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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/cdd__pssm__input_8hpp_source.html below:

NCBI C++ ToolKit: include/algo/blast/api/cdd_pssm_input.hpp Source File

CPssmEngineTest;

& matrix_name =

,

gap_existence = 0,

gap_extension = 0,

& query_title =

);

*

(

) {

&m_QueryData[0];}

(

) {

(m_QueryData.size());}

{

m_DiagnosticsRequest;}

: m_QueryRange(q), m_SubjectRange(s) {}

: m_QueryRange(seg.m_QueryRange),

m_SubjectRange(seg.m_SubjectRange)

FillData(

db_oid,

& profile_data);

Validate(

)

;

IsEmpty(

)

;

AdjustRanges(

d_from,

d_to);

(

)

{

m_QueryRange.GetLength();}

x_FillResidueCounts(

db_oid,

& profile_data);

x_FillObservations(

db_oid,

& profile_data);

(

objects::CDense_seg& denseg,

evalue);

FillData(

& seqdb,

IntersectWith(

vector<TRange>& segments,

Subtract(

& hit);

Validate(

)

;

IsEmpty(

)

;

vector<CHitSegment*>&

(

) {

m_SegmentList;}

{

m_SegmentList;}

->m_SubjectRange.GetFrom() <

->m_SubjectRange.GetFrom();

(

.GetFrom() ==

.GetFrom()) {

.GetTo() <

.GetTo();

.GetFrom() <

.GetFrom();

(

->m_SubjectId->Match(*

->m_SubjectId)) {

->m_Evalue <

->m_Evalue;

*

->m_SubjectId < *

->m_SubjectId;

x_ProcessAlignments(

min_evalue,

max_evalue);

x_FillHitsData(

);

x_CreateMsa(

);

x_RemoveMultipleCdHits(

);

x_ValidateMsa(

)

;

x_ValidateHits(

)

;

x_ExtractQueryForPssm(

);

kRpsScaleFactor = 1000;

class ::CPssmCddInputTest;

static const int kAlphabetSize

The aligner internally works only with the ncbistdaa alphabet.

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

#define NCBI_XBLAST_EXPORT

NULL operations for other cases.

The structures and functions in blast_options.

High level definitions and declarations for the PSSM engine of PSI-BLAST.

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

Represents one alignment segment of a RPS-BLAST hit.

Class used for sorting hits by subject seq-id and e-value.

Class used for sorting hit segments by range.

Class used for sorting ranges.

Strategy for pre-processing RPS-BLAST matches for PSSM computation.

Class for testing methods of CCddInputData class.

Interface for strategy to pre-process multiple alignment of conserved domains matches as input data f...

int GetGapExistence(void)

Get gap existence to use when building PSSM.

CRef< objects::CBioseq > m_QueryBioseq

Query as Bioseq.

TRange m_QueryRange

Segment range on query.

virtual void Process(void)=0

Pre-process CDs used for PSSM computation.

PSICdMsa * GetData(void)

Get data for PSSM computation.

vector< CHit * > m_Hits

RPS-BLAST hits in internal representation.

string m_DbName

CDD database name.

CHit(const objects::CDense_seg &denseg, double evalue)

Constructor.

vector< CHitSegment * > m_SegmentList

List of hit segments.

CConstRef< CSeq_id > m_SubjectId

Seq_id of hit subject.

virtual const PSIDiagnosticsRequest * GetDiagnosticsRequest(void)

Get diagnostics options.

const PSIDiagnosticsRequest * GetDiagnosticsRequest(void)

Get options for PSSM engine diagnostics.

vector< CHitSegment * > & GetSegments(void)

Get hit segments.

CHitSegment(const CHitSegment &seg)

Copy constructor.

CHitSegment & operator=(const CHitSegment &hit)

Fobidding assignment operator.

virtual int GetGapExistence()

Obtain the gap existence value for the underlying matrix used to build the PSSM.

CRef< objects::CBioseq > GetQueryForPssm(void)

Get query as Bioseq.

bool operator()(const TRange &a, const TRange &b) const

PSIBlastOptions m_Opts

Delta BLAST options for PSSM Engine.

vector< PSICdMsaCellData > m_MsaData

Data used for PSSM computation.

void SetMinCddEvalue(double val)

Set minimum e-value threshold for inclusion of CDs in PSSM computation.

double m_MinEvalue

Min e-value threshold for all hits to be included in PSSM computation.

int GetLength(void) const

Get length of the hit segment in residues.

virtual int GetGapExtension()

Obtain the gap extension value for the underlying matrix used to build the PSSM.

PSICdMsaCell ** m_Msa

Pointer to MSA.

CConstRef< objects::CSeq_align_set > m_SeqalignSet

RPS-BLAST hits for the query.

virtual const PSIBlastOptions * GetOptions(void)=0

Get CDD-related PSI-BLAST options.

int m_MsaIdx

Hit index in MSA table.

PSICdMsa m_CddData

MSA of CDs and CD data.

bool operator()(CHit *const &a, CHit *const &b)

vector< Uint1 > m_QueryData

Query sequence.

PSIMsaDimensions m_MsaDimensions

MSA dimensions, used by PSSM engine.

int GetGapExtension(void)

Get gap extension to use when building PSSM.

PSIDiagnosticsRequest * m_DiagnosticsRequest

PSSM engine Diagnostics request.

CHitSegment(TRange q, TRange s)

Constructor.

virtual PSICdMsa * GetData(void)=0

Get CD data for PSSM computation.

int m_GapExtension

Gap extension for underlying scoring system.

const PSIBlastOptions * GetOptions(void)

Get CDD-related PSSM engine options.

vector< double > m_WFreqsData

Buffer for residue frequencies from CDs.

TRange m_SubjectRange

Segment range on subject.

vector< PSICdMsaCell > m_MsaData

MSA data.

Uint4 TFreqs

Type used for residue frequencies stored in CDD.

unsigned char * GetQuery(void)

Get query sequence.

string m_MatrixName

Scoring matrix name.

unsigned int GetQueryLength(void)

Get query length.

string m_QueryTitle

Query title (for PSSM)

bool operator()(const CHitSegment *a, const CHitSegment *b) const

int m_GapExistence

Gap existence for underlying scoring system.

const char * GetMatrixName(void)

Get scoring matrix name.

Uint4 TObsr

Type used for number of independent observations stored in CDD.

const vector< CHitSegment * > & GetSegments(void) const

Get hit segments.

EApplyTo

Master selection for operations involving ranges.

TSeqPos GetLength(const CSeq_id &id, CScope *scope)

Get sequence length if scope not null, else return max possible TSeqPos.

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 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.

Portable reference counted smart and weak pointers using CWeakRef, CRef, CObject and CObjectEx.

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

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

Defines BLAST database access classes.

Base class for the IPssmInputData and IPssmInputFreqRatios interfaces, provided to avoid duplicating ...

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

Alignment cell that represents one column of CD aligned to a position in the query.

Data structure representing multiple alignemnt of CDs and query sequence along with data needed for P...

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

Structure representing the dimensions of the multiple sequence alignment data structure.

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