public EmptyResult MapModuletoApplication(string listId, string attributename, int ordinalposition)
{
string token = HttpContext.Session.GetString("access_token");
List <PatientListModel> listModulesModel = getListofListModel();
List <MappedList> listMappedmodules = APIservice.GetListById <MappedList>(listId.Trim(), "synapsenamespace=meta&synapseentityname=applicationlist&synapseattributename=application_id&attributevalue=", token).OrderBy(o => o.displayorder).ToList();
MappedList Model = new MappedList();
Guid id = Guid.NewGuid();
PatientListModel moduleobj = listModulesModel.Single(s => s.list_id == attributename);
Model.applicationlist_id = id.ToString();
Model.application_id = listId.Trim();
Model.listid = attributename;
Model.listname = moduleobj.listname;
if (listMappedmodules.Count == 0)
{
Model.displayorder = 1;
}
else
{
Model.displayorder = listMappedmodules.Max(x => x.displayorder.Value) + 1;
}
string results = APIservice.PostObject <MappedList>(Model, "synapsenamespace=meta&synapseentityname=applicationlist", token);
listMappedmodules = APIservice.GetListById <MappedList>(listId.Trim(), "synapsenamespace=meta&synapseentityname=applicationlist&synapseattributename=application_id&attributevalue=", token).OrderBy(o => o.displayorder).ToList();;
return(new EmptyResult());
}
public static void AddAssetsOfType <T>(Object o, MappedList <T> graphicsList) where T : Object, IUniqueName
{
graphicsList.ClearList();
graphicsList.AddItems(Instance.GetAllAssetsOfType <T>());
graphicsList.MakeDict();
EditorUtility.SetDirty(o);
AssetDatabase.SaveAssets();
}
public void CreateMatches(SrmSettings settings, IEnumerable <LibKey> libKeys,
MappedList <string, StaticMod> defSetStatic, MappedList <string, StaticMod> defSetHeavy)
{
_dictAAMassPairs = new Dictionary <AATermKey, List <byte[]> >();
_libKeys = libKeys.GetEnumerator();
InitMatcherSettings(settings, defSetStatic, defSetHeavy);
MatcherPepMods = CreateMatcherPeptideSettings();
}
public InsertQuery(Model model, IEnumerable<string> fields)
{
Model = model;
Fields = new MappedList<string, Field>();
foreach (var field in fields)
{
Fields.Add(Model.Fields[field]);
}
}
public GraphicsData()
{
teleportGraphics = new MappedList <TeleportGraphics>();
enemyGraphics = new MappedList <EnemyGraphics>();
raceGraphics = new MappedList <RaceGraphics>();
itemGraphics = new MappedList <ItemGraphics>();
skillGraphics = new MappedList <SkillGraphics>();
animationClips = new MappedList <AnimationClipData>();
}
public GameData()
{
gems = new MappedList <Gem>();
worlds = new MappedList <WorldData>();
races = new MappedList <Race>();
perks = new MappedList <Perk>();
skills = new MappedList <SkillAssetData>();
combos = new MappedList <ComboAssetData>();
items = new MappedList <ItemAssetData>();
enemies = new MappedList <EnemyAssetData>();
}
public void CreateMatches(SrmSettings settings, IEnumerable <string> sequences,
MappedList <string, StaticMod> defSetStatic, MappedList <string, StaticMod> defSetHeavy)
{
_sequences = sequences.GetEnumerator();
InitMatcherSettings(settings, defSetStatic, defSetHeavy);
if (UnmatchedSequences.Count > 0)
{
UnmatchedSequences.Sort();
throw new FormatException(UninterpretedMods);
}
}
public IActionResult SaveDisplayName(string listId, string Modelid, string displayname, bool isdefaultmodule)
{
string token = HttpContext.Session.GetString("access_token");
List <MappedList> Mappedmodule = APIservice.GetListById <MappedList>(listId.Trim(), "synapsenamespace=meta&synapseentityname=applicationlist&synapseattributename=application_id&attributevalue=", token).OrderBy(o => o.displayorder).ToList();
MappedList Model = Mappedmodule.Single(s => s.applicationlist_id == Modelid);
Model.listname = displayname;
string results = APIservice.PostObject <MappedList>(Model, "synapsenamespace=meta&synapseentityname=applicationlist", token);
return(new EmptyResult());
}
public void Index_FirstIsLast()
{
// arrange
var list = new MappedList(_testMap);
list.SetValues(_testValues);
// act
var value = list[0];
// assert
Assert.Equal("baz", value);
}
public void Contains_DoesContain_IsTrue()
{
// arrange
var list = new MappedList(_testMap);
list.SetValues(_testValues);
// act
var result = list.Contains("foo");
// assert
Assert.True(result);
}
public void Count_ReturnsCount()
{
// arrange
var list = new MappedList(_testMap);
list.SetValues(_testValues);
// act
var count = list.Count;
// assert
Assert.Equal(_testValues.Length, count);
}
public void Contains_DoesNotContain_IsFalse()
{
// arrange
var list = new MappedList(_testMap);
list.SetValues(_testValues);
// act
var result = list.Contains("bat");
// assert
Assert.False(result);
}
public static string SaveDisplayName(string listId, string displayname, bool isdefaultmodule)
{
if (isdefaultmodule)
{
}
List <MappedList> Mappedmodule = listMappedmodules;
MappedList Model = Mappedmodule.Single(s => s.applicationlist_id == listId);
Model.listname = displayname;
string results = APIservice.PostObject <MappedList>(Model, "synapsenamespace=meta&synapseentityname=applicationlist");
listMappedmodules = APIservice.GetListById <MappedList>(ApplicationId, "synapsenamespace=meta&synapseentityname=applicationlist&synapseattributename=application_id&attributevalue=").OrderBy(o => o.displayorder).ToList();;
return(results);
}
public static void AddScriptableObjectWrappedDataOfType <T, TWrapper>(Object o, MappedList <T> dataList)
where T : IUniqueName
where TWrapper : ScriptableObjectDataWrapper <T>
{
Debug.Assert(dataList != null);
dataList.ClearList();
var dataWrappers = Instance.GetAllAssetsOfType <TWrapper>();
var data = new List <T>();
foreach (var dataWrapper in dataWrappers)
{
data.Add(dataWrapper.Data);
}
dataList.AddItems(data);
dataList.MakeDict();
EditorUtility.SetDirty(o);
AssetDatabase.SaveAssets();
}
private static IList <ExplicitMod> GetExplicitMods(IList <ComboBox> mods,
MappedList <string, StaticMod> listSettingsMods)
{
List <ExplicitMod> listMods = new List <ExplicitMod>();
for (int i = 0; i < mods.Count; i++)
{
string modName = (string)mods[i].SelectedItem;
if (!string.IsNullOrEmpty(modName))
{
StaticMod settingsMod;
if (listSettingsMods.TryGetValue(modName, out settingsMod))
{
listMods.Add(new ExplicitMod(i, settingsMod));
}
}
}
return(listMods.ToArray());
}
public void Foreach_ListIsBackwards()
{
// arrange
var expected = new[] { "baz", "bar", "foo" };
var list = new MappedList(_testMap);
list.SetValues(_testValues);
// act
var output = new List <string>();
foreach (var value in list)
{
output.Add(value);
}
// assert
var asArray = output.ToArray();
Assert.Equal(expected, asArray);
}
public virtual PeptideModifications GetDocModifications(SrmDocument document)
{
var lightMods = new MappedList <string, StaticMod>();
lightMods.AddRange(DefSetStatic);
var heavyMods = new MappedList <string, StaticMod>();
heavyMods.AddRange(DefSetHeavy);
foreach (var matchPair in Matches)
{
var lightMod = matchPair.Value.StructuralMod;
if (lightMod != null && !lightMods.Contains(lightMod))
{
lightMods.Add(lightMod.ChangeExplicit(true));
}
var heavyMod = matchPair.Value.HeavyMod;
if (heavyMod != null && !heavyMods.Contains(heavyMod))
{
heavyMods.Add(heavyMod.ChangeExplicit(true));
}
}
return(document.Settings.PeptideSettings.Modifications.DeclareExplicitMods(document, lightMods, heavyMods));
}
private static void UpdateMatcher(
StaticMod[] docStatMods, StaticMod[] docHeavyMods,
StaticMod[] globalStatMods, StaticMod[] globalHeavyMods, IEnumerable <string> seqs)
{
docStatMods = docStatMods ?? new StaticMod[0];
docHeavyMods = docHeavyMods ?? new StaticMod[0];
globalStatMods = globalStatMods ?? new StaticMod[0];
globalHeavyMods = globalHeavyMods ?? new StaticMod[0];
MappedList <string, StaticMod> mapGlobalStatMods = new MappedList <string, StaticMod>();
mapGlobalStatMods.AddRange(docStatMods);
mapGlobalStatMods.AddRange(globalStatMods);
MappedList <string, StaticMod> mapGlobalHeavyMods = new MappedList <string, StaticMod>();
mapGlobalHeavyMods.AddRange(docHeavyMods);
mapGlobalHeavyMods.AddRange(globalHeavyMods);
var settings = SrmSettingsList.GetDefault()
.ChangePeptideModifications(mods =>
mods.ChangeStaticModifications(docStatMods));
settings = settings.ChangePeptideModifications(mods =>
mods.ChangeModifications(IsotopeLabelType.heavy, docHeavyMods));
MATCHER.CreateMatches(settings, seqs, mapGlobalStatMods, mapGlobalHeavyMods);
}
internal void InitMatcherSettings(SrmSettings settings,
MappedList <string, StaticMod> defSetStatic, MappedList <string, StaticMod> defSetHeavy)
{
DefSetStatic = defSetStatic;
DefSetHeavy = defSetHeavy;
Settings = settings;
var modifications = settings.PeptideSettings.Modifications;
UserDefinedTypedMods = new Dictionary <StaticMod, IsotopeLabelType>();
// First add modifications found in document settings, then add modifications found in the global settings.
foreach (var type in settings.PeptideSettings.Modifications.GetModificationTypes())
{
// Set the default heavy type to the first heavy type encountered.
if (!ReferenceEquals(type, IsotopeLabelType.light) && DocDefHeavyLabelType == null)
{
DocDefHeavyLabelType = type;
}
InitUserDefTypedModDict(modifications.GetModificationsByName(type.Name), false);
}
InitUserDefTypedModDict(new TypedModifications(IsotopeLabelType.light, DefSetStatic), true);
InitUserDefTypedModDict(new TypedModifications(DocDefHeavyLabelType, DefSetHeavy), true);
Matches = new Dictionary <AAModKey, AAModMatch>();
UnmatchedSequences = new List <string>();
_foundHeavyLabels = new List <StaticMod>();
while (MoveNextSequence())
{
InitModMatches();
}
CleanUpMatches();
Initialized = true;
}
public static void MapModuletoApplication(string listId, string attributename, int ordinalposition)
{
MappedList Model = new MappedList();
Guid id = Guid.NewGuid();
PatientListModel moduleobj = listModulesModel.Single(s => s.list_id == attributename);
Model.applicationlist_id = id.ToString();
Model.application_id = ApplicationId;
Model.listid = attributename;
Model.listname = moduleobj.listname;
if (listMappedmodules.Count == 0)
{
Model.displayorder = 1;
}
else
{
Model.displayorder = listMappedmodules.Max(x => x.displayorder.Value) + 1;
}
string results = APIservice.PostObject <MappedList>(Model, "synapsenamespace=meta&synapseentityname=applicationlist");
listMappedmodules = APIservice.GetListById <MappedList>(ApplicationId, "synapsenamespace=meta&synapseentityname=applicationlist&synapseattributename=application_id&attributevalue=").OrderBy(o => o.displayorder).ToList();;
}
/// <summary>
/// Adds a list of PeptideDocNodes found in the library to the current document.
/// </summary>
public SrmDocument AddPeptides(SrmDocument document, ILongWaitBroker broker, IdentityPath toPath, out IdentityPath selectedPath)
{
if (toPath != null &&
toPath.Depth == (int)SrmDocument.Level.MoleculeGroups &&
ReferenceEquals(toPath.GetIdentity((int)SrmDocument.Level.MoleculeGroups), SequenceTree.NODE_INSERT_ID))
{
toPath = null;
}
SkippedPeptideCount = 0;
var dictCopy = new Dictionary <PeptideSequenceModKey, PeptideMatch>();
// Make heavy mods explicit
if (PeptideMatches.Values.Contains(match => match.NodePep.HasExplicitMods &&
match.NodePep.ExplicitMods.HeavyModifications != null))
{
_matcher.ConvertAllHeavyModsExplicit();
}
// Call ensure mods on all peptides to be added to the document.
var listDefStatMods = new MappedList <string, StaticMod>();
listDefStatMods.AddRange(Properties.Settings.Default.StaticModList);
listDefStatMods.AddRange(document.Settings.PeptideSettings.Modifications.StaticModifications);
var listDefHeavyMods = new MappedList <string, StaticMod>();
listDefHeavyMods.AddRange(Properties.Settings.Default.HeavyModList);
listDefHeavyMods.AddRange(document.Settings.PeptideSettings.Modifications.AllHeavyModifications);
foreach (var key in PeptideMatches.Keys)
{
var match = PeptideMatches[key];
var nodePepDocSet = match.NodePep;
if (_matcher.MatcherPepMods != null)
{
nodePepDocSet = match.NodePep.EnsureMods(_matcher.MatcherPepMods,
document.Settings.PeptideSettings.Modifications,
listDefStatMods, listDefHeavyMods);
}
if (!dictCopy.ContainsKey(nodePepDocSet.SequenceKey))
{
dictCopy.Add(nodePepDocSet.SequenceKey,
new PeptideMatch(nodePepDocSet, match.Proteins,
match.MatchesFilterSettings));
}
}
if (!Properties.Settings.Default.LibraryPeptidesKeepFiltered)
{
// TODO: This removes entire peptides where only a single
// precursor does not match. e.g. the library contains
// a singly charged precursor match, but also doubly charged
dictCopy = dictCopy.Where(match => match.Value.MatchesFilterSettings)
.ToDictionary(match => match.Key, match => match.Value);
}
SrmDocument newDocument = UpdateExistingPeptides(document, dictCopy, toPath, out selectedPath);
toPath = selectedPath;
// If there is an associated background proteome, add peptides that can be
// matched to the proteins from the background proteom.
if (_backgroundProteome != null)
{
newDocument = AddProteomePeptides(newDocument, dictCopy, broker,
toPath, out selectedPath);
}
toPath = selectedPath;
// Add all remaining peptides as a peptide list.
if (_backgroundProteome == null || Properties.Settings.Default.LibraryPeptidesAddUnmatched)
{
var listPeptidesToAdd = dictCopy.Values.ToList();
listPeptidesToAdd.RemoveAll(match => match.Proteins != null && match.Proteins.Count > 0);
if (listPeptidesToAdd.Count > 0)
{
newDocument = AddPeptidesToLibraryGroup(newDocument, listPeptidesToAdd, broker,
toPath, out selectedPath);
if (listPeptidesToAdd.Count > 1000)
{
selectedPath = selectedPath.Parent; // Don't force Skyline to open a massive peptide list, if it wouldn't otherwise
}
}
}
return(newDocument);
}
public void CreateMatches(SrmSettings settings, IEnumerable<string> sequences,
MappedList<string, StaticMod> defSetStatic, MappedList<string, StaticMod> defSetHeavy)
{
_sequences = sequences.GetEnumerator();
InitMatcherSettings(settings, defSetStatic, defSetHeavy);
if (UnmatchedSequences.Count > 0)
{
UnmatchedSequences.Sort();
throw new FormatException(UninterpretedMods);
}
}
protected void AddScriptableObjectWrappedData <T, TWrapper>(MappedList <T> mappedList)
where T : IUniqueName
where TWrapper : ScriptableObjectDataWrapper <T>
{
AssetEditor.AddScriptableObjectWrappedDataOfType <T, TWrapper>(this, mappedList);
}
/// <summary>
/// Create a new set of explicit modifications on a peptide from a list of desired
/// modifications of each type, and the global lists of available modifications.
/// </summary>
/// <param name="nodePep">The peptide to modify</param>
/// <param name="staticMods">Static modifications to be applied</param>
/// <param name="listStaticMods">Global static modifications</param>
/// <param name="heavyMods">All sets of isotope labeled mods to be applied</param>
/// <param name="listHeavyMods">Global isotope labeled mods</param>
/// <param name="implicitOnly">True to create an explicit expression of the implicit modifications</param>
public ExplicitMods(PeptideDocNode nodePep,
IList<StaticMod> staticMods, MappedList<string, StaticMod> listStaticMods,
IEnumerable<TypedModifications> heavyMods, MappedList<string, StaticMod> listHeavyMods,
bool implicitOnly = false)
{
Peptide = nodePep.Peptide;
var modifications = new List<TypedExplicitModifications>();
TypedExplicitModifications staticTypedMods = null;
// Add static mods, if applicable
if (staticMods != null)
{
IList<ExplicitMod> explicitMods = GetImplicitMods(staticMods, listStaticMods);
// If the peptide has variable modifications, make them all override
// the modification state of the default implicit mods
if (!implicitOnly && nodePep.HasVariableMods)
{
explicitMods = MergeExplicitMods(nodePep.ExplicitMods.StaticModifications,
explicitMods, staticMods);
}
staticTypedMods = new TypedExplicitModifications(Peptide,
IsotopeLabelType.light, explicitMods);
modifications.Add(staticTypedMods);
}
foreach (TypedModifications typedMods in heavyMods)
{
var explicitMods = GetImplicitMods(typedMods.Modifications, listHeavyMods);
var typedHeavyMods = new TypedExplicitModifications(Peptide,
typedMods.LabelType, explicitMods);
modifications.Add(typedHeavyMods.AddModMasses(staticTypedMods));
}
_modifications = MakeReadOnly(modifications.ToArray());
}
public virtual PeptideModifications GetDocModifications(SrmDocument document)
{
var lightMods = new MappedList<string, StaticMod>();
lightMods.AddRange(DefSetStatic);
var heavyMods = new MappedList<string, StaticMod>();
heavyMods.AddRange(DefSetHeavy);
foreach (var matchPair in Matches)
{
var lightMod = matchPair.Value.StructuralMod;
if (lightMod != null && !lightMods.Contains(lightMod))
lightMods.Add(lightMod.ChangeExplicit(true));
var heavyMod = matchPair.Value.HeavyMod;
if (heavyMod != null && !heavyMods.Contains(heavyMod))
heavyMods.Add(heavyMod.ChangeExplicit(true));
}
return document.Settings.PeptideSettings.Modifications.DeclareExplicitMods(document, lightMods, heavyMods);
}
/// <summary>
/// Adds a list of PeptideDocNodes found in the library to the current document.
/// </summary>
public SrmDocument AddPeptides(SrmDocument document, ILongWaitBroker broker, IdentityPath toPath, out IdentityPath selectedPath)
{
if (toPath != null &&
toPath.Depth == (int)SrmDocument.Level.MoleculeGroups &&
ReferenceEquals(toPath.GetIdentity((int)SrmDocument.Level.MoleculeGroups), SequenceTree.NODE_INSERT_ID))
{
toPath = null;
}
SkippedPeptideCount = 0;
var dictCopy = new Dictionary<PeptideSequenceModKey, PeptideMatch>();
// Make heavy mods explicit
if (PeptideMatches.Values.Contains(match => match.NodePep.HasExplicitMods
&& match.NodePep.ExplicitMods.HeavyModifications != null))
{
_matcher.ConvertAllHeavyModsExplicit();
}
// Call ensure mods on all peptides to be added to the document.
var listDefStatMods = new MappedList<string, StaticMod>();
listDefStatMods.AddRange(Properties.Settings.Default.StaticModList);
listDefStatMods.AddRange(document.Settings.PeptideSettings.Modifications.StaticModifications);
var listDefHeavyMods = new MappedList<string, StaticMod>();
listDefHeavyMods.AddRange(Properties.Settings.Default.HeavyModList);
listDefHeavyMods.AddRange(document.Settings.PeptideSettings.Modifications.HeavyModifications);
foreach (var key in PeptideMatches.Keys)
{
var match = PeptideMatches[key];
var nodePepDocSet = match.NodePep;
if (_matcher.MatcherPepMods != null)
nodePepDocSet = match.NodePep.EnsureMods(_matcher.MatcherPepMods,
document.Settings.PeptideSettings.Modifications,
listDefStatMods, listDefHeavyMods);
if (!dictCopy.ContainsKey(nodePepDocSet.SequenceKey))
dictCopy.Add(nodePepDocSet.SequenceKey,
new PeptideMatch(nodePepDocSet, match.Proteins,
match.MatchesFilterSettings));
}
if (!Properties.Settings.Default.LibraryPeptidesKeepFiltered)
{
// TODO: This removes entire peptides where only a single
// precursor does not match. e.g. the library contains
// a singly charged precursor match, but also doubly charged
dictCopy = dictCopy.Where(match => match.Value.MatchesFilterSettings)
.ToDictionary(match => match.Key, match => match.Value);
}
SrmDocument newDocument = UpdateExistingPeptides(document, dictCopy, toPath, out selectedPath);
toPath = selectedPath;
// If there is an associated background proteome, add peptides that can be
// matched to the proteins from the background proteom.
if (_backgroundProteome != null)
{
newDocument = AddProteomePeptides(newDocument, dictCopy, broker,
toPath, out selectedPath);
}
toPath = selectedPath;
// Add all remaining peptides as a peptide list.
if (_backgroundProteome == null || Properties.Settings.Default.LibraryPeptidesAddUnmatched)
{
var listPeptidesToAdd = dictCopy.Values.ToList();
listPeptidesToAdd.RemoveAll(match => match.Proteins != null && match.Proteins.Count > 0);
if (listPeptidesToAdd.Count > 0)
{
newDocument = AddPeptidesToLibraryGroup(newDocument, listPeptidesToAdd, broker,
toPath, out selectedPath);
}
}
return newDocument;
}
private static void UpdateMatcher(
StaticMod[] docStatMods, StaticMod[] docHeavyMods,
StaticMod[] globalStatMods, StaticMod[] globalHeavyMods, IEnumerable<string> seqs)
{
docStatMods = docStatMods ?? new StaticMod[0];
docHeavyMods = docHeavyMods ?? new StaticMod[0];
globalStatMods = globalStatMods ?? new StaticMod[0];
globalHeavyMods = globalHeavyMods ?? new StaticMod[0];
MappedList<string, StaticMod> mapGlobalStatMods = new MappedList<string, StaticMod>();
mapGlobalStatMods.AddRange(docStatMods);
mapGlobalStatMods.AddRange(globalStatMods);
MappedList<string, StaticMod> mapGlobalHeavyMods = new MappedList<string, StaticMod>();
mapGlobalHeavyMods.AddRange(docHeavyMods);
mapGlobalHeavyMods.AddRange(globalHeavyMods);
var settings = SrmSettingsList.GetDefault()
.ChangePeptideModifications(mods =>
mods.ChangeStaticModifications(docStatMods));
settings = settings.ChangePeptideModifications(mods =>
mods.ChangeHeavyModifications(docHeavyMods));
MATCHER.CreateMatches(settings, seqs, mapGlobalStatMods, mapGlobalHeavyMods);
}
public void TestModificationMatcher()
{
InitSeqs();
var carbC = StaticModList.GetDefaultsOn()[0];
// Test exception thrown if unable to match - mass.
UpdateMatcherFail(STR_FAIL_MASS);
UpdateMatcherFail(STR_FAIL_NOT_A_NUMBER);
// Test exception thrown if unable to match - name.
UpdateMatcherFail(STR_FAIL_NAME);
// Can't match empty modifications.
UpdateMatcherFail(STR_FAIL_EMPTY_MOD);
UpdateMatcherFail(STR_FAIL_EMPTY_MOD2);
// Can't match double modifications.
UpdateMatcherFail(STR_FAIL_DOUBLE_MOD);
// Test exception thrown if unimod not specified correctly
UpdateMatcherFail(STR_FAIL_UNIMOD);
UpdateMatcherFail(STR_UNKNOWN_UNIMOD);
// Can't phosphorylate tryptophan
UpdateMatcherFail(STR_FAIL_WRONG_AA_UNIMOD);
// Can't put C-terminal modification in middle of peptide
UpdateMatcherFail(STR_FAIL_UNIMOD_TERMINUS);
// Test mods in UniMod match correctly.
UpdateMatcher(StaticModList.GetDefaultsOn(), HeavyModList.GetDefaultsOn(), null, null);
// A sequence with no modifications should not be explicitly modified.
Assert.IsFalse(MATCHER.GetModifiedNode(STR_NO_MODS).HasExplicitMods);
var nodeCysOxi = MATCHER.GetModifiedNode(STR_CYS_AND_OXI);
Assert.IsTrue(nodeCysOxi.HasExplicitMods);
Assert.IsFalse(nodeCysOxi.ExplicitMods.HasHeavyModifications);
// Modifications should match by name.
Assert.IsTrue(MATCHER.GetModifiedNode(STR_MOD_BY_NAME).ExplicitMods.StaticModifications.Contains(mod =>
Equals(mod.Modification.Name, "Phospho (ST)")));
// Test can find terminal modification
Assert.IsTrue(MATCHER.GetModifiedNode(STR_TERM_ONLY).ExplicitMods.HeavyModifications.Contains(mod =>
mod.Modification.EquivalentAll(UniMod.GetModification("Label:13C(6) (C-term R)", false))));
// Test can find matches on terminus that are not terminal
Assert.IsTrue(MATCHER.GetModifiedNode(STR_MOD_BY_NAME).ExplicitMods.StaticModifications.Contains(mod =>
mod.Modification.Terminus == null));
// Test matching negative masses
Assert.IsTrue(MATCHER.GetModifiedNode(STR_AMMONIA_LOSS).ExplicitMods.StaticModifications.Contains(mod =>
mod.Modification.EquivalentAll(UniMod.GetModification("Ammonia-loss (N-term C)", true))));
// General and specific
// If all AAs modified, try for most general modification.
Assert.IsTrue(MATCHER.GetModifiedNode(STR_HEAVY_15)
.ExplicitMods.HeavyModifications.Contains(mod => mod.Modification.Equivalent(LABEL15_N)));
// Updating the settings.
// Peptide settings should change to include new mods.
var docNew = new SrmDocument(SrmSettingsList.GetDefault());
IdentityPath firstAdded;
IdentityPath nextAdded;
docNew = docNew.AddPeptideGroups(new[] { new PeptideGroupDocNode(new PeptideGroup(), "PepGroup1", "",
new[] { MATCHER.GetModifiedNode(STR_MOD_BY_NAME) }) }, true, null, out firstAdded, out nextAdded);
var pepSetNew = MATCHER.GetDocModifications(docNew);
Assert.IsTrue(pepSetNew.StaticModifications.Contains(UniMod.GetModification("Phospho (ST)", true).ChangeExplicit(true)));
// Update the document to the new settings.
var pepSetNew1 = pepSetNew;
var settingsNew2 = docNew.Settings.ChangePeptideModifications(mods => pepSetNew1);
var lightGlobalMods = new MappedList <string, StaticMod>();
lightGlobalMods.AddRange(settingsNew2.PeptideSettings.Modifications.StaticModifications);
var heavyGlobalMods = new MappedList <string, StaticMod>();
heavyGlobalMods.AddRange(settingsNew2.PeptideSettings.Modifications.AllHeavyModifications);
// Match again. Test FoundMatches string should now be empty.
MATCHER.CreateMatches(docNew.Settings.ChangePeptideModifications(mods => pepSetNew1),
new List <string> {
STR_MOD_BY_NAME
}, lightGlobalMods, heavyGlobalMods);
Assert.IsTrue(string.IsNullOrEmpty(MATCHER.FoundMatches));
// Adding 15N to the settings.
UpdateMatcher(new[] { carbC }, new[] { LABEL15_N }, null, null);
// Test sequences with only explicit heavy mods should not have explicit light mods
Assert.IsNull(MATCHER.GetModifiedNode(STR_HEAVY_ONLY).ExplicitMods.StaticModifications);
// Test sequences with only explicit light mods should not have explicit heavy mods
Assert.IsFalse(MATCHER.GetModifiedNode(STR_LIGHT_ONLY).ExplicitMods.HasHeavyModifications);
// Test global mods take precendence over UniMod
UpdateMatcher(new[] { carbC }, null, new[] { OXIDATION_M_GLOBAL }, new[] { LABEL15_N });
Assert.IsTrue(MATCHER.GetModifiedNode(STR_CYS_AND_OXI).ExplicitMods.StaticModifications
.Contains(mod => Equals(mod.Modification, OXIDATION_M_GLOBAL)));
// Test document mods take precendence over UniMod
UpdateMatcher(new[] { carbC, METHIONINE_OXIDATION }, null, new[] { OXIDATION_M_GLOBAL }, new[] { LABEL15_N });
Assert.IsFalse(MATCHER.GetModifiedNode(STR_CYS_AND_OXI).HasExplicitMods);
// Test exception thrown if match doesn't make sense - wrong AA.
UpdateMatcherFail(STR_FAIL_OX_ON_D);
// Test exception thrown if match doesn't make sense - wrong terminus.
_seqs.Add(STR_FAIL_OX_TERM);
AssertEx.ThrowsException <FormatException>(() => UpdateMatcher(new[] { OXIDATION_M_C_TERM }, null, null, null));
_seqs.Remove(STR_FAIL_OX_TERM);
// Heavy 15N - All AAs.
UpdateMatcher(new[] { carbC, METHIONINE_OXIDATION }, new[] { LABEL15_N }, null, null);
// Node should be created from document settings if possible.
Assert.IsNull(MATCHER.GetModifiedNode(STR_HEAVY_15).ExplicitMods);
// Heavy 15N - specific AA.
// If only a specific AA is modified, there must be an explicit mod.
Assert.IsTrue(MATCHER.GetModifiedNode(STR_HEAVY_15_F).HasExplicitMods);
// Test variable mods match correctly.
// Put variable mod in global mod and not on doc - make sure don't get variable mod,
// should get explicit mod in that case.
var variableMetOx = METHIONINE_OXIDATION.ChangeVariable(true);
UpdateMatcher(new[] { carbC }, null, new[] { variableMetOx }, null);
Assert.IsTrue(MATCHER.GetModifiedNode(STR_CYS_AND_OXI).HasExplicitMods);
Assert.IsFalse(MATCHER.GetModifiedNode(STR_CYS_OXI_PHOS).ExplicitMods.IsVariableStaticMods);
Assert.IsFalse(MATCHER.GetModifiedNode(STR_CYS_OXI_PHOS_CAP).ExplicitMods.IsVariableStaticMods);
// Add variable mod to doc
UpdateMatcher(new[] { carbC, variableMetOx }, null, null, null);
// Mod can be created by the settings.
Assert.IsTrue(MATCHER.GetModifiedNode(STR_CYS_AND_OXI).HasExplicitMods);
Assert.IsTrue(MATCHER.GetModifiedNode(STR_CYS_AND_OXI).ExplicitMods.IsVariableStaticMods);
// Mod cannot be created by the settings.
Assert.IsFalse(MATCHER.GetModifiedNode(STR_CYS_OXI_PHOS).ExplicitMods.IsVariableStaticMods);
Assert.IsFalse(MATCHER.GetModifiedNode(STR_CYS_OXI_PHOS_CAP).ExplicitMods.IsVariableStaticMods);
// Add Met Ox to global. Test: +16 finds it.
UpdateMatcher(new[] { carbC }, null, new[] { MET_OX_ROUNDED }, null);
Assert.IsTrue(MATCHER.GetModifiedNode(STR_CYS_AND_OXI).
ExplicitMods.StaticModifications.Contains(mod => Equals(mod.Modification, MET_OX_ROUNDED)));
// Test: +15.99 finds UniMod.
Assert.IsFalse(MATCHER.GetModifiedNode(STR_HEAVY_15).
ExplicitMods.StaticModifications.Contains(mod => Equals(mod.Modification, MET_OX_ROUNDED)));
// Add Methionine Oxidation before Met Ox. Test: +16 finds it.
UpdateMatcher(new[] { carbC }, null, new[] { METHIONINE_OXIDATION, MET_OX_ROUNDED }, null);
Assert.IsFalse(MATCHER.GetModifiedNode(STR_CYS_AND_OXI).
ExplicitMods.StaticModifications.Contains(mod => Equals(mod.Modification, MET_OX_ROUNDED)));
Assert.IsTrue(MATCHER.GetModifiedNode(STR_CYS_AND_OXI).
ExplicitMods.StaticModifications.Contains(mod => Equals(mod.Modification, METHIONINE_OXIDATION)));
// Test long masses rounded.
Assert.IsTrue(MATCHER.GetModifiedNode(STR_METOX_LONG_MASS).ExplicitMods.StaticModifications.Contains(mod =>
Equals(mod.Modification, METHIONINE_OXIDATION)));
// Test UniMod label types
var node = MATCHER.GetModifiedNode(STR_UNIMOD_LABEL);
Assert.IsNotNull(node);
Assert.IsNull(node.ExplicitMods.StaticModifications);
Assert.IsTrue(node.ExplicitMods.HeavyModifications.Contains(mod =>
Equals(mod.Modification, N_TERM_LABEL)));
UpdateMatcherWithNoSequences(new[] { carbC }, new[] { N_TERM_LABEL }, new[] { METHIONINE_OXIDATION, MET_OX_ROUNDED }, null);
var nodeNew = MATCHER.GetModifiedNode(STR_UNIMOD_LABEL);
Assert.IsNotNull(nodeNew);
Assert.IsTrue(nodeNew.TransitionGroups.Any(group => Equals(group.TransitionGroup.LabelType, IsotopeLabelType.heavy)));
UpdateMatcher(new[] { carbC }, null, new[] { METHIONINE_OXIDATION, MET_OX_ROUNDED }, null);
// Test case where there are lots of unimod labels
var nodeUniAll = MATCHER.GetModifiedNode(STR_UNIMOD_ALL);
Assert.AreEqual(nodeUniAll.ExplicitMods.HeavyModifications.Count, 10);
Assert.IsNull(nodeUniAll.ExplicitMods.StaticModifications);
foreach (var mod in nodeUniAll.ExplicitMods.HeavyModifications)
{
Assert.AreEqual(mod.Modification.ShortName, "+01");
Assert.AreEqual(mod.Modification.UnimodId, 994);
}
// Test unimod terminal label
var nodeUniTerm = MATCHER.GetModifiedNode(STR_UNIMOD_TERMINUS);
Assert.AreEqual(nodeUniTerm.ExplicitMods.HeavyModifications.Count, 1);
Assert.IsNull(nodeUniTerm.ExplicitMods.StaticModifications);
Assert.AreEqual(nodeUniTerm.ExplicitMods.HeavyModifications[0].Modification.Terminus, ModTerminus.C);
Assert.AreEqual(nodeUniTerm.ExplicitMods.HeavyModifications[0].Modification.UnimodId, 298);
// Basic multi-label test
var heavyLabelType2 = new IsotopeLabelType("Heavy2", 1);
var typedMod = new TypedModifications(heavyLabelType2, new List <StaticMod> {
LABEL15_N
});
var peptideMods = new PeptideModifications(new List <StaticMod>(), new List <TypedModifications> {
typedMod
});
var settingsMultiLabel = SrmSettingsList.GetDefault().ChangePeptideModifications(mods => peptideMods);
var defSetSetLight = new MappedList <string, StaticMod>();
defSetSetLight.AddRange(StaticModList.GetDefaultsOn());
var defSetHeavy = new MappedList <string, StaticMod>();
defSetHeavy.AddRange(HeavyModList.GetDefaultsOn());
defSetHeavy.Add(LABEL15_N);
MATCHER.CreateMatches(settingsMultiLabel, new List <string> {
STR_HEAVY_15_F
}, defSetSetLight, defSetHeavy);
Assert.IsTrue(MATCHER.GetModifiedNode(STR_HEAVY_15_F).ExplicitMods.GetHeavyModifications().Contains(mod => Equals(mod.LabelType, heavyLabelType2)));
// Peptide settings should not change.
var docNew0 = new SrmDocument(settingsMultiLabel).AddPeptideGroups(new[] { new PeptideGroupDocNode(new PeptideGroup(),
"PepGroup1", "", new[] { MATCHER.GetModifiedNode(STR_HEAVY_15_F) }) }, true, null, out firstAdded, out nextAdded);
var settingsNew = MATCHER.GetDocModifications(docNew0);
Assert.AreEqual(settingsMultiLabel.PeptideSettings.Modifications.ChangeHasHeavyModifications(false),
settingsNew.ChangeHasHeavyModifications(false));
// Finding specific modifications.
// If only specific AA modified, try for most specific modification.
UpdateMatcher(null, null, null, null, new[] { STR_HEAVY_15_F });
Assert.IsTrue(MATCHER.GetModifiedNode(STR_HEAVY_15_F)
.ExplicitMods.HeavyModifications.Contains(mod =>
mod.Modification.AminoAcids.Contains(c => c == 'F')));
// If only some AAs modified, try for most specific modifications.
UpdateMatcher(null, null, null, null, new[] { STR_HEAVY_15_NOT_ALL });
Assert.IsTrue(MATCHER.GetModifiedNode(STR_HEAVY_15_NOT_ALL)
.ExplicitMods.HeavyModifications.Contains(mod =>
mod.Modification.AminoAcids.Contains(c => c == 'I')));
using (var testDir = new TestFilesDir(TestContext, ZIP_FILE))
using (var modMatchDocContainer = InitMatchDocContainer(testDir))
{
var libkeyModMatcher = new LibKeyModificationMatcher();
var anlLibSpec = new BiblioSpecLiteSpec("ANL_Combo", testDir.GetTestPath("ANL_Combined.blib"));
var yeastLibSpec = new BiblioSpecLiteSpec("Yeast", testDir.GetTestPath("Yeast_atlas_small.blib"));
modMatchDocContainer.ChangeLibSpecs(new[] { anlLibSpec, yeastLibSpec });
var docLibraries = modMatchDocContainer.Document.Settings.PeptideSettings.Libraries.Libraries;
int anlLibIndex = docLibraries.IndexOf(library => Equals(library.Name, anlLibSpec.Name));
int yeastLibIndex = docLibraries.IndexOf(library => Equals(library.Name, yeastLibSpec.Name));
libkeyModMatcher.CreateMatches(modMatchDocContainer.Document.Settings,
docLibraries[anlLibIndex].Keys, defSetSetLight, defSetHeavy);
// Test can match 15N
Assert.IsTrue(libkeyModMatcher.Matches.Values.Contains(match =>
match.HeavyMod != null && match.HeavyMod.Equivalent(LABEL15_N)));
var uniModMetOx = UniMod.GetModification("Oxidation (M)", true);
// Test can match Met Ox
Assert.IsTrue(libkeyModMatcher.Matches.Values.Contains(match =>
match.StructuralMod != null && match.StructuralMod.Equivalent(uniModMetOx)));
// Test can match 15N and Met ox!
Assert.IsTrue(libkeyModMatcher.Matches.Contains(match => match.Key.Mass == 17 &&
match.Value.StructuralMod != null && match.Value.StructuralMod.Equivalent(uniModMetOx) &&
match.Value.HeavyMod != null && match.Value.HeavyMod.Equivalent(LABEL15_N)));
// Test can match Cysteine (Implicit) and Met Ox (variable)
libkeyModMatcher.CreateMatches(modMatchDocContainer.Document.Settings,
docLibraries[yeastLibIndex].Keys, defSetSetLight, defSetHeavy);
Assert.IsTrue(libkeyModMatcher.MatcherPepMods.StaticModifications.Contains(mod =>
mod.Formula.Equals(UniMod.GetModification(StaticModList.DEFAULT_NAME, true).Formula) && !mod.IsVariable));
Assert.IsTrue(libkeyModMatcher.MatcherPepMods.StaticModifications.Contains(mod =>
mod.Formula.Equals("O") && mod.IsVariable));
}
}
public void CreateMatches(SrmSettings settings, IEnumerable<LibKey> libKeys,
MappedList<string, StaticMod> defSetStatic, MappedList<string, StaticMod> defSetHeavy)
{
_dictAAMassPairs = new Dictionary<AATermKey, List<byte[]>>();
_libKeys = libKeys.GetEnumerator();
InitMatcherSettings(settings, defSetStatic, defSetHeavy);
MatcherPepMods = CreateMatcherPeptideSettings();
}
/// <summary>
/// Builds a list of <see cref="ExplicitMod"/> objects from the implicit modifications
/// on the document.
/// </summary>
/// <param name="mods">Implicit modifications on the document</param>
/// <param name="listSettingsMods">All modifications available in the settings</param>
/// <returns>List of <see cref="ExplicitMod"/> objects for the implicit modifications</returns>
private ExplicitMod[] GetImplicitMods(IList<StaticMod> mods, MappedList<string, StaticMod> listSettingsMods)
{
List<ExplicitMod> listImplicitMods = new List<ExplicitMod>();
if (!Peptide.IsCustomIon)
{
string seq = Peptide.Sequence;
for (int i = 0; i < seq.Length; i++)
{
char aa = seq[i];
foreach (StaticMod mod in mods)
{
// Skip explicit mods, since only considering implicit
if (mod.IsExplicit || !mod.IsMod(aa, i, seq.Length))
continue;
// Always use the modification from the settings to ensure expected
// equality comparisons.
StaticMod modAdd;
if (listSettingsMods.TryGetValue(mod.Name, out modAdd))
listImplicitMods.Add(new ExplicitMod(i, modAdd));
}
}
}
return listImplicitMods.ToArray();
}
private void AddAssets <T>(MappedList <T> mappedList) where T : Object, IUniqueName
{
AssetEditor.AddAssetsOfType(this, mappedList);
}
public InsertQuery(Model model, MappedList<string, Field> fields)
{
Model = model;
Fields = fields;
}
internal void InitMatcherSettings(SrmSettings settings,
MappedList<string, StaticMod> defSetStatic, MappedList<string, StaticMod> defSetHeavy)
{
DefSetStatic = defSetStatic;
DefSetHeavy = defSetHeavy;
Settings = settings;
var modifications = settings.PeptideSettings.Modifications;
UserDefinedTypedMods = new Dictionary<StaticMod, IsotopeLabelType>();
// First add modifications found in document settings, then add modifications found in the global settings.
foreach (var type in settings.PeptideSettings.Modifications.GetModificationTypes())
{
// Set the default heavy type to the first heavy type encountered.
if (!ReferenceEquals(type, IsotopeLabelType.light) && DocDefHeavyLabelType == null)
DocDefHeavyLabelType = type;
InitUserDefTypedModDict(modifications.GetModificationsByName(type.Name), false);
}
InitUserDefTypedModDict(new TypedModifications(IsotopeLabelType.light, DefSetStatic), true);
InitUserDefTypedModDict(new TypedModifications(DocDefHeavyLabelType, DefSetHeavy), true);
Matches = new Dictionary<AAModKey, AAModMatch>();
UnmatchedSequences = new List<string>();
_foundHeavyLabels = new List<StaticMod>();
while (MoveNextSequence())
{
InitModMatches();
}
CleanUpMatches();
Initialized = true;
}
private static IList<ExplicitMod> GetExplicitMods(IList<ComboBox> mods,
MappedList<string, StaticMod> listSettingsMods)
{
List<ExplicitMod> listMods = new List<ExplicitMod>();
for (int i = 0; i < mods.Count; i++)
{
string modName = (string) mods[i].SelectedItem;
if (!string.IsNullOrEmpty(modName))
{
StaticMod settingsMod;
if (listSettingsMods.TryGetValue(modName, out settingsMod))
listMods.Add(new ExplicitMod(i, settingsMod));
}
}
return listMods.ToArray();
}
public PeptideDocNode EnsureMods(PeptideModifications source, PeptideModifications target,
MappedList<string, StaticMod> defSetStat, MappedList<string, StaticMod> defSetHeavy)
{
// Create explicit mods matching the implicit mods on this peptide for each document.
var sourceImplicitMods = new ExplicitMods(this, source.StaticModifications, defSetStat, source.GetHeavyModifications(), defSetHeavy);
var targetImplicitMods = new ExplicitMods(this, target.StaticModifications, defSetStat, target.GetHeavyModifications(), defSetHeavy);
// If modifications match, no need to create explicit modifications for the peptide.
if (sourceImplicitMods.Equals(targetImplicitMods))
return this;
// Add explicit mods if static mods not implicit in the target document.
IList<ExplicitMod> newExplicitStaticMods = null;
bool preserveVariable = HasVariableMods;
// Preserve non-variable explicit modifications
if (!preserveVariable && HasExplicitMods && ExplicitMods.StaticModifications != null)
{
// If they are not the same as the implicit modifications in the new document
if (!ArrayUtil.EqualsDeep(ExplicitMods.StaticModifications, targetImplicitMods.StaticModifications))
newExplicitStaticMods = ExplicitMods.StaticModifications;
}
else if (!ArrayUtil.EqualsDeep(sourceImplicitMods.StaticModifications, targetImplicitMods.StaticModifications))
{
preserveVariable = false;
newExplicitStaticMods = sourceImplicitMods.StaticModifications;
}
else if (preserveVariable)
{
newExplicitStaticMods = ExplicitMods.StaticModifications;
}
// Drop explicit mods if matching implicit mods are found in the target document.
IList<TypedExplicitModifications> newExplicitHeavyMods = new List<TypedExplicitModifications>();
// For each heavy label type, add explicit mods if static mods not found in the target document.
var newTypedStaticMods = newExplicitStaticMods != null
? new TypedExplicitModifications(Peptide, IsotopeLabelType.light, newExplicitStaticMods)
: null;
foreach (TypedExplicitModifications targetDocMod in targetImplicitMods.GetHeavyModifications())
{
// Use explicit modifications when available. Otherwise, compare against new implicit modifications
IList<ExplicitMod> heavyMods = (HasExplicitMods ? ExplicitMods.GetModifications(targetDocMod.LabelType) : null) ??
sourceImplicitMods.GetModifications(targetDocMod.LabelType);
if (heavyMods != null && !ArrayUtil.EqualsDeep(heavyMods, targetDocMod.Modifications) && heavyMods.Count > 0)
{
var newTypedHeavyMods = new TypedExplicitModifications(Peptide, targetDocMod.LabelType, heavyMods);
newTypedHeavyMods = newTypedHeavyMods.AddModMasses(newTypedStaticMods);
newExplicitHeavyMods.Add(newTypedHeavyMods);
}
}
if (newExplicitStaticMods != null || newExplicitHeavyMods.Count > 0)
return ChangeExplicitMods(new ExplicitMods(Peptide, newExplicitStaticMods, newExplicitHeavyMods, preserveVariable));
return ChangeExplicitMods(null);
}
public UpdateQuery(Model model, MappedList<string, Field> fields)
{
Model = model;
Fields = fields;
}
public void TestModificationMatcher()
{
InitSeqs();
var carbC = StaticModList.GetDefaultsOn()[0];
// Test exception thrown if unable to match - mass.
UpdateMatcherFail(STR_FAIL_MASS);
UpdateMatcherFail(STR_FAIL_NOT_A_NUMBER);
// Test exception thrown if unable to match - name.
UpdateMatcherFail(STR_FAIL_NAME);
// Can't match empty modifications.
UpdateMatcherFail(STR_FAIL_EMPTY_MOD);
UpdateMatcherFail(STR_FAIL_EMPTY_MOD2);
// Can't match double modifications.
UpdateMatcherFail(STR_FAIL_DOUBLE_MOD);
// Test exception thrown if unimod not specified correctly
UpdateMatcherFail(STR_FAIL_UNIMOD);
UpdateMatcherFail(STR_UNKNOWN_UNIMOD);
// Can't phosphorylate tryptophan
UpdateMatcherFail(STR_FAIL_WRONG_AA_UNIMOD);
// Can't put C-terminal modification in middle of peptide
UpdateMatcherFail(STR_FAIL_UNIMOD_TERMINUS);
// Test mods in UniMod match correctly.
UpdateMatcher(StaticModList.GetDefaultsOn(), HeavyModList.GetDefaultsOn(), null, null);
// A sequence with no modifications should not be explicitly modified.
Assert.IsFalse(MATCHER.GetModifiedNode(STR_NO_MODS).HasExplicitMods);
var nodeCysOxi = MATCHER.GetModifiedNode(STR_CYS_AND_OXI);
Assert.IsTrue(nodeCysOxi.HasExplicitMods);
Assert.IsFalse(nodeCysOxi.ExplicitMods.HasHeavyModifications);
// Modifications should match by name.
Assert.IsTrue(MATCHER.GetModifiedNode(STR_MOD_BY_NAME).ExplicitMods.StaticModifications.Contains(mod =>
Equals(mod.Modification.Name, "Phospho (ST)")));
// Test can find terminal modification
Assert.IsTrue(MATCHER.GetModifiedNode(STR_TERM_ONLY).ExplicitMods.HeavyModifications.Contains(mod =>
mod.Modification.EquivalentAll(UniMod.GetModification("Label:13C(6) (C-term R)", false))));
// Test can find matches on terminus that are not terminal
Assert.IsTrue(MATCHER.GetModifiedNode(STR_MOD_BY_NAME).ExplicitMods.StaticModifications.Contains(mod =>
mod.Modification.Terminus == null));
// Test matching negative masses
Assert.IsTrue(MATCHER.GetModifiedNode(STR_AMMONIA_LOSS).ExplicitMods.StaticModifications.Contains(mod =>
mod.Modification.EquivalentAll(UniMod.GetModification("Ammonia-loss (N-term C)", true))));
// General and specific
// If all AAs modified, try for most general modification.
Assert.IsTrue(MATCHER.GetModifiedNode(STR_HEAVY_15)
.ExplicitMods.HeavyModifications.Contains(mod => mod.Modification.Equivalent(LABEL15_N)));
// Updating the settings.
// Peptide settings should change to include new mods.
var docNew = new SrmDocument(SrmSettingsList.GetDefault());
IdentityPath firstAdded;
IdentityPath nextAdded;
docNew = docNew.AddPeptideGroups(new[] { new PeptideGroupDocNode(new PeptideGroup(), "PepGroup1", "",
new[] {MATCHER.GetModifiedNode(STR_MOD_BY_NAME)})}, true, null, out firstAdded, out nextAdded);
var pepSetNew = MATCHER.GetDocModifications(docNew);
Assert.IsTrue(pepSetNew.StaticModifications.Contains(UniMod.GetModification("Phospho (ST)", true).ChangeExplicit(true)));
// Update the document to the new settings.
var pepSetNew1 = pepSetNew;
var settingsNew2 = docNew.Settings.ChangePeptideModifications(mods => pepSetNew1);
var lightGlobalMods = new MappedList<string, StaticMod>();
lightGlobalMods.AddRange(settingsNew2.PeptideSettings.Modifications.StaticModifications);
var heavyGlobalMods = new MappedList<string, StaticMod>();
heavyGlobalMods.AddRange(settingsNew2.PeptideSettings.Modifications.HeavyModifications);
// Match again. Test FoundMatches string should now be empty.
MATCHER.CreateMatches(docNew.Settings.ChangePeptideModifications(mods => pepSetNew1),
new List<string> { STR_MOD_BY_NAME }, lightGlobalMods, heavyGlobalMods);
Assert.IsTrue(string.IsNullOrEmpty(MATCHER.FoundMatches));
// Adding 15N to the settings.
UpdateMatcher(new[] { carbC }, new[] { LABEL15_N }, null, null);
// Test sequences with only explicit heavy mods should not have explicit light mods
Assert.IsNull(MATCHER.GetModifiedNode(STR_HEAVY_ONLY).ExplicitMods.StaticModifications);
// Test sequences with only explicit light mods should not have explicit heavy mods
Assert.IsFalse(MATCHER.GetModifiedNode(STR_LIGHT_ONLY).ExplicitMods.HasHeavyModifications);
// Test global mods take precendence over UniMod
UpdateMatcher(new[] { carbC }, null, new[] { OXIDATION_M_GLOBAL }, new[] { LABEL15_N });
Assert.IsTrue(MATCHER.GetModifiedNode(STR_CYS_AND_OXI).ExplicitMods.StaticModifications
.Contains(mod => Equals(mod.Modification, OXIDATION_M_GLOBAL)));
// Test document mods take precendence over UniMod
UpdateMatcher(new[] { carbC, METHIONINE_OXIDATION }, null, new[] { OXIDATION_M_GLOBAL }, new[] { LABEL15_N });
Assert.IsFalse(MATCHER.GetModifiedNode(STR_CYS_AND_OXI).HasExplicitMods);
// Test exception thrown if match doesn't make sense - wrong AA.
UpdateMatcherFail(STR_FAIL_OX_ON_D);
// Test exception thrown if match doesn't make sense - wrong terminus.
_seqs.Add(STR_FAIL_OX_TERM);
AssertEx.ThrowsException<FormatException>(() => UpdateMatcher(new[] {OXIDATION_M_C_TERM}, null, null, null));
_seqs.Remove(STR_FAIL_OX_TERM);
// Heavy 15N - All AAs.
UpdateMatcher(new[] { carbC, METHIONINE_OXIDATION }, new[] {LABEL15_N}, null, null);
// Node should be created from document settings if possible.
Assert.IsNull(MATCHER.GetModifiedNode(STR_HEAVY_15).ExplicitMods);
// Heavy 15N - specific AA.
// If only a specific AA is modified, there must be an explicit mod.
Assert.IsTrue(MATCHER.GetModifiedNode(STR_HEAVY_15_F).HasExplicitMods);
// Test variable mods match correctly.
// Put variable mod in global mod and not on doc - make sure don't get variable mod,
// should get explicit mod in that case.
var variableMetOx = METHIONINE_OXIDATION.ChangeVariable(true);
UpdateMatcher(new[] { carbC }, null, new[] { variableMetOx }, null);
Assert.IsTrue(MATCHER.GetModifiedNode(STR_CYS_AND_OXI).HasExplicitMods);
Assert.IsFalse(MATCHER.GetModifiedNode(STR_CYS_OXI_PHOS).ExplicitMods.IsVariableStaticMods);
Assert.IsFalse(MATCHER.GetModifiedNode(STR_CYS_OXI_PHOS_CAP).ExplicitMods.IsVariableStaticMods);
// Add variable mod to doc
UpdateMatcher(new[] { carbC, variableMetOx }, null, null, null);
// Mod can be created by the settings.
Assert.IsTrue(MATCHER.GetModifiedNode(STR_CYS_AND_OXI).HasExplicitMods);
Assert.IsTrue(MATCHER.GetModifiedNode(STR_CYS_AND_OXI).ExplicitMods.IsVariableStaticMods);
// Mod cannot be created by the settings.
Assert.IsFalse(MATCHER.GetModifiedNode(STR_CYS_OXI_PHOS).ExplicitMods.IsVariableStaticMods);
Assert.IsFalse(MATCHER.GetModifiedNode(STR_CYS_OXI_PHOS_CAP).ExplicitMods.IsVariableStaticMods);
// Add Met Ox to global. Test: +16 finds it.
UpdateMatcher(new[] {carbC}, null, new[] {MET_OX_ROUNDED}, null);
Assert.IsTrue(MATCHER.GetModifiedNode(STR_CYS_AND_OXI).
ExplicitMods.StaticModifications.Contains(mod => Equals(mod.Modification, MET_OX_ROUNDED)));
// Test: +15.99 finds UniMod.
Assert.IsFalse(MATCHER.GetModifiedNode(STR_HEAVY_15).
ExplicitMods.StaticModifications.Contains(mod => Equals(mod.Modification, MET_OX_ROUNDED)));
// Add Methionine Oxidation before Met Ox. Test: +16 finds it.
UpdateMatcher(new[] { carbC }, null, new[] { METHIONINE_OXIDATION, MET_OX_ROUNDED }, null);
Assert.IsFalse(MATCHER.GetModifiedNode(STR_CYS_AND_OXI).
ExplicitMods.StaticModifications.Contains(mod => Equals(mod.Modification, MET_OX_ROUNDED)));
Assert.IsTrue(MATCHER.GetModifiedNode(STR_CYS_AND_OXI).
ExplicitMods.StaticModifications.Contains(mod => Equals(mod.Modification, METHIONINE_OXIDATION)));
// Test long masses rounded.
Assert.IsTrue(MATCHER.GetModifiedNode(STR_METOX_LONG_MASS).ExplicitMods.StaticModifications.Contains(mod =>
Equals(mod.Modification, METHIONINE_OXIDATION)));
// Test UniMod label types
var node = MATCHER.GetModifiedNode(STR_UNIMOD_LABEL);
Assert.IsNotNull(node);
Assert.IsNull(node.ExplicitMods.StaticModifications);
Assert.IsTrue(node.ExplicitMods.HeavyModifications.Contains(mod =>
Equals(mod.Modification, N_TERM_LABEL)));
UpdateMatcherWithNoSequences(new[] { carbC }, new[] { N_TERM_LABEL }, new[] { METHIONINE_OXIDATION, MET_OX_ROUNDED }, null);
var nodeNew = MATCHER.GetModifiedNode(STR_UNIMOD_LABEL);
Assert.IsNotNull(nodeNew);
Assert.IsTrue(nodeNew.TransitionGroups.Any(group => Equals(group.TransitionGroup.LabelType, IsotopeLabelType.heavy)));
UpdateMatcher(new[] { carbC }, null, new[] { METHIONINE_OXIDATION, MET_OX_ROUNDED }, null);
// Test case where there are lots of unimod labels
var nodeUniAll = MATCHER.GetModifiedNode(STR_UNIMOD_ALL);
Assert.AreEqual(nodeUniAll.ExplicitMods.HeavyModifications.Count, 10);
Assert.IsNull(nodeUniAll.ExplicitMods.StaticModifications);
foreach (var mod in nodeUniAll.ExplicitMods.HeavyModifications)
{
Assert.AreEqual(mod.Modification.ShortName, "+01");
Assert.AreEqual(mod.Modification.UnimodId, 994);
}
// Test unimod terminal label
var nodeUniTerm = MATCHER.GetModifiedNode(STR_UNIMOD_TERMINUS);
Assert.AreEqual(nodeUniTerm.ExplicitMods.HeavyModifications.Count, 1);
Assert.IsNull(nodeUniTerm.ExplicitMods.StaticModifications);
Assert.AreEqual(nodeUniTerm.ExplicitMods.HeavyModifications[0].Modification.Terminus, ModTerminus.C);
Assert.AreEqual(nodeUniTerm.ExplicitMods.HeavyModifications[0].Modification.UnimodId, 298);
// Basic multi-label test
var heavyLabelType2 = new IsotopeLabelType("Heavy2", 1);
var typedMod = new TypedModifications(heavyLabelType2, new List<StaticMod> { LABEL15_N });
var peptideMods = new PeptideModifications(new List<StaticMod>(), new List<TypedModifications> { typedMod });
var settingsMultiLabel = SrmSettingsList.GetDefault().ChangePeptideModifications(mods => peptideMods);
var defSetSetLight = new MappedList<string, StaticMod>();
defSetSetLight.AddRange(StaticModList.GetDefaultsOn());
var defSetHeavy = new MappedList<string, StaticMod>();
defSetHeavy.AddRange(HeavyModList.GetDefaultsOn());
defSetHeavy.Add( LABEL15_N );
MATCHER.CreateMatches(settingsMultiLabel, new List<string> { STR_HEAVY_15_F }, defSetSetLight, defSetHeavy);
Assert.IsTrue(MATCHER.GetModifiedNode(STR_HEAVY_15_F).ExplicitMods.GetHeavyModifications().Contains(mod => Equals(mod.LabelType, heavyLabelType2)));
// Peptide settings should not change.
var docNew0 = new SrmDocument(settingsMultiLabel).AddPeptideGroups(new[] { new PeptideGroupDocNode(new PeptideGroup(),
"PepGroup1", "", new[] {MATCHER.GetModifiedNode(STR_HEAVY_15_F)})}, true, null, out firstAdded, out nextAdded);
var settingsNew = MATCHER.GetDocModifications(docNew0);
Assert.AreEqual(settingsMultiLabel.PeptideSettings.Modifications, settingsNew);
// Finding specific modifications.
// If only specific AA modified, try for most specific modification.
UpdateMatcher(null, null, null, null, new[] { STR_HEAVY_15_F});
Assert.IsTrue(MATCHER.GetModifiedNode(STR_HEAVY_15_F)
.ExplicitMods.HeavyModifications.Contains(mod =>
mod.Modification.AminoAcids.Contains(c => c == 'F')));
// If only some AAs modified, try for most specific modifications.
UpdateMatcher(null, null, null, null, new[] { STR_HEAVY_15_NOT_ALL });
Assert.IsTrue(MATCHER.GetModifiedNode(STR_HEAVY_15_NOT_ALL)
.ExplicitMods.HeavyModifications.Contains(mod =>
mod.Modification.AminoAcids.Contains(c => c == 'I')));
using (var testDir = new TestFilesDir(TestContext, ZIP_FILE))
{
var modMatchDocContainer = InitMatchDocContainer(testDir);
var libkeyModMatcher = new LibKeyModificationMatcher();
var anlLibSpec = new BiblioSpecLiteSpec("ANL_Combo", testDir.GetTestPath("ANL_Combined.blib"));
var yeastLibSpec = new BiblioSpecLiteSpec("Yeast", testDir.GetTestPath("Yeast_atlas_small.blib"));
modMatchDocContainer.ChangeLibSpecs(new[] { anlLibSpec, yeastLibSpec });
var docLibraries = modMatchDocContainer.Document.Settings.PeptideSettings.Libraries.Libraries;
int anlLibIndex = docLibraries.IndexOf(library => Equals(library.Name, anlLibSpec.Name));
int yeastLibIndex = docLibraries.IndexOf(library => Equals(library.Name, yeastLibSpec.Name));
libkeyModMatcher.CreateMatches(modMatchDocContainer.Document.Settings,
docLibraries[anlLibIndex].Keys, defSetSetLight, defSetHeavy);
// Test can match 15N
Assert.IsTrue(libkeyModMatcher.Matches.Values.Contains(match =>
match.HeavyMod != null && match.HeavyMod.Equivalent(LABEL15_N)));
var uniModMetOx = UniMod.GetModification("Oxidation (M)", true);
// Test can match Met Ox
Assert.IsTrue(libkeyModMatcher.Matches.Values.Contains(match =>
match.StructuralMod != null && match.StructuralMod.Equivalent(uniModMetOx)));
// Test can match 15N and Met ox!
Assert.IsTrue(libkeyModMatcher.Matches.Contains(match => match.Key.Mass == 17
&& match.Value.StructuralMod != null && match.Value.StructuralMod.Equivalent(uniModMetOx)
&& match.Value.HeavyMod != null && match.Value.HeavyMod.Equivalent(LABEL15_N)));
// Test can match Cysteine (Implicit) and Met Ox (variable)
libkeyModMatcher.CreateMatches(modMatchDocContainer.Document.Settings,
docLibraries[yeastLibIndex].Keys, defSetSetLight, defSetHeavy);
Assert.IsTrue(libkeyModMatcher.MatcherPepMods.StaticModifications.Contains(mod =>
mod.Formula.Equals(UniMod.GetModification(StaticModList.DEFAULT_NAME, true).Formula) && !mod.IsVariable));
Assert.IsTrue(libkeyModMatcher.MatcherPepMods.StaticModifications.Contains(mod =>
mod.Formula.Equals("O") && mod.IsVariable));
}
}
