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

query_length,

* matrix_name,

& query_title)

: m_GapExistence(gap_existence), m_GapExtension(gap_extension)

( !sset || sset->Get().front()->GetDim() != 2) {

);

memcpy((

*)

, (

*)

, query_length);

);

hit_ids.

();

*

CPsiBlastInputData::x_ExtractAlignmentDataUseBestAlign()

CSeq_align::C_Segs::TDisc::Tdata& hsp_list =

(*itr)->GetSegs().GetDisc().Get();

CSeq_align::C_Segs::TDisc::Tdata::const_iterator best_alignment;

(CSeq_align::C_Segs::TDisc::Tdata, hsp_itr, hsp_list) {

( !(*hsp_itr)->GetSegs().IsDenseg() ) {

);

evalue = s_GetLowestEvalue((*hsp_itr)->GetScore());

(evalue < min_evalue) {

best_alignment = hsp_itr;

(best_alignment != hsp_list.end());

seq_index, min_evalue);

* current_sid =

*

(&(*itr)->GetSeq_id(1));

(last_sid && !current_sid->

(*last_sid)) {

& seg = (*itr)->GetSegs().GetDenseg();

last_sid = current_sid;

msa_index,

(denseg.GetDim() == 2);

kNumSegments = denseg.GetNumseg();

kDimensions = denseg.GetDim();

(seq.size() == 0) {

(denseg.CanGetIds() && denseg.GetIds().size() == 2);

(denseg.GetIds().back()->IsGi()) {

->seqinfo[msa_index].gi = denseg.GetIds().back()->GetGi();

->seqinfo[msa_index].evalue = evalue;

->seqinfo[msa_index].bit_score = bit_score;

(

segmt_idx = 0; segmt_idx < kNumSegments; segmt_idx++) {

query_offset = starts[query_index];

subject_offset = starts[subj_index];

query_index += kDimensions;

subj_index += kDimensions;

subj_seq_idx += lengths[segmt_idx];

(

= 0;

< lengths[segmt_idx];

++) {

(

= 0;

< lengths[segmt_idx];

++, subj_seq_idx++) {

->

[msa_index][query_offset++];

msa_cell.

=

(seq[subj_seq_idx]);

objects::CScope& scope,

& sequence_data)

subj_start_found =

;

kNumSegments = ds.GetNumseg();

kDimensions = ds.GetDim();

(

= 0;

< kNumSegments;

++) {

( !subj_start_found ) {

subj_start = starts[subj_index];

subj_start_found =

;

subjlen += lengths[

];

subj_index += kDimensions;

seqloc(

&

(*ds.GetIds().back()), subj_start,

subj_start+subjlen-1);

sequence_data.erase();

User-defined methods of the data storage class.

Declares the BLAST exception class.

PSIMsa * PSIMsaFree(PSIMsa *msa)

Deallocates the PSIMsa structure.

PSIMsa * PSIMsaNew(const PSIMsaDimensions *dimensions)

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

const unsigned int kQueryIndex

Index into multiple sequence alignment structure for the query sequence.

Defines BLAST error codes (user errors included)

Defines system exceptions occurred while running BLAST.

Auxiliary class to retrieve sequence identifiers its position in the alignment which are below the in...

const CSeq_id & GetSeq_id(TDim row) const

Get seq-id (the first one if segments have different ids).

void Process()

The work to process the alignment is done here.

unsigned int GetNumAlignedSequences() const

Returns the number of sequences that make up the multiple sequence alignment.

#define GAP_IN_ALIGNMENT

Representation of GAP in Seq-align.

CConstRef< objects::CSeq_align_set > m_SeqAlignSet

Pairwise alignment result of a BLAST search.

void x_CopyQueryToMsa()

Copies query sequence data to multiple alignment data structure.

PSIMsa * m_Msa

Structure representing the multiple sequence alignment.

PSIDiagnosticsRequest * m_DiagnosticsRequest

Diagnostics request structure.

virtual const char * GetMatrixName()

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

const PSIBlastOptions * GetOptions()

Obtain the options for the PSSM engine.

PSIMsaDimensions m_MsaDimensions

Multiple sequence alignment dimensions.

PSIBlastOptions m_Opts

Algorithm options.

virtual ~CPsiBlastInputData()

virtual destructor

CRef< objects::CScope > m_Scope

Scope where to retrieve the sequences in the aligment from.

unsigned int x_CountAndSelectQualifyingAlignments()

Examines the sequence alignment and keeps track of those hits which have an HSP with an e-value below...

unsigned int GetQueryLength()

Get the query's length.

CRef< objects::CBioseq > m_QueryBioseq

Query as CBioseq for PSSM.

const Uint1 AMINOACID_TO_NCBISTDAA[]

Translates between ncbieaa and ncbistdaa.

void x_ProcessDenseg(const objects::CDense_seg &denseg, unsigned int msa_index, double evalue, double bit_score)

Iterates over the Dense-seg passed in and extracts alignment information to multiple alignment data s...

const PSIDiagnosticsRequest * GetDiagnosticsRequest()

Obtain the diagnostics data that is requested from the PSSM engine.

const char * GetMatrixName()

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

PSIMsa * GetData()

Obtain the multiple sequence alignment structure.

double GetLowestEvalue(const objects::CDense_seg::TScores &scores, double *bit_score)

Returns the lowest score from the list of scores in CDense_seg::TScores.

void x_ExtractAlignmentData()

Populates the multiple alignment data structure.

unsigned char * m_Query

Pointer to query sequence.

CPsiBlastInputData(const unsigned char *query, unsigned int query_length, CConstRef< objects::CSeq_align_set > sset, CRef< objects::CScope > scope, const PSIBlastOptions &opts, const char *matrix_name=NULL, int gap_existence=0, int gap_opening=0, const PSIDiagnosticsRequest *diags=NULL, const string &query_title="")

Construct a concrete strategy, used to configure the CPssmEngine object.

string m_MatrixName

Underlying matrix to use.

string m_QueryTitle

Title of query.

unsigned char * GetQuery()

Get the query sequence used as master for the multiple sequence alignment in ncbistdaa encoding.

static void x_GetSubjectSequence(const objects::CDense_seg &ds, objects::CScope &scope, string &sequence_data)

Tries to fetch the sequence data for the subject for the segments specified in the Dense-seg.

void x_ExtractQueryForPssm()

Extracts the query bioseq from m_SeqAlignSet.

unsigned int TSeqPos

Type for sequence locations and lengths.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

int TSignedSeqPos

Type for signed sequence position.

const TSeqPos kInvalidSeqPos

Define special value for invalid sequence position.

#define ERR_POST(message)

Error posting with file, line number information but without error codes.

#define NCBI_THROW(exception_class, err_code, message)

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

void Warning(CExceptionArgs_Base &args)

const string AsFastaString(void) const

bool Match(const CSeq_id &sid2) const

Match() - TRUE if SeqIds are equivalent.

void GetSeqData(TSeqPos start, TSeqPos stop, string &buffer) const

Fill the buffer string with the sequence data for the interval [start, stop).

void SetCoding(TCoding coding)

void Reset(void)

Reset reference object.

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 NotEmpty(void) const THROWS_NONE

Check if CConstRef 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

#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.

vector< TSignedSeqPos > TStarts

list< CRef< CSeq_align > > Tdata

const TId & GetId(void) const

Get the Id member data.

const TInt & GetInt(void) const

Get the variant data.

TTitle & SetTitle(void)

Select the variant.

@ eRepr_raw

continuous sequence

@ e_Ncbistdaa

consecutive codes for std aas

Defines a concrete strategy to obtain PSSM input data for PSI-BLAST.

Declarations of auxiliary functions/classes for PSI-BLAST.

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

double inclusion_ethresh

Minimum evalue for inclusion in PSSM calculation.

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

Structure to describe the characteristics of a position in the multiple sequence alignment data struc...

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)

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