/// <summary>
/// Get possible ions for <paramref name="sequence"/>
/// </summary>
/// <param name="sequence"></param>
/// <returns></returns>
public IEnumerable <Ion> GetPossibleIons(Sequence sequence)
{
var cutComposition = sequence.Composition;
var terminalResidue = IsPrefixIon ? sequence[sequence.Count - 1] : sequence[0];
return(BaseIonType.GetPossibleCompositions(terminalResidue)
.Select(offsetComposition => cutComposition + offsetComposition - NeutralLoss.Composition)
.Select(comp => new Ion(comp, Charge)));
}
static BaseIonType()
{
// For A, B, C, X, Y, Z ions: sum of all amino acids + offset
A = new BaseIonType("a", true, new Composition(-1, 0, 0, -1, 0)); // -CO
Ar = new BaseIonType("a.", true, A.OffsetComposition + Composition.Hydrogen);
B = new BaseIonType("b", true, Composition.Zero);
C = new BaseIonType("c", true, Composition.NH3);
//X = new BaseIonType("x", false, Composition.H2O + Composition.CO);
X = new BaseIonType("x", false, new CompositionWithDeltaMass(44.9977) - Composition.Hydrogen);
Xr = new BaseIonType("x.", false, X.OffsetComposition + Composition.Hydrogen);
Y = new BaseIonType("y", false, Composition.H2O);
YM1 = new BaseIonType("y-1", false, Y.OffsetComposition - Composition.Hydrogen);
Z = new BaseIonType("z", false, Composition.H2O - Composition.NH2);
Zr = new BaseIonType("z.", false, Z.OffsetComposition + Composition.Hydrogen);
var aminoAcidSet = new AminoAcidSet();
// D ions have additional options for isoleucine and threonine. All offsets defined as sum of previous residues + offset.
var dIonOffsets = new Dictionary <char, double[]>
{ // Defined in terms of sum of previous residue weights + offset
{ '*', new [] { 44.0500 - Composition.Hydrogen.Mass } }, // For all residues except for V, I and T
{ 'V', new [] { 58.0657 - Composition.Hydrogen.Mass } },
{ 'I', new [] { 58.0657 - Composition.Hydrogen.Mass, 72.0813 - Composition.Hydrogen.Mass } }, // for isoleucine
{ 'T', new [] { 58.0657 - Composition.Hydrogen.Mass, 60.0450 - Composition.Hydrogen.Mass } } // for threonine
};
D = new BaseIonType("d", true, new CompositionWithDeltaMass(44.0500), aminoAcid => DefaultCompositionCalculator(dIonOffsets, aminoAcid));
// V only has one option for all terminal residues. Sum of previous residues + offset
V = new BaseIonType("v", false, new CompositionWithDeltaMass(74.0242), r => new List <Composition> {
r == null ? new CompositionWithDeltaMass(74.0242) : new CompositionWithDeltaMass(74.0242) - r.Composition - Composition.Hydrogen
});
// W ions have additional options for isoleucine and threonine. All offsets defined as sum of previous residues + offset.
var wIonOffsets = new Dictionary <char, double[]>
{ // Defined in terms of sum of previous residue weights + offset
{ '*', new [] { 73.0290 - Composition.Hydrogen.Mass } }, // For all residues except for V, I and T
{ 'V', new [] { 87.0446 - Composition.Hydrogen.Mass } },
{ 'I', new [] { 87.0446 - Composition.Hydrogen.Mass, aminoAcidSet.GetAminoAcid('I').Mass - 12.0238 - Composition.Hydrogen.Mass } }, // for isoleucine
{ 'T', new [] { 87.0446 - Composition.Hydrogen.Mass, aminoAcidSet.GetAminoAcid('T').Mass - 12.0238 - Composition.Hydrogen.Mass } } // for threonine
};
W = new BaseIonType("w", false, new CompositionWithDeltaMass(73.0290), aminoAcid => DefaultCompositionCalculator(wIonOffsets, aminoAcid));
AllBaseIonTypes = new List <BaseIonType> {
A, Ar, B, C, D, V, W, X, Xr, Y, YM1, Z, Zr
};
}
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;
}
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>
/// Get ion type according to the parameters
/// </summary>
/// <param name="baseIonType"></param>
/// <param name="charge"></param>
/// <param name="neutralLoss"></param>
/// <returns></returns>
public IonType GetIonType(BaseIonType baseIonType, int charge, NeutralLoss neutralLoss)
{
var ionTypeName = string.Format("{0}{1}{2}", baseIonType.Symbol, charge, neutralLoss.Name);
return(_ionTypeMap[ionTypeName]);
}
public void ReadConfigurationFile(string configurationFile)
{
var reader = new ConfigFileReader(configurationFile);
// Read program variables
var config = reader.GetNodes("vars").First();
PrecursorCharge = Convert.ToInt32(config.Contents["precursorcharge"]);
PrecursorOffsetThreshold = Convert.ToDouble(config.Contents["precursoroffsetthreshold"]);
WindowWidth = Convert.ToInt32(config.Contents["searchwidth"]);
PrecursorOffsetWidth = Convert.ToInt32(config.Contents["precursoroffsetwidth"]);
RetentionCount = Convert.ToInt32(config.Contents["retentioncount"]);
RelativeIntensityThreshold = Convert.ToDouble(config.Contents["relativeintensitythreshold"]);
SelectedIonThreshold = Convert.ToDouble(config.Contents["selectedionthreshold"]);
MassBinSize = Convert.ToInt32(config.Contents["massbinsize"]);
var actStr = config.Contents["activationmethod"].ToLower();
switch (actStr)
{
case "hcd":
ActivationMethod = ActivationMethod.HCD;
Tolerance = _defaultTolerancePpm;
break;
case "cid":
ActivationMethod = ActivationMethod.CID;
Tolerance = _defaultToleranceTh;
break;
case "etd":
ActivationMethod = ActivationMethod.ETD;
Tolerance = _defaultTolerancePpm;
break;
default:
throw new FormatException("Invalid Activation Method.");
}
var acqStr = config.Contents["acquisitionmethod"].ToLower();
switch (acqStr)
{
case "dia":
AcquisitionMethod = AcquisitionMethod.Dia;
break;
case "dda":
AcquisitionMethod = AcquisitionMethod.Dda;
break;
default:
throw new FormatException("Invalid Acquisition Method.");
}
MassErrorTolerance = _defaultToleranceTh;
MaxRanks = Convert.ToInt32(config.Contents["maxranks"]);
var smoothingRanksStr = config.Contents["smoothingranks"].Split(',');
SmoothingRanks = new int[smoothingRanksStr.Length];
var smoothingWindowSizeStr = config.Contents["smoothingwindowsize"].Split(',');
SmoothingWindowSize = new int[smoothingWindowSizeStr.Length];
if (SmoothingRanks.Length != SmoothingWindowSize.Length)
throw new ArgumentException("SmoothingRanks and SmoothingWindowSize unequal lengths.");
for (int i = 0; i < SmoothingRanks.Length; i++)
{
if (smoothingRanksStr[i] == "Max") SmoothingRanks[i] = Int32.MaxValue;
else SmoothingRanks[i] = Convert.ToInt32(smoothingRanksStr[i]);
SmoothingWindowSize[i] = Convert.ToInt32(smoothingWindowSizeStr[i]);
}
// Read ion data
var ionInfo = reader.GetNodes("ion").First();
int totalCharges = Convert.ToInt32(ionInfo.Contents["totalcharges"]);
var ionTypeStr = ionInfo.Contents["iontype"].Split(',');
var ions = new BaseIonType[ionTypeStr.Length];
for (int i = 0; i < ionTypeStr.Length; i++)
{
switch (ionTypeStr[i].ToLower())
{
case "a":
ions[i] = BaseIonType.A;
break;
case "b":
ions[i] = BaseIonType.B;
break;
case "c":
ions[i] = BaseIonType.C;
break;
case "x":
ions[i] = BaseIonType.X;
break;
case "y":
ions[i] = BaseIonType.Y;
break;
case "z":
ions[i] = BaseIonType.Z;
break;
}
}
var ionLossStr = ionInfo.Contents["losses"].Split(',');
var ionLosses = new NeutralLoss[ionLossStr.Length];
for (int i = 0; i < ionLossStr.Length; i++)
{
switch (ionLossStr[i].ToLower())
{
case "noloss":
ionLosses[i] = NeutralLoss.NoLoss;
break;
case "nh3":
ionLosses[i] = NeutralLoss.NH3;
break;
case "h2o":
ionLosses[i] = NeutralLoss.H2O;
break;
}
}
_ionTypeFactory = new IonTypeFactory(ions, ionLosses, totalCharges);
IonTypes = _ionTypeFactory.GetAllKnownIonTypes().ToArray();
var tempIonList = new List<IonType>();
if (ionInfo.Contents.ContainsKey("exclusions"))
{
var ionExclusions = ionInfo.Contents["exclusions"].Split(',');
tempIonList.AddRange(IonTypes.Where(ionType => !ionExclusions.Contains(ionType.Name)));
IonTypes = tempIonList.ToArray();
}
// Read input and output file names
var fileInfo = reader.GetNodes("fileinfo").First();
DataSets = fileInfo.Contents["name"].Split(',');
var dataFormat = fileInfo.Contents["format"];
switch (dataFormat)
{
case "mgf":
DataFormat = DataFileFormat.Mgf;
break;
case "icbottomup":
DataFormat = DataFileFormat.IcBottomUp;
break;
case "dia":
DataFormat = DataFileFormat.Dia;
break;
default:
throw new FormatException("Invalid Acquisition Method.");
}
TsvPath = fileInfo.Contents["tsvpath"];
DataPath = fileInfo.Contents["datapath"];
var outPathtemp = fileInfo.Contents["outpath"];
OutputPath = outPathtemp;
OutputFileName = OutputPath + fileInfo.Contents["outputfile"];
}
public int GetIonTypeIndex(BaseIonType ionType)
{
return GetIonTypeIndex(ionType.IsPrefix);
}
/// <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)));
}
// Read Configuration file
private void InitTest(ConfigFileReader reader)
{
// Read program variables
var config = reader.GetNodes("vars").First();
_precursorCharge = Convert.ToInt32(config.Contents["precursorcharge"]);
var actStr = config.Contents["activationmethod"].ToLower();
_combineCharges = (config.Contents.ContainsKey("combinecharges") &&
config.Contents["combinecharges"].ToLower() == "true");
_useDecoy = (config.Contents.ContainsKey("usedecoy") &&
config.Contents["usedecoy"].ToLower() == "true");
_relativeIntensityThreshold = Convert.ToDouble(config.Contents["relativeintensitythreshold"]);
// Read ion data
var ionInfo = reader.GetNodes("ion").First();
int totalCharges = Convert.ToInt32(ionInfo.Contents["totalcharges"]);
var ionTypeStr = ionInfo.Contents["iontype"].Split(',');
var ions = new BaseIonType[ionTypeStr.Length];
for (int i = 0; i < ionTypeStr.Length; i++)
{
switch (ionTypeStr[i].ToLower())
{
case "a":
ions[i] = BaseIonType.A;
break;
case "b":
ions[i] = BaseIonType.B;
break;
case "c":
ions[i] = BaseIonType.C;
break;
case "x":
ions[i] = BaseIonType.X;
break;
case "y":
ions[i] = BaseIonType.Y;
break;
case "z":
ions[i] = BaseIonType.Z;
break;
}
}
var ionLossStr = ionInfo.Contents["losses"].Split(',');
var ionLosses = new NeutralLoss[ionLossStr.Length];
for (int i = 0; i < ionLossStr.Length; i++)
{
switch (ionLossStr[i].ToLower())
{
case "noloss":
ionLosses[i] = NeutralLoss.NoLoss;
break;
case "nh3":
ionLosses[i] = NeutralLoss.NH3;
break;
case "h2o":
ionLosses[i] = NeutralLoss.H2O;
break;
}
}
_ionTypeFactory = new IonTypeFactory(ions, ionLosses, totalCharges);
_ionTypes = _ionTypeFactory.GetAllKnownIonTypes().ToList();
var tempIonList = new List<IonType>();
if (ionInfo.Contents.ContainsKey("exclusions"))
{
var ionExclusions = ionInfo.Contents["exclusions"].Split(',');
tempIonList.AddRange(_ionTypes.Where(ionType => !ionExclusions.Contains(ionType.Name)));
_ionTypes = tempIonList;
}
// Read input and output file names
var fileInfo = reader.GetNodes("fileinfo").First();
_names = fileInfo.Contents["name"].Split(',');
_preTsv = fileInfo.Contents["tsvpath"];
_preRaw = fileInfo.Contents["rawpath"];
var outPathtemp = fileInfo.Contents["outpath"];
_outPre = outPathtemp;
var outFiletemp = fileInfo.Contents["outfile"];
_outFileName = _outPre + outFiletemp;
}
private static double GetScore(BaseIonType baseIonType, double fitScore, double intensity)
{
if (intensity < 0) return -1;
return 0;
}