public void SettingsChangeTranGroups()
{
SrmDocument docFasta = CreateMixedDoc();
SrmSettings settings = docFasta.Settings;
// Add heavy mod
SrmDocument docFasta2 = docFasta.ChangeSettings(settings.ChangePeptideModifications(
m => m.ChangeModifications(IsotopeLabelType.heavy, new[] { new StaticMod("N-Terminal K", "K", ModTerminus.C, "H7", LabelAtoms.None, null, null) })));
CheckNTerminalKGroups(docFasta2);
Assert.AreEqual(docFasta.PeptideCount, docFasta2.PeptideCount);
// Add multiple charges with heavy mod
var newCharges = Adduct.ProtonatedFromCharges(2, 3, 4);
settings = docFasta2.Settings;
SrmDocument docFasta3 = docFasta2.ChangeSettings(settings.ChangeTransitionFilter(
f => f.ChangePeptidePrecursorCharges(newCharges)));
CheckNTerminalKGroups(docFasta3);
Assert.AreEqual(docFasta.PeptideCount, docFasta3.PeptideCount);
// Use charge that will cause filtering on instrument maximum m/z
docFasta2 = docFasta.ChangeSettings(settings.ChangeTransitionFilter(
f => f.ChangePeptidePrecursorCharges(Adduct.ProtonatedFromCharges(1))));
Assert.IsTrue(docFasta.PeptideTransitionGroupCount < docFasta2.PeptideTransitionGroupCount);
Assert.AreEqual(docFasta.PeptideCount, docFasta2.PeptideCount);
}
private static SrmDocument InitWiffDocument(TestFilesDir testFilesDir)
{
const LabelAtoms labelAtoms = LabelAtoms.C13 | LabelAtoms.N15;
List <StaticMod> heavyMods = new List <StaticMod>
{
new StaticMod("Heavy K", "K", ModTerminus.C, null, labelAtoms, null, null),
new StaticMod("Heavy R", "R", ModTerminus.C, null, labelAtoms, null, null),
};
SrmSettings settings = SrmSettingsList.GetDefault();
settings = settings.ChangePeptideModifications(mods => mods.ChangeHeavyModifications(heavyMods));
SrmDocument doc = new SrmDocument(settings);
IdentityPath selectPath;
string path = testFilesDir.GetTestPath("051309_transition list.csv");
// Product m/z out of range
var docError = doc;
List <MeasuredRetentionTime> irtPeptides;
List <SpectrumMzInfo> librarySpectra;
List <TransitionImportErrorInfo> errorList;
var inputs = new MassListInputs(path)
{
FormatProvider = CultureInfo.InvariantCulture,
Separator = TextUtil.SEPARATOR_CSV
};
docError.ImportMassList(inputs, null, out selectPath, out irtPeptides, out librarySpectra, out errorList);
Assert.AreEqual(errorList.Count, 1);
AssertEx.AreComparableStrings(TextUtil.SpaceSeparate(Resources.MassListRowReader_CalcTransitionExplanations_The_product_m_z__0__is_out_of_range_for_the_instrument_settings__in_the_peptide_sequence__1_,
Resources.MassListRowReader_CalcPrecursorExplanations_Check_the_Instrument_tab_in_the_Transition_Settings),
errorList[0].ErrorMessage,
2);
Assert.AreEqual(errorList[0].Column, 1);
Assert.AreEqual(errorList[0].Row, 19);
doc = doc.ChangeSettings(settings.ChangeTransitionInstrument(inst => inst.ChangeMaxMz(1800)));
inputs = new MassListInputs(path)
{
FormatProvider = CultureInfo.InvariantCulture,
Separator = TextUtil.SEPARATOR_CSV
};
doc = doc.ImportMassList(inputs, null, out selectPath);
AssertEx.IsDocumentState(doc, 2, 9, 9, 18, 54);
return(doc);
}
public PeptideDocNode GetModifiedNode(LibKey key, string seqUnmod, SrmSettings settings, SrmSettingsDiff diff)
{
if (string.IsNullOrEmpty(seqUnmod))
{
return(null);
}
var peptide = new Peptide(null, seqUnmod, null, null,
settings.PeptideSettings.Enzyme.CountCleavagePoints(seqUnmod));
// First try and create the match from the settings created to match the library explorer.
Settings = HasMatches
? settings.ChangePeptideModifications(mods => MatcherPepMods)
: settings;
TransitionGroupDocNode nodeGroup;
var nodePep = CreateDocNodeFromSettings(key.Sequence, peptide, diff, out nodeGroup);
if (nodePep != null)
{
if (diff == null)
{
nodePep = (PeptideDocNode)nodePep.ChangeAutoManageChildren(false);
}
else
{
// Keep only the matching transition group, so that modifications
// will be highlighted differently for light and heavy forms.
// Only performed when getting peptides for display in the explorer.
nodePep = (PeptideDocNode)nodePep.ChangeChildrenChecked(
new DocNode[] { nodeGroup });
}
return(nodePep);
}
else if (Matches == null)
{
return(null);
}
bool hasHeavy;
// Create explicit mods from the found matches.
nodePep = CreateDocNodeFromMatches(new PeptideDocNode(peptide),
EnumerateSequenceInfos(key.Key, true), false, out hasHeavy);
if (nodePep == null)
{
return(null);
}
// Call change settings with the matched modification settings to enumerate the children.
nodePep = nodePep.ChangeSettings(settings.ChangePeptideModifications(mods =>
!HasMatches ? settings.PeptideSettings.Modifications : MatcherPepMods), diff ?? SrmSettingsDiff.ALL);
if (nodePep.Children.Count == 0)
{
return(null);
}
// Select the correct child, only for use with the library explorer.
if (diff != null && nodePep.Children.Count > 1)
{
nodePep =
(PeptideDocNode)
nodePep.ChangeChildrenChecked(new List <DocNode> {
nodePep.Children[hasHeavy ? 1 : 0]
});
}
if (diff == null)
{
nodePep = (PeptideDocNode)nodePep.ChangeAutoManageChildren(false);
}
return(nodePep);
}
public ToolOptionsUI(SrmSettings settings)
{
InitializeComponent();
checkBoxShowWizard.Checked = Settings.Default.ShowStartupForm;
powerOfTenCheckBox.Checked = Settings.Default.UsePowerOfTen;
Icon = Resources.Skyline;
_driverServers = new SettingsListBoxDriver <Server>(listboxServers, Settings.Default.ServerList);
_driverServers.LoadList();
_driverRemoteAccounts = new SettingsListBoxDriver <RemoteAccount>(listBoxRemoteAccounts, Settings.Default.RemoteAccountList);
_driverRemoteAccounts.LoadList();
_driverColorSchemes = new SettingsListComboDriver <ColorScheme>(comboColorScheme, Settings.Default.ColorSchemes, true);
_driverColorSchemes.LoadList(Settings.Default.CurrentColorScheme);
var pingPep = new Peptide(@"PING");
var peptide = new PeptideDocNode(pingPep);
var precursor = new TransitionGroupDocNode(new TransitionGroup(pingPep, Adduct.SINGLY_PROTONATED, IsotopeLabelType.light),
new TransitionDocNode[0]);
_pingInput = new PrositIntensityModel.PeptidePrecursorNCE(peptide, precursor, IsotopeLabelType.light, 32);
_settingsNoMod = settings.ChangePeptideModifications(
pm => new PeptideModifications(new StaticMod[0], new TypedModifications[0]));
// Hide ability to turn off live reports
//tabControl.TabPages.Remove(tabMisc);
// Populate the languages list with the languages that Skyline has been localized to
string defaultDisplayName = string.Format(Resources.ToolOptionsUI_ToolOptionsUI_Default___0__,
CultureUtil.GetDisplayLanguage(CultureInfo.InstalledUICulture).DisplayName);
listBoxLanguages.Items.Add(new DisplayLanguageItem(string.Empty, defaultDisplayName));
foreach (var culture in CultureUtil.AvailableDisplayLanguages())
{
listBoxLanguages.Items.Add(new DisplayLanguageItem(culture.Name, culture.DisplayName));
}
for (int i = 0; i < listBoxLanguages.Items.Count; i++)
{
var displayLanguageItem = (DisplayLanguageItem)listBoxLanguages.Items[i];
if (Equals(displayLanguageItem.Key, Settings.Default.DisplayLanguage))
{
listBoxLanguages.SelectedIndex = i;
}
}
comboCompactFormatOption.Items.AddRange(CompactFormatOption.ALL_VALUES.ToArray());
comboCompactFormatOption.SelectedItem = CompactFormatOption.FromSettings();
var iModels = PrositIntensityModel.Models.ToList();
iModels.Insert(0, string.Empty);
var rtModels = PrositRetentionTimeModel.Models.ToList();
rtModels.Insert(0, string.Empty);
tbxPrositServer.Text = PrositConfig.GetPrositConfig().Server;
intensityModelCombo.Items.AddRange(iModels.ToArray());
iRTModelCombo.Items.AddRange(rtModels.ToArray());
prositServerStatusLabel.Text = string.Empty;
if (iModels.Contains(Settings.Default.PrositIntensityModel))
{
intensityModelCombo.SelectedItem = Settings.Default.PrositIntensityModel;
}
if (rtModels.Contains(Settings.Default.PrositRetentionTimeModel))
{
iRTModelCombo.SelectedItem = Settings.Default.PrositRetentionTimeModel;
}
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;
}