public void MultiLabelExplicitSerialTest()
{
// Create a simple document and add two peptides
SrmDocument document = new SrmDocument(SrmSettingsList.GetDefault());
const string pepSequence1 = "QFVLSCVILR";
const string pepSequence2 = "DIEVYCDGAITTK";
var reader = new StringReader(string.Join("\n", new[] { ">peptides1", pepSequence1, pepSequence2 }));
IdentityPath path;
document = document.ImportFasta(reader, true, IdentityPath.ROOT, out path);
Assert.AreEqual(2, document.PeptideCount);
// Add some modifications in two new label types
var modCarb = new StaticMod("Carbamidomethyl Cysteine", "C", null, "C2H3ON");
var modOther = new StaticMod("Another Cysteine", "C", null, "CO8N2");
var staticMods = new[] { modCarb, modOther };
var mod15N = new StaticMod("All 15N", null, null, null, LabelAtoms.N15, null, null);
var modK13C = new StaticMod("13C K", "K", ModTerminus.C, null, LabelAtoms.C13, null, null);
var modR13C = new StaticMod("13C R", "R", ModTerminus.C, null, LabelAtoms.C13, null, null);
var modV13C = new StaticMod("Heavy V", "V", null, null, LabelAtoms.C13 | LabelAtoms.N15, null, null);
var heavyMods = new[] { mod15N, modK13C, modR13C, modV13C };
var labelTypeAA = new IsotopeLabelType("heavy AA", IsotopeLabelType.FirstHeavy);
var labelTypeAll = new IsotopeLabelType("heavy All", IsotopeLabelType.FirstHeavy + 1);
var settings = document.Settings;
settings = settings.ChangePeptideModifications(mods =>
new PeptideModifications(mods.StaticModifications,
new[]
{
new TypedModifications(labelTypeAA, new[] { modK13C, modR13C }),
new TypedModifications(labelTypeAll, new[] { mod15N })
}));
document = document.ChangeSettings(settings);
Assert.AreEqual(6, document.PeptideTransitionGroupCount);
// Add modifications to light and heavy AA in the first peptide
path = document.GetPathTo((int)SrmDocument.Level.Molecules, 0);
var nodePepMod = (PeptideDocNode)document.FindNode(path);
var explicitMod = new ExplicitMods(nodePepMod.Peptide,
new[] { new ExplicitMod(pepSequence1.IndexOf('C'), modOther) },
new[] { new TypedExplicitModifications(nodePepMod.Peptide, labelTypeAA, new ExplicitMod[0]) });
document = document.ChangePeptideMods(path, explicitMod, staticMods, heavyMods);
Assert.AreEqual(5, document.PeptideTransitionGroupCount);
// Add a modification to heavy All in the second peptide
path = document.GetPathTo((int)SrmDocument.Level.Molecules, 1);
nodePepMod = (PeptideDocNode)document.FindNode(path);
explicitMod = new ExplicitMods(nodePepMod.Peptide, null,
new[] { new TypedExplicitModifications(nodePepMod.Peptide, labelTypeAll,
new[] { new ExplicitMod(pepSequence2.IndexOf('V'), modV13C) }) });
document = document.ChangePeptideMods(path, explicitMod, staticMods, heavyMods);
Assert.AreEqual(5, document.PeptideTransitionGroupCount);
AssertEx.Serializable(document, 3, AssertEx.DocumentCloned);
}
public void AddRemoveExplicitModTest()
{
SrmDocument docStudy7 = CreateStudy7Doc();
string transitionList = ExportCsv(docStudy7);
Assert.AreEqual(69, transitionList.Split('\n').Length); // Special test mode may add an extra doc node
var modifications = docStudy7.Settings.PeptideSettings.Modifications;
var listStaticMods = modifications.StaticModifications;
var listHeavyMods = modifications.AllHeavyModifications.ToList();
docStudy7 = docStudy7.ChangeSettings(docStudy7.Settings.ChangeTransitionFilter(filter => filter.ChangeAutoSelect(false)));
// Remove all modifications
int i = 0;
// But save them for later
var removedMods = new Dictionary <int, ExplicitMods>();
foreach (var peptide in docStudy7.Peptides)
{
if (peptide.HasExplicitMods)
{
removedMods.Add(i, peptide.ExplicitMods);
IdentityPath path = docStudy7.GetPathTo((int)SrmDocument.Level.Molecules, i);
docStudy7 = docStudy7.ChangePeptideMods(path, null, listStaticMods, listHeavyMods);
}
i++;
}
// Removes heavy from peptide with c-terminal P
AssertEx.IsDocumentState(docStudy7, 6, 7, 11, 21, 63);
modifications = docStudy7.Settings.PeptideSettings.Modifications;
Assert.AreEqual(2, modifications.AllHeavyModifications.Count());
Assert.AreEqual(0, modifications.AllHeavyModifications.Count(mod => mod.IsExplicit));
Assert.AreEqual(0, docStudy7.Peptides.Count(peptide => peptide.HasExplicitMods));
listHeavyMods = ATOMIC_HEAVY_MODS;
foreach (var pair in removedMods)
{
IdentityPath path = docStudy7.GetPathTo((int)SrmDocument.Level.Molecules, pair.Key);
docStudy7 = docStudy7.ChangePeptideMods(path, pair.Value, listStaticMods, listHeavyMods);
}
AssertEx.IsDocumentState(docStudy7, 11, 7, 11, 21, 63);
// Replace the heavy precursor that was removed
// TODO: Yuck. Would be nice to have a way to do this without duplicating
// so much of the logic in PeptideDocNode and PeptideTreeNode
var pepPath = docStudy7.GetPathTo((int)SrmDocument.Level.Molecules, 10);
var nodePep = (PeptideDocNode)docStudy7.FindNode(pepPath);
var mods = nodePep.ExplicitMods;
var nodeGroupLight = (TransitionGroupDocNode)nodePep.Children[0];
var settings = docStudy7.Settings;
foreach (var tranGroup in nodePep.GetTransitionGroups(settings, mods, false))
{
if (tranGroup.PrecursorAdduct.Equals(nodeGroupLight.TransitionGroup.PrecursorAdduct) &&
!tranGroup.LabelType.IsLight)
{
TransitionDocNode[] transitions = nodePep.GetMatchingTransitions(tranGroup, settings, mods);
var nodeGroup = new TransitionGroupDocNode(tranGroup, transitions);
nodeGroup = nodeGroup.ChangeSettings(settings, nodePep, mods, SrmSettingsDiff.ALL);
docStudy7 = (SrmDocument)docStudy7.Add(pepPath, nodeGroup);
break;
}
}
AssertEx.IsDocumentState(docStudy7, 12, 7, 11, 22, 66);
modifications = docStudy7.Settings.PeptideSettings.Modifications;
Assert.AreEqual(2, modifications.AllHeavyModifications.Count(mod => mod.IsExplicit && mod.Label13C));
Assert.AreEqual(2, modifications.AllHeavyModifications.Count(mod => mod.Formula != null));
Assert.AreEqual(3, docStudy7.Peptides.Count(peptide => peptide.HasExplicitMods));
Assert.AreEqual(2, docStudy7.Peptides.Count(peptide => peptide.HasExplicitMods &&
peptide.ExplicitMods.StaticModifications.Count > 0 &&
peptide.ExplicitMods.StaticModifications[0].Modification.AAs[0] == 'C'));
Assert.AreEqual(2, docStudy7.Peptides.Count(peptide => peptide.HasExplicitMods &&
peptide.ExplicitMods.HeavyModifications[0].Modification.AAs[0] == 'V' &&
peptide.ExplicitMods.HeavyModifications[0].Modification.Label13C));
Assert.AreEqual(1, docStudy7.Peptides.Count(peptide => peptide.HasExplicitMods &&
peptide.ExplicitMods.HeavyModifications[0].Modification.AAs[0] == 'L' &&
peptide.ExplicitMods.HeavyModifications[0].Modification.Label13C));
AssertEx.NoDiff(transitionList, ExportCsv(docStudy7));
}
public void ModifyExplicitModTest()
{
SrmDocument docStudy7 = CreateStudy7Doc();
var settings = docStudy7.Settings.ChangeTransitionFilter(filter => filter.ChangeAutoSelect(false));
var listStaticMods = settings.PeptideSettings.Modifications.StaticModifications;
var listHeavyMods = new List <StaticMod>(settings.PeptideSettings.Modifications.AllHeavyModifications);
// Change an explicit heavy modification to something new
var modV = new StaticMod("Heavy V", "V", null, LabelAtoms.C13 | LabelAtoms.N15);
listHeavyMods.Add(modV);
IdentityPath path = docStudy7.GetPathTo((int)SrmDocument.Level.Molecules, 0);
var peptideMod = (PeptideDocNode)docStudy7.FindNode(path);
var explicitMods = peptideMod.ExplicitMods;
explicitMods = explicitMods.ChangeHeavyModifications(new[] { explicitMods.HeavyModifications[0].ChangeModification(modV) });
var docHeavyV = docStudy7.ChangePeptideMods(path, explicitMods, listStaticMods, listHeavyMods);
var modSettings = docHeavyV.Settings.PeptideSettings.Modifications;
Assert.AreEqual(5, modSettings.AllHeavyModifications.Count());
Assert.AreEqual(4, modSettings.AllHeavyModifications.Count(mod => mod.Formula != null));
Assert.AreEqual(1, modSettings.AllHeavyModifications.Count(mod => mod.Label13C && mod.Label15N));
Assert.AreEqual(3, docHeavyV.Peptides.Count(peptide => peptide.HasExplicitMods));
Assert.AreEqual(1, docHeavyV.Peptides.Count(peptide => peptide.HasExplicitMods &&
peptide.ExplicitMods.HeavyModifications[0].Modification.AAs[0] == 'V' &&
peptide.ExplicitMods.HeavyModifications[0].Modification.Label13C));
Assert.AreEqual(1, docHeavyV.Peptides.Count(peptide => peptide.HasExplicitMods &&
peptide.ExplicitMods.HeavyModifications[0].Modification.AAs[0] == 'V' &&
peptide.ExplicitMods.HeavyModifications[0].Modification.Label13C &&
peptide.ExplicitMods.HeavyModifications[0].Modification.Label15N));
// Change an explicit heavy modification to something new
listHeavyMods = new List <StaticMod>(settings.PeptideSettings.Modifications.AllHeavyModifications);
modV = listHeavyMods[2] = ATOMIC_HEAVY_MODS[2];
explicitMods = peptideMod.ExplicitMods;
explicitMods = explicitMods.ChangeHeavyModifications(new[] { explicitMods.HeavyModifications[0].ChangeModification(modV) });
var doc13V = docStudy7.ChangePeptideMods(path, explicitMods, listStaticMods, listHeavyMods);
modSettings = doc13V.Settings.PeptideSettings.Modifications;
Assert.AreEqual(4, modSettings.AllHeavyModifications.Count());
Assert.AreEqual(3, modSettings.AllHeavyModifications.Count(mod => mod.Formula != null));
Assert.AreEqual(1, modSettings.AllHeavyModifications.Count(mod => mod.Label13C));
Assert.AreEqual(3, doc13V.Peptides.Count(peptide => peptide.HasExplicitMods));
Assert.AreEqual(2, doc13V.Peptides.Count(peptide => peptide.HasExplicitMods &&
peptide.ExplicitMods.HeavyModifications[0].Modification.AAs[0] == 'V' &&
peptide.ExplicitMods.HeavyModifications[0].Modification.Label13C));
// No change to the peptide, but change an orthoganal modification
path = docStudy7.GetPathTo((int)SrmDocument.Level.Molecules, docStudy7.Peptides.Count() - 1);
peptideMod = (PeptideDocNode)docStudy7.FindNode(path);
doc13V = docStudy7.ChangePeptideMods(path, peptideMod.ExplicitMods, listStaticMods, listHeavyMods);
modSettings = doc13V.Settings.PeptideSettings.Modifications;
Assert.AreEqual(4, modSettings.AllHeavyModifications.Count());
Assert.AreEqual(3, modSettings.AllHeavyModifications.Count(mod => mod.Formula != null));
Assert.AreEqual(1, modSettings.AllHeavyModifications.Count(mod => mod.Label13C));
Assert.AreEqual(3, doc13V.Peptides.Count(peptide => peptide.HasExplicitMods));
Assert.AreEqual(2, doc13V.Peptides.Count(peptide => peptide.HasExplicitMods &&
peptide.ExplicitMods.HeavyModifications[0].Modification.AAs[0] == 'V' &&
peptide.ExplicitMods.HeavyModifications[0].Modification.Label13C));
// No change to the peptide, but remove all other modifications from global lists
var docClear = docStudy7.ChangePeptideMods(path, peptideMod.ExplicitMods,
new StaticMod[0], new[] { listHeavyMods[3] });
Assert.AreSame(docClear, docStudy7);
// Remove explicit modifications from the global lists
listHeavyMods.RemoveRange(2, 2);
// Mimic the way PeptideSettingsUI would change the settings
var docRemoveExplicit = docStudy7.ChangeSettings(docStudy7.Settings.ChangePeptideModifications(
mods => mods.ChangeModifications(IsotopeLabelType.heavy, listHeavyMods)
.DeclareExplicitMods(docStudy7, listStaticMods, listHeavyMods)));
// Test expected changes
modSettings = docRemoveExplicit.Settings.PeptideSettings.Modifications;
Assert.AreEqual(2, modSettings.AllHeavyModifications.Count());
Assert.AreEqual(3, docRemoveExplicit.Peptides.Count(peptide => peptide.HasExplicitMods));
// Should leave no heavy modifications on the explicitly modified peptides
Assert.AreEqual(0, docRemoveExplicit.Peptides.Count(peptide => peptide.HasExplicitMods &&
peptide.ExplicitMods.HeavyModifications.Count > 0));
}
public void MultiLabelExplicitSerialTest()
{
// Create a simple document and add two peptides
SrmDocument document = new SrmDocument(SrmSettingsList.GetDefault());
const string pepSequence1 = "QFVLSCVILR";
const string pepSequence2 = "DIEVYCDGAITTK";
var reader = new StringReader(string.Join("\n", new[] {">peptides1", pepSequence1, pepSequence2}));
IdentityPath path;
document = document.ImportFasta(reader, true, IdentityPath.ROOT, out path);
Assert.AreEqual(2, document.PeptideCount);
// Add some modifications in two new label types
var modCarb = new StaticMod("Carbamidomethyl Cysteine", "C", null, "C2H3ON");
var modOther = new StaticMod("Another Cysteine", "C", null, "CO8N2");
var staticMods = new[] {modCarb, modOther};
var mod15N = new StaticMod("All 15N", null, null, null, LabelAtoms.N15, null, null);
var modK13C = new StaticMod("13C K", "K", ModTerminus.C, null, LabelAtoms.C13, null, null);
var modR13C = new StaticMod("13C R", "R", ModTerminus.C, null, LabelAtoms.C13, null, null);
var modV13C = new StaticMod("Heavy V", "V", null, null, LabelAtoms.C13 | LabelAtoms.N15, null, null);
var heavyMods = new[] { mod15N, modK13C, modR13C, modV13C };
var labelTypeAA = new IsotopeLabelType("heavy AA", IsotopeLabelType.FirstHeavy);
var labelTypeAll = new IsotopeLabelType("heavy All", IsotopeLabelType.FirstHeavy + 1);
var settings = document.Settings;
settings = settings.ChangePeptideModifications(mods =>
new PeptideModifications(mods.StaticModifications,
new[]
{
new TypedModifications(labelTypeAA, new[] {modK13C, modR13C}),
new TypedModifications(labelTypeAll, new[] {mod15N})
}));
document = document.ChangeSettings(settings);
Assert.AreEqual(6, document.PeptideTransitionGroupCount);
// Add modifications to light and heavy AA in the first peptide
path = document.GetPathTo((int) SrmDocument.Level.Molecules, 0);
var nodePepMod = (PeptideDocNode) document.FindNode(path);
var explicitMod = new ExplicitMods(nodePepMod.Peptide,
new[] {new ExplicitMod(pepSequence1.IndexOf('C'), modOther)},
new[] {new TypedExplicitModifications(nodePepMod.Peptide, labelTypeAA, new ExplicitMod[0])});
document = document.ChangePeptideMods(path, explicitMod, staticMods, heavyMods);
Assert.AreEqual(5, document.PeptideTransitionGroupCount);
// Add a modification to heavy All in the second peptide
path = document.GetPathTo((int)SrmDocument.Level.Molecules, 1);
nodePepMod = (PeptideDocNode)document.FindNode(path);
explicitMod = new ExplicitMods(nodePepMod.Peptide, null,
new[] { new TypedExplicitModifications(nodePepMod.Peptide, labelTypeAll,
new[] {new ExplicitMod(pepSequence2.IndexOf('V'), modV13C)}) });
document = document.ChangePeptideMods(path, explicitMod, staticMods, heavyMods);
Assert.AreEqual(5, document.PeptideTransitionGroupCount);
AssertEx.Serializable(document, 3, AssertEx.DocumentCloned);
}