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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/msmerge_8cpp_source.html below:

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

omemorystream << *OldSearch;

omemorystream.

();

imemorystream >> *

;

((*

().begin())->CanGetMoresettings() && (*

().begin())->GetMoresettings().CanGet()) {

((*

().begin())->GetSpectra().Get().size() == 0)

((*iSpectrum)->GetNumber() > Max)

Max = (*iSpectrum)->GetNumber();

((*iSpectrum)->GetNumber() < Min)

Min = (*iSpectrum)->GetNumber();

(*

().begin())->SetSpectra().Set().push_back(*iSpectrum);

(*

().begin())->SetHitsets().push_back(*iHits);

(*

().begin())->SetMoresettings().Set().push_back(OldSettings);

((*OldSearch->GetRequest().begin())->CanGetMoresettings() &&

(*OldSearch->GetRequest().begin())->GetMoresettings().CanGet()) {

(*

().begin())->SetMoresettings().Set().push_back(*iSettings);

((*

().begin())->GetSettings().GetDb() != Name ||

(*

().begin())->GetDbversion() != Size)

((*

().begin())->CanGetMoresettings() && (*

().begin())->GetMoresettings().CanGet()) {

((*iSettings)->GetDb() != Name)

;

((*

().begin())->CanGetMoresettings() && (*

().begin())->GetMoresettings().CanGet()) {

(*iHits)->SetSettingid() += Min;

(*iHits)->SetNumber() += Min;

(*iSpectrum)->SetNumber() += Min;

().insert((*iMSBioseq)->GetOid());

MSBioseq->SetOid() = oid;

(*

().begin())->SetBioseqs().Set().push_back(MSBioseq);

Min, Max, OldMin, OldMax;

OldSearch->FindMinMaxSearchSettingId(OldMin, OldMax);

OldSearch->RenumberSearchSettingId(Max - OldMin + 1);

OldSearch->FindMinMaxSpectrumNumber(OldMin, OldMax);

OldSearch->RenumberSpectrumNumber(Max - OldMin + 1);

OldSearch->PopulateOidList();

set_difference(OldSearch->GetOids().begin(), OldSearch->GetOids().end(),

().begin(),

().end(),

inserter(Diff, Diff.begin()));

(*iDiff, (*OldSearch->GetResponse().begin())->GetBioseqs().GetBioseqByOid(*iDiff));

In-memory stream (a la strstream or stringstream)

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

generic exception class for omssa

const string FileEnding(const ESerialDataFormat FileType) const

return a file ending based on encoding type

void PopulateOidList(void)

fill in the oid list from existing object

void AppendBioseq(const int oid, CConstRef< CBioseq > Bioseq)

add a bioseq to the bioseq list

void RenumberOneSearchSettingId(CMSSearchSettings &SearchSettings, const int Min)

renumber one search setting

void FindMinMaxForOneSetting(const CMSSearchSettings &SearchSettings, int &Min, int &Max) const

helper function for FindMinMaxSearchSettingId

void AppendSearch(CRef< COMSSASearch > OldSearch)

add a search to this object

const TOid & GetOids(void) const

get the oid list

void FindMinMaxSearchSettingId(int &Min, int &Max) const

find the maximum and minimum search setting id in this search

void RenumberSearchSettingId(const int Min)

renumber search settings by adding a minimum value

void CopySpectra(CRef< COMSSASearch > OldSearch)

copy a spectra from old search into this search

void RenumberSpectrumNumber(const int Min)

renumber spectrum numbers by adding a minimum value

void FindMinMaxSpectrumNumber(int &Min, int &Max) const

find the maximum and minimum spectrum number in this search

const bool CheckLibraryNameAndSize(const string Name, const int Size) const

check for matching library name and size in all search settings

void CopySettings(CRef< COMSSASearch > OldSearch)

copy Settings from old search into new this search

TOid & SetOids(void)

set the oid list

void CopyHitsets(CRef< COMSSASearch > OldSearch)

copy Hitsets from old search into new this search

CObjectIStreamAsnBinary –.

CObjectOStreamAsnBinary –.

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

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define NON_CONST_ITERATE(Type, Var, Cont)

Non constant version of ITERATE macro.

#define NCBI_THROW(exception_class, err_code, message)

Generic macro to throw an exception, given the exception class, error code and message string.

ESerialDataFormat

Data file format.

@ eSerial_AsnText

ASN.1 text.

@ eSerial_AsnBinary

ASN.1 binary.

void SetReferenceSchema(bool use_schema=true)

Make generated XML document reference XML schema.

void SetWriteNamedIntegersByValue(bool set)

Set up writing named integers (in ANS.1 sense) by value only.

TObjectType * GetPointerOrNull(void) const THROWS_NONE

Get pointer value.

#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

TSettingid GetSettingid(void) const

Get the Settingid member data.

const TRequest & GetRequest(void) const

Get the Request member data.

list< CRef< CMSSpectrum > > Tdata

list< CRef< CMSSearchSettings > > Tdata

const TResponse & GetResponse(void) const

Get the Response member data.

list< CRef< CMSBioseq > > Tdata

vector< CRef< CMSHitSet > > THitsets

TResponse & SetResponse(void)

Assign a value to Response data member.

TRequest & SetRequest(void)

Assign a value to Request data member.

void SetSettingid(TSettingid value)

Assign a value to Settingid data member.

CObjectOStream * SetUpOutputFile(CObjectOStream *os, ESerialDataFormat DataFormat)

sets up output file based on DataFormat in particular, initializes xml stream appropriately

const TYPE & Get(const CNamedParameterList *param)

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

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

Int4 TOid

Ordinal ID in BLAST databases.

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