/// <summary>
/// Constructor
/// </summary>
/// <param name="aminoAcidSet"></param>
/// <param name="shiftedMass"></param>
/// <param name="isForward"></param>
/// <param name="maxSequenceLength"></param>
/// <param name="maxSequenceMass"></param>
public ShiftedSequenceGraph(AminoAcidSet aminoAcidSet, double shiftedMass, bool isForward, int maxSequenceLength, double maxSequenceMass = 50000.0)
{
AminoAcidSet = aminoAcidSet;
_modificationParams = aminoAcidSet.GetModificationParams();
_isForward = isForward;
_index = 0;
_maxSeqIndex = maxSequenceLength + 2; // shift + Term + length
_maxSequenceMass = maxSequenceMass;
_aminoAcidSequence = new AminoAcid[_maxSeqIndex];
var shiftAa = new AminoAcid('\0', "Shift", new CompositionWithDeltaMass(shiftedMass));
_aminoAcidSequence[0] = shiftAa;
ShiftMass = shiftedMass;
_fragmentComposition = new Composition.Composition[_maxSeqIndex];
_fragmentComposition[0] = shiftAa.Composition;
_graph = new Node[_maxSeqIndex][];
_graph[0] = new[] { new Node(0) };
_nodeComposition = new Composition.Composition[_maxSeqIndex][];
_compNodeComposition = new Composition.Composition[_maxSeqIndex][];
for (var i = 0; i < _maxSeqIndex; i++)
{
_compNodeComposition[i] = new Composition.Composition[_modificationParams.NumModificationCombinations];
_nodeComposition[i] = new Composition.Composition[_modificationParams.NumModificationCombinations];
}
IsValid = true;
}
protected IntRange GetMinMaxChargeRange(Composition.Composition fragmentComposition)
{
var mostAbundantIsotopeIndex = fragmentComposition.GetMostAbundantIsotopeZeroBasedIndex();
var fragmentIonMostAbuMass = fragmentComposition.Mass + Constants.C13MinusC12 * mostAbundantIsotopeIndex;
return(GetMinMaxChargeRange(fragmentIonMostAbuMass));
}
public ShiftedSequenceGraph(AminoAcidSet aminoAcidSet, double shiftedMass, bool isForward, int maxSequenceLength, double maxSequenceMass = 50000.0)
{
_aminoAcidSet = aminoAcidSet;
_modificationParams = aminoAcidSet.GetModificationParams();
_isForward = isForward;
_index = 0;
_maxSeqIndex = maxSequenceLength + 2; // shift + Term + length
_maxSequenceMass = maxSequenceMass;
_aminoAcidSequence = new AminoAcid[_maxSeqIndex];
var shiftAa = new AminoAcid('\0', "Shift", new CompositionWithDeltaMass(shiftedMass));
_aminoAcidSequence[0] = shiftAa;
ShiftMass = shiftedMass;
_fragmentComposition = new Composition.Composition[_maxSeqIndex];
_fragmentComposition[0] = shiftAa.Composition;
_graph = new Node[_maxSeqIndex][];
_graph[0] = new[] { new Node(0) };
_nodeComposition = new Composition.Composition[_maxSeqIndex][];
_compNodeComposition = new Composition.Composition[_maxSeqIndex][];
for (var i = 0; i < _maxSeqIndex; i++)
{
_compNodeComposition[i] = new Composition.Composition[_modificationParams.NumModificationCombinations];
_nodeComposition[i] = new Composition.Composition[_modificationParams.NumModificationCombinations];
}
IsValid = true;
}
public AminoAcid(char residue, string name, Composition.Composition comp)
{
Residue = residue;
Name = name;
Composition = comp;
Mass = Composition.Mass;
_nominalMass = Composition.NominalMass;
}
/// <summary>
/// Constructor
/// </summary>
/// <param name="prefixComposition"></param>
/// <param name="prefixResidue"></param>
/// <param name="suffixComposition"></param>
/// <param name="suffixResidue"></param>
public Cleavage(Composition.Composition prefixComposition, AminoAcid prefixResidue, Composition.Composition suffixComposition, AminoAcid suffixResidue)
{
PrefixComposition = prefixComposition;
SuffixComposition = suffixComposition;
PrefixResidue = prefixResidue;
SuffixResidue = suffixResidue;
}
public IonType(string name, Composition.Composition offsetComposition,
int charge, bool isPrefixIon)
{
Name = name;
OffsetComposition = offsetComposition;
Charge = charge;
IsPrefixIon = isPrefixIon;
BaseIonType = null;
_offsetMass = offsetComposition.Mass;
}
/// <summary>
/// Gets all possible compositions of the current sequence
/// </summary>
/// <returns>all possible compositions</returns>
public Composition.Composition[] GetSequenceCompositions()
{
var numCompositions = _graph[_index].Length;
var compositions = new Composition.Composition[numCompositions];
for (var modIndex = 0; modIndex < numCompositions; modIndex++)
{
compositions[modIndex] = GetComposition(_index, modIndex);
}
return compositions;
}
/// <summary>
/// Gets all possible compositions of the current sequence
/// </summary>
/// <returns>all possible compositions</returns>
public Composition.Composition[] GetSequenceCompositions()
{
var numCompositions = _graph[_index].Length;
var compositions = new Composition.Composition[numCompositions];
for (var modIndex = 0; modIndex < numCompositions; modIndex++)
{
compositions[modIndex] = GetComposition(_index, modIndex);
}
return(compositions);
}
public static Modification RegisterAndGetModification(string name, Composition.Composition composition)
{
var mod = Get(name);
if (mod != null)
{
return(mod);
}
mod = new Modification(-1, composition, name);
Register(mod);
return(mod);
}
/// <summary>
/// Build a sequence from the supplied list of amino acids
/// </summary>
/// <param name="aaArr"></param>
public Sequence(IEnumerable <AminoAcid> aaArr)
{
var aminoAcids = aaArr as IList <AminoAcid> ?? aaArr.ToList();
PrefixComposition = new Composition.Composition[aminoAcids.Count + 1];
PrefixComposition[0] = Data.Composition.Composition.Zero;
for (var i = 0; i < aminoAcids.Count; i++)
{
var aa = aminoAcids[i] ?? AminoAcid.Empty;
Add(aa);
PrefixComposition[i + 1] = PrefixComposition[i] + aa.Composition;
}
Composition = PrefixComposition[aminoAcids.Count];
_prefixMass = PrefixComposition.Select(c => c.Mass).ToArray();
}
private readonly double _offsetMass; // duplication but stored for performance
internal IonType(
string name,
Composition.Composition offsetComposition,
int charge,
BaseIonType baseIonType,
NeutralLoss neutralLoss
)
{
Name = name;
_offsetMass = offsetComposition.Mass;
OffsetComposition = offsetComposition;
Charge = charge;
IsPrefixIon = baseIonType.IsPrefix;
BaseIonType = baseIonType;
NeutralLoss = neutralLoss;
}
/// <summary>
/// Generate a sequence graph for the provided data
/// </summary>
/// <param name="aminoAcidSet"></param>
/// <param name="nTerm"></param>
/// <param name="sequence"></param>
/// <param name="cTerm"></param>
protected SequenceGraph(AminoAcidSet aminoAcidSet, AminoAcid nTerm, string sequence, AminoAcid cTerm)
{
_aminoAcidSet = aminoAcidSet;
_sequence = sequence;
_nTerm = nTerm;
_modificationParams = aminoAcidSet.GetModificationParams();
_maxSeqIndex = sequence.Length + 3; // init + C-term + sequence length + N-term
_index = 0;
_aminoAcidSequence = new AminoAcid[_maxSeqIndex];
_aminoAcidSequence[0] = AminoAcid.Empty;
_suffixComposition = new Composition.Composition[_maxSeqIndex];
_suffixComposition[0] = Composition.Composition.Zero;
_graph = new Node[_maxSeqIndex][];
_graph[0] = new[] { new Node(0) };
_nodeComposition = new Composition.Composition[_maxSeqIndex][]; //, _modificationParams.NumModificationCombinations];
_compNodeComposition = new Composition.Composition[_maxSeqIndex][]; //, _modificationParams.NumModificationCombinations];
for (var i = 0; i < _maxSeqIndex; i++)
{
_compNodeComposition[i] = new Composition.Composition[_modificationParams.NumModificationCombinations];
_nodeComposition[i] = new Composition.Composition[_modificationParams.NumModificationCombinations];
}
NumNTermCleavages = 0;
IsValid = true;
SetNTerminalAminoAcid(nTerm);
AddAminoAcid(cTerm.Residue);
for (var i = sequence.Length - 1; i >= 0; i--)
{
if (AddAminoAcid(sequence[i]) == false)
{
IsValid = false;
break;
}
}
if (IsValid)
{
AddAminoAcid(nTerm.Residue);
}
}
protected IEnumerable <DeconvolutedPeak> FindMatchedPeaks(Composition.Composition fragmentComposition,
double corrThreshold, double distThreshold)
{
var mostAbundantIsotopeIndex = fragmentComposition.GetMostAbundantIsotopeZeroBasedIndex();
var fragmentIonMass = fragmentComposition.Mass;
//var matchedPeak = new MatchedFragmentPeak();
//var deconvPeak = new DeconvolutedPeak()
if (fragmentIonMass < Ms2Spectrum.Peaks.First().Mz)
{
yield break;
}
var prevObservedCharge = 0;
var fragmentIonMostAbuMass = fragmentIonMass + Constants.C13MinusC12 * mostAbundantIsotopeIndex;
var chargeRange = GetMinMaxChargeRange(fragmentIonMostAbuMass);
for (var charge = chargeRange.Min; charge <= chargeRange.Max; charge++)
{
var ion = new Ion(fragmentComposition, charge);
var observedPeaks = Ms2Spectrum.GetAllIsotopePeaks(ion, Tolerance, RelativeIsotopeIntensityThreshold);
if (observedPeaks == null)
{
if (prevObservedCharge > 0 && charge - prevObservedCharge > 1)
{
yield break;
}
continue;
}
var distCorr = GetDistCorr(ion, observedPeaks);
if (distCorr.Item2 < corrThreshold && distCorr.Item1 > distThreshold)
{
if (prevObservedCharge > 0 && charge - prevObservedCharge > 1)
{
yield break;
}
continue;
}
var matchedPeak = new DeconvolutedPeak(fragmentIonMass, observedPeaks[mostAbundantIsotopeIndex].Intensity, charge, distCorr.Item2, distCorr.Item1, observedPeaks);
prevObservedCharge = charge;
yield return(matchedPeak);
}
}
/*
* protected Peak[] FindMostAbundantPeak(Composition.Composition fragmentComposition,
* double corrThreshold, double distThreshold,
* out int observedCharge, out double envelopeCorr, out double envelopeDist)
* {
* //Peak[] intenseObservedPeaks = null;
* var mostAbundantIsotopeIndex = fragmentComposition.GetMostAbundantIsotopeZeroBasedIndex();
* var fragmentIonMass = fragmentComposition.Mass;
* observedCharge = 0;
* envelopeCorr = 0d;
* envelopeDist = 1.0d;
*
* if (fragmentIonMass < Ms2Spectrum.Peaks.First().Mz) return null;
*
* var fragmentIonMostAbuMass = fragmentIonMass + Constants.C13MinusC12 * mostAbundantIsotopeIndex;
* var chargeRange = GetMinMaxChargeRange(fragmentIonMostAbuMass);
*
* for (var charge = chargeRange.Min; charge <= chargeRange.Max; charge++)
* {
* var ion = new Ion(fragmentComposition, charge);
*
* var observedPeaks = Ms2Spectrum.GetAllIsotopePeaks(ion, Tolerance, RelativeIsotopeIntensityThreshold);
* if (observedPeaks == null) continue;
*
* var distCorr = GetDistCorr(ion, observedPeaks);
* if (distCorr.Item2 < corrThreshold && distCorr.Item1 > distThreshold) continue;
* //var mostAbuPeak = observedPeaks[mostAbundantIsotopeIndex];
* //if (intenseObservedPeaks == null || mostAbuPeak.Intensity > intenseObservedPeaks[mostAbundantIsotopeIndex].Intensity)
* //{
* //intenseObservedPeaks = observedPeaks;
* observedCharge = charge;
* envelopeDist = distCorr.Item1;
* envelopeCorr = distCorr.Item2;
* return observedPeaks;
* //}
* }
* return null;
* }
*/
protected Peak[] FindMostIntensePeak(Composition.Composition fragmentComposition, double corrThreshold, double distThreshold, out int observedCharge, out double envelopeCorr, out double envelopeDist)
{
Peak[] intenseObservedPeaks = null;
var mostAbundantIsotopeIndex = fragmentComposition.GetMostAbundantIsotopeZeroBasedIndex();
var fragmentIonMass = fragmentComposition.Mass;
observedCharge = 0;
envelopeCorr = 0d;
envelopeDist = 1.0d;
if (fragmentIonMass < Ms2Spectrum.Peaks.First().Mz)
{
return(null);
}
var fragmentIonMostAbuMass = fragmentIonMass + Constants.C13MinusC12 * mostAbundantIsotopeIndex;
var chargeRange = GetMinMaxChargeRange(fragmentIonMostAbuMass);
for (var charge = chargeRange.Min; charge <= chargeRange.Max; charge++)
{
var ion = new Ion(fragmentComposition, charge);
var observedPeaks = Ms2Spectrum.GetAllIsotopePeaks(ion, Tolerance, RelativeIsotopeIntensityThreshold);
if (observedPeaks == null)
{
continue;
}
var distCorr = GetDistCorr(ion, observedPeaks);
if (distCorr.Item2 < corrThreshold && distCorr.Item1 > distThreshold)
{
continue;
}
var mostAbuPeak = observedPeaks[mostAbundantIsotopeIndex];
if (intenseObservedPeaks == null || mostAbuPeak.Intensity > intenseObservedPeaks[mostAbundantIsotopeIndex].Intensity)
{
intenseObservedPeaks = observedPeaks;
observedCharge = charge;
envelopeDist = distCorr.Item1;
envelopeCorr = distCorr.Item2;
}
}
return(intenseObservedPeaks);
}
/// <summary>
/// Find a neutral monoisotopic peak corrsponding to a single compound/
/// </summary>
/// <param name="composition">The compound to look for.</param>
/// <param name="tolerance">The peak tolerance to use.</param>
/// <returns>The neutral monoisotopic peak.</returns>
public DeconvolutedPeak FindPeak(Composition.Composition composition, Tolerance tolerance)
{
double mass = composition.Mass;
DeconvolutedPeak deconvolutedPeak = null;
double maxIntensity = 0.0;
for (int charge = this.minCharge; charge <= this.maxCharge; charge++)
{
var ion = new Ion(composition, charge);
var isotopePeaks = this.spectrum.GetAllIsotopePeaks(ion, tolerance);
var intensity = isotopePeaks.Max(peak => peak.Intensity);
var corrCos = this.GetCorrCos(ion, isotopePeaks);
if (intensity > maxIntensity)
{
deconvolutedPeak = new DeconvolutedPeak(mass, intensity, charge, corrCos.Item1, corrCos.Item2, isotopePeaks);
}
}
return(deconvolutedPeak);
}
// Added by Chris
/// <summary>
/// Register a new modification or update existing modification.
/// </summary>
/// <param name="name">The name of the modification.</param>
/// <param name="composition">The composition of the modification.</param>
/// <returns>Registered modification.</returns>
public static Modification UpdateAndGetModification(string name, Composition.Composition composition)
{
if (NameToModMap.ContainsKey(name))
{
NameToModMap.Remove(name);
}
var massStr = string.Format("{0:N3}", composition.Mass);
if (MassToModMap.ContainsKey(massStr))
{
MassToModMap.Remove(massStr);
}
var modification = new Modification(-1, composition, name);
Register(modification);
return(modification);
}
// Added by Chris
/// <summary>
/// Register a new modification or update existing modification.
/// </summary>
/// <param name="name">The name of the modification.</param>
/// <param name="composition">The composition of the modification.</param>
/// <returns>Registered modification.</returns>
public static Modification UpdateAndGetModification(string name, Composition.Composition composition)
{
// Names should be case-insensitive.
var lowerName = name.ToLower();
if (NameToModMap.ContainsKey(lowerName))
{
NameToModMap.Remove(lowerName);
}
var massStr = string.Format(MOD_MASS_FORMAT_STRING, composition.Mass);
if (MassToModMap.ContainsKey(massStr))
{
MassToModMap.Remove(massStr);
}
// Use original-cased name in modification object.
var modification = new Modification(-1, composition, name);
Register(modification);
return(modification);
}
/// <summary>
/// Get possible ions for <paramref name="cutComposition"/> and <paramref name="terminalResidue"/>
/// </summary>
/// <param name="cutComposition"></param>
/// <param name="terminalResidue"></param>
/// <returns></returns>
public IEnumerable <Ion> GetPossibleIons(Composition.Composition cutComposition, AminoAcid terminalResidue)
{
return(BaseIonType.GetPossibleCompositions(terminalResidue)
.Select(offsetComposition => cutComposition + offsetComposition - NeutralLoss.Composition)
.Select(comp => new Ion(comp, Charge)));
}
public abstract double GetFragmentScore(Composition.Composition prefixFragmentComposition, Composition.Composition suffixFragmentComposition);
private BaseIonType(string symbol, bool isPrefix, Composition.Composition offsetComposition)
{
Symbol = symbol;
IsPrefix = isPrefix;
OffsetComposition = offsetComposition;
}
public double GetMz(Composition.Composition prefixComposition)
{
Debug.Assert(prefixComposition != null, "prefixComposition must not be null");
return(GetMz(prefixComposition.Mass));
}
public Cleavage(Composition.Composition prefixComposition, Composition.Composition suffixComposition)
{
PrefixComposition = prefixComposition;
SuffixComposition = suffixComposition;
}
protected SequenceGraph(AminoAcidSet aminoAcidSet, AminoAcid nTerm, string sequence, AminoAcid cTerm)
{
_aminoAcidSet = aminoAcidSet;
_sequence = sequence;
_nTerm = nTerm;
_modificationParams = aminoAcidSet.GetModificationParams();
_maxSeqIndex = sequence.Length + 3; // init + C-term + sequence length + N-term
_index = 0;
_aminoAcidSequence = new AminoAcid[_maxSeqIndex];
_aminoAcidSequence[0] = AminoAcid.Empty;
_suffixComposition = new Composition.Composition[_maxSeqIndex];
_suffixComposition[0] = Composition.Composition.Zero;
_graph = new Node[_maxSeqIndex][];
_graph[0] = new[] { new Node(0) };
_nodeComposition = new Composition.Composition[_maxSeqIndex][]; //, _modificationParams.NumModificationCombinations];
_compNodeComposition = new Composition.Composition[_maxSeqIndex][]; //, _modificationParams.NumModificationCombinations];
for (var i = 0; i < _maxSeqIndex; i++)
{
_compNodeComposition[i] = new Composition.Composition[_modificationParams.NumModificationCombinations];
_nodeComposition[i] = new Composition.Composition[_modificationParams.NumModificationCombinations];
}
NumNTermCleavages = 0;
IsValid = true;
SetNTerminalAminoAcid(nTerm);
AddAminoAcid(cTerm.Residue);
for (var i = sequence.Length - 1; i >= 0; i--)
{
if (AddAminoAcid(sequence[i]) == false)
{
IsValid = false;
break;
}
}
if (IsValid) AddAminoAcid(nTerm.Residue);
}
/// <summary>
/// Get the peak that matches <paramref name="composition"/> and <paramref name="tolerance"/>
/// </summary>
/// <param name="composition"></param>
/// <param name="tolerance"></param>
/// <returns></returns>
public DeconvolutedPeak FindPeak(Composition.Composition composition, Tolerance tolerance)
{
return(base.FindPeak(composition.Mass, tolerance) as DeconvolutedPeak);
}
/// <summary>
/// Constructor
/// </summary>
/// <param name="name"></param>
/// <param name="symbol"></param>
/// <param name="composition"></param>
public NeutralLoss(string name, string symbol, Composition.Composition composition)
{
Symbol = symbol;
Name = name;
Composition = composition;
}
public Ion GetIon(Composition.Composition cutComposition)
{
return(new Ion(cutComposition + OffsetComposition, Charge));
}
/// <summary>
/// Constructor
/// </summary>
/// <param name="accessionNum"></param>
/// <param name="composition"></param>
/// <param name="name"></param>
public Modification(int accessionNum, Composition.Composition composition, string name)
{
AccessionNum = accessionNum;
Composition = composition;
Name = name;
}
public NeutralLoss(string name, Composition.Composition composition)
{
Name = name;
Composition = composition;
}
public Ion(Composition.Composition composition, int charge)
{
Composition = composition;
Charge = charge;
}
protected override void WriteXmlBase(System.Xml.XmlWriter writer)
{
base.WriteXmlBase(writer);
string prefix = RmXmlSerializer.UseOpenEhrPrefix(writer);
string xsiPrefix = RmXmlSerializer.UseXsiPrefix(writer);
writer.WriteStartElement("uid", RmXmlSerializer.OpenEhrNamespace);
this.Uid.WriteXml(writer);
writer.WriteEndElement();
if (this.Data != null)
{
writer.WriteStartElement("data", RmXmlSerializer.OpenEhrNamespace);
OpenEhr.RM.Common.Archetyped.Impl.Locatable dataLocatable = this.Data
as OpenEhr.RM.Common.Archetyped.Impl.Locatable;
if (dataLocatable == null)
{
throw new NotSupportedException("Only support locatable as version data: "
+ Data.GetType().Name);
}
string dataType = ((IRmType)dataLocatable).GetRmTypeName();
if (!string.IsNullOrEmpty(prefix))
{
dataType = prefix + ":" + dataType;
}
writer.WriteAttributeString(xsiPrefix, "type", RmXmlSerializer.XsiNamespace, dataType);
Composition.Composition com = this.Data as Composition.Composition;
com.WriteXml(writer);
writer.WriteEndElement();
}
if (this.PrecedingVersionUid != null)
{
writer.WriteStartElement("preceding_version_uid", RmXmlSerializer.OpenEhrNamespace);
this.PrecedingVersionUid.WriteXml(writer);
writer.WriteEndElement();
}
// otherInputVersionUids
if (this.OtherInputVersionUids != null)
{
foreach (ObjectVersionId objectVersionId in this.OtherInputVersionUids)
{
writer.WriteStartElement("other_input_version_uids", RmXmlSerializer.OpenEhrNamespace);
objectVersionId.WriteXml(writer);
writer.WriteEndElement();
}
}
// attestation
if (this.Attestations != null)
{
foreach (Generic.Attestation a in this.Attestations)
{
writer.WriteStartElement("attestations", RmXmlSerializer.OpenEhrNamespace);
a.WriteXml(writer);
writer.WriteEndElement();
}
}
writer.WriteStartElement("lifecycle_state", RmXmlSerializer.OpenEhrNamespace);
this.LifecycleState.WriteXml(writer);
writer.WriteEndElement();
}
