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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/rps__aux_8hpp_source.html below:

NCBI C++ ToolKit: include/algo/blast/api/rps_aux.hpp Source File

33 #ifndef ALGO_BLAST_API__RPS_AUX___HPP 34 #define ALGO_BLAST_API__RPS_AUX___HPP 82

fObservationsFile = 16,

90

fRpsBlast = fLookupTableFile | fPssmFile | fAuxInfoFile,

93

fDeltaBlast = fFrequenciesFile | fObservationsFile,

96

fRpsBlastWithCBS = fRpsBlast | fFreqRatiosFile

116 double

GetScalingFactor()

const

;

120 const char

* GetMatrixName()

const

;

128 int

GetGapOpeningCost()

const

;

131 int

GetGapExtensionCost()

const

;

137 void

x_Init(

const string

& rps_dbname,

int flags

);

Routines for creating protein BLAST lookup tables.

Defines to provide correct exporting from BLAST DLL in Windows.

#define NCBI_XBLAST_EXPORT

NULL operations for other cases.

RPS BLAST structure definitions.

Wrapper class to manage the BlastRPSAuxInfo structure, as currently there aren't any allocation or de...

Wrapper class to manage the BlastRPSInfo structure, as currently there aren't any allocation or deall...

This class represents the .aux file in a RPS-BLAST file, which contains information about the scoring...

This class represents the .freq file in a RPS-BLAST file, which contains the frequency ratios for the...

This class represents the .wcounts file in a RPS-BLAST file, which contains the weighted residue freq...

This class represents the .loo file in a RPS-BLAST file, which contains the pre-computed lookup table...

This class represents the .obsr file in a RPS-BLAST file, which contains the numbers of independent o...

This class represents the .rps file in a RPS-BLAST file, which contains the PSSMs for the database.

CRef< CRpsLookupTblFile > m_LutFile

The lookup table RPS-BLAST file (.loo)

CRef< CRpsFreqRatiosFile > m_FreqRatiosFile

Frequency ratios file (.freq) used for composition based statistics and cobalt.

unique_ptr< BlastRPSInfo > m_RpsInfo

Pointer which contains pointers to data managed by the data members above.

CRef< CRpsAuxFile > m_AuxFile

The auxiliary RPS-BLAST file (.aux)

CRef< CRpsPssmFile > m_PssmFile

The PSSM RPS-BLAST file (.rps)

CRef< CRpsObsrFile > m_ObsrFile

Number of independent observations file (.obsr) used by delta-blast.

CBlastRPSInfo & operator=(const CBlastRPSInfo &rhs)

Prohibit assignment operator.

CRef< CRpsFreqsFile > m_FreqsFile

Weighted residue frequencies file (.wcounts) used by delta-blast.

CBlastRPSInfo(const CBlastRPSInfo &rhs)

Prohibit copy-constructor.

EOpenFlags

Flags for opening database files.

#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.

The RPS engine uses this structure to access all of the RPS blast related data (assumed to be collect...

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