private static SequenceMods GetShuffledPeptideSequence(SequenceMods seqMods)
{
string sequence = seqMods.Sequence;
char finalA = sequence.Last();
string sequencePrefix = sequence.Substring(0, sequence.Length - 1);
int lenPrefix = sequencePrefix.Length;
// Calculate a random shuffling of the current positions
int[] newIndices = new int[lenPrefix];
do
{
for (int i = 0; i < lenPrefix; i++)
newIndices[i] = i;
for (int i = 0; i < lenPrefix; i++)
Helpers.Swap(ref newIndices[RANDOM.Next(newIndices.Length)], ref newIndices[RANDOM.Next(newIndices.Length)]);
// Move the amino acids to their new positions
char[] shuffledArray = new char[lenPrefix];
for (int i = 0; i < lenPrefix; i++)
shuffledArray[newIndices[i]] = sequencePrefix[i];
seqMods.Sequence = new string(shuffledArray) + finalA;
}
// Make sure random shuffling did not just result in the same sequence
while (seqMods.Sequence.Equals(sequence));
if (seqMods.Mods != null)
{
var shuffledStaticMods = GetShuffledMods(seqMods.Mods.StaticModifications, lenPrefix, newIndices);
var typedStaticMods = GetStaticTypedMods(seqMods.Peptide, shuffledStaticMods);
seqMods.Mods = new ExplicitMods(seqMods.Peptide,
shuffledStaticMods,
GetShuffledHeavyMods(seqMods, typedStaticMods, lenPrefix, newIndices),
seqMods.Mods.IsVariableStaticMods);
}
return seqMods;
}
private static SequenceMods GetReversedPeptideSequence(SequenceMods seqMods)
{
string sequence = seqMods.Sequence;
char finalA = sequence.Last();
sequence = sequence.Substring(0, sequence.Length - 1);
int lenSeq = sequence.Length;
char[] reversedArray = sequence.ToCharArray();
Array.Reverse(reversedArray);
seqMods.Sequence = new string(reversedArray) + finalA;
if (seqMods.Mods != null)
{
var reversedStaticMods = GetReversedMods(seqMods.Mods.StaticModifications, lenSeq);
var typedStaticMods = GetStaticTypedMods(seqMods.Peptide, reversedStaticMods);
seqMods.Mods = new ExplicitMods(seqMods.Peptide,
reversedStaticMods,
GetReversedHeavyMods(seqMods, typedStaticMods, lenSeq),
seqMods.Mods.IsVariableStaticMods);
}
return seqMods;
}
private static IEnumerable<TypedExplicitModifications> GetShuffledHeavyMods(SequenceMods seqMods,
TypedExplicitModifications typedStaticMods, int lenSeq, int[] newIndices)
{
var shuffledHeavyMods = seqMods.Mods.GetHeavyModifications().Select(typedMod =>
new TypedExplicitModifications(seqMods.Peptide, typedMod.LabelType,
GetShuffledMods(typedMod.Modifications, lenSeq, newIndices)));
foreach (var typedMods in shuffledHeavyMods)
{
yield return typedMods.AddModMasses(typedStaticMods);
}
}
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);
}
