/// <summary>
/// Initializes a new instance of the <see cref="ProFormaTagGroup" /> class.
/// </summary>
/// <param name="name">The name.</param>
/// <param name="key">The key.</param>
/// <param name="evidenceType">Type of the evidence.</param>
/// <param name="value">The value.</param>
/// <param name="members">The members.</param>
public ProFormaTagGroup(string name, ProFormaKey key, ProFormaEvidenceType evidenceType, string value,
IList <ProFormaMembershipDescriptor> members)
{
this.Name = name;
this.Key = key;
this.EvidenceType = evidenceType;
this.Value = value;
this.Members = members;
}
public void ModificationAccessionNumbers_4_2_2(string proFormaString, ProFormaEvidenceType modType)
{
var term = _parser.ParseString(proFormaString);
Assert.AreEqual("EMEVEESPEK", term.Sequence);
Assert.AreEqual(2, term.Tags.Count);
var desc1 = term.Tags[0].Descriptors.Single();
var desc2 = term.Tags[1].Descriptors.Single();
Assert.AreEqual(modType, desc1.EvidenceType);
Assert.AreEqual(modType, desc2.EvidenceType);
}
private void FindById(IProteoformModificationLookup lookup, ProFormaKey key, ProFormaEvidenceType evidenceType,
int correctId, string extraPrefix)
{
Assert.IsNotNull(lookup.GetModification(new ProFormaDescriptor(key, evidenceType, $"{extraPrefix}{correctId}")));
Assert.IsNotNull(lookup.GetModification(new ProFormaDescriptor(key, evidenceType, $"{correctId}")));
Assert.Throws <ProteoformModificationLookupException>(
() => lookup.GetModification(new ProFormaDescriptor(key, evidenceType, "-1")));
Assert.Throws <ProteoformModificationLookupException>(
() => lookup.GetModification(new ProFormaDescriptor(key, evidenceType, $"{extraPrefix}0")));
Assert.Throws <ProteoformModificationLookupException>(
() => lookup.GetModification(new ProFormaDescriptor(key, evidenceType, $"{extraPrefix}2200")));
}
private void FindByName(IProteoformModificationLookup lookup, ProFormaEvidenceType evidenceType,
bool isDefault, string correctName)
{
if (isDefault)
{
Assert.IsNotNull(lookup.GetModification(new ProFormaDescriptor(ProFormaKey.Name, ProFormaEvidenceType.None, correctName)));
}
Assert.IsNotNull(lookup.GetModification(new ProFormaDescriptor(ProFormaKey.Name, evidenceType, correctName)));
Assert.Throws <ProteoformModificationLookupException>(
() => lookup.GetModification(new ProFormaDescriptor(ProFormaKey.Name, ProFormaEvidenceType.None, "Something")));
Assert.Throws <ProteoformModificationLookupException>(
() => lookup.GetModification(new ProFormaDescriptor(ProFormaKey.Name, evidenceType, "Something")));
}
private void DescriptorHandling(IProteoformModificationLookup lookup, ProFormaEvidenceType key, bool isDefault)
{
// If the key is a specific mod type, always handle
Assert.IsTrue(lookup.CanHandleDescriptor(new ProFormaDescriptor(ProFormaKey.Name, key, "Anything")));
Assert.IsTrue(lookup.CanHandleDescriptor(new ProFormaDescriptor(ProFormaKey.Name, key, "")));
Assert.IsTrue(lookup.CanHandleDescriptor(new ProFormaDescriptor(ProFormaKey.Name, key, null)));
// If using modification name, must have no ending or end in proper ending
Assert.IsTrue(lookup.CanHandleDescriptor(new ProFormaDescriptor(ProFormaKey.Name, key, "Something")));
Assert.IsFalse(lookup.CanHandleDescriptor(new ProFormaDescriptor(ProFormaKey.Name, "Something")));
Assert.IsFalse(lookup.CanHandleDescriptor(new ProFormaDescriptor(ProFormaKey.Name, ProFormaEvidenceType.Brno, "Something")));
// This is malformed and must be interpreted as a mod "name" ... will fail when looking up modification
//Assert.AreEqual(lookup.CanHandleDescriptor(new ProFormaDescriptor(ProFormaKey.Name, $"Something [{key}]")), isDefault);
}
public void Crosslinks_4_2_3_Disulfides(string proFormaString, ProFormaKey proFormaKey, ProFormaEvidenceType evidenceType, string value)
{
var term = _parser.ParseString(proFormaString);
Assert.IsNull(term.Tags);
Assert.AreEqual(1, term.TagGroups?.Count);
var tagGroup = term.TagGroups.Single();
Assert.AreEqual("XL1", tagGroup.Name);
Assert.AreEqual(proFormaKey, tagGroup.Key);
Assert.AreEqual(evidenceType, tagGroup.EvidenceType);
Assert.AreEqual(value, tagGroup.Value);
Assert.AreEqual(2, tagGroup.Members.Count);
Assert.AreEqual(6, tagGroup.Members[0].ZeroBasedStartIndex);
Assert.AreEqual(11, tagGroup.Members[1].ZeroBasedStartIndex);
}
public ProFormaTagGroupChangingValue(string name, ProFormaKey key, ProFormaEvidenceType evidenceType,
IList <ProFormaMembershipDescriptor> members) : base(name, key, evidenceType, string.Empty, members)
{
}
private void InvalidIdHandling(string id, IProteoformModificationLookup lookup, ProFormaKey key,
ProFormaEvidenceType evidenceType = ProFormaEvidenceType.None)
{
Assert.Throws <ProteoformModificationLookupException>(
() => lookup.GetModification(new ProFormaDescriptor(key, evidenceType, id)));
}
/// <summary>
/// Initializes a new instance of the <see cref="ProFormaDescriptor" /> class.
/// </summary>
/// <param name="key">The key.</param>
/// <param name="evidenceType">Type of the evidence.</param>
/// <param name="value">The value.</param>
public ProFormaDescriptor(ProFormaKey key, ProFormaEvidenceType evidenceType, string value)
{
this.Key = key;
this.EvidenceType = evidenceType;
this.Value = value;
}