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

void (*

)(

TotalSeq,

Completed,

* Anything);

InitBlast(

*blastdb,

use_mmap =

);

ResetGlobals(

);

*CallbackData = 0);

*CallbackData = 0);

& SetRankScore(

);

& SetPoissonOnly(

);

GetPoissonOnly(

)

;

& SetIterative(

);

GetIterative(

)

;

*

(

);

(

);

cout <<

;

DoubleCompare(list<CMSMatchedPeakSet *> &SingleForward,

list<CMSMatchedPeakSet *> &SingleBackward,

list<CMSMatchedPeakSet *> &Double,

MatchAndSort(

* Peaks,

TSeriesChargePairList::const_iterator &iPairList,

list<CMSMatchedPeakSet *> &SingleForward,

list<CMSMatchedPeakSet *> &SingleBackward);

CountModSites(

&NumModSites,

SetIons(list <EMSIonSeries> & Ions);

CreateLadders(

*

,

iSearch,

position,

*Masses,

iMissed,

& AA,

CompareLadders(

iMod,

CompareLaddersTop(

iMod,

InitModIndex(

*ModIndex,

MakeBoolMask(

*ModIndex,

iMod);

MakeBoolMap(

*ModMask,

*ModIndex,

& iMod,

& NumMod);

CalcModIndex(

*ModIndex,

MakeIntFromBoolMap(

*ModMask,

& NumMod);

Getnumseq(

)

;

MakeModString(

& seqstring,

& modseqstring,

*MSHit);

WriteBioseqs(

);

DeleteVariableOverlap(

& NumMod,

UpdateWithNewPep(

Missed,

*PepStart[],

*PepEnd[],

CreateModCombinations(

Missed,

*PepStart[],

NumMassAndMask[],

InitLadders(std::list <EMSIonSeries> & Ions);

MakeOidSet(

);

ReSearch(

Number)

;

& SetRestrictedSearch(

);

GetRestrictedSearch(

)

;

GetLadderCalc(

)

;

& SetLadderCalc(

);

ClearLadderCalc(

Max);

SetLadderContainer(

);

GetLadderContainer(

)

;

j(0),

, NumFixed;

(

= 0;

< NumMod;

++) {

(ModList[

].GetFixed() == 1) {

*OldSite(0);

(

= 0;

< NumMod && j - NumFixed <= iMod;

++) {

(ModList[

].GetFixed() != 1 && ModList[

].GetSite() != OldSite) {

(j = 0; j < NumMod; j++)

(j = 0; j <= iMod; j++)

ModMask[ModIndex[j]] =

;

(; j <= iMod; j++)

retval |= 1 << ModIndex[j];

(j = 0; j < NumMod; j++)

(ModMask[j]) retval |= 1 << j;

& iMod,

& NumMod,

(j = NumFixed; j <= iMod + NumFixed; j++) {

OldIndex = ModIndex[j];

(j == iMod + NumFixed) TopSite = 0;

TopSite = ModList[ModIndex[j+1]].

();

}

(ModList[ModIndex[j]].GetFixed() == 1);

(ModIndex[j] < NumMod && ModList[ModIndex[j]].GetSite() != TopSite) {

*OldSite(0);

(

= NumFixed;

< j;

++) {

(ModList[Low].GetFixed() == 1 ||

OldSite == ModList[Low].GetSite())

OldSite = ModList[ModIndex[

]].

();

ModIndex[j] = OldIndex;

SaveOneFile(

&MySearch,

Filename,

ReadModFiles(

& ModFileName,

& UserModFileName,

&

,

ReadTaxFile(

& Filename,

& TaxNameMap);

ReadFile(

& Filename,

LoadAnyFile(

& MySearch,

* SearchEngineIterative = 0);

ReadSearchRequest(

& Filename,

ReadCompleteSearch(

& Filename,

SaveAnyFile(

& MySearch,

CreateSearchSettings(

FileName,

class to contain preliminary hits.

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

container for a set of matches

class to hold spectral data for filtering and statistical characterization

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

TSite GetSite(void) const

Get the site position.

class to hold various helper functions for CSearch

map< int, string > TTaxNameMap

read in taxonomy file

bool & SetRankScore(void)

Sets the scoring to use rank statistics.

unsigned MakeBoolMask(int *ModIndex, int iMod)

bool & SetIterative(void)

Sets iterate search.

CMSResponse::TOidSet & SetOidSet(void)

get the oidset

const CLadderContainer & GetLadderContainer(void) const

get the ladder container

const bool GetIterative(void) const

Gets iterate search.

Int1 & SetLadderCalc(int i)

Set the bit that indicates whether a ladder was calculated.

CRef< CMSSearchSettings > MySettings

Search params.

AutoPtr< Int1, ArrayDeleter< Int1 > > LadderCalc

bool array that indicates if the ladders been calculated

CLadderContainer & SetLadderContainer(void)

set the ladder container

bool CalcModIndex(int *ModIndex, int &iMod, int &NumMod, int NumFixed, int NumModSites, CMod CModList[])

void MakeBoolMap(bool *ModMask, int *ModIndex, int &iMod, int &NumMod)

CRef< CMSResponse > MyResponse

Search response.

CRef< CMSResponse > & SetResponse(void)

Set search response.

bool RestrictedSearch

is this a oid restricted search

CRef< CSeqDB > rdfp

blast library

bool UseRankScore

boolean to turn on rank scoring

bool CheckFixed(int i, int NumFixed, CMod ModList[], int *ModIndex)

Checks to see that given modindex points to a site shared by a fixed mod.

CConstRef< CMSRequest > GetRequest(void) const

Get search request.

CLadderContainer LadderContainer

ion series mass ladders

Int1 GetLadderCalc(int i) const

Get the bit that indicates whether a ladder was calculated.

unsigned MakeIntFromBoolMap(bool *ModMask, int &NumMod)

CRef< CMSRequest > MyRequest

Search request.

TMassMask & SetMassAndMask(int i, int j)

Set the mask and mass of mod bit array.

void ClearLadderCalc(int Max)

Clear the ladder calc array up to max index.

CMassArray PrecursorMassArray

CConstRef< CCleave > GetEnzyme(void) const

Get search enzyme.

bool & SetRestrictedSearch(void)

is this search restricted to the oid set?

CRef< CMSRequest > & SetRequest(void)

Set search request.

void InitModIndex(int *ModIndex, int &iMod, int NumMod, int NumModSites, CMod ModList[])

CConstRef< CMSSearchSettings > GetSettings(void) const

Get search settings.

CConstRef< CMSResponse > GetResponse(void) const

Get search response.

const bool GetPoissonOnly(void) const

Gets the scoring to use rank statistics only with Poisson.

const CMSResponse::TOidSet & GetOidSet(void) const

get the oidset

const bool GetRestrictedSearch(void) const

is this search restricted to the oid set?

static int iSearchGlobal

Tracks the iSearch number for all search threads.

CRef< CCleave > & SetEnzyme(void)

Set search enzyme.

CMSResponse::TOidSet OidSet

set of oids to be searched

CRef< CMSSearchSettings > & SetSettings(void)

Set search settings.

CRef< CMSModSpecSet > initModset

TOMSSACallback initCallback

const int Getnumseq(void) const

CRef< CMSRequest > initRequestIn

These are so CSearch::Main() can call CSearch::Search() in a threaded run, this requires CSearch::Set...

CRef< CMSResponse > initResponseIn

int MaxModPerPep

maximum number of mod combinations per peptide

bool Iterative

boolean to turn on iterative search

AutoPtr< TMassMask, ArrayDeleter< TMassMask > > MassAndMask

contains bit mask of modifications and resulting mass

bool & SetPoissonOnly(void)

Sets the scoring to use rank statistics only with Poisson.

static int MaxMZ

maximum m/z value of all spectra precursors used to bound non-specific cleavage searches

static CRef< CMSPeakSet > SharedPeakSet

CRef< CCleave > Enzyme

the enzyme in use

bool PoissonOnly

boolean to only use Poisson score when using Rank scoring

CRef< CMSSearchSettings > initSettingsIn

int ThreadNum

The threadid number.

Include a standard set of the NCBI C++ Toolkit most basic headers.

string Path(const string &dir, const string &file)

element_type * get(void) const

Get pointer.

ESerialDataFormat

Data file format.

int8_t Int1

1-byte (8-bit) signed integer

#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.

virtual void OnExit(void)

Override this to execute finalization code.

virtual void * Main(void)=0

Derived (user-created) class must provide a real thread function.

#define NCBI_XOMSSA_EXPORT

list< CRef< CMSOutFile > > TOutfiles

EMSSpectrumFileType

Access to EMSSpectrumFileType's attributes (values, names) as defined in spec.

EMSPeakListTypes

enum that describes type of peak list

Defines the CNcbiApplication and CAppException classes for creating NCBI applications.

Defines command line argument related classes.

Defines NCBI C++ diagnostic APIs, classes, and macros.

Defines unified interface to application:

Defines classes: CDirEntry, CFile, CDir, CSymLink, CMemoryFile, CFileUtil, CFileLock,...

Floating-point support routines.

Multi-threading – classes, functions, and features.

Useful/utility classes and methods.

struct _MassMask TMassMask

void(* TOMSSACallback)(int TotalSeq, int Completed, void *Anything)

progress callback for CSearch

multimap< double, CMSHit * > TScoreList

Defines BLAST database access classes.

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