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

* matrix_name

,

query_length

,

msa_master_idx

)

: m_Query(0), m_GapExistence(gap_existence), m_GapExtension(gap_extension)

m_MsaDimensions.query_length = query_length;

m_Query.reset(

[query_length]);

memcpy((

*) m_Query.get(), (

*)

, query_length);

m_Opts.ignore_unaligned_positions =

;

( !m_Query || msa_master_idx != 0) {

x_ExtractQueryFromMsa(msa_master_idx);

x_ValidateQueryInMsa();

(m_MsaDimensions.query_length);

m_MsaDimensions.num_seqs =

(m_AsciiMsa.size() - 1);

m_MatrixName =

(matrix_name ? matrix_name :

);

*m_DiagnosticsRequest = *diags;

m_DiagnosticsRequest =

;

reader.

(

,

);

(

(e.GetMsg(),

) !=

)) {

(

);

+=

;

+=

;

retval.

().reserve(query_length);

back_inserter(retval.

()));

back_inserter(retval.

()));

);

kAligmentLength =

.front().size();

(; seq_idx <

.size(); seq_idx++) {

query_idx = 0;

(

align_idx = 0;

(query_res == kMaskingRes && kCurrentRes ==

) {

query_res = kCurrentRes;

(query_res != kCurrentRes) {

(

align_idx = 0; align_idx < kAligmentLength; align_idx++) {

(

);

+=

;

oss <<

kQueryLength =

(

.size() - kNumGaps);

query_idx = 0;

(query_idx == kQueryLength);

& ascii_query =

.front();

query_idx = 0;

(

, residue, ascii_query) {

kAlignmentLength =

.front().size();

(; seq_index <

.size(); seq_index++) {

query_idx = 0;

(

align_idx = 0; align_idx < kAlignmentLength; align_idx++) {

kCurrentRes =

[seq_index][align_idx];

kGapResidue = 0;

kLongGapLen = 10;

(i < m_Msa->dimensions->query_length &&

(i < m_Msa->dimensions->query_length) {

(i < m_Msa->dimensions->query_length &&

k =

(

) + 1;

(k < m_Msa->dimensions->query_length &&

(k -

>= kLongGapLen) {

(

j=

(

);j < k;j++) {

(k >= 0 &&

->

[seq_index][k].

== kGapResidue) {

Declares the BLAST exception class.

const Uint1 kProtMask

NCBISTDAA element used to mask residues in BLAST.

PSIMsa * PSIMsaFree(PSIMsa *msa)

Deallocates the PSIMsa structure.

PSIDiagnosticsRequest * PSIDiagnosticsRequestNew(void)

Allocates a PSIDiagnosticsRequest structure, setting all fields to false.

PSIMsa * PSIMsaNew(const PSIMsaDimensions *dimensions)

Allocates and initializes the multiple sequence alignment data structure for use as input to the PSSM...

PSIDiagnosticsRequest * PSIDiagnosticsRequestFree(PSIDiagnosticsRequest *diags_request)

Deallocates the PSIDiagnosticsRequest structure passed in.

const unsigned int kQueryIndex

Index into multiple sequence alignment structure for the query sequence.

class CAlnReader supports importing a large variety of text-based alignment formats into standard dat...

const vector< string > & GetSeqs(void) const

void Read(bool guess, bool generate_local_ids=false, objects::ILineErrorListener *pErrorListener=nullptr)

void SetClustal(EAlphabet alpha)

CRef< objects::CSeq_entry > GetSeqEntry(TFastaFlags fasta_flags=objects::CFastaReader::fAddMods, objects::ILineErrorListener *pErrorListener=nullptr)

Defines BLAST error codes (user errors included)

Defines system exceptions occurred while running BLAST.

CNcbiOstrstreamToString class helps convert CNcbiOstrstream to a string Sample usage:

@ eFormat

Some of these are pretty specialized.

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

static TSeqPos Convert(const CSeq_data &in_seq, CSeq_data *out_seq, CSeq_data::E_Choice to_code, TSeqPos uBeginIdx=0, TSeqPos uLength=0, bool bAmbig=false, Uint4 seed=17734276)

static void s_GetQuerySequenceData(const CBioseq &bioseq, size_t query_length, CNCBIstdaa &retval)

Auxiliary function to retrieve the sequence data in NCBI-stdaa format from the bioseq.

static const char kGapChar('-')

The representation of a gap in ASCII format.

PSIMsaDimensions m_MsaDimensions

Multiple sequence alignment dimensions.

void x_ValidateQueryInMsa()

Searches the query sequence (m_Query) in the aligned sequences (m_AsciiMsa) and moves the first insta...

unsigned int GetQueryLength()

Get the query's length.

void Process()

The work to process the alignment is done here.

CRef< objects::CSeq_entry > m_SeqEntry

CSeq_entry obtained from the multiple sequence alignment.

void x_CopyQueryToMsa()

Copies query sequence data to multiple alignment data structure.

TAutoUint1ArrayPtr m_Query

Pointer to query sequence.

void x_ExtractQueryForPssm()

Extracts the query bioseq from m_SeqEntry.

static bool s_AreSequencesEqual(const CNCBIstdaa &sequence, Uint1 *query)

Returns true iff sequence is identical to query.

CRef< objects::CBioseq > m_QueryBioseq

Query as CBioseq for PSSM.

const Uint1 AMINOACID_TO_NCBISTDAA[]

Translates between ncbieaa and ncbistdaa.

void x_ReadAsciiMsa(CNcbiIstream &input_file)

Reads the multiple sequence alignment from the input file.

PSIDiagnosticsRequest * m_DiagnosticsRequest

Diagnostics request structure.

void x_ExtractAlignmentData()

Populates the multiple alignment data structure.

PSIMsa * m_Msa

Structure representing the multiple sequence alignment.

vector< string > m_AsciiMsa

The raw multiple sequence alignment in ASCII read from the input file.

const char NCBISTDAA_TO_AMINOACID[]

Translates between ncbieaa and ncbistdaa.

virtual ~CPsiBlastInputClustalW()

virtual destructor

void x_ExtractQueryFromMsa(unsigned int msa_master_idx=0)

Extracts the query sequence from the multiple sequence alignment, assuming it's the first one,...

void reset(element_type *p=0, EOwnership ownership=eTakeOwnership)

Reset will delete the old pointer (if owned), set content to the new value, and assume the ownership ...

unsigned int TSeqPos

Type for sequence locations and lengths.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

element_type * get(void) const

Get pointer.

void swap(NCBI_NS_NCBI::pair_base_member< T1, T2 > &pair1, NCBI_NS_NCBI::pair_base_member< T1, T2 > &pair2)

#define NCBI_THROW(exception_class, err_code, message)

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

const TPrim & Get(void) const

CBeginInfo Begin(C &obj)

Get starting point of object hierarchy.

void Reset(void)

Reset reference object.

bool NotEmpty(void) const THROWS_NONE

Check if CRef is not empty – pointing to an object and has a non-null value.

bool Empty(void) const THROWS_NONE

Check if CRef is empty – not pointing to any object, which means having a null value.

uint8_t Uint1

1-byte (8-bit) unsigned integer

uint32_t Uint4

4-byte (32-bit) unsigned integer

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define USING_SCOPE(ns)

Use the specified namespace.

#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::istream CNcbiIstream

Portable alias for istream.

static SIZE_TYPE Find(const CTempString str, const CTempString pattern, ECase use_case=eCase, EDirection direction=eForwardSearch, SIZE_TYPE occurrence=0)

Find the pattern in the string.

TErrCode GetErrCode(void) const

Get error code.

const TInst & GetInst(void) const

Get the Inst member data.

bool IsNcbistdaa(void) const

Check if variant Ncbistdaa is selected.

const TNcbistdaa & GetNcbistdaa(void) const

Get the variant data.

const TSeq_data & GetSeq_data(void) const

Get the Seq_data member data.

@ e_Ncbistdaa

consecutive codes for std aas

unsigned int

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

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

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

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

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

Options used in protein BLAST only (PSI, PHI, RPS and translated BLAST) Some of these possibly should...

Structure to allow requesting various diagnostics data to be collected by PSSM engine.

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.

PSIMsaCell ** data

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

PSIMsaDimensions * dimensions

dimensions of the msa

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