public bool Equals(MeasuredIon other)
{
if (ReferenceEquals(null, other))
{
return(false);
}
if (ReferenceEquals(this, other))
{
return(true);
}
return(base.Equals(other) &&
Equals(other.Fragment, Fragment) &&
Equals(other.Restrict, Restrict) &&
other.Terminus.Equals(Terminus) &&
other.MinFragmentLength.Equals(MinFragmentLength) &&
Equals(other.SettingsCustomIon, SettingsCustomIon) &&
Equals(other.Charge, Charge) &&
other.IsOptional == IsOptional);
}
private void TestSettingIonsUI()
{
var ions = new MeasuredIon[0];
var ionList = new MeasuredIonList();
ionList.AddRange(ions);
Settings.Default.MeasuredIonList = ionList;
RunUI(() => SkylineWindow.ModifyDocument("Change measured ions", document => document.ChangeSettings(
document.Settings.ChangeTransitionFilter(filter => filter.ChangeMeasuredIons(ions)))));
var tranSettings = ShowDialog<TransitionSettingsUI>(SkylineWindow.ShowTransitionSettingsUI);
var editMeasuredIonList =
ShowDialog<EditListDlg<SettingsListBase<MeasuredIon>, MeasuredIon>>(
tranSettings.EditSpecialTransitionsList);
var editMeasuredIon1 = ShowDialog<EditMeasuredIonDlg>(editMeasuredIonList.AddItem);
RunUI(() =>
{
editMeasuredIon1.SwitchToCustom();
editMeasuredIon1.TextName = "Water";
editMeasuredIon1.Formula = "H2O";
});
var errorDlg = ShowDialog<MessageDlg>(() => editMeasuredIon1.Charge = -1); // Negative charge states are valid for small molecule only, not for reporter ions
AssertEx.AreComparableStrings(String.Format(Resources.MessageBoxHelper_ValidateDecimalTextBox__0__must_be_greater_than_or_equal_to__1__, String.Empty, 1), errorDlg.Message);
RunUI(() => errorDlg.OkDialog()); // Dismiss the warning
RunUI(() =>
{
editMeasuredIon1.Charge = 1;
});
OkDialog(editMeasuredIon1,editMeasuredIon1.OkDialog);
var editMeasuredIon2 = ShowDialog<EditMeasuredIonDlg>(editMeasuredIonList.AddItem);
RunUI(() =>
{
editMeasuredIon2.SwitchToCustom();
editMeasuredIon2.TextName = "Carbon";
editMeasuredIon2.Charge = 1;
editMeasuredIon2.Formula = "CO2";
});
OkDialog(editMeasuredIon2,editMeasuredIon2.OkDialog);
OkDialog(editMeasuredIonList,editMeasuredIonList.OkDialog);
RunUI(() =>
{
tranSettings.SetListAlwaysAdd(0,true);
tranSettings.SetListAlwaysAdd(0,true);
tranSettings.SetListAlwaysAdd(1,true);
});
OkDialog(tranSettings,tranSettings.OkDialog);
IdentityPath path;
var newDoc = SkylineWindow.Document.ImportFasta(new StringReader(">peptide1\nPEPMCIDEPR"),
true, IdentityPath.ROOT, out path);
TransitionGroupDocNode nodeGroup = newDoc.PeptideTransitionGroups.ElementAt(0);
var water = new MeasuredIon("Water", "H2O", null, null, 1);
var carbon = new MeasuredIon("Carbon", "CO2", null, null, 1,true);
var filteredWaterNodes = TransitionGroupTreeNode.GetChoices(nodeGroup, newDoc.Settings,
newDoc.Peptides.ElementAt(0).ExplicitMods, true)
.Cast<TransitionDocNode>()
.Where(node => Equals(node.Transition.CustomIon, water.CustomIon));
Assert.AreEqual(1,filteredWaterNodes.Count());
var filteredCarbonNodes =
TransitionGroupTreeNode.GetChoices(nodeGroup, newDoc.Settings,
newDoc.Peptides.ElementAt(0).ExplicitMods, true)
.Cast<TransitionDocNode>()
.Where(node => Equals(node.Transition.CustomIon, carbon.CustomIon));
var unfilteredCarbonNodes =
TransitionGroupTreeNode.GetChoices(nodeGroup, newDoc.Settings,
newDoc.Peptides.ElementAt(0).ExplicitMods, false)
.Cast<TransitionDocNode>()
.Where(node => Equals(node.Transition.CustomIon, carbon.CustomIon));
Assert.AreEqual(0, filteredCarbonNodes.Count());
Assert.AreEqual(1, unfilteredCarbonNodes.Count());
}
public void OkDialog()
{
var helper = new MessageBoxHelper(this);
string name;
if (!helper.ValidateNameTextBox(textName, out name))
return;
if (_existing.Contains(m => !ReferenceEquals(_measuredIon, m) && Equals(name, m.Name)))
{
helper.ShowTextBoxError(textName, Resources.EditMeasuredIonDlg_OkDialog_The_special_ion__0__already_exists, name);
return;
}
if (radioFragment.Checked)
{
string cleavage;
if (!ValidateAATextBox(helper, textFragment, false, out cleavage))
return;
string restrict;
if (!ValidateAATextBox(helper, textRestrict, true, out restrict))
return;
SequenceTerminus direction = (comboDirection.SelectedIndex == 0 ?
SequenceTerminus.C : SequenceTerminus.N);
int minAas;
if (!helper.ValidateNumberTextBox(textMinAas, MeasuredIon.MIN_MIN_FRAGMENT_LENGTH,
MeasuredIon.MAX_MIN_FRAGMENT_LENGTH, out minAas))
return;
_measuredIon = new MeasuredIon(name, cleavage, restrict, direction, minAas);
}
else
{
var customIon = ValidateCustomIon(name);
if (customIon == null)
return;
_measuredIon = customIon;
}
DialogResult = DialogResult.OK;
}
public void ReporterIonTest()
{
// Test the code that updates old-style formulas
Assert.AreEqual("C5C'H13N2", BioMassCalc.AddH("C5C'H12N2"));
Assert.AreEqual("CO2H", BioMassCalc.AddH("CO2"));
var docOriginal = new SrmDocument(SrmSettingsList.GetDefault().ChangeTransitionInstrument(instrument => instrument.ChangeMinMz(10))); // H2O2 is not very heavy!
IdentityPath path;
SrmDocument docPeptide = docOriginal.ImportFasta(new StringReader(">peptide1\nPEPMCIDEPR"),
true, IdentityPath.ROOT, out path);
// One of the prolines should have caused an extra transition
Assert.AreEqual(4, docPeptide.PeptideTransitionCount);
Assert.IsTrue(docPeptide.PeptideTransitions.Contains(nodeTran => nodeTran.Transition.Ordinal == 8));
const string formula = "H2O2"; // This was H2O, but that falls below mz=10 at z > 1
const string hydrogenPeroxide = "Hydrogen Perxoide";
var reporterIons = new[] { new MeasuredIon(hydrogenPeroxide, formula, null, null, 1), new MeasuredIon(hydrogenPeroxide, formula, null, null, 2), new MeasuredIon(hydrogenPeroxide, formula, null, null, 3), MeasuredIonList.NTERM_PROLINE };
SrmDocument docReporterIon = docPeptide.ChangeSettings(docPeptide.Settings.ChangeTransitionFilter(filter =>
filter.ChangeMeasuredIons(reporterIons)));
AssertEx.IsDocumentTransitionCount(docReporterIon, 7);
//Check With Monoisotopic
double mass = BioMassCalc.MONOISOTOPIC.CalculateMassFromFormula(formula);
for (int i = 0; i < 3; i ++)
{
TransitionDocNode tranNode = docReporterIon.MoleculeTransitions.ElementAt(i);
Transition tran = tranNode.Transition;
Assert.AreEqual(reporterIons[i].CustomIon, tran.CustomIon);
Assert.AreEqual(tran.Charge, i + 1);
Assert.AreEqual(BioMassCalc.MONOISOTOPIC.CalculateIonMz(formula, i + 1), tranNode.Mz, BioMassCalc.MassElectron/100);
Assert.AreEqual(BioMassCalc.CalculateIonMz(mass, i + 1), tranNode.Mz, BioMassCalc.MassElectron / 100);
}
//Check with Average
TransitionPrediction predSettings =
docReporterIon.Settings.TransitionSettings.Prediction.ChangeFragmentMassType(MassType.Average);
TransitionSettings tranSettings = docReporterIon.Settings.TransitionSettings.ChangePrediction(predSettings);
SrmSettings srmSettings = docReporterIon.Settings.ChangeTransitionSettings(tranSettings);
SrmDocument averageDocument = docReporterIon.ChangeSettings(srmSettings);
mass = BioMassCalc.AVERAGE.CalculateMassFromFormula(formula);
for (int i = 0; i < 3; i++)
{
TransitionDocNode tranNode = averageDocument.MoleculeTransitions.ElementAt(i);
Transition tran = tranNode.Transition;
Assert.AreEqual(reporterIons[i].CustomIon, tran.CustomIon);
Assert.AreEqual(tran.Charge, i + 1);
Assert.AreEqual(BioMassCalc.AVERAGE.CalculateIonMz(formula, i + 1), tranNode.Mz, BioMassCalc.MassElectron / 100);
Assert.AreEqual(BioMassCalc.CalculateIonMz(mass, i + 1), tranNode.Mz, BioMassCalc.MassElectron / 100);
}
//Make sure the rest of the transitions aren't reporter ions
for (int i = 3; i < 7; i ++)
{
Transition tran = docReporterIon.MoleculeTransitions.ElementAt(i).Transition;
Assert.AreNotEqual(tran.CustomIon, reporterIons);
}
var optionalIon = new MeasuredIon(hydrogenPeroxide, formula, null, null,1, true);
SrmDocument optionalDoc = docPeptide.ChangeSettings(docPeptide.Settings.ChangeTransitionFilter(filter =>
filter.ChangeMeasuredIons(new[] {optionalIon})));
Assert.AreEqual(3, optionalDoc.PeptideTransitionCount);
optionalDoc = optionalDoc.ChangeSettings(optionalDoc.Settings.ChangeTransitionFilter(filter =>
filter.ChangeMeasuredIons(new[] {optionalIon.ChangeIsOptional(false)})));
AssertEx.IsDocumentTransitionCount(optionalDoc, 4);
Assert.AreEqual(optionalIon.ChangeIsOptional(false).CustomIon,
optionalDoc.MoleculeTransitions.ElementAt(0).Transition.CustomIon);
optionalDoc =
optionalDoc.ChangeSettings(
optionalDoc.Settings.ChangeTransitionFilter(
filter => filter.ChangeMeasuredIons(new[] {optionalIon.ChangeIsOptional(true)})));
TransitionGroupDocNode nodeGroup = optionalDoc.MoleculeTransitionGroups.ElementAt(0);
var filteredNodes =
TransitionGroupTreeNode.GetChoices(nodeGroup, optionalDoc.Settings,
optionalDoc.Molecules.ElementAt(0).ExplicitMods, true)
.Cast<TransitionDocNode>()
.Where(node => Equals(node.Transition.CustomIon, optionalIon.CustomIon));
var unfilteredNodes =
TransitionGroupTreeNode.GetChoices(nodeGroup, optionalDoc.Settings,
optionalDoc.Molecules.ElementAt(0).ExplicitMods, false)
.Cast<TransitionDocNode>()
.Where(node => Equals(node.Transition.CustomIon, optionalIon.CustomIon));
Assert.AreEqual(0,filteredNodes.Count());
Assert.AreEqual(1,unfilteredNodes.Count());
}
public bool Equals(MeasuredIon other)
{
if (ReferenceEquals(null, other)) return false;
if (ReferenceEquals(this, other)) return true;
return base.Equals(other) &&
Equals(other.Fragment, Fragment) &&
Equals(other.Restrict, Restrict) &&
other.Terminus.Equals(Terminus) &&
other.MinFragmentLength.Equals(MinFragmentLength) &&
Equals(other.SettingsCustomIon, SettingsCustomIon) &&
Equals(other.Charge, Charge) &&
other.IsOptional == IsOptional;
}
