/// <summary>
///
/// </summary>
/// <param name="abbreviation"></param>
/// <param name="toBase"></param>
/// <param name="fromBase"></param>
/// <param name="mass"></param>
/// <param name="acceleration"></param>
protected ForceBase(string abbreviation,
IUnitConversion toBase, IUnitConversion fromBase,
IMass mass, IAcceleration acceleration)
: base(abbreviation, toBase, fromBase, mass, acceleration)
{
VerifyDimensions();
}
public static int Compare(this IMass mass1, IMass mass2, double epsilon = MassEqualityEpsilon)
{
double difference = mass1.MonoisotopicMass - mass2.MonoisotopicMass;
if (difference < -epsilon)
return -1;
return difference > epsilon ? 1 : 0;
}
public static HashSet <QuantitationChannelSet> GetQuantChannelModifications(Peptide peptide)
{
HashSet <QuantitationChannelSet> sets = new HashSet <QuantitationChannelSet>();
IMass[] mods = peptide.Modifications;
int modLength = mods.Length;
for (int i = 0; i < modLength; i++)
{
if (mods[i] != null)
{
IMass mod = mods[i];
QuantitationChannelSet quantSetMod;
ModificationCollection modCol;
if ((modCol = mod as ModificationCollection) != null)
{
foreach (IMass mod2 in modCol)
{
if ((quantSetMod = mod2 as QuantitationChannelSet) != null)
{
sets.Add(quantSetMod);
}
}
}
else if ((quantSetMod = mod as QuantitationChannelSet) != null)
{
sets.Add(quantSetMod);
}
}
}
return(sets);
}
/// <summary>
///
/// </summary>
/// <param name="abbreviation"></param>
/// <param name="toBase"></param>
/// <param name="fromBase"></param>
/// <param name="mass"></param>
/// <param name="acceleration"></param>
protected ForceBase(string abbreviation,
IUnitConversion toBase, IUnitConversion fromBase,
IMass mass, IAcceleration acceleration)
: base(abbreviation, toBase, fromBase, mass, acceleration)
{
VerifyDimensions();
}
public static bool MassEquals(this IMass mass1, IMass mass2, double epsilon = MassEqualityEpsilon)
{
if (mass1 == null || mass2 == null)
{
return(false);
}
return(Math.Abs(mass1.MonoisotopicMass - mass2.MonoisotopicMass) < epsilon);
}
public MzFeature(Fragment fragment, int charge)
{
this.feature = fragment;
this.charge = charge;
this.mzRange = new MzRange(this.feature.ToMz(this.charge), massTolerance);
this.intensities = new List <double>();
this.spectrumNumbers = new List <int>();
this.spectrumTICs = new List <double>();
}
public MzFeature(Peptide precursor, int charge)
{
this.feature = precursor;
this.charge = charge;
this.mzRange = new MzRange(this.feature.ToMz(this.charge), massTolerance);
this.intensities = new List <double>();
this.spectrumNumbers = new List <int>();
this.spectrumTICs = new List <double>();
}
private static string GetLocalizedString(LocalizedHit hit)
{
StringBuilder sb = new StringBuilder();
IMass[] mods = hit.LocalizedIsoform.GetModifications();
bool first = false;
for (int resNumber = 1; resNumber < mods.Length - 1; resNumber++)
{
IMass mod = mods[resNumber];
if (mod == null)
{
continue;
}
ModificationCollection modCollection = mod as ModificationCollection;
if (modCollection != null)
{
IMass trueMod = mod;
bool passes = false;
foreach (IMass mod2 in modCollection)
{
if (Lotor.QuantifiedModifications.Contains(mod2))
{
trueMod = mod2;
passes = true;
break;
}
}
if (!passes)
{
continue;
}
mod = trueMod;
}
else
{
if (Lotor.FixedModifications.Contains(mod) || !Lotor.QuantifiedModifications.Contains(mod))
{
continue;
}
}
int fullResidueNumber = hit.PSM.StartResidue + resNumber - 1;
char res = hit.LocalizedIsoform.Sequence[resNumber - 1];
if (first)
{
sb.Append(" & ");
}
sb.Append(res);
sb.Append(fullResidueNumber);
sb.Append("[" + mod + "]");
first = true;
}
return(sb.ToString());
}
public static int Compare(this IMass mass1, IMass mass2, double epsilon = MassEqualityEpsilon)
{
double difference = mass1.MonoisotopicMass - mass2.MonoisotopicMass;
if (difference < -epsilon)
{
return(-1);
}
return(difference > epsilon ? 1 : 0);
}
/// <summary>
/// Assigns mass per unit length to objects.
/// </summary>
/// <param name="app">The application.</param>
/// <param name="value">The mass per unit length assigned to the object. [M/L]</param>
/// <param name="replace">True: All existing mass assignments to the object are removed before assigning the specified mass.
/// False: The specified mass is added to any existing mass already assigned to the object.</param>
/// <exception cref="CSiException"><see cref="CSiApiBase.API_DEFAULT_ERROR_CODE" /></exception>
protected void setMass(IMass app,
double value,
bool replace)
{
app.SetMass(Name, value, replace);
if (replace)
{
_mass = value;
}
else
{
_mass += value;
}
}
public void WriteModification(IMass modification, ModificationSites sites, bool fixedModification = true)
{
if (CurrentStage != Stage.SearchSummary)
{
throw new ArgumentException("You must be in the Search Summary stage to write modifications");
}
foreach (ModificationSites singleSite in sites.GetActiveSites())
{
double basemass = 0;
if (singleSite >= ModificationSites.NPep)
{
_writer.WriteStartElement("terminal_modification");
if (singleSite.HasFlag(ModificationSites.NPep) || singleSite.HasFlag(ModificationSites.NProt))
{
_writer.WriteAttributeString("terminus", "N");
basemass += AminoAcidPolymer.DefaultNTerminus.MonoisotopicMass;
}
else
{
_writer.WriteAttributeString("terminus", "C");
basemass += AminoAcidPolymer.DefaultCTerminus.MonoisotopicMass;
}
_writer.WriteAttributeString("protein_terminus", (singleSite.HasFlag(ModificationSites.NProt) || singleSite.HasFlag(ModificationSites.ProtC)) ? "Y" : "N");
}
else
{
string letter = Enum.GetName(typeof(ModificationSites), singleSite);
AminoAcid aa = AminoAcid.GetResidue(letter);
_writer.WriteStartElement("aminoacid_modification");
_writer.WriteAttributeString("aminoacid", letter);
basemass += aa.MonoisotopicMass;
}
double massshift = modification.MonoisotopicMass;
_writer.WriteAttributeString("variable", (fixedModification) ? "N" : "Y");
_writer.WriteAttributeString("mass", (basemass + massshift).ToString());
_writer.WriteAttributeString("massdiff", massshift.ToString());
_writer.WriteAttributeString("description", modification.ToString());
_writer.WriteEndElement();
}
}
private MassDensity(IMass mass, IVolume volume)
: base(mass, volume)
{
}
public static bool TryParse(string input, out IMass output)
{
#region Prepare Variables
string capInput = input.ToUpperInvariant();
string extraction = input.ExtractNumberComponentFromMeasurementString();
double conversion = 0;
#endregion
#region Convert To Double
bool failed = !double.TryParse(extraction, out conversion);
if (failed)
{
Debug.AddDetailMessage("Measurement Input not successfully converted.");
Debug.AddDetailMessage("----" + capInput);
output = new Masses.KiloGram(0);
return(false);
}
#endregion
#endregion
#region Convert To Mass
if (capInput.EndsWithAny(Suffixes.Carat))
{
output = new Masses.Carat(conversion);
return(true);
}
if (capInput.EndsWithAny(Suffixes.CentiGram))
{
output = new Masses.CentiGram(conversion);
return(true);
}
if (capInput.EndsWithAny(Suffixes.DecaGram))
{
output = new Masses.DecaGram(conversion);
return(true);
}
if (capInput.EndsWithAny(Suffixes.Gram))
{
output = new Masses.Gram(conversion);
return(true);
}
if (capInput.EndsWithAny(Suffixes.HectoGram))
{
output = new Masses.HectoGram(conversion);
return(true);
}
if (capInput.EndsWithAny(Suffixes.KiloGram))
{
output = new Masses.KiloGram(conversion);
return(true);
}
if (capInput.EndsWithAny(Suffixes.MetricTonne))
{
output = new Masses.MetricTonne(conversion);
return(true);
}
if (capInput.EndsWithAny(Suffixes.Ounce))
{
output = new Masses.Ounce(conversion);
return(true);
}
if (capInput.EndsWithAny(Suffixes.Pound))
{
output = new Masses.Pound(conversion);
return(true);
}
if (capInput.EndsWithAny(Suffixes.Stone))
{
output = new Masses.Stone(conversion);
return(true);
}
if (capInput.EndsWithAny(Suffixes.UKLongTon))
{
output = new Masses.UKLongTon(conversion);
return(true);
}
if (capInput.EndsWithAny(Suffixes.USShortTon))
{
output = new Masses.USShortTon(conversion);
return(true);
}
#endregion
#region ... Conversion
#region Type Unrecognised
Debug.AddDetailMessage("No Type for input Mass conversion. Break here for details...");
Debug.AddDetailMessage("----" + capInput);
output = new Masses.KiloGram(0);
return(false);
#endregion
}
public static bool TryParse(string value, out IMass output) => objectFactory.TryParse(value, out output);
/// <summary>
///
/// </summary>
/// <param name="mass"></param>
/// <param name="volume"></param>
protected MassDensityBase(IMass mass, IVolume volume)
: base(mass, volume)
{
VerifyDimensions();
}
public void AddVariableModification(IMass modification, string name)
{
_variableMods.Add(name, modification);
}
public Pounds(IMass mass)
: this(mass.To <Pounds>().Value)
{
}
public Kilograms(IMass mass)
: this(mass.To <Kilograms>().Value)
{
}
public void AddVariableModification(IMass modificaiton, IAminoAcid aminoAcid)
{
}
public static bool MassEquals(this IMass mass1, IMass mass2, double epsilon = MassEqualityEpsilon)
{
if (mass1 == null || mass2 == null)
return false;
return Math.Abs(mass1.MonoisotopicMass - mass2.MonoisotopicMass) < epsilon;
}
public void AddVariableModification(IMass modificaiton, Terminus terminus)
{
}
public AccountController(RoleMaster rm, PasswdHesher <IHesh> ph, IRepositoryBuilder rb, IMass sm) : base(rb, rm)
{
MailSender = sm;
PasswdHesh = ph;
}
public Mass(IMass item)
: this(item.MonoisotopicMass)
{
}
private Force(string abbreviation,
IUnitConversion toBase, IUnitConversion fromBase,
IMass mass, IAcceleration acceleration)
: base(abbreviation, toBase, fromBase, mass, acceleration)
{
}
public void AddVariableModification(IMass modification, string name)
{
_variableMods.Add(name, modification);
}
public bool TryParse(string value, out IMass output) => throw new NotImplementedException();
public static IEnumerable <Peptide> GetUniquePeptides(Peptide peptide)
{
HashSet <QuantitationChannelSet> sets = new HashSet <QuantitationChannelSet>();
Dictionary <IQuantitationChannel, HashSet <int> > locations = new Dictionary <IQuantitationChannel, HashSet <int> >();
IMass[] mods = peptide.Modifications;
int modLength = mods.Length;
for (int i = 0; i < modLength; i++)
{
if (mods[i] != null)
{
IMass mod = mods[i];
List <QuantitationChannelSet> channelsets = new List <QuantitationChannelSet>();
QuantitationChannelSet quantSetMod;
ModificationCollection modCol;
if ((modCol = mod as ModificationCollection) != null)
{
foreach (IMass mod2 in modCol)
{
if ((quantSetMod = mod2 as QuantitationChannelSet) != null)
{
channelsets.Add(quantSetMod);
}
}
}
else if ((quantSetMod = mod as QuantitationChannelSet) != null)
{
channelsets.Add(quantSetMod);
}
foreach (QuantitationChannelSet channelset in channelsets)
{
sets.Add(channelset);
foreach (IQuantitationChannel channel in channelset.GetChannels())
{
HashSet <int> residues;
if (locations.TryGetValue(channel, out residues))
{
residues.Add(i);
}
else
{
residues = new HashSet <int> {
i
};
locations.Add(channel, residues);
}
}
}
}
}
if (sets.Count == 0)
{
yield return(new Peptide(peptide, true));
}
else if (sets.Count == 1)
{
foreach (QuantitationChannelSet set in sets)
{
foreach (IQuantitationChannel channel in set.GetChannels())
{
Peptide toReturn = new Peptide(peptide, true);
foreach (int residue in locations[channel])
{
toReturn.SetModification(channel, residue);
}
yield return(toReturn);
}
}
}
else
{
List <HashSet <IQuantitationChannel> > quantChannels = new List <HashSet <IQuantitationChannel> >();
GetUniquePeptides_helper(sets.ToList(), 0, new HashSet <IQuantitationChannel>(), quantChannels);
foreach (HashSet <IQuantitationChannel> channelset in quantChannels)
{
Peptide toReturn = new Peptide(peptide, true);
Dictionary <int, IMass> modsToAdd = new Dictionary <int, IMass>();
foreach (IQuantitationChannel channel in channelset)
{
foreach (int residue in locations[channel])
{
IMass modToAdd;
if (modsToAdd.TryGetValue(residue, out modToAdd))
{
ModificationCollection col = new ModificationCollection(channel, modToAdd);
modsToAdd[residue] = col;
}
else
{
modsToAdd.Add(residue, channel);
}
}
}
foreach (KeyValuePair <int, IMass> kvp in modsToAdd)
{
toReturn.SetModification(kvp.Value, kvp.Key);
}
yield return(toReturn);
}
}
}
public void AddVariableModification(IMass modificaiton, ModificationSites sites)
{
}
public void WriteModification(IMass modification, ModificationSites sites, bool fixedModification = true)
{
if (CurrentStage != Stage.SearchSummary)
throw new ArgumentException("You must be in the Search Summary stage to write modifications");
foreach (ModificationSites singleSite in sites.GetActiveSites())
{
double basemass = 0;
if (singleSite >= ModificationSites.NPep)
{
_writer.WriteStartElement("terminal_modification");
if (singleSite.HasFlag(ModificationSites.NPep) || singleSite.HasFlag(ModificationSites.NProt))
{
_writer.WriteAttributeString("terminus", "N");
basemass += AminoAcidPolymer.DefaultNTerminus.MonoisotopicMass;
}
else
{
_writer.WriteAttributeString("terminus", "C");
basemass += AminoAcidPolymer.DefaultCTerminus.MonoisotopicMass;
}
_writer.WriteAttributeString("protein_terminus", (singleSite.HasFlag(ModificationSites.NProt) || singleSite.HasFlag(ModificationSites.ProtC)) ? "Y" : "N");
}
else
{
string letter = Enum.GetName(typeof(ModificationSites), singleSite);
AminoAcid aa = AminoAcid.GetResidue(letter);
_writer.WriteStartElement("aminoacid_modification");
_writer.WriteAttributeString("aminoacid", letter);
basemass += aa.MonoisotopicMass;
}
double massshift = modification.MonoisotopicMass;
_writer.WriteAttributeString("variable", (fixedModification) ? "N" : "Y");
_writer.WriteAttributeString("mass", (basemass + massshift).ToString());
_writer.WriteAttributeString("massdiff", massshift.ToString());
_writer.WriteAttributeString("description", modification.ToString());
_writer.WriteEndElement();
}
}
public void AddVariableModification(IMass modificaiton, IAminoAcid aminoAcid)
{
}
private MassDensity(IMass mass, ILength cubicLength)
: base(mass, cubicLength)
{
}
public Mass(IMass massToConvertFrom)
{
mMass = (TDataType)(Convert.ChangeType(massToConvertFrom.Value * massToConvertFrom.UnitOfMeasure.GetCompleteMultiplier <TUnitOfMeasure>(1), typeof(TDataType)));
}
/// <summary>
/// Private Constructor
/// </summary>
/// <param name="abbreviation"></param>
/// <param name="toBase"></param>
/// <param name="fromBase"></param>
/// <param name="mass"></param>
/// <param name="acceleration"></param>
private Force(string abbreviation,
IUnitConversion toBase, IUnitConversion fromBase,
IMass mass, IAcceleration acceleration)
: base(abbreviation, toBase, fromBase, mass, acceleration)
{
}
private MassDensity(IMass mass, IVolume volume)
: base(mass, volume)
{
}
/// <summary>
///
/// </summary>
/// <param name="mass"></param>
/// <param name="volume"></param>
protected MassDensityBase(IMass mass, IVolume volume)
: base(mass, volume)
{
VerifyDimensions();
}
private MassDensity(IMass mass, ILength cubicLength)
: base(mass, cubicLength)
{
}
public void AddVariableModification(IMass modification, char residue)
{
}
/// <summary>
/// Converts the object that has a m/z into a mass value based on the charge state
/// </summary>
/// <param name="mz"></param>
/// <param name="charge"></param>
/// <param name="c13Isotope"></param>
/// <returns></returns>
public static double ToMass(this IMass mz, int charge, int c13Isotope = 0)
{
return(Mass.MassFromMz(mz.MonoisotopicMass + c13Isotope * Constants.C13C12Difference, charge));
}
public void AddVariableModification(IMass modificaiton, Terminus terminus)
{
}
private Pressure(string abbreviation, IMass mass, ILength length, ITime time)
: base(abbreviation, mass, length, time)
{
VerifyDimensions();
}
/// <summary>
/// Returns the mass per unit length assignment from objects. [M/L]
/// </summary>
/// <param name="app">The application.</param>
/// <exception cref="CSiException"><see cref="CSiApiBase.API_DEFAULT_ERROR_CODE" /></exception>
protected void getMass(IMass app)
{
_mass = app.GetMass(Name);
}
/// <summary>
/// Assigns mass per unit length to objects.
/// </summary>
/// <param name="app">The application.</param>
/// <param name="value">The mass per unit length assigned to the object. [M/L]</param>
/// <param name="replace">True: All existing mass assignments to the object are removed before assigning the specified mass.
/// False: The specified mass is added to any existing mass already assigned to the object.</param>
/// <exception cref="CSiException"><see cref="CSiApiBase.API_DEFAULT_ERROR_CODE" /></exception>
protected void setMass(IMass app,
double value,
bool replace)
{
app.SetMass(Name, value, replace);
}
public bool TryParse(string value, out IMass output) => Mass.TryParse(value, out output);
private Pressure(string abbreviation, IMass mass, ILength length, ITime time)
: base(abbreviation, mass, length, time)
{
VerifyDimensions();
}
