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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/resfreq_8cpp_source.html below:

NCBI C++ ToolKit: src/algo/cobalt/resfreq.cpp Source File

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vector<string> dbpath;

(

= 0;

< num_rows;

++) {

(num_db_seqs + 1) *

(

));

(

= 0;

< num_rows;

++) {

static const int kAlphabetSize

The aligner internally works only with the ncbistdaa alphabet.

RPS BLAST structure definitions.

EMapChoice

Which collection to retrieve.

@ eGetResFreqs

Retrieve residue frequencies.

@ eGetPssm

Retrieve PSSMs.

CMemoryFile * m_PssmMmap

Memory-mapped PSSM data.

void Clear()

Free previously loaded PSSM or profile data.

Int4 ** m_PssmRows

List of pointers to PSSM columns.

void Load(EMapChoice choice, string dbname, string resfreq_file="")

Load information from a given database.

Int4 * m_SeqOffsets

List of the first offset of each database sequence.

CMemoryFile * m_ResFreqMmap

Memory-mapped residue frequency data.

Int4 ** m_ResFreqRows

List of pointers to profile columns.

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 * GetPtr(void) const

Get pointer to beginning of data.

int32_t Int4

4-byte (32-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.

char * dbname(DBPROCESS *dbproc)

Get name of current database.

Interface for CProfileData.

Defines BLAST database access classes.

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