public GraphFullScan(IDocumentUIContainer documentUIContainer)
{
InitializeComponent();
graphControl.GraphPane = new HeatMapGraphPane
{
MinDotRadius = MIN_DOT_RADIUS,
MaxDotRadius = MAX_DOT_RADIUS
};
Icon = Resources.SkylineData;
_graphHelper = GraphHelper.Attach(graphControl);
_documentContainer = documentUIContainer;
_documentContainer.ListenUI(OnDocumentUIChanged);
_msDataFileScanHelper = new MsDataFileScanHelper(SetSpectra, HandleLoadScanException);
GraphPane.Title.IsVisible = true;
GraphPane.Legend.IsVisible = false;
// Make sure to use italics for "m/z"
AbstractMSGraphItem.SetAxisText(GraphPane.XAxis, Resources.AbstractMSGraphItem_CustomizeXAxis_MZ);
magnifyBtn.Checked = Settings.Default.AutoZoomFullScanGraph;
spectrumBtn.Checked = Settings.Default.SumScansFullScan;
filterBtn.Checked = Settings.Default.FilterDriftTimesFullScan;
spectrumBtn.Visible = false;
filterBtn.Visible = false;
lblScanId.Visible = false; // you might want to show the scan index for debugging
}
public DocumentSettingsDlg(IDocumentUIContainer documentContainer)
{
InitializeComponent();
Icon = Resources.Skyline;
DocumentContainer = documentContainer;
_annotationsListBoxDriver = new SettingsListBoxDriver <AnnotationDef>(
checkedListBoxAnnotations, Settings.Default.AnnotationDefList);
_annotationsListBoxDriver.LoadList(
DocumentContainer.Document.Settings.DataSettings.AnnotationDefs);
_groupComparisonsListBoxDriver = new SettingsListBoxDriver <GroupComparisonDef>(
checkedListBoxGroupComparisons, Settings.Default.GroupComparisonDefList);
_groupComparisonsListBoxDriver.LoadList(
DocumentContainer.Document.Settings.DataSettings.GroupComparisonDefs);
var listDataList = new ListDefList();
listDataList.AddRange(Settings.Default.ListDefList);
listDataList.AddRange(documentContainer.Document.Settings.DataSettings.Lists);
_listsListBoxDriver = new SettingsListBoxDriver <ListData>(
checkedListBoxLists, listDataList);
_listsListBoxDriver.LoadList(documentContainer.Document.Settings.DataSettings.Lists);
var dataSchema = new SkylineDataSchema(documentContainer, DataSchemaLocalizer.INVARIANT);
chooseViewsControl.ViewContext = new SkylineViewContext(dataSchema, new RowSourceInfo[0]);
chooseViewsControl.ShowCheckboxes = true;
chooseViewsControl.CheckedViews =
documentContainer.Document.Settings.DataSettings.ViewSpecList.ViewSpecs.Select(
viewSpec => PersistedViews.MainGroup.Id.ViewName(viewSpec.Name));
}
public StatementCompletionTextBox(IDocumentUIContainer documentUiContainer)
{
MatchTypes = ProteinMatchTypes.ALL;
_documentUiContainer = documentUiContainer;
_imageList.Images.Add(Resources.Protein);
_imageList.Images.Add(Resources.Peptide);
}
public GraphFullScan(IDocumentUIContainer documentUIContainer)
{
InitializeComponent();
graphControl.GraphPane = new HeatMapGraphPane
{
MinDotRadius = MIN_DOT_RADIUS,
MaxDotRadius = MAX_DOT_RADIUS
};
Icon = Resources.SkylineData;
_graphHelper = GraphHelper.Attach(graphControl);
_documentContainer = documentUIContainer;
_documentContainer.ListenUI(OnDocumentUIChanged);
_msDataFileScanHelper = new MsDataFileScanHelper(SetSpectra, HandleLoadScanException);
GraphPane.Title.IsVisible = true;
GraphPane.Legend.IsVisible = false;
// Make sure to use italics for "m/z"
AbstractMSGraphItem.SetAxisText(GraphPane.XAxis, Resources.AbstractMSGraphItem_CustomizeXAxis_MZ);
magnifyBtn.Checked = Settings.Default.AutoZoomFullScanGraph;
spectrumBtn.Checked = Settings.Default.SumScansFullScan;
filterBtn.Checked = Settings.Default.FilterIonMobilityFullScan;
spectrumBtn.Visible = false;
filterBtn.Visible = false;
lblScanId.Visible = false; // you might want to show the scan index for debugging
}
public BuildLibraryDlg(IDocumentUIContainer documentContainer)
{
InitializeComponent();
Icon = Resources.Skyline;
_documentUiContainer = documentContainer;
panelFiles.Visible = false;
textName.Focus();
textPath.Text = Settings.Default.LibraryDirectory;
comboAction.SelectedItem = LibraryBuildAction.Create.GetLocalizedString();
textCutoff.Text = Settings.Default.LibraryResultCutOff.ToString(LocalizationHelper.CurrentCulture);
textAuthority.Text = Settings.Default.LibraryAuthority;
if (documentContainer.Document.PeptideCount == 0)
{
cbFilter.Hide();
}
else
{
cbFilter.Checked = Settings.Default.LibraryFilterDocumentPeptides;
}
cbKeepRedundant.Checked = Settings.Default.LibraryKeepRedundant;
_helper = new MessageBoxHelper(this);
}
public BuildLibraryDlg(IDocumentUIContainer documentContainer)
{
InitializeComponent();
Icon = Resources.Skyline;
_documentUiContainer = documentContainer;
panelFiles.Visible = false;
textName.Focus();
textPath.Text = Settings.Default.LibraryDirectory;
comboAction.SelectedItem = LibraryBuildAction.Create.GetLocalizedString();
textCutoff.Text = Settings.Default.LibraryResultCutOff.ToString(LocalizationHelper.CurrentCulture);
textAuthority.Text = Settings.Default.LibraryAuthority;
if (documentContainer.Document.PeptideCount == 0)
cbFilter.Hide();
else
cbFilter.Checked = Settings.Default.LibraryFilterDocumentPeptides;
cbKeepRedundant.Checked = Settings.Default.LibraryKeepRedundant;
_helper = new MessageBoxHelper(this);
}
// ReSharper restore UnusedMember.Local
// ReSharper restore InconsistentNaming
public ManageResultsDlg(IDocumentUIContainer documentUIContainer, LibraryManager libraryManager)
{
InitializeComponent();
Icon = Resources.Skyline;
DocumentUIContainer = documentUIContainer;
var settings = DocumentUIContainer.Document.Settings;
if (settings.HasResults)
{
foreach (var chromatogramSet in settings.MeasuredResults.Chromatograms)
{
listResults.Items.Add(new ManageResultsAction(chromatogramSet));
}
listResults.SelectedIndices.Add(0);
}
var libraries = settings.PeptideSettings.Libraries;
if (libraries.HasLibraries && libraries.HasDocumentLibrary)
{
DocumentLibrarySpec = libraries.LibrarySpecs.FirstOrDefault(x => x.IsDocumentLibrary);
if (null != DocumentLibrarySpec)
{
DocumentLibrary = libraryManager.TryGetLibrary(DocumentLibrarySpec);
if (null != DocumentLibrary)
{
foreach (var dataFile in DocumentLibrary.LibraryDetails.DataFiles)
{
listLibraries.Items.Add(dataFile);
}
listLibraries.SelectedIndices.Add(0);
}
}
}
if (listLibraries.Items.Count == 0)
{
checkBoxRemoveLibraryRuns.Visible = false;
int heightTabPage = manageResultsTabControl.TabPages[(int)TABS.Replicates].Height;
int changeHeight = heightTabPage - listResults.Bottom - btnRemove.Top;
listResults.Height += changeHeight;
Height -= changeHeight;
manageResultsTabControl.TabPages.RemoveAt((int)TABS.Libraries);
}
else if (listResults.Items.Count == 0)
{
checkBoxRemoveReplicates.Visible = false;
int heightTabPage = manageResultsTabControl.TabPages[(int)TABS.Libraries].Height;
int changeHeight = heightTabPage - listLibraries.Bottom - btnRemoveLibRun.Top;
listLibraries.Height += changeHeight;
Height -= changeHeight;
manageResultsTabControl.TabPages.RemoveAt((int)TABS.Replicates);
}
LibraryRunsRemovedList = new List <string>();
ChromatogramsRemovedList = new List <ChromatogramSet>();
}
public RescoreResultsDlg(IDocumentUIContainer documentUIContainer)
{
InitializeComponent();
DocumentUIContainer = documentUIContainer;
labelMessage.Text =
Resources.RescoreResultsDlg_RescoreResultsDlg_In_certain_cases__you_may_want_to_have_Skyline_re_caclculate_peaks_and_re_score_them_based_on_the_existing_chromatogram_data___Chromatograms_will_not_be_re_imported_from_raw_data_files__but_peak_integration_information_may_change_;
}
public RescoreResultsDlg(IDocumentUIContainer documentUIContainer)
{
InitializeComponent();
DocumentUIContainer = documentUIContainer;
labelMessage.Text =
Resources.RescoreResultsDlg_RescoreResultsDlg_In_certain_cases__you_may_want_to_have_Skyline_re_caclculate_peaks_and_re_score_them_based_on_the_existing_chromatogram_data___Chromatograms_will_not_be_re_imported_from_raw_data_files__but_peak_integration_information_may_change_;
}
// ReSharper restore UnusedMember.Local
// ReSharper restore InconsistentNaming
public ManageResultsDlg(IDocumentUIContainer documentUIContainer, LibraryManager libraryManager)
{
InitializeComponent();
Icon = Resources.Skyline;
DocumentUIContainer = documentUIContainer;
var settings = DocumentUIContainer.Document.Settings;
if (settings.HasResults)
{
foreach (var chromatogramSet in settings.MeasuredResults.Chromatograms)
{
listResults.Items.Add(new ManageResultsAction(chromatogramSet));
}
listResults.SelectedIndices.Add(0);
}
var libraries = settings.PeptideSettings.Libraries;
if (libraries.HasLibraries && libraries.HasDocumentLibrary)
{
DocumentLibrarySpec = libraries.LibrarySpecs.FirstOrDefault(x => x.IsDocumentLibrary);
if (null != DocumentLibrarySpec)
{
DocumentLibrary = libraryManager.TryGetLibrary(DocumentLibrarySpec);
if (null != DocumentLibrary)
{
foreach (var dataFile in DocumentLibrary.LibraryDetails.DataFiles)
{
listLibraries.Items.Add(dataFile);
}
listLibraries.SelectedIndices.Add(0);
}
}
}
if (listLibraries.Items.Count == 0)
{
checkBoxRemoveLibraryRuns.Visible = false;
int heightTabPage = manageResultsTabControl.TabPages[(int) TABS.Replicates].Height;
int changeHeight = heightTabPage - listResults.Bottom - btnRemove.Top;
listResults.Height += changeHeight;
Height -= changeHeight;
manageResultsTabControl.TabPages.RemoveAt((int)TABS.Libraries);
}
else if (listResults.Items.Count == 0)
{
checkBoxRemoveReplicates.Visible = false;
int heightTabPage = manageResultsTabControl.TabPages[(int)TABS.Libraries].Height;
int changeHeight = heightTabPage - listLibraries.Bottom - btnRemoveLibRun.Top;
listLibraries.Height += changeHeight;
Height -= changeHeight;
manageResultsTabControl.TabPages.RemoveAt((int)TABS.Replicates);
}
LibraryRunsRemovedList = new List<string>();
ChromatogramsRemovedList = new List<ChromatogramSet>();
}
public UniquePeptidesDlg(IDocumentUIContainer documentUiContainer)
{
InitializeComponent();
Icon = Resources.Skyline;
DocumentUIContainer = documentUiContainer;
_peptidesInBackgroundProteome = new HashSet <IdentityPath>();
dataGridView1.CurrentCellChanged += dataGridView1_CurrentCellChanged;
}
public MinimizeResultsDlg(IDocumentUIContainer documentUIContainer)
{
InitializeComponent();
Icon = Resources.Skyline;
Settings = new ChromCacheMinimizer.Settings()
.ChangeDiscardUnmatchedChromatograms(true)
.ChangeNoiseTimeRange(null);
DocumentUIContainer = documentUIContainer;
bindingSource1.DataSource = _rowItems = new BindingList <GridRowItem>();
}
public SequenceTreeForm(IDocumentUIContainer documentContainer, bool restoringState)
{
InitializeComponent();
_defaultTabText = TabText;
sequenceTree.LockDefaultExpansion = restoringState;
sequenceTree.InitializeTree(documentContainer);
sequenceTree.LockDefaultExpansion = false;
if (documentContainer.DocumentUI != null)
UpdateResultsUI(documentContainer.DocumentUI.Settings, null);
}
public UniquePeptidesDlg(IDocumentUIContainer documentUiContainer)
{
InitializeComponent();
Icon = Resources.Skyline;
DocumentUIContainer = documentUiContainer;
_targetIsInBackgroundProteome = false;
dataGridView1.CurrentCellChanged += dataGridView1_CurrentCellChanged;
}
public UniquePeptidesDlg(IDocumentUIContainer documentUiContainer)
{
InitializeComponent();
Icon = Resources.Skyline;
DocumentUIContainer = documentUiContainer;
_targetIsInBackgroundProteome = false;
dataGridView1.CurrentCellChanged += dataGridView1_CurrentCellChanged;
}
public MinimizeResultsDlg(IDocumentUIContainer documentUIContainer)
{
InitializeComponent();
Icon = Resources.Skyline;
Settings = new ChromCacheMinimizer.Settings()
.SetDiscardUnmatchedChromatograms(true)
.SetNoiseTimeRange(null);
DocumentUIContainer = documentUIContainer;
bindingSource1.DataSource = _rowItems = new BindingList<GridRowItem>();
}
public ExportLiveReportDlg(IDocumentUIContainer documentUIContainer)
{
InitializeComponent();
Icon = Resources.Skyline;
_documentUiContainer = documentUIContainer;
Debug.Assert(indexLocalizedLanguage == comboLanguage.Items.Count);
comboLanguage.Items.Add(CultureInfo.CurrentUICulture.DisplayName);
Debug.Assert(indexInvariantLanguage == comboLanguage.Items.Count);
comboLanguage.Items.Add(Resources.ExportLiveReportDlg_ExportLiveReportDlg_Invariant);
comboLanguage.SelectedIndex = 0;
}
public ExportLiveReportDlg(IDocumentUIContainer documentUIContainer)
{
InitializeComponent();
Icon = Resources.Skyline;
_documentUiContainer = documentUIContainer;
Debug.Assert(indexLocalizedLanguage == comboLanguage.Items.Count);
comboLanguage.Items.Add(CultureInfo.CurrentUICulture.DisplayName);
Debug.Assert(indexInvariantLanguage == comboLanguage.Items.Count);
comboLanguage.Items.Add(Resources.ExportLiveReportDlg_ExportLiveReportDlg_Invariant);
comboLanguage.SelectedIndex = 0;
}
public SequenceTreeForm(IDocumentUIContainer documentContainer, bool restoringState)
{
InitializeComponent();
_defaultTabText = TabText;
sequenceTree.LockDefaultExpansion = restoringState;
sequenceTree.InitializeTree(documentContainer);
sequenceTree.LockDefaultExpansion = false;
if (documentContainer.DocumentUI != null)
{
UpdateResultsUI(documentContainer.DocumentUI.Settings, null);
}
}
public static FoldChangeBindingSource FindOrCreateBindingSource(IDocumentUIContainer documentContainer,
string groupComparisonName)
{
var form = FindForm <FoldChangeForm>(documentContainer, groupComparisonName);
if (null != form)
{
return(form.FoldChangeBindingSource);
}
return(new FoldChangeBindingSource(new GroupComparisonModel(documentContainer, groupComparisonName)));
}
public ExportReportDlg(IDocumentUIContainer documentUiContainer)
{
_documentUiContainer = documentUiContainer;
InitializeComponent();
CultureInfo = LocalizationHelper.CurrentCulture;
LoadList();
if (listboxReports.Items.Count > 0)
listboxReports.SelectedIndex = 0;
}
public EditGroupComparisonDlg(IDocumentUIContainer documentContainer,
GroupComparisonDef groupComparisonDef, IEnumerable <GroupComparisonDef> existingGroupComparisons)
: this(new GroupComparisonModel(documentContainer, null) { GroupComparisonDef = groupComparisonDef })
{
_originalGroupComparisonDef = groupComparisonDef;
_existingGroupComparisons = existingGroupComparisons;
if (documentContainer == null)
{
btnPreview.Visible = false;
}
_pushChangesToDocument = false;
tbxName.Text = groupComparisonDef.Name ?? string.Empty;
}
public ExportReportDlg(IDocumentUIContainer documentUiContainer)
{
_documentUiContainer = documentUiContainer;
InitializeComponent();
CultureInfo = LocalizationHelper.CurrentCulture;
LoadList();
if (listboxReports.Items.Count > 0)
{
listboxReports.SelectedIndex = 0;
}
}
public GraphSpectrum(IDocumentUIContainer documentUIContainer)
{
InitializeComponent();
Icon = Resources.SkylineData;
_graphHelper = GraphHelper.Attach(graphControl);
_documentContainer = documentUIContainer;
_documentContainer.ListenUI(OnDocumentUIChanged);
_stateProvider = documentUIContainer as IStateProvider ??
new DefaultStateProvider();
if (DocumentUI != null)
{
ZoomSpectrumToSettings();
}
}
public bool ServerSupportsSkydVersion(FolderInformation folderInfo, IDocumentUIContainer _docContainer, IWin32Window parent)
{
var settings = _docContainer.DocumentUI.Settings;
Assume.IsTrue(_docContainer.DocumentUI.IsLoaded);
var cacheVersion = settings.HasResults ? settings.MeasuredResults.CacheVersion : null;
if (cacheVersion == null)
{
// The document may not have any chromatogram data.
return(true);
}
var serverVersionsJson = SupportedVersionsJson(folderInfo.Server);
if (serverVersionsJson == null)
{
// There was an error getting the server-supported skyd version for some reason.
// Perhaps this is an older server that did not understand the request, or
// the returned JSON was malformed. Let the document upload continue.
return(true);
}
int? serverVersion = null;
JToken serverSkydVersion;
if (serverVersionsJson.TryGetValue("SKYD_version", out serverSkydVersion)) // Not L10N
{
int version;
if (int.TryParse(serverSkydVersion.Value <string>(), out version))
{
serverVersion = version;
}
}
if (serverVersion.HasValue && cacheVersion.Value > serverVersion.Value)
{
MessageDlg.Show(parent,
string.Format(
Resources.PublishDocumentDlg_ServerSupportsSkydVersion_,
cacheVersion.Value)
);
return(false);
}
return(true);
}
public GraphSummary(IDocumentUIContainer documentUIContainer, IController controller)
{
InitializeComponent();
Icon = Resources.SkylineData;
graphControl.MasterPane.Border.IsVisible = false;
_controller = controller;
_controller.GraphSummary = this;
_documentContainer = documentUIContainer;
_documentContainer.ListenUI(OnDocumentUIChanged);
_stateProvider = documentUIContainer as IStateProvider ??
new DefaultStateProvider();
UpdateUI();
}
public PublishDocumentDlg(IDocumentUIContainer docContainer, SettingsList <Server> servers, string fileName)
{
IsLoaded = false;
InitializeComponent();
Icon = Resources.Skyline;
_docContainer = docContainer;
_panoramaServers = servers;
tbFilePath.Text = FileEx.GetTimeStampedFileName(fileName);
treeViewFolders.ImageList = new ImageList();
treeViewFolders.ImageList.Images.Add(Resources.Panorama);
treeViewFolders.ImageList.Images.Add(Resources.LabKey);
treeViewFolders.ImageList.Images.Add(Resources.ChromLib);
treeViewFolders.ImageList.Images.Add(Resources.Folder);
ServerTreeStateRestorer = new TreeViewStateRestorer(treeViewFolders);
}
public PublishDocumentDlg(IDocumentUIContainer docContainer, SettingsList<Server> servers, string fileName)
{
IsLoaded = false;
InitializeComponent();
Icon = Resources.Skyline;
_docContainer = docContainer;
_panoramaServers = servers;
tbFilePath.Text = FileEx.GetTimeStampedFileName(fileName);
treeViewFolders.ImageList = new ImageList();
treeViewFolders.ImageList.Images.Add(Resources.Panorama);
treeViewFolders.ImageList.Images.Add(Resources.LabKey);
treeViewFolders.ImageList.Images.Add(Resources.ChromLib);
treeViewFolders.ImageList.Images.Add(Resources.Folder);
ServerTreeStateRestorer = new TreeViewStateRestorer(treeViewFolders);
}
public BuildLibraryDlg(SkylineWindow skylineWindow)
{
InitializeComponent();
Icon = Resources.Skyline;
_skylineWindow = skylineWindow;
_documentUiContainer = skylineWindow;
// Store locations of those controls since we move the irt label/combo around
_actionLabelPos = actionLabel.Location;
_actionComboPos = comboAction.Location;
_iRTLabelPos = iRTPeptidesLabel.Location;
_iRTComboPos = comboStandards.Location;
panelFiles.Visible = false;
textName.Focus();
textPath.Text = Settings.Default.LibraryDirectory;
comboAction.SelectedItem = LibraryBuildAction.Create.GetLocalizedString();
textCutoff.Text = Settings.Default.LibraryResultCutOff.ToString(LocalizationHelper.CurrentCulture);
if (_documentUiContainer.Document.PeptideCount == 0)
{
cbFilter.Hide();
}
else
{
cbFilter.Checked = Settings.Default.LibraryFilterDocumentPeptides;
}
cbKeepRedundant.Checked = Settings.Default.LibraryKeepRedundant;
ceCombo.Items.AddRange(
Enumerable.Range(PrositConstants.MIN_NCE, PrositConstants.MAX_NCE - PrositConstants.MIN_NCE + 1).Select(c => (object)c)
.ToArray());
ceCombo.SelectedItem = Settings.Default.PrositNCE;
_helper = new MessageBoxHelper(this);
_driverStandards = new SettingsListComboDriver <IrtStandard>(comboStandards, Settings.Default.IrtStandardList);
_driverStandards.LoadList(IrtStandard.EMPTY.GetKey());
}
public static FoldChangeForm RestoreFoldChangeForm(IDocumentUIContainer documentContainer, string persistentString)
{
var formContructors = new[]
{
FormConstructor.MakeFormConstructor(() => new FoldChangeGrid()),
FormConstructor.MakeFormConstructor(() => new FoldChangeBarGraph()),
FormConstructor.MakeFormConstructor(() => new FoldChangeVolcanoPlot()),
};
foreach (var formConstructor in formContructors)
{
string prefix = formConstructor.FormType.ToString() + '|';
if (persistentString.StartsWith(prefix))
{
string groupComparisonName = Uri.UnescapeDataString(persistentString.Substring(prefix.Length));
var form = formConstructor.Constructor();
form.SetGroupComparisonName(documentContainer, groupComparisonName);
return(form);
}
}
return(null);
}
public GraphSummary(GraphTypeSummary type, IDocumentUIContainer documentUIContainer, IController controller, int targetResultsIndex, int originalIndex = -1)
{
_targetResultsIndex = targetResultsIndex;
_originalResultsIndex = originalIndex;
InitializeComponent();
Icon = Resources.SkylineData;
graphControl.MasterPane.Border.IsVisible = false;
_controller = controller;
_controller.GraphSummary = this;
_documentContainer = documentUIContainer;
_documentContainer.ListenUI(OnDocumentUIChanged);
_stateProvider = documentUIContainer as IStateProvider ??
new DefaultStateProvider();
Type = type;
Text = Controller.Text + @" - " + Type.CustomToString();
UpdateUI();
}
public GraphSummary(GraphTypeSummary type, IDocumentUIContainer documentUIContainer, IController controller, int targetResultsIndex, int originalIndex = -1)
{
_targetResultsIndex = targetResultsIndex;
_originalResultsIndex = originalIndex;
InitializeComponent();
Icon = Resources.SkylineData;
graphControl.MasterPane.Border.IsVisible = false;
_controller = controller;
_controller.GraphSummary = this;
_documentContainer = documentUIContainer;
_documentContainer.ListenUI(OnDocumentUIChanged);
_stateProvider = documentUIContainer as IStateProvider ??
new DefaultStateProvider();
Type = type;
Text = Controller.Text + @" - " + Type.CustomToString();
Helpers.PeptideToMoleculeTextMapper.TranslateForm(this, _documentContainer.Document.DocumentType); // Use terminology like "Molecule Comparison" instead of "Peptide Comparison" as appropriate
UpdateUI();
}
public ManageResultsDlg(IDocumentUIContainer documentUIContainer, LibraryManager libraryManager)
{
InitializeComponent();
Icon = Resources.Skyline;
DocumentUIContainer = documentUIContainer;
var settings = DocumentUIContainer.Document.Settings;
if (settings.HasResults)
{
foreach (var chromatogramSet in settings.MeasuredResults.Chromatograms)
{
listResults.Items.Add(new ManageResultsAction(chromatogramSet));
}
listResults.SelectedIndices.Add(0);
}
DocumentLibrarySpecs = new List <LibrarySpec>();
DocumentLibraries = new List <Library>();
var libraries = settings.PeptideSettings.Libraries;
if (libraries.HasLibraries && (libraries.HasDocumentLibrary || libraries.HasMidasLibrary))
{
foreach (var documentLibrarySpec in libraries.LibrarySpecs.Where(x => x.IsDocumentLibrary || x is MidasLibSpec))
{
var documentLibrary = libraryManager.TryGetLibrary(documentLibrarySpec);
if (null != documentLibrary)
{
DocumentLibrarySpecs.Add(documentLibrarySpec);
DocumentLibraries.Add(documentLibrary);
foreach (var dataFile in documentLibrary.LibraryFiles.FilePaths)
{
listLibraries.Items.Add(dataFile);
}
}
}
if (listLibraries.Items.OfType <object>().Any())
{
listLibraries.SelectedIndices.Add(0);
}
}
if (listLibraries.Items.Count == 0)
{
checkBoxRemoveLibraryRuns.Visible = false;
int heightTabPage = manageResultsTabControl.TabPages[(int)TABS.Replicates].Height;
int changeHeight = heightTabPage - listResults.Bottom - btnRemove.Top;
listResults.Height += changeHeight;
Height -= changeHeight;
manageResultsTabControl.TabPages.RemoveAt((int)TABS.Libraries);
}
else if (listResults.Items.Count == 0)
{
checkBoxRemoveReplicates.Visible = false;
int heightTabPage = manageResultsTabControl.TabPages[(int)TABS.Libraries].Height;
int changeHeight = heightTabPage - listLibraries.Bottom - btnRemoveLibRun.Top;
listLibraries.Height += changeHeight;
Height -= changeHeight;
manageResultsTabControl.TabPages.RemoveAt((int)TABS.Replicates);
}
LibraryRunsRemovedList = new List <string>();
ChromatogramsRemovedList = new List <ChromatogramSet>();
_renamedReplicates = new Dictionary <string, string>();
}
public StatementCompletionTextBox(IDocumentUIContainer documentUiContainer)
{
MatchTypes = ProteinMatchType.all;
_documentUiContainer = documentUiContainer;
_imageList.Images.Add(Resources.Protein);
_imageList.Images.Add(Resources.Peptide);
}
public PasteDlg(IDocumentUIContainer documentUiContainer)
{
InitializeComponent();
Icon = Resources.Skyline;
DocumentUiContainer = documentUiContainer;
_statementCompletionEditBox = new StatementCompletionTextBox(DocumentUiContainer)
{
MatchTypes = ProteinMatchType.name | ProteinMatchType.description
};
_statementCompletionEditBox.SelectionMade += statementCompletionEditBox_SelectionMade;
gridViewProteins.DataGridViewKey += OnDataGridViewKey;
gridViewPeptides.DataGridViewKey += OnDataGridViewKey;
gridViewTransitionList.DataGridViewKey += OnDataGridViewKey;
}
public void SetGroupComparisonName(IDocumentUIContainer documentContainer, string groupComparisonName)
{
_documentContainer = documentContainer;
_groupComparisonName = groupComparisonName;
Text = TabText = GetTitle(groupComparisonName);
}
public GraphChromatogram(IStateProvider stateProvider, IDocumentUIContainer documentContainer, string name)
{
InitializeComponent();
graphControl.GraphPane = new MSGraphPane();
_graphHelper = GraphHelper.Attach(graphControl);
NameSet = name;
Icon = Resources.SkylineData;
_nameChromatogramSet = name;
_documentContainer = documentContainer;
_documentContainer.ListenUI(OnDocumentUIChanged);
_stateProvider = stateProvider;
// Synchronize the zooming across all graph panes
// Note that this only affects applying ZoomState to a graph pane. Explicit changes
// to Scale Min/Max properties need to be manually applied to each axis.
graphControl.IsSynchronizeXAxes = true;
}
public RefineDlg(IDocumentUIContainer documentContainer)
{
_document = documentContainer.DocumentUI;
_settings = documentContainer.DocumentUI.Settings;
DocumentContainer = documentContainer;
InitializeComponent();
Icon = Resources.Skyline;
// Save text for later use
_removeLabelText = labelLabelType.Text;
_removeTipText = helpTip.GetToolTip(comboRefineLabelType);
// Fill label type comb_o box
comboRefineLabelType.Items.Add(string.Empty);
comboRefineLabelType.Items.Add(IsotopeLabelType.LIGHT_NAME);
foreach (var typedMods in _settings.PeptideSettings.Modifications.GetHeavyModifications())
{
comboRefineLabelType.Items.Add(typedMods.LabelType.Name);
}
comboRefineLabelType.SelectedIndex = 0;
comboReplicateUse.SelectedIndex = 0;
if (!_settings.HasResults)
{
FormUtil.RemoveTabPage(tabResults, helpTip);
}
if (!_settings.HasResults || _settings.MeasuredResults.Chromatograms.Count < 2)
{
FormUtil.RemoveTabPage(tabConsistency, helpTip);
}
else
{
// Consistency tab
textQVal.Enabled = _settings.PeptideSettings.Integration.PeakScoringModel.IsTrained;
numericUpDownDetections.Enabled = textQVal.Enabled;
if (numericUpDownDetections.Enabled)
{
numericUpDownDetections.Minimum = 1;
numericUpDownDetections.Maximum = _document.MeasuredResults.Chromatograms.Count;
numericUpDownDetections.Value = 1;
}
_normalizationMethods.Clear();
_normalizationMethods.Add(NormalizeOption.DEFAULT);
_normalizationMethods.AddRange(NormalizeOption.AvailableNormalizeOptions(_document));
_normalizationMethods.Add(NormalizeOption.NONE);
comboNormalizeTo.Items.Clear();
comboNormalizeTo.Items.AddRange(_normalizationMethods.Select(option => option.Caption).ToArray());
comboNormalizeTo.SelectedIndex = comboNormalizeTo.Items.Count - 1;
comboTransitions.Items.Add(Resources.RefineDlg_RefineDlg_all);
comboTransitions.Items.Add(Resources.RefineDlg_RefineDlg_best);
comboTransitions.SelectedIndex = 0;
var maxTrans = _document.MoleculeTransitionGroups.Select(g => g.TransitionCount).DefaultIfEmpty().Max();
for (int i = 1; i <= maxTrans; i++)
{
comboTransitions.Items.Add(i);
}
if (_document.MoleculeTransitions.Any(t => t.IsMs1))
{
comboTransType.Items.Add(Resources.RefineDlg_RefineDlg_Precursors);
comboTransType.SelectedIndex = comboTransType.Items.Count - 1;
}
if (_document.MoleculeTransitions.Any(t => !t.IsMs1))
{
comboTransType.Items.Add(Resources.RefineDlg_RefineDlg_Products);
comboTransType.SelectedIndex = comboTransType.Items.Count - 1;
}
if (comboTransType.Items.Count == 1)
{
comboTransType.Enabled = false;
}
}
if (_settings.PeptideSettings.Libraries.HasLibraries)
{
labelMinDotProduct.Enabled = textMinDotProduct.Enabled = groupLibCorr.Enabled = true;
}
if (_settings.TransitionSettings.FullScan.IsHighResPrecursor)
{
labelMinIdotProduct.Enabled = textMinIdotProduct.Enabled = groupLibCorr.Enabled = true;
}
// Group Comparisons
_groupComparisonsListBoxDriver = new SettingsListBoxDriver <GroupComparisonDef>(
checkedListBoxGroupComparisons, Settings.Default.GroupComparisonDefList);
_groupComparisonsListBoxDriver.LoadList(
_document.Settings.DataSettings.GroupComparisonDefs);
if (_document.PeptideTransitions.Any(t => t.IsMs1))
{
comboMSGroupComparisons.Items.Add(Resources.RefineDlg_MSLevel_1);
comboMSGroupComparisons.SelectedIndex = comboMSGroupComparisons.Items.Count - 1;
}
if (_document.PeptideTransitions.Any(t => !t.IsMs1))
{
comboMSGroupComparisons.Items.Add(Resources.RefineDlg_MSLevel_2);
comboMSGroupComparisons.SelectedIndex = comboMSGroupComparisons.Items.Count - 1;
}
if (comboMSGroupComparisons.Items.Count == 1)
{
comboMSGroupComparisons.Enabled = false;
}
}
public static FoldChangeGrid ShowFoldChangeGrid(DockPanel dockPanel, Rectangle rcFloating, IDocumentUIContainer documentContainer,
string groupComparisonName)
{
var grid = FindForm <FoldChangeGrid>(documentContainer, groupComparisonName);
if (grid != null)
{
grid.Activate();
return(grid);
}
grid = new FoldChangeGrid();
grid.SetBindingSource(FindOrCreateBindingSource(documentContainer, groupComparisonName));
grid.Show(dockPanel, rcFloating);
return(grid);
}
