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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/msa2pssm__unit__test_8cpp_source.html below:

NCBI C++ ToolKit: src/algo/blast/unit_tests/api/msa2pssm_unit_test.cpp Source File

;

ifstream

(

);

kQuerySize = 10;

[] = { 3, 9, 14, 20, 6, 23, 1, 7, 16, 5 };

unique_ptr<CPsiBlastInputClustalW> pssm_input;

ifstream

(

);

os <<

<<

;

BOOST_REQUIRE_MESSAGE(msa->

[0][

].

!=

ifstream

(

);

kQuerySeq(

);

(

, res, kQuerySeq) {

os <<

<<

;

BOOST_REQUIRE_MESSAGE(msa->

[0][

].

!=

ifstream

(

);

os <<

<<

;

os <<

<<

;

os <<

<<

;

os <<

<<

;

BOOST_REQUIRE_MESSAGE(msa->

[0][

].

!=

Contains C++ wrapper classes to structures in algo/blast/core as well as some auxiliary functions to ...

#define BLAST_DEFAULT_MATRIX

Default matrix name: BLOSUM62.

Int2 PSIBlastOptionsNew(PSIBlastOptions **psi_options)

Initialize default options for PSI BLAST.

BOOST_AUTO_TEST_SUITE_END() static int s_GetSegmentFlags(const CBioseq &bioseq)

Defines BLAST error codes (user errors included)

CNcbiOstrstreamToString class helps convert CNcbiOstrstream to a string Sample usage:

Wrapper class for PSIBlastOptions .

This class is a concrete strategy for IPssmInputData which converts the CLUSTALW-style output contain...

Ensure direct dependencies on enough of the core xncbi library to satisfy shared libraries that depen...

PSIMsa * GetData()

Obtain the multiple sequence alignment structure.

unsigned int GetQueryLength()

Get the query's length.

void Process()

The work to process the alignment is done here.

const Uint1 AMINOACID_TO_NCBISTDAA[]

Translates between ncbieaa and ncbistdaa.

const char * GetMatrixName()

Obtain the name of the underlying matrix to use when building the PSSM.

unsigned int TSeqPos

Type for sequence locations and lengths.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

uint8_t Uint1

1-byte (8-bit) unsigned integer

uint32_t Uint4

4-byte (32-bit) unsigned integer

position_type GetToOpen(void) const

TTo GetTo(void) const

Get the To member data.

TFrom GetFrom(void) const

Get the From member data.

unsigned int

A callback function used to compare two keys in a database.

BOOST_AUTO_TEST_CASE(QueryNotFoundInMsa)

Defines a concrete strategy to obtain PSSM input data for PSI-BLAST from a multiple sequence alignmen...

Magic spell ;-) needed for some weird compilers... very empiric.

#define TRUE

bool replacment for C indicating true.

#define FALSE

bool replacment for C indicating false.

std::istream & in(std::istream &in_, double &x_)

BOOST_AUTO_TEST_SUITE(psiblast_iteration)

Boolean is_aligned

Is this letter part of the alignment?

Uint1 letter

Preferred letter at this position, in ncbistdaa encoding.

Uint4 num_seqs

Number of distinct sequences aligned with the query (does not include the query)

Uint4 query_length

Length of the query.

Multiple sequence alignment (msa) data structure containing the raw data needed by the PSSM engine to...

PSIMsaCell ** data

actual data, dimensions are (dimensions->num_seqs+1) by (dimensions->query_length)

PSIMsaDimensions * dimensions

dimensions of the msa

Utility stuff for more convenient using of Boost.Test library.

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