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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/msms_8hpp_source.html below:

NCBI C++ ToolKit: src/algo/ms/omssa/msms.hpp Source File

[] = {0.0, 71.03711, 0.0, 103.00919, 115.02694, 129.04259, 147.06841, 57.02147, 137.05891, 113.08406, 128.09496, 113.08406, 131.04049, 114.04293, 97.05276, 128.05858, 156.10111, 87.03203, 101.04768, 99.06841, 186.07931, 0.0, 163.06333, 0.0, 149.903 , 0.0, 113.08406, 237.14776, 0.0 };

[] = {0.0, 71.08, 0.0, 103.15, 115.09, 129.12, 147.18, 57.05, 137.14, 113.16, 128.17, 113.16, 131.20, 114.10, 97.12, 128.13, 156.19, 87.08, 101.11, 99.13, 186.21, 0.0, 163.18, 0.0, 150.044, 0.0, 113.16, 237.30, 0.0 };

[] = {0.0, 72.034144893, 0.0, 104.006224893, 116.023974893, 130.039624893, 148.065444893, 58.018494893, 140.050014679, 114.081094893, 130.089029786, 114.081094893, 132.037524893, 116.036999786, 98.049794893, 130.052649786, 160.089239572, 88.029064893, 102.044714893, 100.065444893, 188.073379786, 0.0, 164.060364893, 0.0, 150.8964, 0.0, 114.081094893, 240.1388649, 0.0 };

[] = {1.007825, 1.007825, 1.007825, 17.00274, 17.00274, 17.00274, 0, 0, 0, 0, 1.007825, 17.00274, 1.007825};

[] = { -27.994915, 0.0, 17.02655, 27.994915, 2.01565, -14.003075, 0, 0, 0, 0, -26.98709, -15.9994, -70.981405};

*

GetMass(

)

;

*

GetIntMass(

)

;

*

GetMap(

)

;

& operator= (

& rhs);

GetSite(

)

;

& SetSite(

);

GetPrecursorDelta(

)

;

& SetPrecursorDelta(

);

GetProductDelta(

)

;

& SetProductDelta(

);

GetEnum(

)

;

& SetEnum(

);

GetFixed(

)

;

& SetFixed(

);

= (

*)-1;

(GetErrCode()) {

CalcAndCut(

*SeqStart,

**PepStart,

*IntCalcMass,

*PrecursorIntCalcMass,

CheckCleave(

*iPepStart,

*iSeqStart);

CheckCleaveChar(

*iPepStart)

;

CalcMass(

SeqChar,

*IntCalcMass

EndMass(

*Masses

findfirst(

* Seq,

,

SeqLen);

CheckNonSpecificMods(

ModType,

*iPepStart,

*iPepStart,

& NumMod,

SeqChar,

MaxNumMod,

*iPepStart,

GetTopDown(

)

;

*

(

)

;

* & SetStop(

);

GetNonSpecific(

)

;

GetCleaveNum(

)

;

* GetCleaveOffset(

)

;

GetNMethionine(

)

;

& SetNMethionine(

);

GetCleaveAt(

)

;

GetCheckProline(

)

;

* GetCleaveSense(

)

;

(iPepStart == iSeqStart &&

&& *(iPepStart) ==

) {

(iPepStart ==

())

;

*IntCalcMass

SeqChar,

MaxNumMod,

ModList[],

*iPepStart,

iMods < VariableMods.

(ModType).

(); ++iMods) {

(SeqChar == Modset->

(VariableMods.

(ModType)[iMods], iChar) && NumMod < MaxNumMod) {

ModList[NumMod].

() = iPepStart;

(setfixed) ModList[NumMod].

() = 1;

ModList[NumMod].

() = 0;

& NumMod,

MaxNumMod,

*iPepStart,

iMods < VariableMods.

(ModType).

(); ++iMods) {

(NumMod < MaxNumMod) {

ModList[NumMod].

() = iPepStart;

(setfixed) ModList[NumMod].

() = 1;

ModList[NumMod].

() = 0;

& NumMod,

SeqChar,

MaxNumMod,

*iPepStart,

iPepStart,

, Modset);

iPepStart,

, Modset);

(Specific, VariableMods, NumMod, SeqChar, MaxNumMod, ModList,

iPepStart,

, Modset);

(Specific, FixedMods, NumMod, SeqChar, MaxNumMod, ModList,

iPepStart,

, Modset);

const int kNumUniqueAA

@MSMod.hpp User-defined methods of the data storage class.

const char *const GetMap(void) const

return the map for translating AA char to AA number

eMSEnzymes_aspn_de Asp-N that cuts at D and E

eMSEnzymes_chymotrypsin_p chymotrypsin without proline rule

factory to return back object for enzyme

const char *& SetStop(void)

Set the enzyme stop value.

const char * CleaveOffset

what is the cleavage offset

bool CheckProline

Should we apply the proline rule (no cleavage before proline)

void CheckNonSpecificMods(EMSModType ModType, CMSMod &VariableMods, int &NumMod, int MaxNumMod, CMod ModList[], const char *iPepStart, bool setfixed, CRef< CMSModSpecSet > &Modset)

looks for non-specific ptms

bool CheckCleave(const char *iPepStart, const char *iSeqStart)

Check to see if we are at a cleavage point Used by CalcAndCut.

bool GetNonSpecific(void) const

Is this a non-specific search?

const char * Stop

Stop Stop position for no-enzyme and semi-tryptic searches.

bool NMethionine

n-terminal methionine cleavage

void CalcMass(char SeqChar, int *Masses, const int *IntCalcMass)

bool & SetNMethionine(void)

Set n-term methionine cleavage.

const char * GetCleaveOffset(void) const

Get the the cleave offset, 0 = cterm, 1 = nterm.

void CheckMods(EMSModType NonSpecificIn, EMSModType Specific, CMSMod &VariableMods, CMSMod &FixedMods, int &NumMod, char SeqChar, int MaxNumMod, CMod ModList[], const char *iPepStart, CRef< CMSModSpecSet > &Modset)

checks all mods for a particular type

const char * GetStop(void) const

Get the enzyme stop value.

bool NonSpecific

Is this a non-specific search?

bool GetCheckProline(void) const

Should we check for proline?

bool GetNMethionine(void) const

Is there n-term methionine cleavage?

void EndMass(int *Masses)

const string GetCleaveAt(void) const

What are the cleavage chars?

const char * CleaveAt

where to cleave.

bool GetTopDown(void) const

Is the enzyme really a top-down search?

bool CheckCleaveChar(const char *iPepStart) const

is the character given one of the cleavage chars?

const char * GetCleaveSense(void) const

Should we check for proline?

int GetCleaveNum(void) const

Get the number of cleavage chars.

bool TopDown

TopDown does this signify a top-down search.

int kCleave

How many cleavage characters.

void CheckAAMods(EMSModType ModType, CMSMod &VariableMods, int &NumMod, char SeqChar, int MaxNumMod, CMod ModList[], const char *iPepStart, bool setfixed, CRef< CMSModSpecSet > &Modset)

looks for amino acid specific ptms

eMSEnzymes_gluc_de Glu-C that cuts at D and E

eMSEnzymes_lysn Cuts N term of lysine

int GetNeutralLoss(int Mod) const

get neutral loss

int GetModNumChars(int Mod) const

get the number of modification AA's

char GetModChar(int Mod, int Number) const

get modification AA's

int GetModMass(int Mod) const

get modification mass

const TModLists & GetAAMods(EMSModType Type) const

double CalcMass[kNumUniqueAA]

const int *const GetIntMass(void) const

const double *const GetMass(void) const

int IntCalcMass[kNumUniqueAA]

contains information for a post translational modification at a particular sequence site

TMass & SetProductDelta(void)

Set the site postion.

TMass & SetPrecursorDelta(void)

Set the site postion.

int TMass

type for masses

int IsFixed

track fixed mods, 1 == fixed

TSite GetSite(void) const

Get the site position.

int TFixed

is the mod fixed?

const char * Site

the position within the peptide of a variable modification

TMass GetPrecursorDelta(void) const

Get the mass to be added to the precursor mass.

TFixed & SetFixed(void)

set mod state (1 = fixed)

CMod(void)

default constructor

int ProductDelta

the modification mass for the product

TEnum GetEnum(void) const

Get mod type.

int TEnum

what is the type of the mod?

TMass GetProductDelta(void) const

Get the mass to be added to the product mass.

void Reset(void)

reset to default values

TSite & SetSite(void)

Set the site postion.

int PrecursorDelta

the modification mass for the precursor

int ModEnum

the modification type (used for saving for output)

TEnum & SetEnum(void)

Set the mod type.

const char * TSite

type for a site on a sequence

TFixed GetFixed(void) const

Is the mod fixed?

const CMod & operator=(const CMod &rhs)

assignment

eMSEnzymes_no_enzyme search without enzyme (precursor mass only)

generic exception class for omssa

NCBI_EXCEPTION_DEFAULT(COMSSAException, CException)

EErrCode

Error types that subsystem can generate.

@ eMSLadderNotFound

ladder not found in CLadderContainer

@ eMSNoMatchException

unmatched sequence library

@ eMSParseException

unable to parse COMSSASearch

virtual const char * GetErrCodeString(void) const override

Translate from the error code value to its string representation.

Chymotrypsin, cuts N terminal at A,F,I,L,M or V.

eMSEnzymes_semi_tryptic semi tryptic search (one end of peptide has to be tryptic)

static SIZE_TYPE Convert(const CTempString &src, TCoding src_coding, TSeqPos pos, TSeqPos length, string &dst, TCoding dst_coding)

eMSEnzymes_thermolysin_p cuts N terminal at A,F,I,L,M or V

eMSEnzymes_top_down top-down search of ETD spectra

whole protein (no cleavage)

std::ofstream out("events_result.xml")

main entry point for tests

virtual const char * GetErrCodeString(void) const

Get error code interpreted as text.

#define EXCEPTION_VIRTUAL_BASE

Do not use virtual base classes in exception declaration at all, because in this case derived class s...

TSeqPos GetStop(const CSeq_loc &loc, CScope *scope, ESeqLocExtremes ext=eExtreme_Positional)

If only one CBioseq is represented by CSeq_loc, returns the position at the stop of the location.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define BEGIN_SCOPE(ns)

Define a new scope.

#define NCBI_XOMSSA_EXPORT

EMSModType

enumerate modification types

EMSEnzymes

enumerate enzymes

const double kNeutron

neutron mass

const double kIonTypeMass[]

std::deque< int > TCleave

const double AverageMass[]

const double MonoN15Mass[]

const int kNumAAIntervals

const double kWater

mass of water

const struct ncbi::grid::netcache::search::fields::SIZE size

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