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NCBI C++ ToolKit: src/algo/blast/api/rps_aux.cpp Source File

vector<double>& karlin_k);

vector<double>& karlin_k)

}

(

bad_alloc&) {

);

file2open(filename_no_extn +

);

(auxfile.bad() || auxfile.fail()) {

+ file2open);

vector<double> karlinK;

>> ignore_me_d;

>> ignore_me_d;

>> ignore_me_i;

>> ignore_me_i;

>> scale_factor;

karlinK.push_back(k);

+ filename);

+ filename_no_extn +

+

+ filename_no_extn +

+

+ filename_no_extn +

+

+ filename_no_extn +

+

+ filename_no_extn +

+

vector<string> dbpath;

path = *dbpath.begin();

);

unique_ptr<BlastRPSInfo> rps_info;

(

bad_alloc&) {

);

= rps_dbname +

\

+ rps_dbname +

;

->aux_info.scale_factor;

->aux_info.orig_score_matrix;

->aux_info.gap_open_penalty;

->aux_info.gap_extend_penalty;

Definitions used throughout BLAST.

#define sfree(x)

Safe free a pointer: belongs to a higher level header.

Declares the BLAST exception class.

#define RPS_MAGIC_NUM_28

Version number for 28-letter alphabet.

struct BlastRPSAuxInfo BlastRPSAuxInfo

information derived from RPS blast '.aux' file

#define RPS_MAGIC_NUM

RPS blast version number.

Defines BLAST error codes (user errors included)

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

Defines system exceptions occurred while running BLAST.

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...

Encapsulates logic of mmap'ing and performing sanity checks on RPS-BLAST database files.

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.

static void FindVolumePaths(const string &dbname, ESeqType seqtype, vector< string > &paths, vector< string > *alias_paths=NULL, bool recursive=true, bool expand_links=true)

Find volume paths.

void x_Init(const string &rps_dbname, int flags)

Initialize attributes.

int GetGapExtensionCost() const

Returns the gap extension cost associated with the scoring matrix above.

CRef< CRpsLookupTblFile > m_LutFile

The lookup table RPS-BLAST file (.loo)

BlastRPSProfileHeader * m_Data

Header.

CBlastRPSAuxInfo & operator=(const CBlastRPSAuxInfo &rhs)

Prohibit assignment operator.

const BlastRPSAuxInfo * operator()() const

Lend the caller the pointer to the data structure this object manages.

CRef< CRpsFreqRatiosFile > m_FreqRatiosFile

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

BlastRPSProfileHeader * m_Data

The data structure this class manages.

BlastRPSFreqRatiosHeader * m_Data

The data this class manages.

const BlastRPSProfileHeader * operator()() const

Lend the caller the pointer to the data structure this object manages.

BlastRPSAuxInfo * m_Data

The data structure this class manages.

const BlastRPSProfileHeader * operator()() const

Lend the caller the pointer to the data structure this object manages.

static const string kExtension

Extension associated with the RPS-BLAST database PSSM file.

const BlastRPSProfileHeader * operator()() const

Lend the caller the pointer to the data structure this object manages.

unique_ptr< BlastRPSInfo > m_RpsInfo

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

CRpsPssmFile(const string &filename_no_extn)

Parametrized constructor.

double GetScalingFactor() const

Returns the scaling factor used to build RPS-BLAST database.

~CBlastRPSInfo()

Destructor.

CRpsAuxFile(const string &filename_no_extn)

Parametrized constructor.

BlastRPSProfileHeader * m_Data

The data this class manages.

const BlastRPSFreqRatiosHeader * operator()() const

Lend the caller the pointer to the data structure this object manages.

CRpsMmappedFile(const string &filename)

Parametrized constructor.

~CBlastRPSAuxInfo()

Destructor.

void x_DoDestroy()

Deallocates the structure owned by this class.

CRef< CBlastRPSAuxInfo > m_Data

CBlastRPSInfo(const string &rps_dbname)

Parametrized constructor.

CBlastRPSAuxInfo(const string &matrix, int gap_open, int gap_extend, double scale_factor, const vector< double > &karlin_k)

Parametrized constructor.

CBlastRPSAuxInfo(const CBlastRPSAuxInfo &rhs)

Prohibit copy-constructor.

CRef< CRpsAuxFile > m_AuxFile

The auxiliary RPS-BLAST file (.aux)

static const string kExtension

Extension associated with the RPS-BLAST database auxiliary file.

CRpsObsrFile(const string &filename_no_extn)

Parametrized constructor.

CRef< CBlastRPSAuxInfo > x_ReadFromFile(CNcbiIfstream &input)

Auxiliary method to read the contents of the file into m_Data.

static const string kExtension

Extension associated with the RPS-BLAST database PSSM file.

const BlastRPSInfo * operator()() const

Accessor for the underlying C structure (managed by this class)

CRpsFreqRatiosFile(const string &filename_no_extn)

Parametrized constructor.

virtual ~CRpsFreqRatiosFile()

CRef< CRpsPssmFile > m_PssmFile

The PSSM RPS-BLAST file (.rps)

static const string kExtension

Extension associated with the RPS-BLAST database PSSM file.

BlastRPSLookupFileHeader * m_Data

The data structure this class manages.

const BlastRPSLookupFileHeader * operator()() const

Lend the caller the pointer to the data structure this object manages.

const char * GetMatrixName() const

Returns the name of the scoring matrix used to build the RPS-BLAST database.

CRef< CRpsObsrFile > m_ObsrFile

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

CRpsFreqsFile(const string &filename_no_extn)

Parametrized constructor.

CRpsLookupTblFile(const string &filename_no_extn)

Parametrized constructor.

CRef< CRpsFreqsFile > m_FreqsFile

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

static const string kExtension

Extension associated with the RPS-BLAST database PSSM file.

unique_ptr< CMemoryFile > m_MmappedFile

The data structure this class manages.

static const string kExtension

Extension associated with the RPS-BLAST database lookup table file.

const BlastRPSAuxInfo * operator()() const

Lend the caller the pointer to the data structure this object manages.

int GetGapOpeningCost() const

Returns the gap opening cost associated with the scoring matrix above.

@ fFrequenciesFile

Open residue frequencies file.

@ fFreqRatiosFile

Open file with frequency ratios.

@ fObservationsFile

Open file with numbers of independent observations.

@ fRpsBlast

Flags set for RPS-BLAST.

@ fAuxInfoFile

Open auxiliary information file.

@ fPssmFile

Open pssm file.

#define NCBI_THROW(exception_class, err_code, message)

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

#define NCBI_RETHROW(prev_exception, exception_class, err_code, message)

Generic macro to re-throw an exception.

void Reset(void)

Reset reference object.

#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.

IO_PREFIX::ifstream CNcbiIfstream

Portable alias for ifstream.

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

void copy(Njn::Matrix< S > *matrix_, const Njn::Matrix< T > &matrix0_)

Declares auxiliary classes to manage RPS-BLAST related C-structures.

Defines BLAST database access classes.

static SLJIT_INLINE sljit_ins msg(sljit_gpr r, sljit_s32 d, sljit_gpr x, sljit_gpr b)

information derived from RPS blast '.aux' file

Int4 gap_extend_penalty

gap extend penalty used in deriving PSSMs

double * karlin_k

one Karlin value for each DB sequence

double scale_factor

the PSSMs are scaled by this amount, and so all scores and all cutoff values must be similarly scaled...

Int4 gap_open_penalty

gap open penalty used in deriving PSSMs

char * orig_score_matrix

score matrix used to derive PSSMs

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

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