public static bool?OverwriteAnnotations(List <AnnotationDef> annotations)
{
List <string> annotationTitles = annotations.Select(annotation => annotation.GetKey()).ToList();
string annotationMultiMessage = TextUtil.LineSeparate(Resources.ConfigureToolsDlg_OverwriteAnnotations_Annotations_with_the_following_names_already_exist_, String.Empty,
"{0}", String.Empty); // Not L10N
string annotationSingleMessage =
TextUtil.LineSeparate(Resources.ConfigureToolsDlg_OverwriteAnnotations_An_annotation_with_the_following_name_already_exists_, String.Empty, "{0}", String.Empty); // Not L10N
string annotationMessage = annotations.Count == 1 ? annotationSingleMessage : annotationMultiMessage;
string question = Resources.ConfigureToolsDlg_OverwriteAnnotations_Do_you_want_to_overwrite_or_keep_the_existing_annotations_;
string messageFormat = TextUtil.LineSeparate(annotationMessage, question);
DialogResult result = MultiButtonMsgDlg.Show(
null,
String.Format(messageFormat, TextUtil.LineSeparate(annotationTitles)),
Resources.ConfigureToolsDlg_OverwriteOrInParallel_Overwrite,
Resources.ConfigureToolsDlg_OverwriteAnnotations_Keep_Existing, true);
switch (result)
{
case DialogResult.Cancel:
return(null);
case DialogResult.Yes:
return(true);
case DialogResult.No:
return(false);
}
return(false);
}
public void Cancel()
{
if (!Unsaved)
{
DialogResult = DialogResult.Cancel;
}
else
{
DialogResult result = MultiButtonMsgDlg.Show(
this,
Resources.ConfigureToolsDlg_Cancel_Do_you_wish_to_Save_changes_,
MultiButtonMsgDlg.BUTTON_YES, MultiButtonMsgDlg.BUTTON_NO, true);
switch (result)
{
case DialogResult.Yes:
if (SaveTools())
{
DialogResult = DialogResult.OK;
}
break;
case DialogResult.No:
DialogResult = DialogResult.Cancel;
break;
}
}
}
/// <summary>
/// Shows a dialog prompting user to decide whether to use embedded spectra when external spectra are preferred but cannot be found.
/// Returns 'normal' if the user wants Embedded spectra, 'option1' to retry finding the external spectra, or to 'cancel' to abort the library build.
/// </summary>
public static UpdateProgressResponse ShowLibraryMissingExternalSpectraError(Control parentWindow, Exception errorException)
{
// E.g. could not find external raw data for MaxQuant msms.txt; ask user if they want to retry with "prefer embedded spectra" option
if (!BiblioSpecLiteBuilder.IsLibraryMissingExternalSpectraError(errorException, out string spectrumFilename, out string resultsFilepath))
{
throw new InvalidOperationException(@"IsLibraryMissingExternalSpectraError returned false");
}
// TODO: parse supported file extensions from BiblioSpec or ProteoWizard
var dialogResult = MultiButtonMsgDlg.Show(parentWindow,
string.Format(Resources.VendorIssueHelper_ShowLibraryMissingExternalSpectraError_Could_not_find_an_external_spectrum_file_matching__0__in_the_same_directory_as_the_MaxQuant_input_file__1__,
spectrumFilename, resultsFilepath) +
string.Format(Resources.VendorIssueHelper_ShowLibraryMissingExternalSpectraError_ButtonDescriptionsSupportsExtensions__0__, BiblioSpecLiteBuilder.BiblioSpecSupportedFileExtensions),
Resources.BiblioSpecLiteBuilder_Embedded,
Resources.AlertDlg_GetDefaultButtonText__Retry, true);
switch (dialogResult)
{
case DialogResult.Cancel: return(UpdateProgressResponse.cancel);
case DialogResult.Yes: return(UpdateProgressResponse.normal);
case DialogResult.No: return(UpdateProgressResponse.option1);
default:
throw new ArgumentOutOfRangeException();
}
}
private void EnsureChorusAccount()
{
if (_chorusAccounts.Any())
{
return;
}
DialogResult buttonPress = MultiButtonMsgDlg.Show(
this,
TextUtil.LineSeparate(
Resources.OpenDataSourceDialog_EnsureChorusAccount_No_Chorus_acounts_have_been_specified,
Resources.OpenDataSourceDialog_EnsureChorusAccount_Press_Register_to_register_for_an_account_on_the_Chorus_Project,
Resources.OpenDataSourceDialog_EnsureChorusAccount_Press_Add_to_use_specify_an_existing_Chorus_account),
Resources.OpenDataSourceDialog_EnsureChorusAccount_Register, Resources.OpenDataSourceDialog_EnsureChorusAccount_Add, true);
if (buttonPress == DialogResult.Cancel)
{
return;
}
if (buttonPress == DialogResult.Yes)
{
// person intends to register
WebHelpers.OpenLink(this, "https://chorusproject.org/pages/register.html"); // Not L10N
}
var newAccount = _chorusAccounts.NewItem(this, _chorusAccounts, null);
if (null != newAccount)
{
_chorusAccounts.Add(newAccount);
}
}
public void OkDialog()
{
var chosenLists = new HashSet <string>(_listsListBoxDriver.Chosen.Select(data => data.ListName));
var removedListsWithData = DocumentContainer.Document.Settings.DataSettings.Lists
.Where(list => !chosenLists.Contains(list.ListName) && list.RowCount > 0).ToArray();
if (removedListsWithData.Any())
{
string message;
if (removedListsWithData.Length == 1)
{
var list = removedListsWithData[0];
message = string.Format(
Resources.DocumentSettingsDlg_OkDialog_The_list___0___has__1__items_in_it__If_you_remove_that_list_from_your_document__those_items_will_be_deleted__Are_you_sure_you_want_to_delete_those_items_from_that_list_,
list.ListName, list.RowCount);
}
else
{
message = TextUtil.LineSeparate(new[]
{
Resources.DocumentSettingsDlg_OkDialog_The_following_lists_have_items_in_them_which_will_be_deleted_when_you_remove_the_lists_from_your_document_
}
.Concat(removedListsWithData.Select(list =>
string.Format(Resources.DocumentSettingsDlg_OkDialog_List___0___with__1__items, list.ListName, list.RowCount)))
.Concat(new[] { Resources.DocumentSettingsDlg_OkDialog_Are_you_sure_you_want_to_delete_those_items_from_those_lists_ }));
}
if (MultiButtonMsgDlg.Show(this, message, MultiButtonMsgDlg.BUTTON_OK) == DialogResult.Cancel)
{
return;
}
}
Settings.Default.ListDefList.Clear();
Settings.Default.ListDefList.AddRange(_listsListBoxDriver.List.Select(list => list.DeleteAllRows()));
DialogResult = DialogResult.OK;
}
private bool SetCalibrationPeptides(ICollection <PeptideDocNode> exclude)
{
CheckDisposed();
var document = Program.ActiveDocumentUI;
if (!document.Settings.HasResults)
{
MessageDlg.Show(this, Resources.CalibrateIrtDlg_UseResults_The_document_must_contain_results_to_calibrate_a_standard);
return(false);
}
var targetResolver = TargetResolver.MakeTargetResolver(document);
_gridViewDriver.TargetResolver = targetResolver;
var peptides = document.Molecules.Where(nodePep => nodePep.SchedulingTime.HasValue).ToArray();
var count = peptides.Length;
if (exclude != null && exclude.Count > 0)
{
peptides = peptides.Where(nodePep => !exclude.Contains(nodePep)).ToArray();
count = peptides.Length;
if (count < MIN_STANDARD_PEPTIDES)
{
MessageDlg.Show(this,
ModeUIAwareStringFormat(
Resources.CalibrateIrtDlg_SetCalibrationPeptides_The_document_contains_results_for__0__peptide_s__not_in_this_standard__which_is_less_than_the_minimum_requirement_of__1__to_calibrate_a_standard_,
count, MIN_STANDARD_PEPTIDES));
return(false);
}
else if (count < MIN_SUGGESTED_STANDARD_PEPTIDES)
{
if (MultiButtonMsgDlg.Show(this,
ModeUIAwareStringFormat(
Resources.CalibrateIrtDlg_SetCalibrationPeptides_The_document_only_contains_results_for__0__peptide_s__not_in_this_standard__It_is_recommended_to_use_at_least__1__peptides_to_calibrate_a_standard__Are_you_sure_you_wish_to_continue_,
count, MIN_SUGGESTED_STANDARD_PEPTIDES),
MultiButtonMsgDlg.BUTTON_YES, MultiButtonMsgDlg.BUTTON_NO, false) != DialogResult.Yes)
{
return(false);
}
}
}
if (count > 20)
{
using (var dlg = new AddIrtStandardsDlg(count, exclude != null && exclude.Count > 0))
{
if (dlg.ShowDialog(this) != DialogResult.OK)
{
return(false);
}
count = dlg.StandardCount;
}
}
_gridViewDriver.Recalculate(document, count, exclude);
return(true);
}
public void OkDialog()
{
var reader = new StringReader(ProteinsText);
var notFoundLines = new List <string>();
var acceptedProteins = new HashSet <string>();
var setProteinNames = GetProteinNames();
string line;
while ((line = reader.ReadLine()) != null)
{
line = line.Trim();
if (string.IsNullOrEmpty(line))
{
continue;
}
if (!setProteinNames.Contains(line))
{
notFoundLines.Add(line);
}
else
{
acceptedProteins.Add(line);
}
}
if (acceptedProteins.Count == 0)
{
MessageDlg.Show(this, Resources.RefineListDlgProtein_OkDialog_None_of_the_specified_proteins_are_in_the_document_);
return;
}
if (notFoundLines.Count > 0)
{
string message;
if (notFoundLines.Count == 1)
{
message = string.Format(Resources.RefineListDlgProtein_OkDialog_The_protein___0___is_not_in_the_document__Do_you_want_to_continue_, notFoundLines[0]);
}
else if (notFoundLines.Count < 15)
{
message = TextUtil.LineSeparate(Resources.RefineListDlgProtein_OkDialog_The_following_proteins_are_not_in_the_document_, string.Empty,
TextUtil.LineSeparate(notFoundLines), string.Empty,
Resources.RefineListDlgProtein_OkDialog_Do_you_want_to_continue);
}
else
{
message = string.Format(Resources.RefineListDlgProtein_OkDialog_Of_the_specified__0__proteins__1__are_not_in_the_document__Do_you_want_to_continue_,
notFoundLines.Count + acceptedProteins.Count, notFoundLines.Count);
}
if (MultiButtonMsgDlg.Show(this, message, MultiButtonMsgDlg.BUTTON_OK) != DialogResult.OK)
{
return;
}
}
AcceptedProteins = acceptedProteins;
DialogResult = DialogResult.OK;
}
public void ResetAllSettings()
{
if (MultiButtonMsgDlg.Show(this,
string.Format(
Resources
.ToolOptionsUI_btnResetSettings_Click_Are_you_sure_you_want_to_clear_all_saved_settings__This_will_immediately_return__0__to_its_original_configuration_and_cannot_be_undone_,
Program.Name), MultiButtonMsgDlg.BUTTON_OK) == DialogResult.OK)
{
Settings.Default.Reset();
}
}
public void RemovePeaks(SrmDocument.DOCUMENT_TYPE docType, BoundDataGridView dataGridView)
{
var parent = FormUtil.FindTopLevelOwner(dataGridView);
var selectedPeaks = GetSelectedPeaks(dataGridView).Distinct().ToArray();
if (selectedPeaks.Length == 0)
{
MessageDlg.Show(parent, Resources.RemovePeaksAction_RemovePeaks_No_peaks_are_selected);
return;
}
var lookup = selectedPeaks.ToLookup(tuple => tuple.Item1, tuple => tuple.Item2).ToArray();
string message = GetConfirmRemoveMessage(docType, selectedPeaks.Length, lookup.Length);
if (MultiButtonMsgDlg.Show(parent, message, MultiButtonMsgDlg.BUTTON_OK) != DialogResult.OK)
{
return;
}
var skylineWindow = GetSkylineWindow(dataGridView);
lock (skylineWindow.GetDocumentChangeLock())
{
skylineWindow.ModifyDocument(Resources.RemovePeaksAction_RemovePeaks_Remove_peaks,
doc =>
{
var longOperationRunner = new LongOperationRunner
{
ParentControl = parent,
JobTitle = Resources.RemovePeaksAction_RemovePeaks_Removing_Peaks
};
SrmDocument resultDocument = doc;
doc = doc.BeginDeferSettingsChanges();
longOperationRunner.Run(broker =>
{
for (int iGroup = 0; iGroup < lookup.Length; iGroup++)
{
broker.ProgressValue = iGroup * 100 / lookup.Length;
if (broker.IsCanceled)
{
return;
}
doc = RemovePeaks(doc, lookup[iGroup]);
}
resultDocument = doc.EndDeferSettingsChanges(resultDocument, null);
});
return(resultDocument);
},
docPair => AuditLogEntry.CreateSingleMessageEntry(
new MessageInfo(MessageType.removed_peaks, docPair.NewDocumentType, selectedPeaks.Length, lookup.Length)));
}
}
protected void DeleteSkylineDocNodes(Control owner, ICollection <SkylineDocNode> docNodes)
{
if (docNodes.Count == 0)
{
return;
}
var confirmationMessages = docNodes.Select(node => node.GetDeleteConfirmation(docNodes.Count)).Distinct()
.ToArray();
string message = confirmationMessages.Length == 1
? confirmationMessages[0]
: SkylineDocNode.GetGenericDeleteConfirmation(docNodes.Count);
if (MultiButtonMsgDlg.Show(owner, message, MultiButtonMsgDlg.BUTTON_OK) != DialogResult.OK)
{
return;
}
DeleteDocNodes(new HashSet <IdentityPath>(docNodes.Select(node => node.IdentityPath)));
}
/// <summary>
/// Returns true if the tools are saved
/// </summary>
private bool PromptForSave()
{
if (Unsaved)
{
DialogResult toSave = MultiButtonMsgDlg.Show(
this,
string.Format(Resources.ConfigureToolsDlg_AddFromFile_You_must_save_changes_before_installing_tools__Would_you_like_to_save_changes_),
MultiButtonMsgDlg.BUTTON_YES, Resources.ConfigureToolsDlg_AddFromFile_Cancel, false);
switch (toSave)
{
case (DialogResult.Yes):
SaveTools();
return(true);
case (DialogResult.No):
return(false);
}
}
return(true);
}
public static void DeleteSkylineDocNodes(SkylineWindow skylineWindow, BoundDataGridView dataGridView, IEnumerable <SkylineDocNode> docNodesToDelete)
{
var docNodes = (ICollection <SkylineDocNode>)DistinctNodes(docNodesToDelete).ToList();
if (docNodes.Count == 0)
{
return;
}
var owner = FormUtil.FindTopLevelOwner(dataGridView);
var confirmationMessages = docNodes.Select(node => node.GetDeleteConfirmation(docNodes.Count)).Distinct()
.ToArray();
string message = confirmationMessages.Length == 1
? confirmationMessages[0]
: SkylineDocNode.GetGenericDeleteConfirmation(docNodes.Count);
if (MultiButtonMsgDlg.Show(owner, message, MultiButtonMsgDlg.BUTTON_OK) != DialogResult.OK)
{
return;
}
DeleteDocNodes(skylineWindow, new HashSet <IdentityPath>(docNodes.Select(node => node.IdentityPath)));
}
public override void Delete()
{
var selectedItems = GetSelectedListItems(BoundDataGridView);
if (selectedItems.Count == 0)
{
return;
}
string message = string.Format(Resources.ListViewContext_Delete_Are_you_sure_you_want_to_delete_the__0__selected_items_from_the_list___1___, selectedItems.Count, ListName);
if (MultiButtonMsgDlg.Show(BoundDataGridView, message, MultiButtonMsgDlg.BUTTON_OK) != DialogResult.OK)
{
return;
}
SkylineDataSchema.ModifyDocument(EditDescription.Message(ListRef.PROTOTYPE.ChangeName(ListName), string.Format(Resources.ListViewContext_Delete_Delete_from_list___0__, ListName)),
doc =>
{
var listData = doc.Settings.DataSettings.FindList(ListName);
listData = listData.DeleteItems(selectedItems);
return(doc.ChangeSettings(
doc.Settings.ChangeDataSettings(doc.Settings.DataSettings.ReplaceList(listData))));
}, AuditLogEntry.SettingsLogFunction);
}
public bool ValidateNewRow(RowItem rowItem, out bool cancelRowEdit)
{
cancelRowEdit = false;
var listItem = rowItem.Value as ListItem;
if (listItem == null)
{
return(true);
}
var values = ((ListItem.NewRecordData)listItem.GetRecord()).UncommittedValues;
if (values.Count == 0)
{
return(true);
}
try
{
ListItemId listItemId;
var listData = SkylineDataSchema.Document.Settings.DataSettings.FindList(ListName);
listData.AddRow(values, out listItemId);
return(true);
}
catch (Exception exception)
{
if (MultiButtonMsgDlg.Show(BoundDataGridView,
TextUtil.LineSeparate(Resources.ListViewContext_ValidateNewRow_The_new_row_could_not_be_added_because_of_the_following_error_,
exception.Message, Resources.ListViewContext_ValidateNewRow_Press_OK_to_continue_editing_your_row__or_Cancel_to_throw_away_the_new_row_)
, MultiButtonMsgDlg.BUTTON_OK) == DialogResult.Cancel)
{
cancelRowEdit = true;
}
return(false);
}
}
public void OkDialog()
{
var helper = new MessageBoxHelper(this);
string name;
if (!helper.ValidateNameTextBox(_editing ? (Control)textName : comboMod, out name))
{
return;
}
// Allow updating the original modification
if (!_editing || !Equals(name, Modification.Name))
{
if (!ModNameAvailable(name))
{
helper.ShowTextBoxError(_editing ? (Control)textName : comboMod,
Resources.EditStaticModDlg_OkDialog_The_modification__0__already_exists, name);
return;
}
}
string aas = comboAA.Text;
if (string.IsNullOrEmpty(aas))
{
aas = null;
}
else
{
// Use the cleanest possible format.
var sb = new StringBuilder();
foreach (string aaPart in aas.Split(SEPARATOR_AA))
{
string aa = aaPart.Trim();
if (aa.Length == 0)
{
continue;
}
if (sb.Length > 0)
{
sb.Append(", "); // Not L10N
}
sb.Append(aa);
}
}
string termString = comboTerm.SelectedItem.ToString();
ModTerminus?term = null;
if (!string.IsNullOrEmpty(termString))
{
term = (ModTerminus)Enum.Parse(typeof(ModTerminus), termString);
}
if (cbVariableMod.Checked && aas == null && term == null)
{
MessageDlg.Show(this, Resources.EditStaticModDlg_OkDialog_Variable_modifications_must_specify_amino_acid_or_terminus);
comboAA.Focus();
return;
}
string formula = null;
double? monoMass = null;
double? avgMass = null;
LabelAtoms labelAtoms = LabelAtoms.None;
if (cbChemicalFormula.Checked)
{
formula = Formula;
}
else
{
labelAtoms = LabelAtoms;
}
// Get the losses to know whether any exist below
IList <FragmentLoss> losses = null;
if (listNeutralLosses.Items.Count > 0)
{
losses = Losses.ToArray();
}
if (!string.IsNullOrEmpty(formula))
{
try
{
SequenceMassCalc.FormulaMass(BioMassCalc.MONOISOTOPIC, formula, SequenceMassCalc.MassPrecision);
}
catch (ArgumentException x)
{
_formulaBox.ShowTextBoxErrorFormula(helper, x.Message);
return;
}
}
else if (labelAtoms == LabelAtoms.None)
{
formula = null;
// Allow formula and both masses to be empty, if losses are present
if (NotZero(_formulaBox.MonoMass) || NotZero(_formulaBox.AverageMass) || losses == null)
{
// TODO: Maximum and minimum masses should be formalized and applied everywhere
double mass;
if (!_formulaBox.ValidateMonoText(helper, -1500, 5000, out mass))
{
return;
}
monoMass = mass;
if (!_formulaBox.ValidateAverageText(helper, -1500, 5000, out mass))
{
return;
}
avgMass = mass;
}
// Loss-only modifications may not be variable
else if (cbVariableMod.Checked)
{
MessageDlg.Show(this, Resources.EditStaticModDlg_OkDialog_The_variable_checkbox_only_applies_to_precursor_modification_Product_ion_losses_are_inherently_variable);
cbVariableMod.Focus();
return;
}
}
else if (aas == null && term.HasValue)
{
MessageDlg.Show(this, Resources.EditStaticModDlg_OkDialog_Labeled_atoms_on_terminal_modification_are_not_valid);
return;
}
RelativeRT relativeRT = RelativeRT.Matching;
if (comboRelativeRT.Visible && comboRelativeRT.SelectedItem != null)
{
relativeRT = RelativeRTExtension.GetEnum(comboRelativeRT.SelectedItem.ToString());
}
// Store state of the chemical formula checkbox for next use.
if (cbChemicalFormula.Visible)
{
Settings.Default.ShowHeavyFormula = _formulaBox.FormulaVisible;
}
var newMod = new StaticMod(name,
aas,
term,
cbVariableMod.Checked,
formula,
labelAtoms,
relativeRT,
monoMass,
avgMass,
losses);
foreach (StaticMod mod in _existing)
{
if (newMod.Equivalent(mod) && !(_editing && mod.Equals(_originalModification)))
{
if (DialogResult.OK == MultiButtonMsgDlg.Show(
this,
TextUtil.LineSeparate(Resources.EditStaticModDlg_OkDialog_There_is_an_existing_modification_with_the_same_settings,
string.Format("'{0}'.", mod.Name), // Not L10N
string.Empty,
Resources.EditStaticModDlg_OkDialog_Continue),
MultiButtonMsgDlg.BUTTON_OK))
{
Modification = newMod;
DialogResult = DialogResult.OK;
}
return;
}
}
var uniMod = UniMod.GetModification(name, IsStructural);
// If the modification name is not found in Unimod, check if there exists a modification in Unimod that matches
// the dialog modification, and prompt the user to to use the Unimod modification instead.
if (uniMod == null)
{
var matchingMod = UniMod.FindMatchingStaticMod(newMod, IsStructural);
if (matchingMod != null &&
(ModNameAvailable(matchingMod.Name) ||
(_editing && Equals(matchingMod.Name, Modification.Name))))
{
var result = MultiButtonMsgDlg.Show(
this,
TextUtil.LineSeparate(Resources.EditStaticModDlg_OkDialog_There_is_a_Unimod_modification_with_the_same_settings,
string.Empty,
string.Format(Resources.EditStaticModDlg_OkDialog_Click__Unimod__to_use_the_name___0___, matchingMod.Name),
string.Format(Resources.EditStaticModDlg_OkDialog_Click__Custom__to_use_the_name___0___, name)),
Resources.EditStaticModDlg_OkDialog_Unimod,
Resources.EditStaticModDlg_OkDialog_Custom,
true);
if (result == DialogResult.Yes)
{
newMod = matchingMod.MatchVariableAndLossInclusion(newMod); // Unimod
}
if (result == DialogResult.Cancel)
{
return;
}
}
}
else
{
// If the dialog modification matches the modification of the same name in Unimod,
// use the UnimodId.
if (newMod.Equivalent(uniMod))
{
newMod = uniMod.MatchVariableAndLossInclusion(newMod);
}
else
{
// Finally, if the modification name is found in Unimod, but the modification in Unimod does not
// match the dialog modification, prompt the user to use the Unimod modification definition instead.
if (DialogResult.OK != MultiButtonMsgDlg.Show(
this,
TextUtil.LineSeparate(string.Format(Resources.EditStaticModDlg_OkDialog_This_modification_does_not_match_the_Unimod_specifications_for___0___, name),
string.Empty,
Resources.EditStaticModDlg_OkDialog_Use_non_standard_settings_for_this_name),
MultiButtonMsgDlg.BUTTON_OK))
{
return;
}
}
}
_modification = newMod;
DialogResult = DialogResult.OK;
}
public void OkDialog()
{
IrtType irtType = GetIrtType();
if (textCalculatorName.Text.Length == 0)
{
MessageDlg.Show(this, Resources.CreateIrtCalculatorDlg_OkDialog_Calculator_name_cannot_be_empty);
return;
}
if (_existing.Select(spec => spec.Name).Contains(textCalculatorName.Text))
{
var replaceResult = MultiButtonMsgDlg.Show(this, Resources.CreateIrtCalculatorDlg_OkDialog_A_calculator_with_that_name_already_exists___Do_you_want_to_replace_it_,
MultiButtonMsgDlg.BUTTON_YES,
MultiButtonMsgDlg.BUTTON_NO,
false);
if (replaceResult == DialogResult.No)
{
return;
}
}
if (irtType == IrtType.existing)
{
try
{
if (!File.Exists(textOpenDatabase.Text))
{
MessageDlg.Show(this, Resources.CreateIrtCalculatorDlg_OkDialog_iRT_database_field_must_contain_a_path_to_a_valid_file_);
textOpenDatabase.Focus();
return;
}
var db = IrtDb.GetIrtDb(textOpenDatabase.Text, null);
if (db == null)
{
throw new DatabaseOpeningException(string.Format(Resources.CreateIrtCalculatorDlg_OkDialog_Cannot_read_the_database_file__0_, textOpenDatabase.Text));
}
}
catch (Exception x)
{
MessageDlg.ShowWithException(this, string.Format(Resources.CreateIrtCalculatorDlg_OkDialog_Failed_to_open_the_database_file___0_, x.Message), x);
return;
}
}
else if (irtType == IrtType.separate_list)
{
if (textNewDatabase.Text.Length == 0)
{
MessageDlg.Show(this, Resources.CreateIrtCalculatorDlg_OkDialog_iRT_database_field_must_not_be_empty_);
textNewDatabase.Focus();
return;
}
if (!CreateIrtDatabase(textNewDatabase.Text))
{
return;
}
}
else
{
if (textNewDatabaseProteins.Text.Length == 0)
{
MessageDlg.Show(this, Resources.CreateIrtCalculatorDlg_OkDialog_iRT_database_field_must_not_be_empty_);
textNewDatabaseProteins.Focus();
return;
}
if (comboBoxProteins.SelectedIndex == -1)
{
MessageDlg.Show(this, Resources.CreateIrtCalculatorDlg_OkDialog_Please_select_a_protein_containing_the_list_of_standard_peptides_for_the_iRT_calculator_);
comboBoxProteins.Focus();
return;
}
if (!CreateIrtDatabase(textNewDatabaseProteins.Text))
{
return;
}
}
// Make a version of the document with the new calculator in it
var databaseFileName = irtType == IrtType.existing ? textOpenDatabase.Text :
irtType == IrtType.separate_list ? textNewDatabase.Text :
textNewDatabaseProteins.Text;
var calculator = new RCalcIrt(textCalculatorName.Text, databaseFileName);
// CONSIDER: Probably can't use just a static default like 10 below
var retentionTimeRegression = new RetentionTimeRegression(calculator.Name, calculator, null, null, RetentionTimeRegression.DEFAULT_WINDOW, new List <MeasuredRetentionTime>());
var docNew = Document.ChangeSettings(Document.Settings.ChangePeptidePrediction(prediction =>
prediction.ChangeRetentionTime(retentionTimeRegression)));
// Import transition list of standards, if applicable
if (irtType == IrtType.separate_list)
{
try
{
if (!File.Exists(textImportText.Text))
{
MessageDlg.Show(this, Resources.CreateIrtCalculatorDlg_OkDialog_Transition_list_field_must_contain_a_path_to_a_valid_file_);
return;
}
IdentityPath selectPath;
List <MeasuredRetentionTime> irtPeptides;
List <TransitionImportErrorInfo> errorList;
var inputs = new MassListInputs(textImportText.Text);
docNew = docNew.ImportMassList(inputs, null, out selectPath, out irtPeptides, out _librarySpectra, out errorList);
if (errorList.Any())
{
throw new InvalidDataException(errorList[0].ErrorMessage);
}
_dbIrtPeptides = irtPeptides.Select(rt => new DbIrtPeptide(rt.PeptideSequence, rt.RetentionTime, true, TimeSource.scan)).ToList();
IrtFile = textImportText.Text;
}
catch (Exception x)
{
MessageDlg.ShowWithException(this, string.Format(Resources.CreateIrtCalculatorDlg_OkDialog_Error_reading_iRT_standards_transition_list___0_, x.Message), x);
return;
}
}
else if (irtType == IrtType.protein)
{
PeptideGroupDocNode selectedGroup = comboBoxProteins.SelectedItem as PeptideGroupDocNode;
// ReSharper disable PossibleNullReferenceException
_irtPeptideSequences = new HashSet <Target>(selectedGroup.Peptides.Select(pep => pep.ModifiedTarget));
// ReSharper restore PossibleNullReferenceException
}
Document = docNew;
DialogResult = DialogResult.OK;
}
public void OkDialog()
{
var helper = new MessageBoxHelper(this);
string name;
if (!helper.ValidateNameTextBox(textName, out name))
{
return;
}
if (_existing.Contains(en => !ReferenceEquals(_isolationScheme, en) && Equals(name, en.Name)))
{
helper.ShowTextBoxError(textName,
Resources.EditIsolationSchemeDlg_OkDialog_The_isolation_scheme_named__0__already_exists, name);
return;
}
if (rbUseResultsData.Checked)
{
double?precursorFilter = null;
bool filterMargin = Equals(comboIsolationWidth.SelectedItem, IsolationWidthType.RESULTS_WITH_MARGIN);
if (!Equals(comboIsolationWidth.SelectedItem, IsolationWidthType.RESULTS))
{
double minFilt = filterMargin ? 0 : TransitionFullScan.MIN_PRECURSOR_MULTI_FILTER;
double maxFilt = filterMargin
? TransitionFullScan.MAX_PRECURSOR_MULTI_FILTER_MARGIN
: TransitionFullScan.MAX_PRECURSOR_MULTI_FILTER;
double precFilt;
if (!helper.ValidateDecimalTextBox(textPrecursorFilterMz,
minFilt, maxFilt, out precFilt))
{
return;
}
precursorFilter = precFilt;
}
try
{
_isolationScheme = new IsolationScheme(name, SpecialHandling, precursorFilter, null, filterMargin);
}
catch (InvalidDataException exception)
{
MessageDlg.ShowException(this, exception);
return;
}
}
else
{
// Validate prespecified windows.
List <IsolationWindow> windowList;
if ((windowList = GetIsolationWindows()) == null)
{
return;
}
// Must be at least one window.
if (windowList.Count == 0)
{
_gridViewDriver.SelectCell(COLUMN_START, 0);
MessageDlg.Show(this,
Resources
.EditIsolationSchemeDlg_OkDialog_Specify_Start_and_End_values_for_at_least_one_isolation_window);
gridIsolationWindows.Focus();
_gridViewDriver.EditCell();
return;
}
int?windowsPerScan = null;
if (Equals(SpecialHandling, IsolationScheme.SpecialHandlingType.MULTIPLEXED))
{
int x;
if (!helper.ValidateNumberTextBox(textWindowsPerScan,
IsolationScheme.MIN_MULTIPLEXED_ISOLATION_WINDOWS,
IsolationScheme.MAX_MULTIPLEXED_ISOLATION_WINDOWS,
out x))
{
return;
}
windowsPerScan = x;
}
// Check for overlap and gaps
var sortedWindowList = windowList.OrderBy(o => o.Start).ToList();
bool gapsOk = false;
bool overlapsOk = false;
bool overlap = Overlap;
int increment = overlap ? 2 : 1;
int subtraction = overlap ? 3 : 1;
const double tolerance = 0.0001;
for (int i = 0; i < sortedWindowList.Count - subtraction; i += increment)
{
for (int j = 0; j < increment; j++)
{
IsolationWindow current = sortedWindowList.ElementAt(i + j);
IsolationWindow next = sortedWindowList.ElementAt(i + j + increment);
if (!gapsOk && next.Start - current.End > tolerance)
{
if (MultiButtonMsgDlg.Show(this,
Resources
.EditIsolationSchemeDlg_OkDialog_There_are_gaps_in_a_single_cycle_of_your_extraction_windows__Do_you_want_to_continue_,
MultiButtonMsgDlg.BUTTON_YES, MultiButtonMsgDlg.BUTTON_NO, false) !=
DialogResult.Yes)
{
return;
}
gapsOk = true;
}
else if (!overlapsOk && current.End - next.Start > tolerance)
{
if (MultiButtonMsgDlg.Show(this,
Resources.EditIsolationSchemeDlgOkDialogThereAreOverlapsContinue,
MultiButtonMsgDlg.BUTTON_YES,
MultiButtonMsgDlg.BUTTON_NO, false) != DialogResult.Yes)
{
return;
}
overlapsOk = true;
}
}
}
try
{
_isolationScheme = new IsolationScheme(name, windowList, SpecialHandling, windowsPerScan);
}
catch (InvalidDataException exception)
{
MessageDlg.ShowException(this, exception);
return;
}
}
DialogResult = DialogResult.OK;
}
/// <summary>
/// UI for warning about unrecognized peptides in imported file
/// </summary>
/// <param name="parent"></param>
/// <returns></returns>
public bool UnrecognizedPeptidesCancel(IWin32Window parent)
{
const int itemsToShow = 10;
var peptides = UnrecognizedPeptides.ToList();
if (peptides.Any())
{
var sb = new StringBuilder();
sb.AppendLine(peptides.Count == 1
? Resources.PeakBoundaryImporter_UnrecognizedPeptidesCancel_The_following_peptide_in_the_peak_boundaries_file_was_not_recognized_
: string.Format(Resources.SkylineWindow_ImportPeakBoundaries_The_following__0__peptides_in_the_peak_boundaries_file_were_not_recognized__,
peptides.Count));
sb.AppendLine();
int peptidesToShow = Math.Min(peptides.Count, itemsToShow);
for (int i = 0; i < peptidesToShow; ++i)
{
sb.AppendLine(peptides[i]);
}
if (peptidesToShow < peptides.Count)
{
sb.AppendLine("..."); // Not L10N
}
sb.AppendLine();
sb.Append(peptides.Count == 1
? Resources.PeakBoundaryImporter_UnrecognizedPeptidesCancel_Continue_peak_boundary_import_ignoring_this_peptide_
: Resources.SkylineWindow_ImportPeakBoundaries_Continue_peak_boundary_import_ignoring_these_peptides_);
var dlgPeptides = MultiButtonMsgDlg.Show(parent, sb.ToString(), MultiButtonMsgDlg.BUTTON_OK);
if (dlgPeptides == DialogResult.Cancel)
{
return(false);
}
}
var files = UnrecognizedFiles.ToList();
if (files.Any())
{
var sb = new StringBuilder();
sb.AppendLine(files.Count == 1
? Resources.PeakBoundaryImporter_UnrecognizedPeptidesCancel_The_following_file_name_in_the_peak_boundaries_file_was_not_recognized_
: string.Format(Resources.SkylineWindow_ImportPeakBoundaries_The_following__0__file_names_in_the_peak_boundaries_file_were_not_recognized_,
files.Count));
sb.AppendLine();
int filesToShow = Math.Min(files.Count, itemsToShow);
for (int i = 0; i < filesToShow; ++i)
{
sb.AppendLine(files[i]);
}
if (filesToShow < files.Count)
{
sb.AppendLine("..."); // Not L10N
}
sb.AppendLine();
sb.Append(files.Count == 1
? Resources.PeakBoundaryImporter_UnrecognizedPeptidesCancel_Continue_peak_boundary_import_ignoring_this_file_
: Resources.SkylineWindow_ImportPeakBoundaries_Continue_peak_boundary_import_ignoring_these_files_);
var dlgFiles = MultiButtonMsgDlg.Show(parent, sb.ToString(), MultiButtonMsgDlg.BUTTON_OK);
if (dlgFiles == DialogResult.Cancel)
{
return(false);
}
}
var charges = UnrecognizedChargeStates.ToList();
if (charges.Any())
{
var sb = new StringBuilder();
sb.AppendLine(files.Count == 1
? Resources.PeakBoundaryImporter_UnrecognizedPeptidesCancel_The_following_peptide__file__and_charge_state_combination_was_not_recognized_
: string.Format(Resources.PeakBoundaryImporter_UnrecognizedPeptidesCancel_The_following__0__peptide__file__and_charge_state_combinations_were_not_recognized_,
charges.Count()));
sb.AppendLine();
int chargesToShow = Math.Min(charges.Count, itemsToShow);
for (int i = 0; i < chargesToShow; ++i)
{
sb.AppendLine(charges[i].PrintLine(' ')); // Not L10N
}
if (chargesToShow < charges.Count)
{
sb.AppendLine("..."); // Not L10N
}
sb.AppendLine();
sb.Append(files.Count == 1
? Resources.PeakBoundaryImporter_UnrecognizedPeptidesCancel_Continue_peak_boundary_import_ignoring_these_charge_states_
: Resources.PeakBoundaryImporter_UnrecognizedPeptidesCancel_Continue_peak_boundary_import_ignoring_this_charge_state_);
var dlgFiles = MultiButtonMsgDlg.Show(parent, sb.ToString(), MultiButtonMsgDlg.BUTTON_OK);
if (dlgFiles == DialogResult.Cancel)
{
return(false);
}
}
return(true);
}
public override void Delete()
{
if (null == BoundDataGridView)
{
return;
}
var selectedRows = GetSelectedRows <FoldChangeBindingSource.FoldChangeRow>(BoundDataGridView);
if (!selectedRows.Any())
{
MessageDlg.Show(BoundDataGridView, GroupComparisonStrings.GroupComparisonViewContext_Delete_No_rows_are_selected);
return;
}
var docNodes = new Dictionary <IdentityPath, SkylineDocNode>();
foreach (var row in selectedRows)
{
if (row.Peptide != null)
{
docNodes[row.Peptide.IdentityPath] = row.Peptide;
}
else
{
docNodes[row.Protein.IdentityPath] = row.Protein;
}
}
string message;
if (docNodes.Count == 1)
{
var peptide = docNodes.Values.First() as Peptide;
if (null != peptide)
{
message = string.Format(GroupComparisonStrings.GroupComparisonViewContext_Delete_Are_you_sure_you_want_to_delete_the_peptide__0_, peptide);
}
else
{
var protein = docNodes.Values.First() as Protein;
message = string.Format(GroupComparisonStrings.GroupComparisonViewContext_Delete_Are_you_sure_you_want_to_delete_the_protein__0_, protein);
}
}
else
{
if (docNodes.Values.First() is Peptide)
{
message = string.Format(GroupComparisonStrings.GroupComparisonViewContext_Delete_Are_you_sure_you_want_to_delete_these__0__peptides, docNodes.Count);
}
else
{
message = string.Format(GroupComparisonStrings.GroupComparisonViewContext_Delete_Are_you_sure_you_want_to_delete_these__0__proteins, docNodes.Count);
}
}
if (MultiButtonMsgDlg.Show(BoundDataGridView, message, Resources.OK) != DialogResult.OK)
{
return;
}
var identityPathsToDelete = new HashSet <IdentityPath>(docNodes.Keys);
var skylineWindow = ((SkylineDataSchema)DataSchema).SkylineWindow;
if (null != skylineWindow)
{
skylineWindow.ModifyDocument(GroupComparisonStrings.GroupComparisonViewContext_Delete_Delete_items, doc => DeleteProteins(doc, identityPathsToDelete));
}
}
private bool GetPackages()
{
ICollection <string> downloadablePackages = new Collection <string>();
ICollection <string> localPackages = new Collection <string>();
AssignPackagesToInstall(ref downloadablePackages, ref localPackages);
IEnumerable <string> packagePaths = null;
try
{
// download packages
using (var waitDlg = new LongWaitDlg {
ProgressValue = 0
})
{
waitDlg.PerformWork(this, 500, longWaitBroker => packagePaths = DownloadPackages(longWaitBroker, downloadablePackages));
}
// separate packages
ICollection <string> exePaths = new Collection <string>();
ICollection <string> sourcePaths = new Collection <string>();
foreach (var package in (packagePaths == null) ? localPackages : packagePaths.Concat(localPackages))
{
if (package.EndsWith(@".exe"))
{
exePaths.Add(package);
}
else
{
sourcePaths.Add(package);
}
}
// first install executable packages, if any
if (exePaths.Count != 0)
{
using (var waitDlg = new LongWaitDlg(null, false)
{
Message = Resources.PythonInstaller_GetPackages_Installing_Packages
})
{
waitDlg.PerformWork(this, 500, () => InstallExecutablePackages(exePaths));
}
}
// then install source paths, if any
if (sourcePaths.Count != 0)
{
// try and find the path to the pip package manager .exe
string pipPath = PythonUtil.GetPipPath(_version);
// if it can't be found, install it
if (pipPath == null || TestingPip)
{
DialogResult result = MultiButtonMsgDlg.Show(
this,
Resources.PythonInstaller_InstallPackages_Skyline_uses_the_Python_tool_setuptools_and_the_Python_package_manager_Pip_to_install_packages_from_source__Click_install_to_begin_the_installation_process_,
Resources.PythonInstaller_InstallPackages_Install);
if (result == DialogResult.OK && GetPip())
{
pipPath = PythonUtil.GetPipPath(_version);
MessageDlg.Show(this, Resources.PythonInstaller_InstallPackages_Pip_installation_complete_);
}
else
{
MessageDlg.Show(this, Resources.PythonInstaller_InstallPackages_Python_package_installation_cannot_continue__Canceling_tool_installation_);
return(false);
}
}
using (var waitDlg = new LongWaitDlg(null, false)
{
Message = Resources.PythonInstaller_GetPackages_Installing_Packages
})
{
waitDlg.PerformWork(this, 500, () => InstallSourcePackages(sourcePaths, pipPath));
}
}
MessageDlg.Show(this, Resources.PythonInstaller_GetPackages_Package_installation_completed_);
return(true);
}
catch (TargetInvocationException ex)
{
if (ex.InnerException is ToolExecutionException)
{
MessageDlg.ShowException(this, ex);
return(false);
}
throw;
}
}
public void OkDialog()
{
var reader = new StringReader(textPeptides.Text);
var standardPeptides = new List <DbIrtPeptide>();
var invalidLines = new List <string>();
string line;
while ((line = reader.ReadLine()) != null)
{
line = line.Trim();
// Skip blank lines
if (string.IsNullOrEmpty(line))
{
continue;
}
DbIrtPeptide peptide = null;
var target = TargetResolver.ResolveTarget(line);
if (target == null || !_dictSequenceToPeptide.TryGetValue(target, out peptide)) // CONSIDER(bspratt) - small molecule equivalent?
{
invalidLines.Add(line);
}
standardPeptides.Add(peptide);
}
if (invalidLines.Count > 0)
{
string message;
if (invalidLines.Count == 1)
{
message = ModeUIAwareStringFormat(Resources.ChangeIrtPeptidesDlg_OkDialog_The_sequence__0__is_not_currently_in_the_database,
invalidLines[0]);
MessageBox.Show(this, message, Program.Name);
}
else
{
message = TextUtil.LineSeparate(GetModeUIHelper().Translate(Resources.ChangeIrtPeptidesDlg_OkDialog_The_following_sequences_are_not_currently_in_the_database),
string.Empty,
TextUtil.LineSeparate(invalidLines),
string.Empty,
GetModeUIHelper().Translate(Resources.ChangeIrtPeptidesDlg_OkDialog_Standard_peptides_must_exist_in_the_database));
MessageBox.Show(this, message, Program.Name);
}
return;
}
ReplacementProtein = null;
var selected = (ComboBoxProtein)comboProteins.SelectedItem;
if (selected.IsNotNull)
{
var removedPeptides = selected.RemovedPeptides(TargetResolver, textPeptides.Lines).ToArray();
if (removedPeptides.Any())
{
switch (MultiButtonMsgDlg.Show(this, TextUtil.LineSeparate(
Resources.ChangeIrtPeptidesDlg_OkDialog_The_following_peptides_were_removed_,
TextUtil.LineSeparate(removedPeptides.Select(nodePep => nodePep.ModifiedSequenceDisplay)),
Resources.ChangeIrtPeptidesDlg_OkDialog_Would_you_like_to_remove_them_from_the_document_),
MultiButtonMsgDlg.BUTTON_YES, MultiButtonMsgDlg.BUTTON_NO, true))
{
case DialogResult.Yes:
ReplacementProtein = selected.RemovePeptides(TargetResolver, textPeptides.Lines);
break;
case DialogResult.No:
break;
case DialogResult.Cancel:
return;
}
}
}
_standardPeptides = standardPeptides.ToArray();
DialogResult = DialogResult.OK;
}
public void UploadSharedZipFile(Control parent, Server server, string zipFilePath, string folderPath)
{
Uri result = null;
if (server == null)
{
return;
}
try
{
var isCanceled = false;
using (var waitDlg = new LongWaitDlg {
Text = Resources.PublishDocumentDlg_UploadSharedZipFile_Uploading_File
})
{
waitDlg.PerformWork(parent, 1000, longWaitBroker =>
{
result = SendZipFile(server, folderPath,
zipFilePath, longWaitBroker);
if (longWaitBroker.IsCanceled)
{
isCanceled = true;
}
});
}
if (!isCanceled) // if user not canceled
{
String message = Resources.WebPanoramaPublishClient_UploadSharedZipFile_Publish_succeeded__would_you_like_to_view_the_file_in_Panorama_;
if (MultiButtonMsgDlg.Show(parent, message, MultiButtonMsgDlg.BUTTON_YES, MultiButtonMsgDlg.BUTTON_NO, false)
== DialogResult.Yes)
{
Process.Start(result.ToString());
}
}
}
catch (Exception x)
{
var panoramaEx = x.InnerException as PanoramaImportErrorException;
if (panoramaEx != null)
{
var message = Resources.WebPanoramaPublishClient_UploadSharedZipFile_An_error_occured_while_publishing_to_Panorama__would_you_like_to_go_to_Panorama_;
if (MultiButtonMsgDlg.Show(parent, message, MultiButtonMsgDlg.BUTTON_YES, MultiButtonMsgDlg.BUTTON_NO, false)
== DialogResult.Yes)
{
Process.Start(panoramaEx.JobUrl.ToString());
}
}
else
{
MessageDlg.ShowException(parent, x);
}
}
// Change PanoramaUrl setting to the successful url used
var uriString = server.GetKey() + folderPath;
uriString = Uri.EscapeUriString(uriString);
var window = parent as SkylineWindow;
if (window != null && Uri.IsWellFormedUriString(uriString, UriKind.Absolute)) // cant do Uri.isWellFormed because of port and ip
{
window.ChangeDocPanoramaUri(new Uri(uriString));
}
}
public bool SetCalibrationPeptides()
{
CheckDisposed();
var document = Program.ActiveDocumentUI;
if (!document.Settings.HasResults)
{
MessageDlg.Show(this, Resources.CalibrateIrtDlg_UseResults_The_document_must_contain_results_to_calibrate_a_standard);
return(false);
}
var targetResolver = TargetResolver.MakeTargetResolver(document);
_gridViewDriver.TargetResolver = targetResolver;
var docTargets = document.Molecules.Where(nodePep => nodePep.SchedulingTime.HasValue).Select(nodePep => nodePep.ModifiedTarget).Distinct().ToArray();
var count = docTargets.Length;
// If calibrating against another standard, exclude peptides in that standard
var excludePeps = SelectedRegressionOption?.MatchedRegressionPeptides?.Select(match => match.Item2.ModifiedTarget).ToHashSet();
var exclude = excludePeps != null && excludePeps.Count > 0;
if (exclude)
{
docTargets = docTargets.Where(target => !excludePeps.Contains(target)).ToArray();
count = docTargets.Length;
}
if (count < MIN_STANDARD_PEPTIDES)
{
MessageDlg.Show(this,
ModeUIAwareStringFormat(!exclude
? Resources.CalibrateIrtDlg_UseResults_The_document_contains_results_for__0__peptides__which_is_less_than_the_minimum_requirement_of__1__to_calibrate_a_standard_
: Resources.CalibrateIrtDlg_SetCalibrationPeptides_The_document_contains_results_for__0__peptide_s__not_in_this_standard__which_is_less_than_the_minimum_requirement_of__1__to_calibrate_a_standard_,
count, MIN_STANDARD_PEPTIDES));
return(false);
}
else if (count < MIN_SUGGESTED_STANDARD_PEPTIDES)
{
if (MultiButtonMsgDlg.Show(this,
ModeUIAwareStringFormat(!exclude
? Resources.CalibrateIrtDlg_UseResults_The_document_contains_results_for__0__peptides__but_using_fewer_than__1__standard_peptides_is_not_recommended__Are_you_sure_you_want_to_continue_
: Resources.CalibrateIrtDlg_UseResults_The_document_contains_results_for__0__peptides_not_in_this_standard__but_using_fewer_than__1__standard_peptides_is_not_recommended__Are_you_sure_you_want_to_continue_,
count, MIN_SUGGESTED_STANDARD_PEPTIDES),
MultiButtonMsgDlg.BUTTON_YES, MultiButtonMsgDlg.BUTTON_NO, false) != DialogResult.Yes)
{
return(false);
}
}
else if (count > 20)
{
using (var dlg = new AddIrtStandardsDlg(count, excludePeps != null && excludePeps.Count > 0))
{
if (dlg.ShowDialog(this) != DialogResult.OK)
{
return(false);
}
count = dlg.StandardCount;
}
}
_gridViewDriver.Recalculate(document, count, SelectedRegressionOption, excludePeps);
return(true);
}
public void OkDialog()
{
var reader = new StringReader(PeptidesText);
var invalidLines = new List <string>();
var notFoundLines = new List <string>();
var acceptedPeptides = new List <LibraryKey>();
var peptideSequences = GetPeptideSequences();
string line;
while ((line = reader.ReadLine()) != null)
{
line = line.Trim();
if (string.IsNullOrEmpty(line))
{
continue;
}
int foundAt;
var charge = Transition.GetChargeFromIndicator(line,
TransitionGroup.MIN_PRECURSOR_CHARGE, TransitionGroup.MAX_PRECURSOR_CHARGE, out foundAt);
if (!charge.IsEmpty)
{
line = line.Substring(0, foundAt);
}
Target target;
try
{
// CONSIDER(bspratt) small molecule equivalent?
if (!FastaSequence.IsExSequence(line))
{
invalidLines.Add(line);
continue;
}
line = SequenceMassCalc.NormalizeModifiedSequence(line);
target = new Target(line);
}
catch (Exception)
{
invalidLines.Add(line);
continue;
}
if (!peptideSequences.ContainsKey(target))
{
notFoundLines.Add(line);
}
else
{
acceptedPeptides.Add(new LibKey(target, charge).LibraryKey);
}
}
if (invalidLines.Count > 0)
{
if (invalidLines.Count == 1)
{
MessageDlg.Show(this, string.Format(Resources.RefineListDlg_OkDialog_The_sequence__0__is_not_a_valid_peptide, invalidLines[0]));
}
else
{
MessageDlg.Show(this, TextUtil.LineSeparate(Resources.RefineListDlg_OkDialog_The_following_sequences_are_not_valid_peptides, string.Empty, TextUtil.LineSeparate(invalidLines)));
}
return;
}
if (acceptedPeptides.Count == 0)
{
MessageDlg.Show(this, Resources.RefineListDlg_OkDialog_None_of_the_specified_peptides_are_in_the_document);
return;
}
if (notFoundLines.Count > 0)
{
string message;
if (notFoundLines.Count == 1)
{
message = string.Format(Resources.RefineListDlg_OkDialog_The_peptide__0__is_not_in_the_document_Do_you_want_to_continue, notFoundLines[0]);
}
else if (notFoundLines.Count < 15)
{
message = TextUtil.LineSeparate(Resources.RefineListDlg_OkDialog_The_following_peptides_are_not_in_the_document, string.Empty,
TextUtil.LineSeparate(notFoundLines), string.Empty,
Resources.RefineListDlg_OkDialog_Do_you_want_to_continue);
}
else
{
message = string.Format(Resources.RefineListDlg_OkDialog_Of_the_specified__0__peptides__1__are_not_in_the_document_Do_you_want_to_continue,
notFoundLines.Count + acceptedPeptides.Count, notFoundLines.Count);
}
if (MultiButtonMsgDlg.Show(this, message, MultiButtonMsgDlg.BUTTON_OK) != DialogResult.OK)
{
return;
}
}
AcceptedPeptides = acceptedPeptides.ToArray();
DialogResult = DialogResult.OK;
}
public void UseResults()
{
if (!_document.Settings.HasResults)
{
MessageDlg.Show(this, Resources.CalibrateIrtDlg_UseResults_The_document_must_contain_results_to_calibrate_a_standard);
return;
}
var count = _document.Molecules.Where(nodePep => nodePep.SchedulingTime.HasValue).Select(nodePep => nodePep.ModifiedTarget).Distinct().Count();
if (count < CalibrateIrtDlg.MIN_STANDARD_PEPTIDES)
{
MessageDlg.Show(this,
string.Format(
Resources.CalibrateIrtDlg_UseResults_The_document_contains_results_for__0__peptides__which_is_less_than_the_minimum_requirement_of__1__to_calibrate_a_standard_,
count, CalibrateIrtDlg.MIN_STANDARD_PEPTIDES));
return;
}
else if (count < CalibrateIrtDlg.MIN_SUGGESTED_STANDARD_PEPTIDES)
{
if (MultiButtonMsgDlg.Show(this,
string.Format(
Resources.CalibrateIrtDlg_UseResults_The_document_contains_results_for__0__peptides__but_using_fewer_than__1__standard_peptides_is_not_recommended__Are_you_sure_you_want_to_continue_,
count, CalibrateIrtDlg.MIN_SUGGESTED_STANDARD_PEPTIDES),
MultiButtonMsgDlg.BUTTON_YES, MultiButtonMsgDlg.BUTTON_NO, false) != DialogResult.Yes)
{
return;
}
}
else if (count > 20)
{
using (var dlg = new AddIrtStandardsDlg(count, false))
{
if (dlg.ShowDialog(this) != DialogResult.OK)
{
return;
}
count = dlg.StandardCount;
}
}
if (!_picker.HasScoredPeptides)
{
using (var longWaitDlg = new LongWaitDlg {
Text = Resources.CalibrationGridViewDriver_FindEvenlySpacedPeptides_Calculating_scores
})
{
longWaitDlg.PerformWork(this, 1000, pm => _picker.ScorePeptides(_document, pm));
if (longWaitDlg.IsCanceled)
{
return;
}
}
}
var useCirt = false;
if (_picker.TryGetCirtRegression(count, out _, out _))
{
switch (MultiButtonMsgDlg.Show(this, string.Format(
Resources.CalibrationGridViewDriver_FindEvenlySpacedPeptides_This_document_contains__0__CiRT_peptides__Would_you_like_to_use__1__of_them_as_your_iRT_standards_,
_picker.CirtPeptideCount, count), MultiButtonMsgDlg.BUTTON_YES, MultiButtonMsgDlg.BUTTON_NO, true))
{
case DialogResult.Yes:
useCirt = true;
break;
case DialogResult.No:
break;
case DialogResult.Cancel:
return;
}
}
comboProteins.SelectedIndex = 0;
PeptideLines = _picker.Pick(count, null, useCirt).Select(pep => pep.Target.ToString()).ToArray();
}
public static bool?OverwriteOrInParallel(Control parent,
string toolCollectionName,
string toolCollectionVersion,
List <ReportOrViewSpec> reportList,
string foundVersion,
string newCollectionName)
{
string message;
string buttonText;
if (toolCollectionName != null)
{
RelativeVersion relativeVersion = DetermineRelativeVersion(toolCollectionVersion, foundVersion);
string toolMessage;
switch (relativeVersion)
{
case RelativeVersion.upgrade:
toolMessage = TextUtil.LineSeparate(Resources.ConfigureToolsDlg_OverwriteOrInParallel_The_tool__0__is_currently_installed_, String.Empty,
String.Format(Resources.ConfigureToolsDlg_OverwriteOrInParallel_Do_you_wish_to_upgrade_to__0__or_install_in_parallel_, foundVersion));
buttonText = Resources.ConfigureToolsDlg_OverwriteOrInParallel_Upgrade;
break;
case RelativeVersion.olderversion:
toolMessage =
TextUtil.LineSeparate(
String.Format(Resources.ConfigureToolsDlg_OverwriteOrInParallel_This_is_an_older_installation_v_0__of_the_tool__1_, foundVersion, @"{0}"),
String.Empty,
String.Format(Resources.ConfigureToolsDlg_OverwriteOrInParallel_Do_you_wish_to_overwrite_with_the_older_version__0__or_install_in_parallel_,
foundVersion));
buttonText = Resources.ConfigureToolsDlg_OverwriteOrInParallel_Overwrite;
break;
case RelativeVersion.reinstall:
toolMessage = TextUtil.LineSeparate(Resources.ConfigureToolsDlg_OverwriteOrInParallel_The_tool__0__is_already_installed_,
String.Empty,
Resources.ConfigureToolsDlg_OverwriteOrInParallel_Do_you_wish_to_reinstall_or_install_in_parallel_);
buttonText = Resources.ConfigureToolsDlg_OverwriteOrInParallel_Reinstall;
break;
default:
toolMessage =
TextUtil.LineSeparate(
Resources.ConfigureToolsDlg_OverwriteOrInParallel_The_tool__0__is_in_conflict_with_the_new_installation,
String.Empty,
Resources.ConfigureToolsDlg_OverwriteOrInParallel_Do_you_wish_to_overwrite_or_install_in_parallel_);
buttonText = Resources.ConfigureToolsDlg_OverwriteOrInParallel_Overwrite; // Or update?
break;
}
message = String.Format(toolMessage, toolCollectionName);
}
else //Warn about overwritng report.
{
List <string> reportTitles = reportList.Select(sp => sp.GetKey()).ToList();
string reportMultiMessage = TextUtil.LineSeparate(Resources.ConfigureToolsDlg_OverwriteOrInParallel_This_installation_would_modify_the_following_reports, String.Empty,
@"{0}", String.Empty);
string reportSingleMessage = TextUtil.LineSeparate(Resources.ConfigureToolsDlg_OverwriteOrInParallel_This_installation_would_modify_the_report_titled__0_, String.Empty);
string reportMessage = reportList.Count == 1 ? reportSingleMessage : reportMultiMessage;
string question = Resources.ConfigureToolsDlg_OverwriteOrInParallel_Do_you_wish_to_overwrite_or_install_in_parallel_;
buttonText = Resources.ConfigureToolsDlg_OverwriteOrInParallel_Overwrite;
string reportMessageFormat = TextUtil.LineSeparate(reportMessage, question);
message = String.Format(reportMessageFormat, TextUtil.LineSeparate(reportTitles));
}
DialogResult result = MultiButtonMsgDlg.Show(
parent, message, buttonText, Resources.ConfigureToolsDlg_OverwriteOrInParallel_In_Parallel, true);
switch (result)
{
case DialogResult.Cancel:
return(null);
case DialogResult.Yes:
return(true);
case DialogResult.No:
return(false);
}
return(false);
}
public void OkDialog()
{
bool isModel = radioButtonModel.Checked;
if (isModel)
{
var model = _driverPeakScoringModel.SelectedItem;
if (model == null)
{
MessageDlg.Show(this, Resources.PeakBoundaryCompareTest_DoTest_Must_select_a_model_for_comparison_);
return;
}
if (!model.IsTrained)
{
MessageDlg.Show(this, Resources.AddPeakCompareDlg_OkDialog_Model_must_be_trained_before_it_can_be_used_for_peak_boundary_comparison_);
return;
}
BoundaryComparer = new ComparePeakBoundaries(model);
}
else
{
string displayName = textName.Text;
if (displayName.Length == 0)
{
MessageDlg.Show(this, Resources.AddPeakCompareDlg_OkDialog_Comparison_name_cannot_be_empty_);
return;
}
string filePath = textFilePath.Text;
if (filePath.Length == 0)
{
MessageDlg.Show(this, Resources.AddPeakCompareDlg_OkDialog_File_path_cannot_be_empty_);
return;
}
if (!File.Exists(filePath))
{
MessageDlg.Show(this, Resources.AddPeakCompareDlg_OkDialog_File_path_field_must_contain_a_path_to_a_valid_file_);
return;
}
BoundaryComparer = new ComparePeakBoundaries(displayName, filePath);
}
var compNames = _existing.Select(comp => comp.Name);
if (compNames.Contains(BoundaryComparer.Name) && (_current == null || _current.Name != BoundaryComparer.Name))
{
var message = isModel
? Resources.AddPeakCompareDlg_OkDialog_The_selected_model_is_already_included_in_the_list_of_comparisons__Please_choose_another_model_
: Resources.AddPeakCompareDlg_OkDialog_There_is_already_an_imported_file_with_the_current_name___Please_choose_another_name;
MessageDlg.Show(this, message);
return;
}
using (var longWaitDlg = new LongWaitDlg
{
Text = isModel ? Resources.AddPeakCompareDlg_OkDialog_Comparing_Models : Resources.AddPeakCompareDlg_OkDialog_Comparing_Imported_Files
})
{
try
{
longWaitDlg.PerformWork(this, 1000, pm => BoundaryComparer.GenerateComparison(Document, pm));
if (BoundaryComparer.Matches.Count == 0)
{
throw new IOException(Resources.AddPeakCompareDlg_OkDialog_Document_has_no_eligible_chromatograms_for_analysis___Valid_chromatograms_must_not_be_decoys_or_iRT_standards_);
}
if (BoundaryComparer.Matches.All(match => match.IsMissingPickedPeak))
{
throw new IOException(Resources.AddPeakCompareDlg_OkDialog_The_selected_file_or_model_does_not_assign_peak_boundaries_to_any_chromatograms_in_the_document___Please_select_a_different_model_or_file_);
}
if (BoundaryComparer.HasNoQValues && BoundaryComparer.HasNoScores)
{
throw new IOException(Resources.AddPeakCompareDlg_OkDialog_The_current_file_or_model_has_no_q_values_or_scores_to_analyze___Either_q_values_or_scores_are_necessary_to_compare_peak_picking_tools_);
}
if (BoundaryComparer.CountMissing > 0)
{
var missingMessage = string.Format(Resources.AddPeakCompareDlg_OkDialog_The_imported_file_does_not_contain_any_peak_boundaries_for__0__transition_group___file_pairs___These_chromatograms_will_be_treated_as_if_no_boundary_was_selected_,
BoundaryComparer.CountMissing);
var dlgMissing = MultiButtonMsgDlg.Show(this, missingMessage, MultiButtonMsgDlg.BUTTON_OK);
if (dlgMissing == DialogResult.Cancel)
{
return;
}
}
// Show a warning message and give a chance to cancel, if there are unrecognized peptides
if (BoundaryComparer.Importer != null && !BoundaryComparer.Importer.UnrecognizedPeptidesCancel(this))
{
return;
}
}
catch (Exception x)
{
string initMessage = isModel
? Resources.AddPeakCompareDlg_OkDialog_Error_comparing_model_peak_boundaries___0_
: Resources.AddPeakCompareDlg_OkDialog_Error_applying_imported_peak_boundaries___0_;
MessageDlg.ShowWithException(this, string.Format(initMessage, x.Message), x);
return;
}
}
DialogResult = DialogResult.OK;
}
private List <MeasuredPeptide> PickPeptides(SrmDocument doc, int count, ICollection <Target> exclude, RegressionOption currentRegression, out RegressionOption cirt)
{
cirt = null;
if (!_picker.HasScoredPeptides)
{
using (var longWaitDlg = new LongWaitDlg {
Text = Resources.CalibrationGridViewDriver_FindEvenlySpacedPeptides_Calculating_scores
})
{
longWaitDlg.PerformWork(_parent, 1000, pm => _picker.ScorePeptides(doc, pm));
if (longWaitDlg.IsCanceled)
{
return(null);
}
}
}
RegressionLine cirtRegression = null;
var useCirt = false;
var cirtUsePredefined = false;
if (_picker.TryGetCirtRegression(count, out var tryCirtRegression, out var matchedPeptides))
{
var currentIsCirt = currentRegression != null && currentRegression.IsCirtDiscovered;
switch (MultiButtonMsgDlg.Show(_parent, string.Format(
Resources.CalibrationGridViewDriver_FindEvenlySpacedPeptides_This_document_contains__0__CiRT_peptides__Would_you_like_to_use__1__of_them_as_your_iRT_standards_,
_picker.CirtPeptideCount, count), MultiButtonMsgDlg.BUTTON_YES, MultiButtonMsgDlg.BUTTON_NO, true))
{
case DialogResult.Yes:
cirtRegression = tryCirtRegression;
useCirt = true;
if (currentRegression?.RegressionLine == null || currentIsCirt)
{
switch (MultiButtonMsgDlg.Show(_parent,
Resources.CalibrationGridViewDriver_FindEvenlySpacedPeptides_Would_you_like_to_use_the_predefined_iRT_values_,
Resources.CalibrationGridViewDriver_FindEvenlySpacedPeptides_Predefined_values,
Resources.CalibrationGridViewDriver_FindEvenlySpacedPeptides_Calculate_from_regression,
true))
{
case DialogResult.Yes:
cirtUsePredefined = true;
break;
case DialogResult.No:
break;
case DialogResult.Cancel:
return(null);
}
}
break;
case DialogResult.No:
if (currentIsCirt)
{
cirtRegression = tryCirtRegression;
}
break;
case DialogResult.Cancel:
return(null);
}
}
var bestPeptides = _picker.Pick(count, exclude, useCirt);
if (cirtRegression != null)
{
var standardPeptides = bestPeptides.Select(pep => new StandardPeptide
{
Irt = cirtUsePredefined ? _picker.CirtIrt(pep.Target).Value : double.NaN,
RetentionTime = pep.RetentionTime,
Target = pep.Target
}).ToList();
cirt = new RegressionOption(Resources.CalibrationGridViewDriver_CiRT_option_name, cirtRegression,
matchedPeptides.ToList(), standardPeptides, false, false);
}
return(bestPeptides);
}
private void populateListViewFromDirectory(MsDataFileUri directory)
{
_abortPopulateList = false;
listView.Cursor = Cursors.Default;
_waitingForData = false;
listView.Items.Clear();
var listSourceInfo = new List <SourceInfo>();
if (null == directory || directory is MsDataFilePath && string.IsNullOrEmpty(((MsDataFilePath)directory).FilePath))
{
foreach (DriveInfo driveInfo in DriveInfo.GetDrives())
{
string label = string.Empty;
string sublabel = driveInfo.Name;
ImageIndex imageIndex = ImageIndex.Folder;
_driveReadiness[sublabel] = false;
try
{
switch (driveInfo.DriveType)
{
case DriveType.Fixed:
imageIndex = ImageIndex.LocalDrive;
label = Resources.OpenDataSourceDialog_populateListViewFromDirectory_Local_Drive;
if (driveInfo.VolumeLabel.Length > 0)
{
label = driveInfo.VolumeLabel;
}
break;
case DriveType.CDRom:
imageIndex = ImageIndex.OpticalDrive;
label = Resources.OpenDataSourceDialog_populateListViewFromDirectory_Optical_Drive;
if (driveInfo.IsReady && driveInfo.VolumeLabel.Length > 0)
{
label = driveInfo.VolumeLabel;
}
break;
case DriveType.Removable:
imageIndex = ImageIndex.OpticalDrive;
label = Resources.OpenDataSourceDialog_populateListViewFromDirectory_Removable_Drive;
if (driveInfo.IsReady && driveInfo.VolumeLabel.Length > 0)
{
label = driveInfo.VolumeLabel;
}
break;
case DriveType.Network:
label = Resources.OpenDataSourceDialog_populateListViewFromDirectory_Network_Share;
break;
}
_driveReadiness[sublabel] = IsDriveReady(driveInfo);
}
catch (Exception)
{
label += string.Format(@" ({0})", Resources.OpenDataSourceDialog_populateListViewFromDirectory_access_failure);
}
string name = driveInfo.Name;
if (label != string.Empty)
{
name = string.Format(@"{0} ({1})", label, name);
}
listSourceInfo.Add(new SourceInfo(new MsDataFilePath(driveInfo.RootDirectory.FullName))
{
type = DataSourceUtil.FOLDER_TYPE,
imageIndex = imageIndex,
name = name,
dateModified = GetDriveModifiedTime(driveInfo)
});
}
}
else if (directory is RemoteUrl)
{
RemoteUrl remoteUrl = directory as RemoteUrl;
if (string.IsNullOrEmpty(remoteUrl.ServerUrl))
{
foreach (var remoteAccount in _remoteAccounts)
{
listSourceInfo.Add(new SourceInfo(remoteAccount.GetRootUrl())
{
name = remoteAccount.GetKey(),
type = DataSourceUtil.FOLDER_TYPE,
imageIndex = ImageIndex.MyNetworkPlaces,
});
}
}
else
{
RemoteAccount remoteAccount = GetRemoteAccount(remoteUrl);
if (RemoteSession == null || !Equals(remoteAccount, RemoteSession.Account))
{
RemoteSession = RemoteSession.CreateSession(remoteAccount);
}
RemoteServerException exception;
bool isComplete = _remoteSession.AsyncFetchContents(remoteUrl, out exception);
foreach (var item in _remoteSession.ListContents(remoteUrl))
{
var imageIndex = DataSourceUtil.IsFolderType(item.Type)
? ImageIndex.Folder
: ImageIndex.MassSpecFile;
listSourceInfo.Add(new SourceInfo(item.MsDataFileUri)
{
name = item.Label,
type = item.Type,
imageIndex = imageIndex,
dateModified = item.LastModified,
size = item.FileSize
});
}
if (null != exception)
{
if (MultiButtonMsgDlg.Show(this, exception.Message, Resources.OpenDataSourceDialog_populateListViewFromDirectory_Retry) != DialogResult.Cancel)
{
RemoteSession.RetryFetchContents(remoteUrl);
isComplete = false;
}
}
if (!isComplete)
{
listView.Cursor = Cursors.WaitCursor;
_waitingForData = true;
}
}
}
else if (directory is MsDataFilePath)
{
MsDataFilePath msDataFilePath = (MsDataFilePath)directory;
DirectoryInfo dirInfo = new DirectoryInfo(msDataFilePath.FilePath);
try
{
// subitems: Name, Type, Spectra, Size, Date Modified
var arraySubDirInfo = dirInfo.GetDirectories();
Array.Sort(arraySubDirInfo, (d1, d2) => string.Compare(d1.Name, d2.Name, StringComparison.CurrentCultureIgnoreCase));
var arrayFileInfo = dirInfo.GetFiles();
Array.Sort(arrayFileInfo, (f1, f2) => string.Compare(f1.Name, f2.Name, StringComparison.CurrentCultureIgnoreCase));
// Calculate information about the files, allowing the user to cancel
foreach (var info in arraySubDirInfo)
{
listSourceInfo.Add(getSourceInfo(info));
Application.DoEvents();
if (_abortPopulateList)
{
//MessageBox.Show( "abort" );
break;
}
}
if (!_abortPopulateList)
{
foreach (var info in arrayFileInfo)
{
listSourceInfo.Add(getSourceInfo(info));
Application.DoEvents();
if (_abortPopulateList)
{
//MessageBox.Show( "abort" );
break;
}
}
}
}
catch (Exception x)
{
var message = TextUtil.LineSeparate(
Resources.OpenDataSourceDialog_populateListViewFromDirectory_An_error_occurred_attempting_to_retrieve_the_contents_of_this_directory,
x.Message);
// Might throw access violation.
MessageDlg.ShowWithException(this, message, x);
return;
}
}
// Populate the list
var items = new List <ListViewItem>();
foreach (var sourceInfo in listSourceInfo)
{
if (sourceInfo != null &&
(sourceTypeComboBox.SelectedIndex == 0 ||
sourceTypeComboBox.SelectedItem.ToString() == sourceInfo.type ||
// Always show folders
sourceInfo.isFolder))
{
ListViewItem item = new ListViewItem(sourceInfo.ToArray(), (int)sourceInfo.imageIndex)
{
Tag = sourceInfo,
};
item.SubItems[2].Tag = sourceInfo.size;
item.SubItems[3].Tag = sourceInfo.dateModified;
items.Add(item);
}
}
listView.Items.AddRange(items.ToArray());
}
private bool CheckPassToolInternal(int toolIndex)
{
ToolDescription tool;
if (toolIndex < ToolList.Count && toolIndex >= 0)
{
tool = ToolList[toolIndex];
}
else
{
return(true);
}
if (tool.Title == string.Empty)
{
MessageDlg.Show(this, Resources.ConfigureToolsDlg_CheckPassTool_You_must_enter_a_valid_title_for_the_tool);
textTitle.Focus();
return(false);
}
//Ensure the tool Title is unique.
if (!IsUniqueTitle(tool.Title))
{
MessageDlg.Show(this, Resources.ConfigureToolsDlg_CheckPassToolInternal_Tool_titles_must_be_unique__please_enter_a_unique_title_for_this_tool_);
textTitle.Focus();
return(false);
}
if (tool.Command == string.Empty)
{
MessageDlg.Show(this, string.Format(Resources.ConfigureToolsDlg_CheckPassTool_The_command_cannot_be_blank__please_enter_a_valid_command_for__0_, tool.Title));
textCommand.Focus();
return(false);
}
if (tool.IsWebPage)
{
try
{
// ReSharper disable ObjectCreationAsStatement
new Uri(tool.Command);
// ReSharper restore ObjectCreationAsStatement
}
catch (Exception)
{
MessageDlg.Show(this, Resources.ConfigureToolsDlg_CheckPassToolInternal_Please_specify_a_valid_URL_);
textCommand.Focus();
return(false);
}
return(true);
}
//If it is not a $(ProgramPath()) macro then do other checks.
if (ToolMacros.GetProgramPathContainer(tool.Command) == null)
{
string supportedTypes = String.Join("; ", EXTENSIONS); // Not L10N
supportedTypes = supportedTypes.Replace(".", "*."); // Not L10N
if (!CheckExtension(tool.Command))
{
MessageDlg.Show(this, string.Format(TextUtil.LineSeparate(
Resources.ConfigureToolsDlg_CheckPassTool_The_command_for__0__must_be_of_a_supported_type,
Resources.ConfigureToolsDlg_CheckPassTool_Supported_Types___1_,
Resources.ConfigureToolsDlg_CheckPassTool_if_you_would_like_the_command_to_launch_a_link__make_sure_to_include_http____or_https___),
tool.Title, supportedTypes));
textCommand.Focus();
return(false);
}
string adjustedCommand = tool.Command;
if (adjustedCommand.Contains(ToolMacros.TOOL_DIR))
{
if (String.IsNullOrEmpty(tool.ToolDirPath))
{
MessageDlg.Show(this,
Resources.ConfigureToolsDlg_CheckPassToolInternal__ToolDir__is_not_a_valid_macro_for_a_tool_that_was_not_installed_and_therefore_does_not_have_a_Tool_Directory_);
textCommand.Focus();
return(false);
}
else
{
adjustedCommand = adjustedCommand.Replace(ToolMacros.TOOL_DIR, tool.ToolDirPath);
}
}
if (!File.Exists(adjustedCommand))
{
if (DialogResult.Yes == MultiButtonMsgDlg.Show(
this,
string.Format(TextUtil.LineSeparate(
Resources.ConfigureToolsDlg_CheckPassTool__The_command_for__0__may_not_exist_in_that_location__Would_you_like_to_edit_it__,
Resources.ConfigureToolsDlg_CheckPassTool__Note__if_you_would_like_the_command_to_launch_a_link__make_sure_to_include_http____or_https___),
tool.Title),
MultiButtonMsgDlg.BUTTON_YES, MultiButtonMsgDlg.BUTTON_NO, false))
{
textCommand.Focus();
return(false);
}
}
}
if (tool.Arguments.Contains(ToolMacros.INPUT_REPORT_TEMP_PATH) && string.IsNullOrEmpty(tool.ReportTitle))
{
MessageDlg.Show(this, TextUtil.LineSeparate(
string.Format(Resources.ConfigureToolsDlg_CheckPassToolInternal_You_have_provided__0__as_an_argument_but_have_not_selected_a_report_, ToolMacros.INPUT_REPORT_TEMP_PATH),
string.Format(Resources.ConfigureToolsDlg_CheckPassToolInternal_Please_select_a_report_or_remove__0__from_arguments_, ToolMacros.INPUT_REPORT_TEMP_PATH)));
comboReport.Focus();
return(false);
}
return(true);
}
