public void TerminusModification()
{
Peptide pepA = new Peptide("DERLEK");
pepA.AddModification(new OldSchoolChemicalFormulaModification(ChemicalFormula.ParseFormula("SO")), Terminus.N);
Assert.AreEqual("[OS]-DERLEK", pepA.ToString());
}
public void PeptideCloneWithoutModifications()
{
Peptide pepA = new Peptide("DER[Fe]EK");
Peptide pepB = new Peptide(pepA, false);
Assert.AreEqual("DEREK", pepB.ToString());
}
private void ShowHalfLifeForm(Peptide peptide, string proteinName, string cohort)
{
if (0 != (GetKeyState(0x10) & 0x8000))
{
var halfLifeRowDataForm = new HalfLifeRowDataForm(_form.Workspace)
{
Protein = proteinName,
};
if (peptide != null)
{
halfLifeRowDataForm.Peptide = peptide.ToString();
}
var resultData = HalfLives[cohort].Value;
halfLifeRowDataForm.RowDatas = resultData.RowDatas;
halfLifeRowDataForm.Show(_form.DockPanel, _form.DockState);
return;
}
var halfLifeForm = new HalfLifeForm(_form.Workspace)
{
Peptide = peptide == null ? "" : peptide.Sequence,
ProteinName = proteinName,
Cohort = cohort,
};
halfLifeForm.SetHalfLifeSettings(_form.HalfLifeSettings);
for (int i = 0; i < _form.checkedListBoxTimePoints.Items.Count; i++)
{
halfLifeForm.SetTimePointExcluded((double)_form.checkedListBoxTimePoints.Items[i],
!_form.checkedListBoxTimePoints.GetItemChecked(i));
}
halfLifeForm.Show(_form.DockPanel, _form.DockState);
}
public void ClearModificationsBySites()
{
var peptide = new Peptide("AC[Fe]DEFGHIKLMNP[Fe]QRSTV[Fe]WY");
peptide.ClearModifications(ModificationSites.C | ModificationSites.V);
Assert.AreEqual("ACDEFGHIKLMNP[Fe]QRSTVWY", peptide.ToString());
}
public void ClearModificationsBySites()
{
var peptide = new Peptide("AC[Fe]DEFGHIKLMNP[Fe]QRSTV[Fe]WY");
peptide.ClearModifications(ModificationSites.C | ModificationSites.V);
Assert.AreEqual("ACDEFGHIKLMNP[Fe]QRSTVWY", peptide.ToString());
}
public void ClearMods()
{
Peptide pepA = new Peptide("DE[Al]R[Fe]EK");
pepA.ClearModifications(new OldSchoolChemicalFormulaModification(ChemicalFormula.ParseFormula("Al")));
Assert.AreEqual("DER[Fe]EK", pepA.ToString());
pepA.ClearModifications(new OldSchoolChemicalFormulaModification(ChemicalFormula.ParseFormula("C")));
Assert.AreEqual("DER[Fe]EK", pepA.ToString());
pepA.ClearModifications();
Assert.AreEqual("DEREK", pepA.ToString());
pepA.ClearModifications();
Assert.AreEqual("DEREK", pepA.ToString());
pepA.ClearModifications(ModificationSites.Any);
Assert.AreEqual("DEREK", pepA.ToString());
pepA.ClearModifications(Terminus.C);
Assert.AreEqual("DEREK", pepA.ToString());
}
public void ParseDoubleModificationToString()
{
Peptide peptide = new Peptide("THGEAK[25.132]K");
Assert.AreEqual("THGEAK[25.132]K", peptide.ToString());
}
public void EmptyStringPeptideConstructorToString()
{
Peptide peptide = new Peptide();
Assert.AreEqual(string.Empty, peptide.ToString());
}
public override String ToString()
{
return(Peptide.ToString());
}
public void EmptyStringPeptideConstructorToString()
{
Peptide peptide = new Peptide();
Assert.AreEqual(string.Empty, peptide.ToString());
}
public void PeptideCloneWithoutModifications()
{
Peptide pepA = new Peptide("DER[Fe]EK");
Peptide pepB = new Peptide(pepA, false);
Assert.AreEqual("DEREK", pepB.ToString());
}
public void ParseNamedChemicalModificationToString()
{
Peptide peptide = new Peptide("THGEAK[Acetyl]K");
Assert.AreEqual("THGEAK[Acetyl]K", peptide.ToString());
}
public void ParseDoubleModificationToString()
{
Peptide peptide = new Peptide("THGEAK[25.132]K");
Assert.AreEqual("THGEAK[25.132]K", peptide.ToString());
}
private void ShowHalfLifeForm(Peptide peptide, string proteinName, string cohort)
{
if (0 != (GetKeyState(0x10) & 0x8000))
{
var halfLifeRowDataForm = new HalfLifeRowDataForm(_form.Workspace)
{
Protein = proteinName,
};
if (peptide != null)
{
halfLifeRowDataForm.Peptide = peptide.ToString();
}
var resultData = HalfLives[cohort].Value;
halfLifeRowDataForm.RowDatas = resultData.RowDatas;
halfLifeRowDataForm.Show(_form.DockPanel, _form.DockState);
return;
}
var halfLifeForm = new HalfLifeForm(_form.Workspace)
{
Peptide = peptide == null ? "" : peptide.Sequence,
ProteinName = proteinName,
Cohort = cohort,
};
halfLifeForm.SetHalfLifeSettings(_form.HalfLifeSettings);
for (int i = 0; i < _form.checkedListBoxTimePoints.Items.Count; i++)
{
halfLifeForm.SetTimePointExcluded((double)_form.checkedListBoxTimePoints.Items[i],
!_form.checkedListBoxTimePoints.GetItemChecked(i));
}
halfLifeForm.Show(_form.DockPanel, _form.DockState);
}
public void SetAminoAcidModification()
{
ChemicalFormula formula = new ChemicalFormula("Fe");
_mockPeptideEveryAminoAcid.SetModification(formula, AminoAcid.Asparagine);
Assert.AreEqual("ACDEFGHIKLMN[Fe]PQRSTVWY", _mockPeptideEveryAminoAcid.ToString());
}
public void ParseNamedChemicalModificationToString()
{
Peptide peptide = new Peptide("THGEAK[Acetyl]K");
Assert.AreEqual("THGEAK[Acetyl]K", peptide.ToString());
}
