public AddIrtSpectralLibrary(IEnumerable <LibrarySpec> librarySpecs)
{
InitializeComponent();
comboLibrary.Items.AddRange(librarySpecs.Cast <object>().ToArray());
ComboHelper.AutoSizeDropDown(comboLibrary);
}
public AddIrtCalculatorDlg(IEnumerable <RCalcIrt> calculators)
{
InitializeComponent();
comboLibrary.Items.AddRange(calculators.Cast <object>().ToArray());
ComboHelper.AutoSizeDropDown(comboLibrary);
}
public DefineAnnotationDlg(IEnumerable <AnnotationDef> existing)
{
InitializeComponent();
Icon = Resources.Skyline;
checkedListBoxAppliesTo.Items.Clear();
comboAppliesTo.Items.Clear();
foreach (var annotationTarget in new[]
{
AnnotationDef.AnnotationTarget.protein,
AnnotationDef.AnnotationTarget.peptide,
AnnotationDef.AnnotationTarget.precursor,
AnnotationDef.AnnotationTarget.transition,
AnnotationDef.AnnotationTarget.replicate,
AnnotationDef.AnnotationTarget.precursor_result,
AnnotationDef.AnnotationTarget.transition_result,
})
{
var item = new AnnotationTargetItem(annotationTarget, ModeUI);
checkedListBoxAppliesTo.Items.Add(item);
comboAppliesTo.Items.Add(item);
}
comboType.Items.AddRange(ListPropertyType.ListPropertyTypes().ToArray());
comboType.SelectedIndex = 0;
ComboHelper.AutoSizeDropDown(comboType);
_existing = existing;
_dataSchema = BrowsingDataSchema.GetBrowsingDataSchema();
availableFieldsTree1.RootColumn = NullRootColumn;
}
public AddOptimizationLibraryDlg(IEnumerable <OptimizationLibrary> libraries)
{
InitializeComponent();
comboLibrary.Items.AddRange(libraries.Cast <object>().ToArray());
ComboHelper.AutoSizeDropDown(comboLibrary);
if (comboLibrary.Items.Count > 0)
{
comboLibrary.SelectedIndex = 0;
}
}
private int ResetResultsCombo(List <string> listNames, ToolStripComboBox combo)
{
object selected = combo.SelectedItem;
combo.Items.Clear();
foreach (string name in listNames)
{
combo.Items.Add(name);
}
ComboHelper.AutoSizeDropDown(combo);
return(selected != null?combo.Items.IndexOf(selected) : -1);
}
public ImportIonMobilityFromSpectralLibraryDlg(IEnumerable <LibrarySpec> librarySpecs, CollisionalCrossSectionGridViewDriver gridViewDriver)
{
InitializeComponent();
comboLibrary.Items.AddRange(librarySpecs.Cast <object>().ToArray());
if ((comboLibrary.Items.Count == 1) && (Source == SpectralLibrarySource.settings))
{
comboLibrary.SelectedIndex = 0; // The obvious choice
}
ComboHelper.AutoSizeDropDown(comboLibrary);
_gridViewDriver = gridViewDriver;
}
private void UpdateCombo()
{
var documentRetentionTimes = Document.Settings.DocumentRetentionTimes;
var newItems = documentRetentionTimes.RetentionTimeSources.Values.Select(retentionTimeSource => new DataFileKey(retentionTimeSource)).ToArray();
if (newItems.SequenceEqual(comboAlignAgainst.Items.Cast <DataFileKey>()))
{
return;
}
var selectedIndex = comboAlignAgainst.SelectedIndex;
comboAlignAgainst.Items.Clear();
comboAlignAgainst.Items.AddRange(newItems.Cast <object>().ToArray());
ComboHelper.AutoSizeDropDown(comboAlignAgainst);
bool updateRows = true;
if (comboAlignAgainst.Items.Count > 0)
{
if (selectedIndex < 0)
{
if (SkylineWindow.SelectedResultsIndex >= 0 && Document.Settings.HasResults)
{
var chromatogramSet =
Document.Settings.MeasuredResults.Chromatograms[SkylineWindow.SelectedResultsIndex];
foreach (var msDataFileInfo in chromatogramSet.MSDataFileInfos)
{
var retentionTimeSource = documentRetentionTimes.RetentionTimeSources.Find(msDataFileInfo);
if (retentionTimeSource == null)
{
continue;
}
selectedIndex =
newItems.IndexOf(
dataFileKey => Equals(retentionTimeSource, dataFileKey.RetentionTimeSource));
break;
}
}
}
selectedIndex = Math.Min(comboAlignAgainst.Items.Count - 1,
Math.Max(0, selectedIndex));
if (comboAlignAgainst.SelectedIndex != selectedIndex)
{
comboAlignAgainst.SelectedIndex = selectedIndex;
updateRows = false; // because the selection change will cause an update
}
}
if (updateRows)
{
UpdateRows();
}
}
private void UpdateToolbar()
{
if (_spectra == null || _spectra.Count < 2)
{
toolBar.Visible = false;
}
else
{
// Check to see if the list of files has changed.
var listNames = _spectra.Select(spectrum => spectrum.Identity).ToArray();
var listExisting = new List <string>();
foreach (var item in comboSpectrum.Items)
{
listExisting.Add(item.ToString());
}
if (!ArrayUtil.EqualsDeep(listNames, listExisting))
{
// If it has, update the list, trying to maintain selection, if possible.
object selected = comboSpectrum.SelectedItem;
// Unless the current selected index is the one matching the one currently
// in use by the precursor (zero), then try to stay viewing the in-use spectrum (zero)
int selectedIndex = comboSpectrum.SelectedIndex;
_inToolbarUpdate = true;
comboSpectrum.Items.Clear();
foreach (string name in listNames)
{
comboSpectrum.Items.Add(name);
}
if (selectedIndex == 0 || selected == null ||
comboSpectrum.Items.IndexOf(selected) == -1)
{
comboSpectrum.SelectedIndex = 0;
}
else
{
comboSpectrum.SelectedItem = selected;
}
_inToolbarUpdate = false;
ComboHelper.AutoSizeDropDown(comboSpectrum);
}
// Show the toolbar after updating the spectra
if (!toolBar.Visible)
{
toolBar.Visible = true;
}
}
FireSelectedSpectrumChanged(false);
}
public SchedulingOptionsDlg(SrmDocument document, Func<int, bool> canTriggerReplicate)
{
InitializeComponent();
Icon = Resources.Skyline;
_document = document;
_canTriggerReplicate = canTriggerReplicate;
foreach (var chromatogramSet in document.Settings.MeasuredResults.Chromatograms)
{
comboReplicateNames.Items.Add(chromatogramSet);
}
ComboHelper.AutoSizeDropDown(comboReplicateNames);
radioSingleDataSet.Checked = !Settings.Default.ScheduleAvergeRT;
}
public void LoadList(string selectedItemLast)
{
try
{
Combo.BeginUpdate();
Combo.Items.Clear();
foreach (TItem item in List.ToArrayStd())
{
string name = List.GetDisplayName(item);
int i = Combo.Items.Add(name);
if (Equals(Combo.Items[i].ToString(), selectedItemLast))
{
Combo.SelectedIndex = i;
}
}
// If nothing was added, add a blank to avoid starting with "Add..." selected.
if (Combo.Items.Count == 0)
{
Combo.Items.Add(string.Empty);
}
if (IsVisibleEditting)
{
if (List is IItemEditor <TItem> )
{
Combo.Items.Add(Resources.SettingsListComboDriver_Add);
Combo.Items.Add(Resources.SettingsListComboDriver_Edit_current);
}
Combo.Items.Add(Resources.SettingsListComboDriver_Edit_list);
}
if (Combo.SelectedIndex < 0)
{
Combo.SelectedIndex = 0;
}
ComboHelper.AutoSizeDropDown(Combo);
}
finally
{
Combo.EndUpdate();
}
}
public DefineAnnotationDlg(IEnumerable <AnnotationDef> existing)
{
InitializeComponent();
Icon = Resources.Skyline;
checkedListBoxAppliesTo.Items.Clear();
foreach (var annotationTarget in new[]
{
AnnotationDef.AnnotationTarget.protein,
AnnotationDef.AnnotationTarget.peptide,
AnnotationDef.AnnotationTarget.precursor,
AnnotationDef.AnnotationTarget.transition,
AnnotationDef.AnnotationTarget.replicate,
AnnotationDef.AnnotationTarget.precursor_result,
AnnotationDef.AnnotationTarget.transition_result,
})
{
checkedListBoxAppliesTo.Items.Add(new AnnotationTargetItem(annotationTarget, GetModeUIHelper().ModeUI));
}
comboType.Items.AddRange(ListPropertyType.ListPropertyTypes().ToArray());
comboType.SelectedIndex = 0;
ComboHelper.AutoSizeDropDown(comboType);
_existing = existing;
}
private void LoadFragmentIonEntries()
{
cbFragmentIons.Items.AddRange(ImportPeptideSearch.SearchEngine.FragmentIons);
ComboHelper.AutoSizeDropDown(cbFragmentIons);
cbFragmentIons.SelectedIndex = 0;
}
public void UpdateResultsUI(SrmSettings settingsNew, SrmSettings settingsOld)
{
if (_updateLockCountDoc > 0)
{
return;
}
var results = settingsNew.MeasuredResults;
if (settingsOld == null || !ReferenceEquals(results, settingsOld.MeasuredResults))
{
if (results == null || results.Chromatograms.Count < 2)
{
if (toolBarResults.Visible)
{
toolBarResults.Visible = false;
}
// Make sure the combo contains the results name, if one is
// available, because graph handling depends on this.
if (results != null && results.Chromatograms.Count > 0)
{
string resultsName = results.Chromatograms[0].Name;
if (ComboResults.Items.Count != 1 || !Equals(ComboResults.SelectedItem, resultsName))
{
ComboResults.Items.Clear();
ComboResults.Items.Add(resultsName);
ComboResults.SelectedIndex = 0;
}
}
}
else
{
// Check to see if the list of files has changed.
var listNames = new List <string>();
foreach (var chromSet in results.Chromatograms)
{
listNames.Add(chromSet.Name);
}
var listExisting = new List <string>();
foreach (var item in ComboResults.Items)
{
listExisting.Add(item.ToString());
}
if (!ArrayUtil.EqualsDeep(listNames, listExisting))
{
// If it has, update the list, trying to maintain selection, if possible.
object selected = ComboResults.SelectedItem;
ComboResults.Items.Clear();
foreach (string name in listNames)
{
ComboResults.Items.Add(name);
}
if (selected == null || ComboResults.Items.IndexOf(selected) == -1)
{
ComboResults.SelectedIndex = 0;
}
else
{
ComboResults.SelectedItem = selected;
}
ComboHelper.AutoSizeDropDown(ComboResults);
}
// Show the toolbar after updating the files
if (!toolBarResults.Visible)
{
toolBarResults.Visible = true;
EnsureResultsComboSize();
}
}
}
}
private int UpdateComboItems(ComboBox combo, IEnumerable <StaticMod> listSettingsMods,
IList <ExplicitMod> listExplicitMods, IList <StaticMod> listDocMods, int indexAA,
bool selectEither, bool select)
{
string seq = NodePeptide.Peptide.Target.Sequence;
char aa = seq[indexAA];
int iSelected = -1;
string explicitName = null;
if (listExplicitMods != null)
{
int indexMod = listExplicitMods.IndexOf(mod => mod.IndexAA == indexAA);
if (indexMod != -1)
{
explicitName = listExplicitMods[indexMod].Modification.Name;
}
}
List <string> listItems = new List <string> {
string.Empty
};
foreach (StaticMod mod in listSettingsMods)
{
if (!mod.IsMod(aa, indexAA, seq.Length))
{
continue;
}
listItems.Add(mod.Name);
// If the peptide is explicitly modified, then the explicit modifications
// indicate the combo selections.
if (listExplicitMods != null)
{
if (Equals(explicitName, mod.Name))
{
iSelected = listItems.Count - 1;
}
}
// If it is not explicitly modified, or no modification was found in the
// explicit set, and using the implicit modifications is allowed (variable mods)
// check the implicit modifications for an applicable mod
if (listExplicitMods == null || (selectEither && iSelected == -1))
{
// If the modification is present in the document, then it should be selected by default.
StaticMod modCurrent = mod;
if (listDocMods != null && listDocMods.IndexOf(modDoc =>
!modDoc.IsExplicit && Equals(modDoc.Name, modCurrent.Name)) != -1)
{
iSelected = listItems.Count - 1;
}
}
}
listItems.Add(Resources.SettingsListComboDriver_Add);
listItems.Add(Resources.SettingsListComboDriver_Edit_list);
if (!EqualsItems(combo, listItems))
{
combo.Items.Clear();
listItems.ForEach(item => combo.Items.Add(item));
// If not just the blank, add and edit items, make sure the drop-down is wid enough
if (listItems.Count > 3)
{
ComboHelper.AutoSizeDropDown(combo);
}
}
if (select)
{
combo.SelectedIndex = iSelected;
}
return(iSelected);
}
private void PopulateComboBoxes()
{
foreach (var comboBox in ComboBoxes)
{
comboBox.Text = string.Empty;
comboBox.Items.AddRange(new object[] {
Resources.ImportTransitionListColumnSelectDlg_PopulateComboBoxes_Ignore_Column,
Resources.ImportTransitionListColumnSelectDlg_PopulateComboBoxes_Decoy,
Resources.ImportTransitionListColumnSelectDlg_PopulateComboBoxes_iRT,
Resources.ImportTransitionListColumnSelectDlg_PopulateComboBoxes_Label_Type,
Resources.ImportTransitionListColumnSelectDlg_PopulateComboBoxes_Library_Intensity,
Resources.ImportTransitionListColumnSelectDlg_PopulateComboBoxes_Peptide_Modified_Sequence,
Resources.ImportTransitionListColumnSelectDlg_PopulateComboBoxes_Precursor_m_z,
Resources.ImportTransitionListColumnSelectDlg_PopulateComboBoxes_Product_m_z,
Resources.ImportTransitionListColumnSelectDlg_PopulateComboBoxes_Protein_Name,
Resources.ImportTransitionListColumnSelectDlg_PopulateComboBoxes_Fragment_Name,
// Commented out for consistency because there is no product charge column
// Resources.ImportTransitionListColumnSelectDlg_PopulateComboBoxes_Precursor_Charge
});
comboBox.SelectedIndex = 0;
comboBox.SelectedIndexChanged += ComboChanged;
ComboHelper.AutoSizeDropDown(comboBox);
}
var columns = Importer.RowReader.Indices;
// It's not unusual to see lines like "744.8 858.39 10 APR.AGLCQTFVYGGCR.y7.light 105 40" where protein, peptide, and label are all stuck together,
// so that all three lay claim to a single column. In such cases, prioritize peptide.
columns.PrioritizePeptideColumn();
var headers = Importer.RowReader.Indices.Headers;
// Checks if the headers of the current list are the same as the headers of the previous list,
// because if they are then we want to prioritize user headers
bool sameHeaders = false;
if (headers != null)
{
sameHeaders = (headers.ToList().SequenceEqual(Settings.Default.CustomImportTransitionListHeaders));
}
// If there are items on our saved column list and the file does not contain headers (or the headers are the same as the previous file),
// and the number of columns matches the saved column count then the combo box text is set using that list
if ((Settings.Default.CustomImportTransitionListColumnsList.Count != 0) && ((headers == null) || (sameHeaders)) && Importer.RowReader.Lines[0].ParseDsvFields(Importer.Separator).Length == Settings.Default.CustomImportTransitionListColumnCount)
{
for (int i = 0; i < Settings.Default.CustomImportTransitionListColumnsList.Count; i++)
{
// The method is called for every tuplet on the list. Item 1 is the index position and item 2 is the name
SetComboBoxText(Settings.Default.CustomImportTransitionListColumnsList[i].Item1, Settings.Default.CustomImportTransitionListColumnsList[i].Item2);
ComboChanged(ComboBoxes[i], new EventArgs());
}
}
else
{
SetComboBoxText(columns.DecoyColumn, Resources.ImportTransitionListColumnSelectDlg_PopulateComboBoxes_Decoy);
SetComboBoxText(columns.IrtColumn, Resources.ImportTransitionListColumnSelectDlg_PopulateComboBoxes_iRT);
SetComboBoxText(columns.LabelTypeColumn, Resources.ImportTransitionListColumnSelectDlg_PopulateComboBoxes_Label_Type);
SetComboBoxText(columns.LibraryColumn, Resources.ImportTransitionListColumnSelectDlg_PopulateComboBoxes_Library_Intensity);
SetComboBoxText(columns.PeptideColumn, Resources.ImportTransitionListColumnSelectDlg_PopulateComboBoxes_Peptide_Modified_Sequence);
SetComboBoxText(columns.PrecursorColumn, Resources.ImportTransitionListColumnSelectDlg_PopulateComboBoxes_Precursor_m_z);
SetComboBoxText(columns.ProductColumn, Resources.ImportTransitionListColumnSelectDlg_PopulateComboBoxes_Product_m_z);
SetComboBoxText(columns.ProteinColumn, Resources.ImportTransitionListColumnSelectDlg_PopulateComboBoxes_Protein_Name);
SetComboBoxText(columns.FragmentNameColumn, Resources.ImportTransitionListColumnSelectDlg_PopulateComboBoxes_Fragment_Name);
// Commented out for consistency because there is no product charge column
// SetComboBoxText(columns.PrecursorChargeColumn, Resources.ImportTransitionListColumnSelectDlg_PopulateComboBoxes_Precursor_Charge);
}
}
private void EnsureResultsComboSize()
{
comboResults.Width = toolBarResults.Width - labelResults.Width - 6;
ComboHelper.AutoSizeDropDown(comboResults);
}
public override void UpdateUI()
{
var document = _graphSummary.DocumentUIContainer.DocumentUI;
if (!document.Settings.HasResults)
{
return;
}
var groupsVisible = AreaGraphController.GroupByGroup != null;
toolStripLabel1.Visible = toolStripComboGroup.Visible = groupsVisible;
var detectionsVisiblePrev = toolStripLabel2.Visible && toolStripNumericDetections.Visible && toolStripLabel3.Visible;
var detectionsVisible = AreaGraphController.ShouldUseQValues(document);
toolStripLabel2.Visible = toolStripNumericDetections.Visible = toolStripLabel3.Visible = detectionsVisible;
if (detectionsVisible)
{
toolStripNumericDetections.NumericUpDownControl.Minimum = 2;
if (AreaGraphController.GroupByGroup == null || AreaGraphController.GroupByAnnotation == null)
{
toolStripNumericDetections.NumericUpDownControl.Maximum = document.MeasuredResults.Chromatograms.Count;
}
else
{
toolStripNumericDetections.NumericUpDownControl.Maximum = AnnotationHelper.GetReplicateIndices(document, ReplicateValue.FromPersistedString(document.Settings, AreaGraphController.GroupByGroup), AreaGraphController.GroupByAnnotation).Length;
}
if (!detectionsVisiblePrev)
{
toolStripNumericDetections.NumericUpDownControl.Value = 2;
}
}
if (groupsVisible)
{
var annotations = new[] { Resources.GraphSummary_UpdateToolbar_All }.Concat(
AnnotationHelper.GetPossibleAnnotations(document,
ReplicateValue.FromPersistedString(document.Settings, AreaGraphController.GroupByGroup))
.Except(new object[] { null })).ToArray();
toolStripComboGroup.Items.Clear();
// ReSharper disable once CoVariantArrayConversion
toolStripComboGroup.Items.AddRange(annotations);
if (AreaGraphController.GroupByAnnotation != null)
{
toolStripComboGroup.SelectedItem = AreaGraphController.GroupByAnnotation;
}
else
{
toolStripComboGroup.SelectedIndex = 0;
}
ComboHelper.AutoSizeDropDown(toolStripComboGroup);
}
toolStripComboNormalizedTo.Items.Clear();
_normalizationMethods.Clear();
_normalizationMethods.Add(NormalizeOption.DEFAULT);
_normalizationMethods.AddRange(NormalizeOption.AvailableNormalizeOptions(_graphSummary.DocumentUIContainer.DocumentUI));
_normalizationMethods.Add(NormalizeOption.NONE);
toolStripComboNormalizedTo.Items.AddRange(_normalizationMethods.Select(item => item.Caption).ToArray());
toolStripComboNormalizedTo.SelectedIndex = _normalizationMethods.IndexOf(AreaGraphController.AreaCVNormalizeOption);
ComboHelper.AutoSizeDropDown(toolStripComboNormalizedTo);
}