Settings for digestion, ion calculation and VectorSearch. More...

Public Member Functions
	Settings (int MaxCleavages=2, int MinPepLength=5, int MaxPepLength=30, int MaxPrecursorCharge=4, string MaxFragmentCharge="+1", int MaxNeutralLosses=1, int MaxNeutralLossMods=2, bool DecoySearch=true, int TopN=1000, float Tolerance=0.02f, bool Normalize=false, bool UseGaussian=true, string Mode="CPU_SMi32")
	Settings constructor to set the specified search parameters.

bool	addFixedModification (string aminoAcid, double mass)
	Add a fixed modification to the fixed modification dictionary.

bool	addVariableModification (string aminoAcid, double mass)
	Add a variable modification to the variable modification dictionary.

string	modificationsToString (bool variable=false)
	Returns a string representation of the modifications.

override string	ToString ()
	Returns a string representation of the settings.

Properties
int	MAX_CLEAVAGES `[get, set]`
	Maximum number of missed cleavages allowed during digestion.

int	MIN_PEP_LENGTH `[get, set]`
	Minimum peptide length.

int	MAX_PEP_LENGTH `[get, set]`
	Maximum peptide length.

int	MAX_PRECURSOR_CHARGE `[get, set]`
	Maximum considered precursor ion charge.

string	MAX_FRAGMENT_CHARGE `[get, set]`
	Maximum considered fragment ion charge.

int	MAX_NEUTRAL_LOSSES `[get, set]`
	Maximum number of considered neutral losses.

int	MAX_NEUTRAL_LOSS_MODS `[get, set]`
	Maximum number of considered neutral loss modifications.

Dictionary< string, double >	FIXED_MODIFICATIONS `[get, set]`
	Dictionary for fixed modifications that maps amino acids to their possible modification masses.

Dictionary< string, double >	VARIABLE_MODIFICATIONS `[get, set]`
	Dictionary for variable modifications that maps amino acids to their possible modification masses.

bool	DECOY_SEARCH `[get, set]`
	Whether or not decoy search should be performed.

int	TOP_N `[get, set]`
	The top n candidates that should be returned by the VectorSearch.

float	TOLERANCE `[get, set]`
	The tolerance used for the VectorSearch.

bool	NORMALIZE `[get, set]`
	Whether or not scores should be normalized by the VectorSearch.

bool	USE_GAUSSIAN `[get, set]`
	Whether or not peaks should be modelled as gaussian distributions by the VectorSearch.

string	MODE `[get, set]`
	The search approach used by the VectorSearch.

Detailed Description

Settings for digestion, ion calculation and VectorSearch.

Definition at line 8 of file Settings.cs.

Constructor & Destructor Documentation

◆ Settings()

CandidateSearch.util.Settings.Settings	(	int	MaxCleavages = `2`,
		int	MinPepLength = `5`,
		int	MaxPepLength = `30`,
		int	MaxPrecursorCharge = `4`,
		string	MaxFragmentCharge = `"+1"`,
		int	MaxNeutralLosses = `1`,
		int	MaxNeutralLossMods = `2`,
		bool	DecoySearch = `true`,
		int	TopN = `1000`,
		float	Tolerance = `0::02f`,
		bool	Normalize = `false`,
		bool	UseGaussian = `true`,
		string	Mode = `"CPU_SMi32"`
	)

Settings constructor to set the specified search parameters.

Parameters

MaxCleavages	Maximum number of missed cleavages allowed during digestion.
MinPepLength	Minimum peptide length.
MaxPepLength	Maximum peptide length.
MaxPrecursorCharge	Maximum considered precursor ion charge.
MaxFragmentCharge	Maximum considered fragment ion charge.
MaxNeutralLosses	Maximum number of considered neutral losses.
MaxNeutralLossMods	Maximum number of considered neutral loss modifications.
DecoySearch	Whether or not decoy search should be performed.
TopN	The top n candidates that should be returned by the VectorSearch.
Tolerance	The tolerance used for the VectorSearch.
Normalize	Whether or not scores should be normalized by the VectorSearch.
UseGaussian	Whether or not peaks should be modelled as gaussian distributions by the VectorSearch.
Mode	The search approach used by the VectorSearch.

Definition at line 94 of file Settings.cs.

Member Function Documentation

◆ addFixedModification()

bool CandidateSearch.util.Settings.addFixedModification	(	string	aminoAcid,
		double	mass
	)

Add a fixed modification to the fixed modification dictionary.

Parameters

aminoAcid	The amino acid that will be modified.
mass	The mass of the modification.

Returns: True if there is no modification for that amino acid yet, false if there already exists a modification for that amino acid.

Definition at line 125 of file Settings.cs.

◆ addVariableModification()

bool CandidateSearch.util.Settings.addVariableModification	(	string	aminoAcid,
		double	mass
	)

Add a variable modification to the variable modification dictionary.

Parameters

aminoAcid	The amino acid that can be modified.
mass	The mass of the modification.

Returns: True if there is no modification for that amino acid yet, false if there already exists a modification for that amino acid.

Definition at line 140 of file Settings.cs.

◆ modificationsToString()

string CandidateSearch.util.Settings.modificationsToString ( bool variable = false )

Returns a string representation of the modifications.

Parameters

variable Whether to process fixed or variable modifications.

Returns: The string representation of the specified modification set.

Definition at line 154 of file Settings.cs.

◆ ToString()

override string CandidateSearch.util.Settings.ToString ( )

Returns a string representation of the settings.

Returns: The string representation of the settings.

Definition at line 178 of file Settings.cs.

Property Documentation

◆ DECOY_SEARCH

bool CandidateSearch.util.Settings.DECOY_SEARCH

getset

Whether or not decoy search should be performed.

Definition at line 54 of file Settings.cs.

◆ FIXED_MODIFICATIONS

Dictionary<string, double> CandidateSearch.util.Settings.FIXED_MODIFICATIONS

getset

Dictionary for fixed modifications that maps amino acids to their possible modification masses.

Definition at line 44 of file Settings.cs.

◆ MAX_CLEAVAGES

int CandidateSearch.util.Settings.MAX_CLEAVAGES

getset

Maximum number of missed cleavages allowed during digestion.

Definition at line 14 of file Settings.cs.

◆ MAX_FRAGMENT_CHARGE

string CandidateSearch.util.Settings.MAX_FRAGMENT_CHARGE

getset

Maximum considered fragment ion charge.

Definition at line 32 of file Settings.cs.

◆ MAX_NEUTRAL_LOSS_MODS

int CandidateSearch.util.Settings.MAX_NEUTRAL_LOSS_MODS

getset

Maximum number of considered neutral loss modifications.

Definition at line 40 of file Settings.cs.

◆ MAX_NEUTRAL_LOSSES

int CandidateSearch.util.Settings.MAX_NEUTRAL_LOSSES

getset

Maximum number of considered neutral losses.

Definition at line 36 of file Settings.cs.

◆ MAX_PEP_LENGTH

int CandidateSearch.util.Settings.MAX_PEP_LENGTH

getset

Maximum peptide length.

Definition at line 22 of file Settings.cs.

◆ MAX_PRECURSOR_CHARGE

int CandidateSearch.util.Settings.MAX_PRECURSOR_CHARGE

getset

Maximum considered precursor ion charge.

Definition at line 28 of file Settings.cs.

◆ MIN_PEP_LENGTH

int CandidateSearch.util.Settings.MIN_PEP_LENGTH

getset

Minimum peptide length.

Definition at line 18 of file Settings.cs.

◆ MODE

string CandidateSearch.util.Settings.MODE

getset

The search approach used by the VectorSearch.

Definition at line 76 of file Settings.cs.

◆ NORMALIZE

bool CandidateSearch.util.Settings.NORMALIZE

getset

Whether or not scores should be normalized by the VectorSearch.

Definition at line 68 of file Settings.cs.

◆ TOLERANCE

float CandidateSearch.util.Settings.TOLERANCE

getset

The tolerance used for the VectorSearch.

Definition at line 64 of file Settings.cs.

◆ TOP_N

int CandidateSearch.util.Settings.TOP_N

getset

The top n candidates that should be returned by the VectorSearch.

Definition at line 60 of file Settings.cs.

◆ USE_GAUSSIAN

bool CandidateSearch.util.Settings.USE_GAUSSIAN

getset

Whether or not peaks should be modelled as gaussian distributions by the VectorSearch.

Definition at line 72 of file Settings.cs.

◆ VARIABLE_MODIFICATIONS

Dictionary<string, double> CandidateSearch.util.Settings.VARIABLE_MODIFICATIONS

getset

Dictionary for variable modifications that maps amino acids to their possible modification masses.

Definition at line 48 of file Settings.cs.

The documentation for this class was generated from the following file:

C:/Users/P42587/Documents/GitHub/CandidateSearch/util/Settings.cs

Public Member Functions

Properties

Detailed Description

Constructor & Destructor Documentation

◆ Settings()

Member Function Documentation

◆ addFixedModification()

◆ addVariableModification()

◆ modificationsToString()

◆ ToString()

Property Documentation

◆ DECOY_SEARCH

◆ FIXED_MODIFICATIONS

◆ MAX_CLEAVAGES

◆ MAX_FRAGMENT_CHARGE

◆ MAX_NEUTRAL_LOSS_MODS

◆ MAX_NEUTRAL_LOSSES

◆ MAX_PEP_LENGTH

◆ MAX_PRECURSOR_CHARGE

◆ MIN_PEP_LENGTH

◆ MODE

◆ NORMALIZE

◆ TOLERANCE

◆ TOP_N

◆ USE_GAUSSIAN

◆ VARIABLE_MODIFICATIONS