShowDialog <ImportResultsDlg>(SkylineWindow.ImportResults);
RunUI(() =>
{
var rawFiles = DataSourceUtil.GetDataSources(TestFilesDirs[0].FullPath).First().Value;
var namedPathSets = from rawFile in rawFiles
select new KeyValuePair <string, MsDataFileUri[]>(
rawFile.GetFileNameWithoutExtension(), new[] { rawFile });
importResultsDlg.NamedPathSets = namedPathSets.ToArray();
});
OkDialog(importResultsDlg, importResultsDlg.OkDialog);
WaitForGraphs();
RunUI(() =>
{
SkylineWindow.SelectedPath = SkylineWindow.Document.GetPathTo((int)SrmDocument.Level.Molecules, 0);
Settings.Default.ArrangeGraphsOrder = GroupGraphsOrder.Document.ToString();
Settings.Default.ArrangeGraphsReversed = false;
SkylineWindow.ArrangeGraphsTabbed();
SkylineWindow.AutoZoomBestPeak();
});
WaitForCondition(() => Equals(9, SkylineWindow.GraphChromatograms.Count(graphChrom => !graphChrom.IsHidden)),
"unexpected visible graphChromatogram count");
WaitForCondition(10 * 60 * 1000, // ten minutes
() => SkylineWindow.Document.Settings.HasResults && SkylineWindow.Document.Settings.MeasuredResults.IsLoaded);
PauseForScreenShot <AuditLogForm>("Audit Log form with imported data files.", 9);
ShowLastExtraInfo("Extra info form for the import.", 9);
// Peptide Quantitification Settings p. 9
peptideSettingsUi = ShowDialog <PeptideSettingsUI>(SkylineWindow.ShowPeptideSettingsUI);
RunUI(() => peptideSettingsUi.SelectedTab = (PeptideSettingsUI.TABS) 5);
const string quantUnits = "fmol/ul";
RunUI(() =>
{
peptideSettingsUi.QuantRegressionFit = RegressionFit.LINEAR;
peptideSettingsUi.QuantNormalizationMethod = new NormalizationMethod.RatioToLabel(IsotopeLabelType.heavy);
peptideSettingsUi.QuantUnits = quantUnits;
});
OkDialog(peptideSettingsUi, peptideSettingsUi.OkDialog);
PauseForScreenShot <AuditLogForm>("Audit Log form with quantification settings.", 10);
// Specify analyte concentrations of external standards
RunUI(() =>
{
SkylineWindow.AuditLogForm.Close();
SkylineWindow.ShowDocumentGrid(true);
});
var documentGridForm = FindOpenForm <DocumentGridForm>();
RunUI(() =>
{
documentGridForm.ChooseView(Resources.SkylineViewContext_GetDocumentGridRowSources_Replicates);
});
WaitForConditionUI(() => documentGridForm.IsComplete);
var concentrations = new[] { 40, 12.5, 5, 2.5, 1, .5, .25, .1 };
string pasteString = TextUtil.LineSeparate(concentrations.Select((f, i) =>
QuantificationStrings.SampleType_STANDARD_Standard + "\t" + f));
ClipboardEx.SetText(pasteString);
using (new WaitDocumentChange())
{
RunUI(() =>
{
var colSampleType = documentGridForm.FindColumn(PropertyPath.Root.Property("SampleType"));
documentGridForm.DataGridView.CurrentCell = documentGridForm.DataGridView.Rows[1].Cells[colSampleType.Index];
documentGridForm.DataGridView.SendPaste();
});
}
// ReSharper restore AccessToModifiedClosure
WaitForConditionUI(() => documentGridForm.IsComplete);
RunUI(() =>
{
var gridFloatingWindow = documentGridForm.Parent.Parent;
gridFloatingWindow.Size = new Size(370, 315);
gridFloatingWindow.Top = SkylineWindow.Bottom + 20;
});
PauseForScreenShot <DocumentGridForm>("Document grid with concentrations filled in", 11);
RunUI(documentGridForm.Close);
ShowAndPositionAuditLog(true);
PauseForScreenShot <AuditLogForm>("Audit Log form with grid changes", 12);
ShowLastExtraInfo("Extra Info for the analyte data import.", 12);
RunUI(SkylineWindow.AuditLogForm.Close);
const string unknownReplicate = "FOXN1-GST";
RestoreViewOnScreen(13);
ActivateReplicate(unknownReplicate);
SelectNode(SrmDocument.Level.TransitionGroups, 1);
RunUI(() => SkylineWindow.Size = new Size(936, 527));
WaitForGraphs();
PauseForScreenShot("Heavy precursor chromatogram", 13);
RunUI(() =>
{
var pathHeavy = SkylineWindow.DocumentUI.GetPathTo((int)SrmDocument.Level.TransitionGroups, 1);
var graphChrom = SkylineWindow.GetGraphChrom(unknownReplicate);
Assert.IsNotNull(graphChrom);
Assert.AreEqual(unknownReplicate, graphChrom.NameSet);
var firstGroupInfo = graphChrom.ChromGroupInfos.FirstOrDefault();
Assert.IsNotNull(firstGroupInfo, "Missing group info");
var firstChromItem = graphChrom.GraphItems.FirstOrDefault(gci => gci.TransitionChromInfo != null);
Assert.IsNotNull(firstChromItem, "Missing graph item");
var listChanges = new List <ChangedPeakBoundsEventArgs>
{
new ChangedPeakBoundsEventArgs(pathHeavy,
null,
graphChrom.NameSet,
firstGroupInfo.FilePath,
firstChromItem.GetValidPeakBoundaryTime(20.65),
firstChromItem.GetValidPeakBoundaryTime(21.15),
PeakIdentification.FALSE,
PeakBoundsChangeType.both)
};
graphChrom.SimulateChangedPeakBounds(listChanges);
});
ShowAndPositionAuditLog(true, 50, 200);
WaitForConditionUI(500, () => SkylineWindow.AuditLogForm.DataGridView.Rows.Count > 0);
PauseForScreenShot <AuditLogForm>("Audit Log form with changed integration boundary.", 14);
int reasonIndex = 2;
using (new WaitDocumentChange())
{
RunUI(() =>
{
var pathReason = PropertyPath.Root.Property("Reason");
var colReason = SkylineWindow.AuditLogForm.FindColumn(pathReason);
reasonIndex = colReason.Index;
SetCellValue(SkylineWindow.AuditLogForm.DataGridView, 0, reasonIndex,
"Changed peak integration as instructed by the tutorial");
});
}
RunUI(() => SkylineWindow.AuditLogForm.DataGridView.AutoResizeColumn(reasonIndex));
SetGridFormToFullWidth(SkylineWindow.AuditLogForm);
PauseForScreenShot <AuditLogForm>("Audit Log form with updated reason.", 14);
// View the calibration curve p. 15
RunUI(() => SkylineWindow.ShowCalibrationForm());
var calibrationForm = FindOpenForm <CalibrationForm>();
var priorZoomState = ZoomCalibrationCurve(calibrationForm, 0.52);
RunUI(() =>
{
Assert.AreEqual(CalibrationCurveFitter.AppendUnits(QuantificationStrings.Analyte_Concentration, quantUnits), calibrationForm.ZedGraphControl.GraphPane.XAxis.Title.Text);
Assert.AreEqual(string.Format(QuantificationStrings.CalibrationCurveFitter_PeakAreaRatioText__0___1__Peak_Area_Ratio, IsotopeLabelType.light.Title, IsotopeLabelType.heavy.Title),
calibrationForm.ZedGraphControl.GraphPane.YAxis.Title.Text);
VerifyCalibrationCurve(calibrationForm, 5.4065E-1, -2.9539E-1, 0.999);
});
PauseForScreenShot <CalibrationForm>("Calibration curve zoomed", 15);
RunUI(() =>
{
priorZoomState?.ApplyState(calibrationForm.ZedGraphControl.GraphPane);
var chromatograms = SkylineWindow.DocumentUI.Settings.MeasuredResults.Chromatograms;
new [] { 5, 6, 7, 8 }.ForEach((index) =>
{
int replicateIdx = chromatograms.IndexOf((ch) => ch.Name.Equals("Standard_" + index));
Assert.IsTrue(replicateIdx >= 0);
using (var excludeStandardMenu = calibrationForm.MakeExcludeStandardMenuItem(replicateIdx))
{
excludeStandardMenu?.PerformClick();
}
});
});
WaitForGraphs();
RunUI(() => VerifyCalibrationCurve(calibrationForm, 5.52E-1, -6.3678E-1, 1));
OkDialog(calibrationForm, calibrationForm.Close);
PauseForScreenShot <AuditLogForm>("Audit Log with excluded standard records", 16);
PauseForScreenShot <AuditLogForm>("Audit Log Reports menu (manual)", 16);
// TODO(nicksh): Audit log reason field does not currently support fill down
// RunUI(() =>
// {
// SetCellValue(SkylineWindow.AuditLogForm.DataGridView, 0, reasonIndex, "Excluded standard below LOD");
// for (int i = 0; i < 4; i++)
// SkylineWindow.AuditLogForm.DataGridView.Rows[i].Cells[reasonIndex].Selected = true;
// });
// RunUI(() => SkylineWindow.AuditLogForm.DataboundGridControl.FillDown());
RunUI(() =>
{
for (int i = 0; i < 4; i++)
{
SetCellValue(SkylineWindow.AuditLogForm.DataGridView, i, reasonIndex, "Excluded standard below LOD");
}
});
RunUI(() =>
{
SkylineWindow.AuditLogForm.ChooseView(AuditLogStrings.AuditLogForm_MakeAuditLogForm_Undo_Redo);
});
SetGridFormToFullWidth(SkylineWindow.AuditLogForm);
RunUI(() =>
{
var floatingWindow = SkylineWindow.AuditLogForm.Parent.Parent;
floatingWindow.Height = 334;
floatingWindow.Width -= 15;
});
PauseForScreenShot <AuditLogForm>("Audit Log with UndoRedo view.", 17);
if (IsCoverShotMode)
{
RunUI(() =>
{
SkylineWindow.ChangeTextSize(TreeViewMS.LRG_TEXT_FACTOR);
});
RestoreCoverViewOnScreen();
var calibrationCoverForm = WaitForOpenForm <CalibrationForm>();
ZoomCalibrationCurve(calibrationCoverForm, 0.53);
var floatingLogWindow = SkylineWindow.AuditLogForm.Parent.Parent;
var floatingCalWindow = calibrationCoverForm.Parent.Parent;
RunUI(() =>
{
floatingLogWindow.Top = SkylineWindow.Bottom - floatingLogWindow.Height - 8;
floatingLogWindow.Left =
(SkylineWindow.Left + SkylineWindow.Right) / 2 - floatingLogWindow.Width / 2;
floatingCalWindow.Top = SkylineWindow.Top + 8;
floatingCalWindow.Left = SkylineWindow.Right - floatingCalWindow.Width - 8;
SkylineWindow.AuditLogForm.DataGridView.AutoResizeColumn(reasonIndex);
SkylineWindow.AuditLogForm.DataGridView.AutoResizeColumn(reasonIndex - 1);
});
TakeCoverShot();
}
var customizeDialog = ShowDialog <ViewEditor>(SkylineWindow.AuditLogForm.NavBar.CustomizeView);
RunUI(() =>
{
customizeDialog.ViewName = "Custom Columns";
var columnsToAdd = new[]
{
PropertyPath.Parse("SkylineVersion"),
PropertyPath.Parse("User"),
};
foreach (var id in columnsToAdd)
{
Assert.IsTrue(customizeDialog.ChooseColumnsTab.TrySelect(id), "Unable to select {0}", id);
customizeDialog.ChooseColumnsTab.AddSelectedColumn();
}
customizeDialog.Height = 370;
});
PauseForScreenShot <ViewEditor.ChooseColumnsView>("Custom Columns report template", 17);
OkDialog(customizeDialog, customizeDialog.OkDialog);
SetGridFormToFullWidth(SkylineWindow.AuditLogForm);
RunUI(() => SkylineWindow.AuditLogForm.Parent.Parent.Height += 10); // Extra for 2-line headers
PauseForScreenShot <AuditLogForm>("Audit Log with custom view.", 18);
var registrationDialog = ShowDialog <MultiButtonMsgDlg>(() => SkylineWindow.ShowPublishDlg(null));
PauseForScreenShot <MultiButtonMsgDlg>("Upload confirmation dialog.", 19);
var loginDialog = ShowDialog <EditServerDlg>(registrationDialog.ClickNo);
PauseForScreenShot <EditServerDlg>("Login dialog.", 20);
RunUI(() =>
{
loginDialog.URL = SERVER_URL;
loginDialog.Username = PANORAMA_USER_NAME;
});
if (!IsPauseForScreenShots)
{
OkDialog(loginDialog, loginDialog.CancelButton.PerformClick);
}
else
{
PauseTest("Enter password. (manual) No screen shot.");
var publishDialog = ShowDialog <PublishDocumentDlg>(loginDialog.OkDialog);
WaitForCondition(() => publishDialog.IsLoaded);
RunUI(() =>
{
publishDialog.SelectItem(testFolderName);
});
PauseForScreenShot <PublishDocumentDlg>("Folder selection dialog.", 21);
var browserConfirmationDialog = ShowDialog <MultiButtonMsgDlg>(publishDialog.OkDialog);
OkDialog(browserConfirmationDialog, browserConfirmationDialog.ClickYes);
PauseForScreenShot("Uploaded document in Panorama (in browser).");
Regex reDocId = new Regex(@"\?id=([0-9]+)");
Assert.IsTrue(reDocId.IsMatch(publishDialog.PanoramaPublishClient.UploadedDocumentUri.ToString()));
string docId = reDocId.Match(publishDialog.PanoramaPublishClient.UploadedDocumentUri.ToString()).Groups[1].Captures[0].Value;
Uri serverUri = new Uri(SERVER_URL);
Uri requestUri = PanoramaUtil.Call(serverUri, "targetedms", String.Format("{0}/{1}", PANORAMA_FOLDER, testFolderName),
"showSkylineAuditLog", "id=" + docId);
Process.Start(requestUri.ToString());
PauseForScreenShot("Uploaded document audit log in Panorama (in browser).");
}
}
protected override void DoTest()
{
// p. 1 open the file
string documentFile = GetTestPath(@"QuaSAR_Tutorial.sky"); // Not L10N
WaitForCondition(() => File.Exists(documentFile));
RunUI(() => SkylineWindow.OpenFile(documentFile));
var document = SkylineWindow.Document;
AssertEx.IsDocumentState(document, null, 34, 125, 250, 750);
var configureToolsDlg = ShowDialog <ConfigureToolsDlg>(SkylineWindow.ShowConfigureToolsDlg);
RunUI(() =>
{
configureToolsDlg.RemoveAllTools();
configureToolsDlg.SaveTools();
});
PauseForScreenShot("p. 2 - External Tools");
const string installZipName = "QuaSAR-1_0.zip"; // Not L10N
if (IsPauseForScreenShots)
{
var rInstaller = ShowDialog <RInstaller>(() =>
{
configureToolsDlg.RemoveAllTools();
configureToolsDlg.SaveTools();
configureToolsDlg.InstallZipTool(GetTestPath(installZipName));
});
PauseForScreenShot("p. 3 - R Installer");
// cancel as we don't actually want to install R / Packages
OkDialog(rInstaller, rInstaller.CancelButton.PerformClick);
}
RunUI(() =>
{
// bypass the R installer dialogue
configureToolsDlg.TestInstallProgram = (container, collection, script) => @"FakeDirectory\R.exe"; // Not L10N
configureToolsDlg.InstallZipTool(GetTestPath(installZipName));
var installedQuaSAR = configureToolsDlg.ToolList[0];
Assert.AreEqual(QUASAR.Title, installedQuaSAR.Title);
Assert.AreEqual(QUASAR.Command, installedQuaSAR.Command);
Assert.AreEqual(QUASAR.Arguments, installedQuaSAR.Arguments);
Assert.AreEqual(QUASAR.InitialDirectory, installedQuaSAR.InitialDirectory);
Assert.AreEqual(QUASAR.ReportTitle, installedQuaSAR.ReportTitle);
Assert.AreEqual(QUASAR.OutputToImmediateWindow, installedQuaSAR.OutputToImmediateWindow);
});
PauseForScreenShot("p. 4 - External Tools (QuaSAR Installed)");
OkDialog(configureToolsDlg, configureToolsDlg.OkDialog);
RunUI(() => SkylineWindow.PopulateToolsMenu());
var annotationsDlg = ShowDialog <DocumentSettingsDlg>(SkylineWindow.ShowDocumentSettingsDialog);
RunUI(() =>
{
var checkedListBox = annotationsDlg.AnnotationsCheckedListBox;
for (int i = 0; i < checkedListBox.Items.Count; i++)
{
checkedListBox.SetItemChecked(i, true);
}
});
PauseForScreenShot("p. 5 - Annotation Settings");
OkDialog(annotationsDlg, annotationsDlg.OkDialog);
RunUI(() =>
{
Assert.IsTrue(SkylineWindow.Document.Settings.DataSettings.AnnotationDefs.Contains(SAMPLEGROUP));
Assert.IsTrue(SkylineWindow.Document.Settings.DataSettings.AnnotationDefs.Contains(IS_SPIKE));
Assert.IsTrue(SkylineWindow.Document.Settings.DataSettings.AnnotationDefs.Contains(CONCENTRATION));
});
RunUI(() => SkylineWindow.ShowResultsGrid(true));
RunUI(() =>
{
SkylineWindow.SelectedPath =
SkylineWindow.DocumentUI.GetPathTo((int)SrmDocument.Level.MoleculeGroups, 0);
});
WaitForGraphs();
DataGridViewColumn colSampleId = null, colConcentration = null, colIsConc = null;
DataGridView resultsGrid = FindOpenForm <LiveResultsGrid>().DataGridView;
WaitForConditionUI(() => 0 != resultsGrid.ColumnCount);
RunUI(() =>
{
colSampleId =
resultsGrid.Columns.Cast <DataGridViewColumn>()
.First(col => SAMPLEGROUP.Name == col.HeaderText);
colConcentration =
resultsGrid.Columns.Cast <DataGridViewColumn>()
.First(col => CONCENTRATION.Name == col.HeaderText);
colIsConc =
resultsGrid.Columns.Cast <DataGridViewColumn>().First(col => IS_SPIKE.Name == col.HeaderText);
});
WaitForCondition(() => resultsGrid != null && colSampleId != null && colConcentration != null && colIsConc != null);
float[] concentrations = { 0f, .001f, .004f, .018f, .075f, .316f, 1.33f, 5.62f, 23.71f, 100 };
string[] sampleIds = { "A", "B", "C", "D", "E", "F", "G", "H", "I", "J" }; // Not L10N
RunUI(() =>
{
Assert.AreEqual(colSampleId.DisplayIndex + 1, colConcentration.DisplayIndex);
Assert.AreEqual(colSampleId.DisplayIndex + 1, colConcentration.DisplayIndex);
StringBuilder clipboardText = new StringBuilder();
for (int i = 0; i < concentrations.Length; i++)
{
for (int j = i * 4; j < (i + 1) * 4; j++)
{
if (clipboardText.Length > 0)
{
clipboardText.Append('\n');
}
clipboardText.Append(sampleIds[i]);
clipboardText.Append('\t');
clipboardText.Append(concentrations[i]);
clipboardText.Append('\t');
clipboardText.Append(10);
}
}
resultsGrid.CurrentCell = resultsGrid.Rows[0].Cells[colSampleId.Index];
ClipboardEx.SetText(clipboardText.ToString());
SendMessage(resultsGrid.Handle, WM_KEYDOWN, (IntPtr)Keys.Control, (IntPtr)0);
SendMessage(resultsGrid.Handle, WM_KEYDOWN, (IntPtr)Keys.V, (IntPtr)0);
SendMessage(resultsGrid.Handle, WM_KEYUP, (IntPtr)Keys.V, (IntPtr)0);
SendMessage(resultsGrid.Handle, WM_KEYUP, (IntPtr)Keys.Control, (IntPtr)0);
});
WaitForGraphs();
PauseForScreenShot("p. 7 - Results Grid");
RunUI(() => SkylineWindow.ShowResultsGrid(false));
if (IsPauseForScreenShots)
{
int formCount = Application.OpenForms.Count;
RunUI(() => SkylineWindow.RunTool(0));
WaitForCondition(() => Application.OpenForms.Count == formCount + 1);
Form argsCollector = Application.OpenForms["QuaSARUI"]; // Not L10N
Assert.IsNotNull(argsCollector);
PauseForScreenShot("p. 8 - Args Collector");
Action actCancel = () => argsCollector.CancelButton.PerformClick();
argsCollector.BeginInvoke(actCancel);
WaitForClosedForm(argsCollector);
}
}
private void btnCopyText_Click(object sender, EventArgs e)
{
ClipboardEx.SetText(SelectedControl.GetErrorLog(cbMoreInfo.Checked));
}
private void DoStudy7Test()
{
// Preparing a Document to Accept the Study 7 Transition List, p. 18
RunUI(() => SkylineWindow.NewDocument());
var peptideSettingsUI1 = ShowDialog <PeptideSettingsUI>(SkylineWindow.ShowPeptideSettingsUI);
if (IsCoverShotMode)
{
var modHeavyK = new StaticMod(HEAVY_K, "K", ModTerminus.C, false, null, LabelAtoms.C13 | LabelAtoms.N15, // Not L10N
RelativeRT.Matching, null, null, null);
AddHeavyMod(modHeavyK, peptideSettingsUI1, "Edit Isotope Modification form", 6);
}
var mod13Cr = new StaticMod("Label:13C(6) (C-term R)", "R", ModTerminus.C, false, null, LabelAtoms.C13,
RelativeRT.Matching, null, null, null);
AddHeavyMod(mod13Cr, peptideSettingsUI1, "Edit Isotope Modification form", 18);
RunUI(() =>
{
peptideSettingsUI1.PickedHeavyMods = new[] { "Label:13C(6) (C-term R)", HEAVY_K };
peptideSettingsUI1.PickedLibraries = new string[0];
peptideSettingsUI1.SelectedBackgroundProteome = Resources.SettingsList_ELEMENT_NONE_None;
peptideSettingsUI1.OkDialog();
});
// Pasting a Transition List into the Document, p. 19.
string clipboardSaveText = string.Empty;
RunUI(() =>
{
var filePath = GetTestPath(@"Study 7\Study7 transition list.xls");
SetExcelFileClipboardText(filePath, "Simple", 6, false);
clipboardSaveText = ClipboardEx.GetText();
});
// We expect this to fail due to instrument settings rather than format issues eg "The product m/z 1519.78 is out of range for the instrument settings, in the peptide sequence YEVQGEVFTKPQLWP. Check the Instrument tab in the Transition Settings."
{
var transitionSelectdgl = ShowDialog <ImportTransitionListColumnSelectDlg>(SkylineWindow.Paste);
var messageDlg = ShowDialog <ImportTransitionListErrorDlg>(transitionSelectdgl.AcceptButton.PerformClick);
AssertEx.AreComparableStrings(TextUtil.SpaceSeparate(Resources.MassListRowReader_CalcTransitionExplanations_The_product_m_z__0__is_out_of_range_for_the_instrument_settings__in_the_peptide_sequence__1_,
Resources.MassListRowReader_CalcPrecursorExplanations_Check_the_Instrument_tab_in_the_Transition_Settings),
messageDlg.ErrorList[0].ErrorMessage,
2);
RunUI(() => messageDlg.Size = new Size(838, 192));
PauseForScreenShot <ImportTransitionListErrorDlg>("Error message form (expected)", 19);
OkDialog(messageDlg, messageDlg.CancelButton.PerformClick); // Acknowledge the error but decline to proceed with import
RunUI(() => transitionSelectdgl.DialogResult = DialogResult.Cancel); // Cancel the import
// Restore the clipboard text after pausing
ClipboardEx.SetText(clipboardSaveText);
}
RunDlg <TransitionSettingsUI>(() => SkylineWindow.ShowTransitionSettingsUI(TransitionSettingsUI.TABS.Instrument), transitionSettingsUI =>
{
transitionSettingsUI.InstrumentMaxMz = 1800;
transitionSettingsUI.OkDialog();
});
PasteTransitionListSkipColumnSelect();
RunUI(SkylineWindow.CollapsePeptides);
PauseForScreenShot("Targets tree (selected from main window)", 20);
// Adjusting Modifications Manually, p. 19.
AdjustModifications("AGLCQTFVYGGCR", true, 'V', 747.348);
PauseForScreenShot("Target tree clipped from main window", 22);
AdjustModifications("IVGGWECEK", true, 'V', 541.763);
AdjustModifications("YEVQGEVFTKPQLWP", false, 'L', 913.974);
RunUI(() => SkylineWindow.SaveDocument(GetTestPath(@"Study 7\Study7.sky")));
// Importing Data from a Multiple Sample WIFF file, p. 23.
var importResultsDlg1 = ShowDialog <ImportResultsDlg>(SkylineWindow.ImportResults);
var openDataSourceDialog1 = ShowDialog <OpenDataSourceDialog>(() => importResultsDlg1.NamedPathSets =
importResultsDlg1.GetDataSourcePathsFile(null));
RunUI(() =>
{
openDataSourceDialog1.CurrentDirectory = new MsDataFilePath(GetTestPath("Study 7"));
openDataSourceDialog1.SelectAllFileType(UseRawFilesOrFullData ? ".wiff" : ".mzML"); // Force true wiff for FullData
});
if (UseRawFilesOrFullData)
{
var importResultsSamplesDlg = ShowDialog <ImportResultsSamplesDlg>(openDataSourceDialog1.Open);
PauseForScreenShot <ImportResultsSamplesDlg>("Choose Samples form", 24);
RunUI(() =>
{
if (IsFullData)
{
importResultsSamplesDlg.CheckAll(true);
importResultsSamplesDlg.ExcludeSample(0); // Blank
importResultsSamplesDlg.ExcludeSample(25); // QC
importResultsSamplesDlg.ExcludeSample(26);
importResultsSamplesDlg.ExcludeSample(27);
importResultsSamplesDlg.ExcludeSample(28);
importResultsSamplesDlg.ExcludeSample(45); // A2
importResultsSamplesDlg.ExcludeSample(46);
importResultsSamplesDlg.ExcludeSample(47);
importResultsSamplesDlg.ExcludeSample(48);
importResultsSamplesDlg.ExcludeSample(49); // gradientwash
importResultsSamplesDlg.ExcludeSample(50);
importResultsSamplesDlg.ExcludeSample(51);
importResultsSamplesDlg.ExcludeSample(52);
importResultsSamplesDlg.ExcludeSample(53); // A3
importResultsSamplesDlg.ExcludeSample(54);
importResultsSamplesDlg.ExcludeSample(55);
importResultsSamplesDlg.ExcludeSample(56);
}
else
{
importResultsSamplesDlg.CheckAll(false);
importResultsSamplesDlg.IncludeSample(1);
importResultsSamplesDlg.IncludeSample(2);
importResultsSamplesDlg.IncludeSample(11);
importResultsSamplesDlg.IncludeSample(12);
}
});
OkDialog(importResultsSamplesDlg, importResultsSamplesDlg.OkDialog);
}
else
{
RunUI(openDataSourceDialog1.Open);
}
{
var importResultsNameDlg = ShowDialog <ImportResultsNameDlg>(importResultsDlg1.OkDialog);
PauseForScreenShot <ImportResultsNameDlg>("Import Results Common prefix form", 25);
OkDialog(importResultsNameDlg, importResultsNameDlg.YesDialog);
}
WaitForCondition(() =>
SkylineWindow.Document.Settings.HasResults && SkylineWindow.Document.Settings.MeasuredResults.IsLoaded);
RestoreViewOnScreen(26);
// Inspecting and Adjusting Peak Integration, p. 24.
RunUI(() =>
{
SkylineWindow.ShowPeakAreaReplicateComparison();
SkylineWindow.ShowGraphRetentionTime(true);
SkylineWindow.Size = new Size(1029, 659);
});
if (!IsPauseForScreenShots && !IsFullData)
{
TestApplyToAll();
}
PauseForScreenShot <GraphSummary.RTGraphView>("Main window with peaks and retention times showing", 26);
CheckReportCompatibility.CheckAll(SkylineWindow.Document);
RunUI(SkylineWindow.EditDelete);
FindNode("IVGGWECEK"); // Not L10N
TransitionGroupTreeNode selNodeGroup = null;
RunUI(() =>
{
selNodeGroup = (TransitionGroupTreeNode)SkylineWindow.SequenceTree.SelectedNode.Nodes[1];
Assert.AreEqual(selNodeGroup.StateImageIndex, (int)SequenceTree.StateImageId.peak_blank);
});
RunDlg <TransitionSettingsUI>(SkylineWindow.ShowTransitionSettingsUI, transitionSettingsUI =>
{
transitionSettingsUI.MZMatchTolerance = 0.065;
transitionSettingsUI.OkDialog();
});
RunUI(() =>
{
Assert.AreEqual((int)SequenceTree.StateImageId.peak, selNodeGroup.StateImageIndex);
SkylineWindow.ToggleIntegrateAll();
});
RunUI(() =>
{
foreach (PeptideDocNode nodePep in SkylineWindow.Document.Molecules)
{
string sequence = nodePep.Peptide.Sequence;
int imageIndex = PeptideTreeNode.GetPeakImageIndex(nodePep, SkylineWindow.SequenceTree);
if ((sequence != null) && (sequence.StartsWith("YLA") || sequence.StartsWith("YEV"))) // Not L10N
{
Assert.AreEqual((int)SequenceTree.StateImageId.keep, imageIndex,
string.Format("Expected keep icon for the peptide {0}, found {1}", sequence, imageIndex));
}
else if (sequence != null)
{
Assert.AreEqual((int)SequenceTree.StateImageId.peak, imageIndex,
string.Format("Expected peak icon for the peptide {0}, found {1}", sequence, imageIndex));
}
else // Custom Ion
{
Assert.AreEqual((int)SequenceTree.StateImageId.peak_blank, imageIndex,
string.Format("Expected peak_blank icon for the custom ion {0}, found {1}", nodePep.ModifiedTarget, imageIndex));
}
}
});
PauseForScreenShot("Main window", 27);
// Data Inspection with Peak Areas View, p. 29.
RestoreViewOnScreen(28);
FindNode("SSDLVALSGGHTFGK"); // Not L10N
RunUI(NormalizeGraphToHeavy);
PauseForScreenShot <GraphSummary.AreaGraphView>("Peak Areas graph metafile", 29);
FindNode((564.7746).ToString(LocalizationHelper.CurrentCulture) + "++"); // ESDTSYVSLK - Not L10N
PauseForScreenShot <GraphSummary.AreaGraphView>("Peak Areas graph metafile", 30);
RunUI(SkylineWindow.ExpandPeptides);
string hgflprLight = (363.7059).ToString(LocalizationHelper.CurrentCulture) + "++"; // HGFLPR - Not L10N
FindNode(hgflprLight);
PauseForScreenShot <GraphSummary.AreaGraphView>("Peak Areas graph metafile", 31);
RunUI(() => SkylineWindow.NormalizeAreaGraphTo(NormalizeOption.TOTAL));
PauseForScreenShot <GraphSummary.AreaGraphView>("Peak Areas graph normalized metafile", 32);
RunUI(() =>
{
SkylineWindow.ShowGraphPeakArea(false);
SkylineWindow.ActivateReplicate("E_03");
SkylineWindow.Size = new Size(757, 655);
});
PauseForScreenShot <GraphChromatogram>("Chromatogram graph metafile with interference", 32);
RunUI(() => SkylineWindow.ShowGraphPeakArea(true));
RunUI(() =>
{
SkylineWindow.ShowPeakAreaPeptideGraph();
SkylineWindow.ShowTotalTransitions();
SkylineWindow.ShowCVValues(true);
SkylineWindow.ShowPeptideOrder(SummaryPeptideOrder.document);
});
PauseForScreenShot <GraphSummary.AreaGraphView>("Peak Areas Peptide Comparison graph metafile", 33);
float[] concentrations = { 0f, 60, 175, 513, 1500, 2760, 4980, 9060, 16500, 30000 };
var documentGrid = ShowDialog <DocumentGridForm>(() => SkylineWindow.ShowDocumentGrid(true));
var pathConcentration = PropertyPath.Parse("AnalyteConcentration");
var pathSampleType = PropertyPath.Parse("SampleType");
RunUI(() => documentGrid.ChooseView(Resources.SkylineViewContext_GetDocumentGridRowSources_Replicates));
WaitForConditionUI(() => documentGrid.RowCount == (IsFullData ? concentrations.Length * 4 : 4) &&
documentGrid.FindColumn(pathConcentration) != null &&
documentGrid.FindColumn(pathSampleType) != null); // Let it initialize
RunUI(() =>
{
// Parent is a DocPane and Parent.Parent is the floating window
documentGrid.Parent.Parent.Size = new Size(585, 325);
var documentGridView = documentGrid.DataGridView;
var colConcentration = documentGrid.FindColumn(pathConcentration);
var colStandardType = documentGrid.FindColumn(pathSampleType);
if (IsFullData)
{
for (int i = 0; i < concentrations.Length; i++)
{
for (int j = i * 4; j < (i + 1) * 4; j++)
{
double?concentration = concentrations[i];
SetCellValue(documentGridView, j, colConcentration.Index, concentration);
SetCellValue(documentGridView, j, colStandardType.Index,
concentration == 0 ? SampleType.BLANK : SampleType.STANDARD);
}
}
}
else
{
SetCellValue(documentGridView, 0, colConcentration.Index, 0.0);
SetCellValue(documentGridView, 0, colStandardType.Index, SampleType.BLANK);
SetCellValue(documentGridView, 1, colConcentration.Index, 0.0);
SetCellValue(documentGridView, 1, colStandardType.Index, SampleType.BLANK);
SetCellValue(documentGridView, 2, colConcentration.Index, 175.0);
SetCellValue(documentGridView, 2, colStandardType.Index, SampleType.STANDARD);
SetCellValue(documentGridView, 3, colConcentration.Index, 175.0);
SetCellValue(documentGridView, 3, colStandardType.Index, SampleType.STANDARD);
}
});
WaitForGraphs();
PauseForScreenShot <DocumentGridForm>("Document grid filled (scrolled to the end)", 35);
RunUI(() => documentGrid.Close());
FindNode("SSDLVALSGGHTFGK"); // Not L10N
RunUI(() =>
{
SkylineWindow.ShowPeakAreaReplicateComparison();
var settings = SkylineWindow.DocumentUI.Settings;
var valConcentration = ReplicateValue.GetAllReplicateValues(settings).Skip(1).First();
SkylineWindow.GroupByReplicateValue(valConcentration);
NormalizeGraphToHeavy();
});
PauseForScreenShot <GraphSummary.AreaGraphView>("Peak Areas graph with CVs metafile", 36);
RunUI(() => SkylineWindow.ShowCVValues(false));
RunUI(() => SkylineWindow.SaveDocument());
PauseForScreenShot <GraphSummary.AreaGraphView>("Peak Areas graph grouped by concentration metafile", 37);
PauseForAuditLog();
// Further Exploration, p. 33.
RunUI(() =>
{
SkylineWindow.OpenFile(GetTestPath(@"Study 7\Study II\Study 7ii (site 52).sky")); // Not L10N
SkylineWindow.ShowPeakAreaPeptideGraph();
SkylineWindow.ShowCVValues(true);
});
WaitForCondition(() => SkylineWindow.Document.Settings.MeasuredResults.IsLoaded);
RestoreViewOnScreen(38);
PauseForScreenShot <GraphSummary.AreaGraphView>("Peak Areas peptide comparison graph metafile", 38);
FindNode("LSEPAELTDAVK");
RunUI(() =>
{
SkylineWindow.ShowGraphPeakArea(false);
SkylineWindow.Width = 920;
SkylineWindow.ShowRTReplicateGraph();
});
PauseForScreenShot <GraphSummary.RTGraphView>("Retention Times replicate graph metafile", 38);
FindNode("INDISHTQSVSAK");
RunUI(SkylineWindow.ShowPeakAreaReplicateComparison);
PauseForScreenShot <GraphSummary.AreaGraphView>("Peak Areas normalized to heave graph metafile", 39);
if (IsCoverShotMode)
{
RunUI(() =>
{
Settings.Default.ChromatogramFontSize = 14;
Settings.Default.AreaFontSize = 14;
SkylineWindow.ChangeTextSize(TreeViewMS.LRG_TEXT_FACTOR);
SkylineWindow.AutoZoomBestPeak();
});
RestoreCoverViewOnScreen();
RunUI(() => SkylineWindow.SequenceTree.SelectedNode = SkylineWindow.SelectedNode.Parent);
WaitForGraphs();
RunUI(() => SkylineWindow.SequenceTree.SelectedNode = SkylineWindow.SelectedNode.Nodes[0]);
RunUI(SkylineWindow.FocusDocument);
TakeCoverShot();
return;
}
RunUI(() => SkylineWindow.NormalizeAreaGraphTo(NormalizeOption.NONE));
WaitForGraphs();
PauseForScreenShot <GraphSummary.AreaGraphView>("Peak Areas no normalization graph metafile", 40);
FindNode(hgflprLight);
RunUI(() =>
{
SkylineWindow.ShowAllTransitions();
NormalizeGraphToHeavy();
});
WaitForGraphs();
PauseForScreenShot <GraphSummary.AreaGraphView>("Area Ratio to Heavy graph showing interference metafile", 41);
RunUI(() => SkylineWindow.ShowGraphPeakArea(false));
RunUI(() => SkylineWindow.ActivateReplicate("E_ 03"));
WaitForGraphs();
PauseForScreenShot <GraphChromatogram>("Chromatogram graph metafile showing slight interference", 41);
}
private void DoStudy7Test()
{
// Preparing a Document to Accept the Study 7 Transition List, p. 15
RunUI(() => SkylineWindow.NewDocument());
var peptideSettingsUI1 = ShowDialog <PeptideSettingsUI>(SkylineWindow.ShowPeptideSettingsUI);
var mod13Cr = new StaticMod("Label:13C(6) (C-term R)", "R", ModTerminus.C, false, null, LabelAtoms.C13,
RelativeRT.Matching, null, null, null);
AddHeavyMod(mod13Cr, peptideSettingsUI1, "Edit Isotope Modification form", 17);
RunUI(() =>
{
peptideSettingsUI1.PickedHeavyMods = new[] { "Label:13C(6) (C-term R)", HEAVY_K };
peptideSettingsUI1.PickedLibraries = new[] { "" };
peptideSettingsUI1.SelectedBackgroundProteome = Resources.SettingsList_ELEMENT_NONE_None;
peptideSettingsUI1.OkDialog();
});
// Pasting a Transition List into the Document, p. 18.
string clipboardSaveText = string.Empty;
RunUI(() =>
{
var filePath = GetTestPath(@"Study 7\Study7 transition list.xls");
SetExcelFileClipboardText(filePath, "Simple", 6, false);
clipboardSaveText = ClipboardEx.GetText();
});
{
var messageDlg = ShowDialog <ImportTransitionListErrorDlg>(SkylineWindow.Paste);
PauseForScreenShot <ImportTransitionListErrorDlg>("Error message form (expected)", 18);
OkDialog(messageDlg, messageDlg.CancelDialog);
// Restore the clipboard text after pausing
ClipboardEx.SetText(clipboardSaveText);
}
RunDlg <TransitionSettingsUI>(() => SkylineWindow.ShowTransitionSettingsUI(TransitionSettingsUI.TABS.Instrument), transitionSettingsUI =>
{
transitionSettingsUI.InstrumentMaxMz = 1800;
transitionSettingsUI.OkDialog();
});
RunUI(() =>
{
SkylineWindow.Paste();
SkylineWindow.CollapsePeptides();
});
PauseForScreenShot("Targets tree (selected from main window)", 19);
// Adjusting Modifications Manually, p. 19.
AdjustModifications("AGLCQTFVYGGCR", true, 'V', 747.348);
PauseForScreenShot("Target tree clipped from main window", 22);
AdjustModifications("IVGGWECEK", true, 'V', 541.763);
AdjustModifications("YEVQGEVFTKPQLWP", false, 'L', 913.974);
RunUI(() => SkylineWindow.SaveDocument(GetTestPath(@"Study 7\Study7.sky")));
// Importing Data from a Multiple Sample WIFF file, p. 23.
var importResultsDlg1 = ShowDialog <ImportResultsDlg>(SkylineWindow.ImportResults);
var openDataSourceDialog1 = ShowDialog <OpenDataSourceDialog>(() => importResultsDlg1.NamedPathSets =
importResultsDlg1.GetDataSourcePathsFile(null));
RunUI(() =>
{
openDataSourceDialog1.CurrentDirectory = new MsDataFilePath(GetTestPath("Study 7"));
openDataSourceDialog1.SelectAllFileType(IsFullData ? ".wiff" : ExtensionTestContext.ExtAbWiff); // Force true wiff for FullData
});
if (UseRawFilesOrFullData)
{
var importResultsSamplesDlg = ShowDialog <ImportResultsSamplesDlg>(openDataSourceDialog1.Open);
PauseForScreenShot <ImportResultsSamplesDlg>("Choose Samples form", 23);
RunUI(() =>
{
if (IsFullData)
{
importResultsSamplesDlg.CheckAll(true);
importResultsSamplesDlg.ExcludeSample(0); // Blank
importResultsSamplesDlg.ExcludeSample(25); // QC
importResultsSamplesDlg.ExcludeSample(26);
importResultsSamplesDlg.ExcludeSample(27);
importResultsSamplesDlg.ExcludeSample(28);
importResultsSamplesDlg.ExcludeSample(45); // A2
importResultsSamplesDlg.ExcludeSample(46);
importResultsSamplesDlg.ExcludeSample(47);
importResultsSamplesDlg.ExcludeSample(48);
importResultsSamplesDlg.ExcludeSample(49); // gradientwash
importResultsSamplesDlg.ExcludeSample(50);
importResultsSamplesDlg.ExcludeSample(51);
importResultsSamplesDlg.ExcludeSample(52);
importResultsSamplesDlg.ExcludeSample(53); // A3
importResultsSamplesDlg.ExcludeSample(54);
importResultsSamplesDlg.ExcludeSample(55);
importResultsSamplesDlg.ExcludeSample(56);
}
else
{
importResultsSamplesDlg.CheckAll(false);
importResultsSamplesDlg.IncludeSample(1);
importResultsSamplesDlg.IncludeSample(2);
importResultsSamplesDlg.IncludeSample(11);
importResultsSamplesDlg.IncludeSample(12);
}
});
OkDialog(importResultsSamplesDlg, importResultsSamplesDlg.OkDialog);
}
else
{
RunUI(openDataSourceDialog1.Open);
}
{
var importResultsNameDlg = ShowDialog <ImportResultsNameDlg>(importResultsDlg1.OkDialog);
PauseForScreenShot <ImportDocResultsDlg>("Import Results Common prefix form", 24);
OkDialog(importResultsNameDlg, importResultsNameDlg.YesDialog);
}
WaitForCondition(() =>
SkylineWindow.Document.Settings.HasResults && SkylineWindow.Document.Settings.MeasuredResults.IsLoaded);
RestoreViewOnScreen(25);
// Inspecting and Adjusting Peak Integration, p. 24.
RunUI(() =>
{
SkylineWindow.ShowPeakAreaReplicateComparison();
SkylineWindow.ShowGraphRetentionTime(true);
});
if (!IsPauseForScreenShots && !IsFullData)
{
TestApplyToAll();
}
PauseForScreenShot <GraphSummary.RTGraphView>("Main window with peaks and retention times showing", 25);
CheckReportCompatibility.CheckAll(SkylineWindow.Document);
RunUI(SkylineWindow.EditDelete);
FindNode("IVGGWECEK"); // Not L10N
TransitionGroupTreeNode selNodeGroup = null;
RunUI(() =>
{
selNodeGroup = (TransitionGroupTreeNode)SkylineWindow.SequenceTree.SelectedNode.Nodes[1];
Assert.AreEqual(selNodeGroup.StateImageIndex, (int)SequenceTree.StateImageId.peak_blank);
});
RunDlg <TransitionSettingsUI>(SkylineWindow.ShowTransitionSettingsUI, transitionSettingsUI =>
{
transitionSettingsUI.MZMatchTolerance = 0.065;
transitionSettingsUI.OkDialog();
});
RunUI(() =>
{
Assert.AreEqual((int)SequenceTree.StateImageId.peak, selNodeGroup.StateImageIndex);
SkylineWindow.ToggleIntegrateAll();
});
RunUI(() =>
{
foreach (PeptideDocNode nodePep in SkylineWindow.Document.Molecules)
{
string sequence = nodePep.Peptide.Sequence;
int imageIndex = PeptideTreeNode.GetPeakImageIndex(nodePep, SkylineWindow.SequenceTree);
if ((sequence != null) && (sequence.StartsWith("YLA") || sequence.StartsWith("YEV"))) // Not L10N
{
Assert.AreEqual((int)SequenceTree.StateImageId.keep, imageIndex,
string.Format("Expected keep icon for the peptide {0}, found {1}", sequence, imageIndex));
}
else if (sequence != null)
{
Assert.AreEqual((int)SequenceTree.StateImageId.peak, imageIndex,
string.Format("Expected peak icon for the peptide {0}, found {1}", sequence, imageIndex));
}
else // Custom Ion
{
Assert.AreEqual((int)SequenceTree.StateImageId.peak_blank, imageIndex,
string.Format("Expected peak_blank icon for the custom ion {0}, found {1}", nodePep.ModifiedTarget, imageIndex));
}
}
});
PauseForScreenShot("Main window", 27);
// Data Inspection with Peak Areas View, p. 27.
FindNode("SSDLVALSGGHTFGK"); // Not L10N
RunUI(NormalizeGraphToHeavy);
RestoreViewOnScreen(28);
PauseForScreenShot <GraphSummary.AreaGraphView>("Peak Areas graph metafile", 28);
FindNode((564.7746).ToString(LocalizationHelper.CurrentCulture) + "++"); // ESDTSYVSLK - Not L10N
PauseForScreenShot <GraphSummary.AreaGraphView>("Peak Areas graph metafile", 29);
RunUI(SkylineWindow.ExpandPeptides);
string hgflprLight = (363.7059).ToString(LocalizationHelper.CurrentCulture) + "++"; // HGFLPR - Not L10N
FindNode(hgflprLight);
PauseForScreenShot <GraphSummary.AreaGraphView>("Peak Areas graph metafile", 30);
RunUI(() => SkylineWindow.NormalizeAreaGraphTo(AreaNormalizeToView.area_percent_view));
PauseForScreenShot <GraphSummary.AreaGraphView>("Peak Areas graph normalized metafile", 31);
RunUI(() => SkylineWindow.ShowGraphPeakArea(false));
RunUI(() => SkylineWindow.ActivateReplicate("E_03"));
PauseForScreenShot <GraphChromatogram>("Chromatogram graph metafile with interference", 31);
RunUI(() => SkylineWindow.ShowGraphPeakArea(true));
RunUI(() =>
{
SkylineWindow.ShowPeakAreaPeptideGraph();
SkylineWindow.ShowTotalTransitions();
SkylineWindow.ShowCVValues(true);
SkylineWindow.ShowPeptideOrder(SummaryPeptideOrder.document);
});
PauseForScreenShot <GraphSummary.AreaGraphView>("Peak Areas Peptide Comparison graph metafile", 32);
// Annotating replicates with concentration values
var chooseAnnotationsDlg = ShowDialog <DocumentSettingsDlg>(SkylineWindow.ShowDocumentSettingsDialog);
var editListDlg = ShowDialog <EditListDlg <SettingsListBase <AnnotationDef>, AnnotationDef> >(chooseAnnotationsDlg.EditAnnotationList);
RunUI(editListDlg.ResetList);
var defineAnnotationDlg = ShowDialog <DefineAnnotationDlg>(editListDlg.AddItem);
RunUI(() =>
{
defineAnnotationDlg.AnnotationName = "Concentration";
defineAnnotationDlg.AnnotationType = AnnotationDef.AnnotationType.number;
defineAnnotationDlg.AnnotationTargets = AnnotationDef.AnnotationTargetSet.Singleton(AnnotationDef.AnnotationTarget.replicate);
});
PauseForScreenShot <DefineAnnotationDlg>("Define Annotation form", 33);
OkDialog(defineAnnotationDlg, defineAnnotationDlg.OkDialog);
OkDialog(editListDlg, () => editListDlg.DialogResult = DialogResult.OK);
RunUI(() => chooseAnnotationsDlg.AnnotationsCheckedListBox.SetItemChecked(0, true));
PauseForScreenShot <DocumentSettingsDlg>("Annotation Settings form", 34);
OkDialog(chooseAnnotationsDlg, chooseAnnotationsDlg.OkDialog);
RunUI(() => SkylineWindow.ShowResultsGrid(true));
RunUI(() =>
{
SkylineWindow.SelectedPath =
SkylineWindow.DocumentUI.GetPathTo((int)SrmDocument.Level.MoleculeGroups, 0);
});
WaitForGraphs();
WaitForConditionUI(() => FindOpenForm <LiveResultsGrid>().IsComplete);
RunUI(() =>
{
Settings.Default.ResultsGridSynchSelection = false;
var resultsGrid = FindOpenForm <LiveResultsGrid>().DataGridView;
var colConcentration =
// ReSharper disable LocalizableElement
resultsGrid.Columns.Cast <DataGridViewColumn>().First(col => "Concentration" == col.HeaderText); // Not L10N
// ReSharper restore LocalizableElement
if (IsFullData)
{
float[] concentrations = { 0f, 60, 175, 513, 1500, 2760, 4980, 9060, 16500, 30000 };
for (int i = 0; i < concentrations.Length; i++)
{
for (int j = i * 4; j < (i + 1) * 4; j++)
{
SetCellValue(resultsGrid, j, colConcentration.Index, concentrations[i]);
}
}
}
else
{
SetCellValue(resultsGrid, 0, colConcentration.Index, 0f);
SetCellValue(resultsGrid, 1, colConcentration.Index, 0f);
SetCellValue(resultsGrid, 2, colConcentration.Index, 175f);
SetCellValue(resultsGrid, 3, colConcentration.Index, 175f);
}
});
WaitForGraphs();
PauseForScreenShot <LiveResultsGrid>("Results grid with annotations (scrolled to the end)", 35);
FindNode("SSDLVALSGGHTFGK"); // Not L10N
RunUI(() =>
{
SkylineWindow.ShowPeakAreaReplicateComparison();
SkylineWindow.GroupByReplicateAnnotation("Concentration");
NormalizeGraphToHeavy();
});
PauseForScreenShot <GraphSummary.AreaGraphView>("Peak Areas graph with CVs metafile", 36);
RunUI(() => SkylineWindow.ShowCVValues(false));
RunUI(() => SkylineWindow.SaveDocument());
PauseForScreenShot <GraphSummary.AreaGraphView>("Peak Areas graph grouped by concentration metafile", 36);
PauseForAuditLog();
// Further Exploration, p. 33.
RunUI(() =>
{
SkylineWindow.OpenFile(GetTestPath(@"Study 7\Study II\Study 7ii (site 52).sky")); // Not L10N
SkylineWindow.ShowPeakAreaPeptideGraph();
SkylineWindow.ShowCVValues(true);
});
WaitForCondition(() => SkylineWindow.Document.Settings.MeasuredResults.IsLoaded);
PauseForScreenShot <GraphSummary.AreaGraphView>("Peak Areas peptide comparison graph metafile", 37);
FindNode("LSEPAELTDAVK");
RunUI(SkylineWindow.ShowRTReplicateGraph);
PauseForScreenShot <GraphSummary.RTGraphView>("Retention Times replicate graph metafile", 38);
FindNode("INDISHTQSVSAK");
RunUI(SkylineWindow.ShowPeakAreaReplicateComparison);
PauseForScreenShot <GraphSummary.AreaGraphView>("Peak Areas normalized to heave graph metafile", 38);
RunUI(() => SkylineWindow.NormalizeAreaGraphTo(AreaNormalizeToView.none));
WaitForGraphs();
PauseForScreenShot <GraphSummary.AreaGraphView>("Peak Areas no normalization graph metafile", 39);
FindNode(hgflprLight);
RunUI(() =>
{
SkylineWindow.ShowAllTransitions();
NormalizeGraphToHeavy();
});
WaitForGraphs();
PauseForScreenShot <GraphSummary.AreaGraphView>("Area Ratio to Heavy graph showing interference metafile", 40);
RunUI(() => SkylineWindow.ShowGraphPeakArea(false));
RunUI(() => SkylineWindow.ActivateReplicate("E_ 03"));
WaitForGraphs();
PauseForScreenShot <GraphChromatogram>("Chromatogram graph metafile showing slight interference", 40);
}
public void CopyMessage()
{
ClipboardEx.SetText(GetTitleAndMessageDetail());
}
