private PeptideSettings ValidateNewSettings(bool showMessages)
{
var helper = new MessageBoxHelper(this, showMessages);
// Validate and hold digestion settings
Enzyme enzyme = Settings.Default.GetEnzymeByName(comboEnzyme.SelectedItem.ToString());
Helpers.AssignIfEquals(ref enzyme, _peptideSettings.Enzyme);
int maxMissedCleavages =
int.Parse(comboMissedCleavages.SelectedItem.ToString());
bool excludeRaggedEnds = cbRaggedEnds.Checked;
DigestSettings digest = new DigestSettings(maxMissedCleavages, excludeRaggedEnds);
Helpers.AssignIfEquals(ref digest, Digest);
var backgroundProteomeSpec = _driverBackgroundProteome.SelectedItem;
BackgroundProteome backgroundProteome = BackgroundProteome.NONE;
if (!backgroundProteomeSpec.IsNone)
{
backgroundProteome = new BackgroundProteome(backgroundProteomeSpec, true);
if (backgroundProteome.DatabaseInvalid)
{
var message = TextUtil.LineSeparate(string.Format(Resources.PeptideSettingsUI_ValidateNewSettings_Failed_to_load_background_proteome__0__,
backgroundProteomeSpec.Name),
string.Format(Resources.PeptideSettingsUI_ValidateNewSettings_The_file__0__may_not_be_a_valid_proteome_file,
backgroundProteomeSpec.DatabasePath));
MessageDlg.Show(this, message);
tabControl1.SelectedIndex = 0;
_driverBackgroundProteome.Combo.Focus();
return null;
}
}
Helpers.AssignIfEquals(ref backgroundProteome, _peptideSettings.BackgroundProteome);
// Validate and hold prediction settings
string nameRT = comboRetentionTime.SelectedItem.ToString();
RetentionTimeRegression retentionTime =
Settings.Default.GetRetentionTimeByName(nameRT);
if (retentionTime != null && retentionTime.Calculator != null)
{
RetentionScoreCalculatorSpec retentionCalc =
Settings.Default.GetCalculatorByName(retentionTime.Calculator.Name);
// Just in case the calculator in use in the current documet got removed,
// never set the calculator to null. Just keep using the one we have.
if (retentionCalc != null && !ReferenceEquals(retentionCalc, retentionTime.Calculator))
retentionTime = retentionTime.ChangeCalculator(retentionCalc);
}
bool useMeasuredRT = cbUseMeasuredRT.Checked;
double? measuredRTWindow = null;
if (!string.IsNullOrEmpty(textMeasureRTWindow.Text))
{
double measuredRTWindowOut;
const double minWindow = PeptidePrediction.MIN_MEASURED_RT_WINDOW;
const double maxWindow = PeptidePrediction.MAX_MEASURED_RT_WINDOW;
if (!helper.ValidateDecimalTextBox(tabControl1, (int) TABS.Prediction,
textMeasureRTWindow, minWindow, maxWindow, out measuredRTWindowOut))
return null;
measuredRTWindow = measuredRTWindowOut;
}
string nameDt = comboDriftTimePredictor.SelectedItem.ToString();
DriftTimePredictor driftTimePredictor =
Settings.Default.GetDriftTimePredictorByName(nameDt);
if (driftTimePredictor != null && driftTimePredictor.IonMobilityLibrary != null)
{
IonMobilityLibrarySpec ionMobilityLibrary =
Settings.Default.GetIonMobilityLibraryByName(driftTimePredictor.IonMobilityLibrary.Name);
// Just in case the library in use in the current documet got removed,
// never set the library to null. Just keep using the one we have.
if (ionMobilityLibrary != null && !ReferenceEquals(ionMobilityLibrary, driftTimePredictor.IonMobilityLibrary))
driftTimePredictor = driftTimePredictor.ChangeLibrary(ionMobilityLibrary);
}
bool useLibraryDriftTime = cbUseSpectralLibraryDriftTimes.Checked;
double? libraryDTResolvingPower = null;
if (useLibraryDriftTime || !string.IsNullOrEmpty(textSpectralLibraryDriftTimesResolvingPower.Text))
{
double libraryDTWindowOut;
if (!helper.ValidateDecimalTextBox(tabControl1, (int)TABS.Prediction,
textSpectralLibraryDriftTimesResolvingPower, null, null, out libraryDTWindowOut))
return null;
string errmsg = EditDriftTimePredictorDlg.ValidateResolvingPower(libraryDTWindowOut);
if (errmsg != null)
{
helper.ShowTextBoxError(tabControl1, (int)TABS.Prediction, textSpectralLibraryDriftTimesResolvingPower, errmsg);
return null;
}
libraryDTResolvingPower = libraryDTWindowOut;
}
var prediction = new PeptidePrediction(retentionTime, driftTimePredictor, useMeasuredRT, measuredRTWindow, useLibraryDriftTime, libraryDTResolvingPower);
Helpers.AssignIfEquals(ref prediction, Prediction);
// Validate and hold filter settings
int excludeNTermAAs;
if (!helper.ValidateNumberTextBox(tabControl1, (int) TABS.Filter, textExcludeAAs,
PeptideFilter.MIN_EXCLUDE_NTERM_AA, PeptideFilter.MAX_EXCLUDE_NTERM_AA, out excludeNTermAAs))
return null;
int minPeptideLength;
if (!helper.ValidateNumberTextBox(tabControl1, (int) TABS.Filter, textMinLength,
PeptideFilter.MIN_MIN_LENGTH, PeptideFilter.MAX_MIN_LENGTH, out minPeptideLength))
return null;
int maxPeptideLength;
if (!helper.ValidateNumberTextBox(tabControl1, (int)TABS.Filter, textMaxLength,
Math.Max(PeptideFilter.MIN_MAX_LENGTH, minPeptideLength), PeptideFilter.MAX_MAX_LENGTH, out maxPeptideLength))
return null;
PeptideExcludeRegex[] exclusions = _driverExclusion.Chosen;
bool autoSelect = cbAutoSelect.Checked;
PeptideFilter filter;
try
{
filter = new PeptideFilter(excludeNTermAAs,
minPeptideLength,
maxPeptideLength,
exclusions,
autoSelect);
}
catch (InvalidDataException x)
{
if (showMessages)
MessageDlg.ShowException(this, x);
return null;
}
Helpers.AssignIfEquals(ref filter, Filter);
// Validate and hold libraries
PeptideLibraries libraries;
IList<LibrarySpec> librarySpecs = _driverLibrary.Chosen;
if (librarySpecs.Count == 0)
libraries = new PeptideLibraries(PeptidePick.library, null, null, false, librarySpecs, new Library[0]);
else
{
int? peptideCount = null;
if (cbLimitPeptides.Checked)
{
int peptideCountVal;
if (!helper.ValidateNumberTextBox(textPeptideCount, PeptideLibraries.MIN_PEPTIDE_COUNT,
PeptideLibraries.MAX_PEPTIDE_COUNT, out peptideCountVal))
return null;
peptideCount = peptideCountVal;
}
PeptidePick pick = (PeptidePick) comboMatching.SelectedIndex;
IList<Library> librariesLoaded = new Library[librarySpecs.Count];
bool documentLibrary = false;
if (Libraries != null)
{
// Use existing library spec's, if nothing was changed.
// Avoid changing the libraries, just because the the picking
// algorithm changed.
if (ArrayUtil.EqualsDeep(librarySpecs, Libraries.LibrarySpecs))
{
librarySpecs = Libraries.LibrarySpecs;
librariesLoaded = Libraries.Libraries;
}
documentLibrary = Libraries.HasDocumentLibrary;
// Otherwise, leave the list of loaded libraries empty,
// and let the LibraryManager refill it. This ensures a
// clean save of library specs only in the user config, rather
// than a mix of library specs and libraries.
}
PeptideRankId rankId = (PeptideRankId) comboRank.SelectedItem;
if (comboRank.SelectedIndex == 0)
rankId = null;
libraries = new PeptideLibraries(pick, rankId, peptideCount, documentLibrary, librarySpecs, librariesLoaded);
}
Helpers.AssignIfEquals(ref libraries, Libraries);
// Validate and hold modifications
int maxVariableMods;
if (!helper.ValidateNumberTextBox(tabControl1, (int)TABS.Modifications, textMaxVariableMods,
PeptideModifications.MIN_MAX_VARIABLE_MODS, PeptideModifications.MAX_MAX_VARIABLE_MODS, out maxVariableMods))
return null;
int maxNeutralLosses;
if (!helper.ValidateNumberTextBox(tabControl1, (int)TABS.Modifications, textMaxNeutralLosses,
PeptideModifications.MIN_MAX_NEUTRAL_LOSSES, PeptideModifications.MAX_MAX_NEUTRAL_LOSSES, out maxNeutralLosses))
return null;
var standardTypes = _driverLabelType.InternalStandardTypes;
PeptideModifications modifications = new PeptideModifications(
_driverStaticMod.Chosen, maxVariableMods, maxNeutralLosses,
_driverLabelType.GetHeavyModifications(), standardTypes);
// Should not be possible to change explicit modifications in the background,
// so this should be safe. CONSIDER: Document structure because of a library load?
modifications = modifications.DeclareExplicitMods(_parent.DocumentUI,
Settings.Default.StaticModList, Settings.Default.HeavyModList);
Helpers.AssignIfEquals(ref modifications, _peptideSettings.Modifications);
PeptideIntegration integration = new PeptideIntegration(_driverPeakScoringModel.SelectedItem);
Helpers.AssignIfEquals(ref integration, Integration);
QuantificationSettings quantification = QuantificationSettings.DEFAULT
.ChangeNormalizationMethod(comboNormalizationMethod.SelectedItem as NormalizationMethod ?? NormalizationMethod.NONE)
.ChangeRegressionWeighting(comboWeighting.SelectedItem as RegressionWeighting)
.ChangeRegressionFit(comboRegressionFit.SelectedItem as RegressionFit)
.ChangeMsLevel(_quantMsLevels[comboQuantMsLevel.SelectedIndex])
.ChangeUnits(tbxQuantUnits.Text);
return new PeptideSettings(enzyme, digest, prediction, filter, libraries, modifications, integration, backgroundProteome)
.ChangeAbsoluteQuantification(quantification);
}
public PeptideSettings ChangeFilter(PeptideFilter prop)
{
return ChangeProp(ImClone(this), im => im.Filter = prop);
}
public bool Equals(PeptideFilter obj)
{
if (ReferenceEquals(null, obj)) return false;
if (ReferenceEquals(this, obj)) return true;
return obj.ExcludeNTermAAs == ExcludeNTermAAs &&
obj.MinPeptideLength == MinPeptideLength &&
obj.MaxPeptideLength == MaxPeptideLength &&
obj.AutoSelect.Equals(AutoSelect) &&
ArrayUtil.EqualsDeep(obj._exclusions, _exclusions);
}
public PeptideSettings(Enzyme enzyme,
DigestSettings digestSettings,
PeptidePrediction prediction,
PeptideFilter filter,
PeptideLibraries libraries,
PeptideModifications modifications,
PeptideIntegration integration,
BackgroundProteome backgroundProteome
)
{
Enzyme = enzyme;
DigestSettings = digestSettings;
Prediction = prediction;
Filter = filter;
Libraries = libraries;
Modifications = modifications;
Integration = integration;
BackgroundProteome = backgroundProteome;
Quantification = QuantificationSettings.DEFAULT;
}