private static void ValidateDecoys(SrmDocument document, SrmDocument decoysDoc, bool modifiesSequences)
{
AssertEx.IsDocumentState(decoysDoc, 1, document.PeptideGroupCount + 1, document.PeptideCount * 2,
document.PeptideTransitionGroupCount * 2, document.PeptideTransitionCount * 2);
// Check for the existence of the Decoys peptide group and that everything under it is marked as a decoy.
var nodePeptideGroupDecoy = decoysDoc.PeptideGroups.Single(nodePeptideGroup => nodePeptideGroup.IsDecoy);
var dictModsToPep = document.Peptides.ToDictionary(nodePep => nodePep.ModifiedSequence);
foreach (var nodePep in nodePeptideGroupDecoy.Peptides)
{
Assert.AreEqual(true, nodePep.IsDecoy);
PeptideDocNode nodePepSource = null;
if (!modifiesSequences)
{
Assert.IsNull(nodePep.SourceKey);
}
else
{
Assert.IsNotNull(nodePep.SourceKey, string.Format("Source key for {0}{1} is null", nodePep.ModifiedSequence,
nodePep.IsDecoy ? " - decoy" : string.Empty));
Assert.IsTrue(FastaSequence.IsExSequence(nodePep.SourceKey.Sequence));
Assert.AreEqual(nodePep.SourceKey.ModifiedSequence,
SequenceMassCalc.NormalizeModifiedSequence(nodePep.SourceKey.ModifiedSequence));
if (nodePep.HasExplicitMods)
{
Assert.IsNotNull(nodePep.SourceKey.ExplicitMods);
}
Assert.IsTrue(dictModsToPep.TryGetValue(nodePep.SourceTextId, out nodePepSource));
var sourceKey = new ModifiedSequenceMods(nodePepSource.Peptide.Sequence, nodePepSource.ExplicitMods);
Assert.AreEqual(sourceKey.ExplicitMods, nodePep.SourceExplicitMods);
}
for (int i = 0; i < nodePep.TransitionGroupCount; i++)
{
var nodeGroup = nodePep.TransitionGroups.ElementAt(i);
Assert.AreEqual(true, nodeGroup.IsDecoy);
TransitionGroupDocNode nodeGroupSource = null;
double shift = SequenceMassCalc.GetPeptideInterval(nodeGroup.TransitionGroup.DecoyMassShift);
if (nodePepSource != null && nodeGroup.TransitionGroup.DecoyMassShift.HasValue)
{
nodeGroupSource = nodePepSource.TransitionGroups.ElementAt(i);
Assert.AreEqual(nodeGroupSource.PrecursorMz + shift, nodeGroup.PrecursorMz, SequenceMassCalc.MassTolerance);
}
for (int j = 0; j < nodeGroup.TransitionCount; j++)
{
var nodeTran = nodeGroup.Transitions.ElementAt(j);
Assert.IsTrue(nodeTran.IsDecoy);
if (nodeTran.Transition.IsPrecursor())
{
Assert.AreEqual(nodeGroup.TransitionGroup.DecoyMassShift, nodeTran.Transition.DecoyMassShift);
if (nodeGroupSource != null)
{
Assert.AreEqual(nodeGroupSource.Transitions.ElementAt(j).Mz + shift, nodeTran.Mz, SequenceMassCalc.MassTolerance);
}
}
}
}
}
// Check that the resulting document persists correctly by passing the SrmDocument to AssertEx.IsSerializable().
AssertEx.Serializable(decoysDoc);
}
private static SrmDocument GenerateDecoysFunc(SrmDocument document, int numDecoys, bool multiCycle,
Func<SequenceMods, SequenceMods> genDecoySequence)
{
// Loop through the existing tree in random order creating decoys
var settings = document.Settings;
var enzyme = settings.PeptideSettings.Enzyme;
var decoyNodePepList = new List<PeptideDocNode>();
var setDecoyKeys = new HashSet<PeptideModKey>();
while (numDecoys > 0)
{
int startDecoys = numDecoys;
foreach (var nodePep in document.Peptides.ToArray().RandomOrder())
{
if (numDecoys == 0)
break;
// Decoys should not be based on standard peptides
if (nodePep.GlobalStandardType != null)
continue;
// If the non-terminal end of the peptide sequence is all a single character, skip this peptide,
// since it can't support decoy generation.
var sequence = nodePep.Peptide.Sequence;
if (genDecoySequence != null && sequence.Substring(0, sequence.Length - 1).Distinct().Count() == 1)
continue;
var seqMods = new SequenceMods(nodePep);
if (genDecoySequence != null)
{
seqMods = genDecoySequence(seqMods);
}
var peptide = nodePep.Peptide;
var decoyPeptide = new Peptide(null, seqMods.Sequence, null, null, enzyme.CountCleavagePoints(seqMods.Sequence), true);
if (seqMods.Mods != null)
seqMods.Mods = seqMods.Mods.ChangePeptide(decoyPeptide);
foreach (var comparableGroups in PeakFeatureEnumerator.ComparableGroups(nodePep))
{
var decoyNodeTranGroupList = GetDecoyGroups(nodePep, decoyPeptide, seqMods.Mods, comparableGroups, document,
Equals(seqMods.Sequence, peptide.Sequence));
if (decoyNodeTranGroupList.Count == 0)
continue;
var nodePepNew = new PeptideDocNode(decoyPeptide, settings, seqMods.Mods,
null, nodePep.ExplicitRetentionTime, decoyNodeTranGroupList.ToArray(), false);
if (!Equals(nodePep.ModifiedSequence, nodePepNew.ModifiedSequence))
{
var sourceKey = new ModifiedSequenceMods(nodePep.ModifiedSequence, nodePep.ExplicitMods);
nodePepNew = nodePepNew.ChangeSourceKey(sourceKey);
}
// Avoid adding duplicate peptides
if (setDecoyKeys.Contains(nodePepNew.Key))
continue;
setDecoyKeys.Add(nodePepNew.Key);
decoyNodePepList.Add(nodePepNew);
numDecoys--;
}
}
// Stop if not multi-cycle or the number of decoys has not changed.
if (!multiCycle || startDecoys == numDecoys)
break;
}
var decoyNodePepGroup = new PeptideGroupDocNode(new PeptideGroup(true), Annotations.EMPTY, PeptideGroup.DECOYS,
null, decoyNodePepList.ToArray(), false);
decoyNodePepGroup = decoyNodePepGroup.ChangeSettings(document.Settings, SrmSettingsDiff.ALL);
return (SrmDocument)document.Add(decoyNodePepGroup);
}
private static void ValidateDecoys(SrmDocument document, SrmDocument decoysDoc, bool modifiesSequences)
{
AssertEx.IsDocumentState(decoysDoc, 1, document.PeptideGroupCount + 1, document.PeptideCount*2,
document.PeptideTransitionGroupCount*2, document.PeptideTransitionCount*2);
// Check for the existence of the Decoys peptide group and that everything under it is marked as a decoy.
var nodePeptideGroupDecoy = decoysDoc.PeptideGroups.Single(nodePeptideGroup => nodePeptideGroup.IsDecoy);
var dictModsToPep = document.Peptides.ToDictionary(nodePep => nodePep.ModifiedSequence);
foreach (var nodePep in nodePeptideGroupDecoy.Peptides)
{
Assert.AreEqual(true, nodePep.IsDecoy);
PeptideDocNode nodePepSource = null;
if (!modifiesSequences)
Assert.IsNull(nodePep.SourceKey);
else
{
Assert.IsNotNull(nodePep.SourceKey, string.Format("Source key for {0}{1} is null", nodePep.ModifiedSequence,
nodePep.IsDecoy ? " - decoy" : string.Empty));
Assert.IsTrue(FastaSequence.IsExSequence(nodePep.SourceKey.Sequence));
Assert.AreEqual(nodePep.SourceKey.ModifiedSequence,
SequenceMassCalc.NormalizeModifiedSequence(nodePep.SourceKey.ModifiedSequence));
if (nodePep.HasExplicitMods)
Assert.IsNotNull(nodePep.SourceKey.ExplicitMods);
Assert.IsTrue(dictModsToPep.TryGetValue(nodePep.SourceTextId, out nodePepSource));
var sourceKey = new ModifiedSequenceMods(nodePepSource.Peptide.Sequence, nodePepSource.ExplicitMods);
Assert.AreEqual(sourceKey.ExplicitMods, nodePep.SourceExplicitMods);
}
for (int i = 0; i < nodePep.TransitionGroupCount; i++)
{
var nodeGroup = nodePep.TransitionGroups.ElementAt(i);
Assert.AreEqual(true, nodeGroup.IsDecoy);
TransitionGroupDocNode nodeGroupSource = null;
double shift = SequenceMassCalc.GetPeptideInterval(nodeGroup.TransitionGroup.DecoyMassShift);
if (nodePepSource != null && nodeGroup.TransitionGroup.DecoyMassShift.HasValue)
{
nodeGroupSource = nodePepSource.TransitionGroups.ElementAt(i);
Assert.AreEqual(nodeGroupSource.PrecursorMz + shift, nodeGroup.PrecursorMz, SequenceMassCalc.MassTolerance);
}
for (int j = 0; j < nodeGroup.TransitionCount; j++)
{
var nodeTran = nodeGroup.Transitions.ElementAt(j);
Assert.IsTrue(nodeTran.IsDecoy);
if (nodeTran.Transition.IsPrecursor())
{
Assert.AreEqual(nodeGroup.TransitionGroup.DecoyMassShift, nodeTran.Transition.DecoyMassShift);
if (nodeGroupSource != null)
{
Assert.AreEqual(nodeGroupSource.Transitions.ElementAt(j).Mz + shift, nodeTran.Mz, SequenceMassCalc.MassTolerance);
}
}
}
}
}
// Check that the resulting document persists correctly by passing the SrmDocument to AssertEx.IsSerializable().
AssertEx.Serializable(decoysDoc);
}
public PeptideDocNode ChangeSourceKey(ModifiedSequenceMods prop)
{
return ChangeProp(ImClone(this), im => im.SourceKey = prop);
}
public PeptideDocNode(Peptide id,
SrmSettings settings,
ExplicitMods mods,
ModifiedSequenceMods sourceKey,
string standardType,
int? rank,
ExplicitRetentionTimeInfo explicitRetentionTimeInfo,
Annotations annotations,
Results<PeptideChromInfo> results,
TransitionGroupDocNode[] children,
bool autoManageChildren)
: base(id, annotations, children, autoManageChildren)
{
ExplicitMods = mods;
SourceKey = sourceKey;
GlobalStandardType = standardType;
Rank = rank;
ExplicitRetentionTime = explicitRetentionTimeInfo;
Results = results;
BestResult = CalcBestResult();
if (settings != null)
{
var calcPre = settings.GetPrecursorCalc(IsotopeLabelType.light, ExplicitMods);
ModifiedSequence = calcPre.GetModifiedSequence(Peptide.Sequence, false);
ModifiedSequenceDisplay = calcPre.GetModifiedSequence(Peptide.Sequence, true);
}
}
public PeptideDocNode(Peptide id, SrmSettings settings, ExplicitMods mods, ModifiedSequenceMods sourceKey, ExplicitRetentionTimeInfo explicitRetentionTime,
TransitionGroupDocNode[] children, bool autoManageChildren)
: this(id, settings, mods, sourceKey, null, null, explicitRetentionTime, Annotations.EMPTY, null, children, autoManageChildren)
{
}
