Home - News ( United States | United Kingdom | Italy | Germany ) - Football scores

Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/score__builder_8cpp_source.html below:

NCBI C++ ToolKit: src/algo/align/util/score_builder.cpp Source File

);

);

);

m_EffectiveSearchSpace(0)

: m_EffectiveSearchSpace(0)

: m_EffectiveSearchSpace(0)

);

+

+

);

[16] = {0, 8, 4, 0, 2, 0, 0, 0, 1};

);

);

computed_score = 0;

( !bsh1 || !bsh2 ) {

);

);

(start1 == -1 || start2 == -1) {

computed_score -= gap_open + gap_extend * seg_len;

(

pos = 0; pos < seg_len; ++pos) {

c1 = vec1[start1 + pos];

c2 = vec2[start2 + pos];

computed_score += matrix[c1][c2];

);

scaled_up =

;

(gap_open == 0 && gap_extend == 0) {

gap_extend =

/ 2 - mismatch;

(start1 == -1 || start2 == -1) {

computed_score -= gap_open + gap_extend * seg_len;

(strand1 > strand2) {

(

pos = 0; pos < seg_len; ++pos) {

c1 = vec1[start1 + pos];

c2 = vec2[start2 + seg_len - 1 - pos];

(strand1 < strand2) {

(

pos = 0; pos < seg_len; ++pos) {

c1 = vec1[start1 + seg_len - 1 - pos];

c2 = vec2[start2 + pos];

(

pos = 0; pos < seg_len; ++pos) {

c1 = vec1[start1 + pos];

c2 = vec2[start2 + pos];

computed_score += (c1 == c2) ?

: mismatch;

computed_score =

(0, computed_score);

computed_score;

( !bsh1 || !bsh2 ) {

);

unique_ptr<CSeq_align> swapped_align_ptr;

swapped_align_ptr->

(align);

swapped_align_ptr->SwapRows(0,1);

align_ptr = swapped_align_ptr.get();

list<CRef<CPairwiseAln> > pairs;

pairs.push_back(aln);

);

list<CRef<CPairwiseAln> > pairs;

sub_align.

(align);

sub_align.

().SetSpliced().SetExons().clear();

sub_align.

().SetSpliced().SetExons().push_back(exon);

(exon->IsSetAcceptor_before_exon() || pairs.empty()) {

pairs.push_back(aln);

pairs.back()->push_back(*

);

( !prot_bsh || !genomic_bsh ) {

);

this_pair_score = -1;

CPairwiseAln::const_iterator

= aln->end();

(

!= aln->end()) {

q_gap = range_it->GetFirstFrom() -

->GetFirstTo() - 1;

->GetSecondFrom() - range_it->GetSecondTo() - 1 :

range_it->GetSecondFrom() -

->GetSecondTo() - 1);

gap =

(q_gap - s_gap);

s_start = s_range.

();

s_end = s_range.

();

q_pos = q_range.

();

new_offs = q_pos % 3;

( ; offs != new_offs; offs = (offs + 1) % 3) {

( ; s_start <= s_end; ++s_start, ++q_pos, ++vec_it) {

this_score = matrix[

][xlate];

this_pair_score += this_score;

offs = (offs + 1) % 3;

(list<int>, gap_bases, gaps) {

(new_score > 0 ) {

this_pair_score = new_score;

this_pair_score -= 1;

score += this_pair_score;

d == numeric_limits<double>::quiet_NaN()) {

(d > 1e35 || d < -1e35) {

d == numeric_limits<double>::quiet_NaN()) {

(d > 1e35 || d < -1e35) {

flipped_BTOP.insert(0, match_str);

);

BTOP, flipped_BTOP;

(

.empty()) {

(

idx = 0; idx <

.size(); ++idx) {

flipped_BTOP.insert(flipped_BTOP.begin(), complement[0]);

flipped_BTOP.insert(flipped_BTOP.begin(),

);

}

(

.empty()) {

(

idx = 0; idx <

.size(); ++idx) {

flipped_BTOP.insert(flipped_BTOP.begin(),

);

flipped_BTOP.insert(flipped_BTOP.begin(), complement[0]);

(

idx = 0; idx <

.size(); ++idx) {

);

query_complement;

idx, 1, query_complement);

subject_complement;

idx, 1, subject_complement);

flipped_BTOP.insert(flipped_BTOP.begin(),

subject_complement[0]);

flipped_BTOP.insert(flipped_BTOP.begin(),

query_complement[0]);

pair<string,string>(

? BTOP : flipped_BTOP);

((*ext_it)->GetType().IsStr() &&

(*ext_it)->GetType().GetStr() ==

)

tracebacks = *ext_it;

tracebacks->

().SetStr(

);

align.

().push_back(tracebacks);

}

(tracebacks->

(

) && tracebacks->

(

))

tracebacks->

(

).

().SetStr(traceback_strings.first);

tracebacks->

(

).

().SetStr(traceback_strings.second);

((*ext_it)->GetType().IsStr() &&

(*ext_it)->GetType().GetStr() ==

)

field =

== 0 ?

:

;

((*ext_it)->HasField(field)) {

(*ext_it)->GetField(field).GetData().GetStr();

(!stored_traceback.empty()) {

stored_traceback;

== 0 ? traceback_strings.first : traceback_strings.second;

align.

().SetDenseg().SetScores().clear();

align.

().SetDisc().Set()) {

align.

().SetSpliced().SetExons()) {

(*exon_iter)->SetScores().Set().clear();

align.

().SetSparse().SetRow_scores().clear();

(*std_iter)->SetScores().clear();

align.

().clear();

stringstream cleanStr;

checksum.

(cleanStr.str());

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

CRef< CPairwiseAln > CreatePairwiseAlnFromSeqAlign(const objects::CSeq_align &seq_align)

A simple API that assumes that the seq_align has exactly two rows and you want to create a pairwise w...

CRef< CSeq_align > ConvertSeq_align(const CSeq_align &src, CSeq_align::TSegs::E_Choice dst_choice, CSeq_align::TDim anchor_row=-1, CScope *scope=NULL)

Convert source alignment to a new type.

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

Declarations of static arrays used to define some NCBI encodings to be used in a toolkit independent ...

The structures and functions in blast_options.

Int2 BLAST_FillScoringOptions(BlastScoringOptions *options, EBlastProgramType program, Boolean greedy_extension, Int4 penalty, Int4 reward, const char *matrix, Int4 gap_open, Int4 gap_extend)

Fill non-default values in the BlastScoringOptions structure.

Int2 BlastScoringOptionsNew(EBlastProgramType program, BlastScoringOptions **options)

Allocate memory for BlastScoringOptions and fill with default values.

BlastScoringOptions * BlastScoringOptionsFree(BlastScoringOptions *options)

Deallocate memory for BlastScoringOptions.

Declares the CBlastOptionsHandle and CBlastOptionsFactory classes.

EBlastProgramType

Defines the engine's notion of the different applications of the BLAST algorithm.

Utilities initialize/setup BLAST.

Int2 Blast_ScoreBlkMatrixInit(EBlastProgramType program_number, const BlastScoringOptions *scoring_options, BlastScoreBlk *sbp, GET_MATRIX_PATH get_path)

Initializes the substitution matrix in the BlastScoreBlk according to the scoring options specified.

Definitions and prototypes used by blast_stat.c to calculate BLAST statistics.

BlastScoreBlk * BlastScoreBlkFree(BlastScoreBlk *sbp)

Deallocates BlastScoreBlk as well as all associated structures.

Int2 Blast_KarlinBlkGappedCalc(Blast_KarlinBlk *kbp, Int4 gap_open, Int4 gap_extend, const char *matrix_name, Blast_Message **error_return)

Fills in lambda, H, and K values, as calculated by Stephen Altschul in Methods in Enzy.

Blast_KarlinBlk * Blast_KarlinBlkNew(void)

Callocs a Blast_KarlinBlk.

Int2 Blast_KarlinBlkNuclGappedCalc(Blast_KarlinBlk *kbp, Int4 gap_open, Int4 gap_extend, Int4 reward, Int4 penalty, Blast_KarlinBlk *kbp_ungap, Boolean *round_down, Blast_Message **error_return)

Retrieves Karlin-Altschul parameters from precomputed tables, given the substitution and gap scores.

double BLAST_KarlinStoE_simple(Int4 S, Blast_KarlinBlk *kbp, Int8 searchsp)

Calculates the Expect value based upon the search space and some Karlin-Altschul parameters.

Int2 Blast_ScoreBlkKbpIdealCalc(BlastScoreBlk *sbp)

Calculates the Karlin-Altschul parameters assuming standard residue compositions for the query and su...

BlastScoreBlk * BlastScoreBlkNew(Uint1 alphabet, Int4 number_of_contexts)

Allocates and initializes BlastScoreBlk.

EProgram

This enumeration is to evolve into a task/program specific list that specifies sets of default parame...

@ eVecScreen

Vector screening.

@ eBlastn

Nucl-Nucl (traditional blastn)

@ ePHIBlastn

Nucleotide PHI BLAST.

@ eBlastp

Protein-Protein.

@ eTblastn

Protein-Translated nucl.

@ eMegablast

Nucl-Nucl (traditional megablast)

@ eDiscMegablast

Nucl-Nucl using discontiguous megablast.

Checksum and hash calculation classes.

TSignedSeqPos GetStart(TNumrow row, TNumseg seg, int offset=0) const

TSeqPos GetLen(TNumseg seg, int offset=0) const

CDense_seg::TNumseg TNumseg

int StrandSign(TNumrow row) const

TNumseg GetNumSegs(void) const

const CBioseq_Handle & GetBioseqHandle(TNumrow row) const

string & GetSegSeqString(string &buffer, TNumrow row, TNumseg seg, TNumseg offset=0) const

Handle to the options to the BLAST algorithm.

Encapsulates ALL the BLAST algorithm's options.

CChecksum – Checksum calculator.

static const CTrans_table & GetTransTable(int id)

A pairwise aln is a collection of ranges for a pair of rows.

double ComputeScore(CScope &scope, const CSeq_align &align, CSeq_align::EScoreType score)

int GetBlastScoreProtToNucl(CScope &scope, const CSeq_align &align, list< CRef< CPairwiseAln > > &pairs)

int ComputeTieBreaker(const CSeq_align &align)

void AddTracebacks(CScope &scope, CSeq_align &align)

enum blast::EProgram m_BlastType

~CScoreBuilder()

Destructor.

void AddScore(CScope &scope, CSeq_align &align, EScoreType score)

deprecated: use CSeq_align::EScoreType directly

double GetBlastBitScore(CScope &scope, const CSeq_align &align)

Compute the BLAST bit score.

struct BlastScoreBlk * m_ScoreBlk

int GetBlastScore(CScope &scope, const CSeq_align &align)

Compute the BLAST score of the alignment.

void AddTieBreaker(CSeq_align &align)

int GetBlastScoreDenseg(CScope &scope, const CSeq_align &align)

void x_Initialize(blast::CBlastOptionsHandle &options)

double ComputeScore(CScope &scope, const CSeq_align &align, const CRangeCollection< TSeqPos > &ranges, CSeq_align::EScoreType score)

int GetBlastScoreSpliced(CScope &scope, const CSeq_align &align)

Int8 m_EffectiveSearchSpace

int GetBlastScoreStd(CScope &scope, const CSeq_align &align)

string GetTraceback(const CSeq_align &align, CSeq_align::TDim row)

double GetBlastEValue(CScope &scope, const CSeq_align &align)

Compute the BLAST e-value.

CScoreBuilder()

Default constructor.

static SIZE_TYPE Complement(const string &src, TCoding src_coding, TSeqPos pos, TSeqPos length, string &dst)

EScoreType

enum controlling known named scores

void SetNamedScore(const string &id, int score)

TDim CheckNumRows(void) const

Validatiors.

const CSeq_id & GetSeq_id(TDim row) const

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

ENa_strand GetSeqStrand(TDim row) const

Get strand (the first one if segments have different strands).

char GetStartResidue(int state) const

char GetCodonResidue(int state) const

static int NextCodonState(int state, unsigned char ch)

bool HasField(const string &str, const string &delim=".", NStr::ECase use_case=NStr::eCase) const

Verify that a named field exists.

CUser_field & SetField(const string &str, const string &delim=".", const string &obj_subtype=kEmptyStr, NStr::ECase use_case=NStr::eCase)

Access a named field in this user object.

static DLIST_TYPE *DLIST_NAME() prev(DLIST_LIST_TYPE *list, DLIST_TYPE *item)

#define BLASTNA_SEQ_CODE

Identifies the blastna alphabet, for use in blast only.

static CBlastOptionsHandle * Create(EProgram program, EAPILocality locality=CBlastOptions::eLocal)

Creates an options handle object configured with default options for the requested program,...

EBlastProgramType EProgramToEBlastProgramType(EProgram p)

Convert EProgram to EBlastProgramType.

int GetGapExtensionCost() const

#define BLASTAA_SEQ_CODE

== Seq_code_ncbistdaa

const Uint1 AMINOACID_TO_NCBISTDAA[]

Translates between ncbieaa and ncbistdaa.

EProgram GetProgram() const

Accessors/Mutators for individual options.

const CBlastOptions & GetOptions() const

Return the object which this object is a handle for.

int GetMismatchPenalty() const

int GetMatchReward() const

int GetGapOpeningCost() const

const char * GetMatrixName() const

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.

#define NON_CONST_ITERATE(Type, Var, Cont)

Non constant version of ITERATE macro.

void AddLine(const char *line, size_t len)

Uint4 GetChecksum(void) const

Return calculated checksum.

#define NCBI_ASSERT(expr, mess)

#define NCBI_THROW(exception_class, err_code, message)

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

virtual void Assign(const CSerialObject &source, ESerialRecursionMode how=eRecursive)

Set object to copy of another one.

#define MSerial_AsnText

I/O stream manipulators –.

static CSeq_id_Handle GetHandle(const CSeq_id &id)

Normal way of getting a handle, works for any seq-id.

const COrg_ref & GetOrg_ref(const CBioseq_Handle &handle)

Return the org-ref associated with a given sequence.

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

TMol GetSequenceType(void) const

CRef< CSeq_loc > GetRangeSeq_loc(TSeqPos start, TSeqPos stop, ENa_strand strand=eNa_strand_unknown) const

Return CSeq_loc referencing the given range and strand on the bioseq If start == 0,...

@ eCoding_Iupac

Set coding to printable coding (Iupacna or Iupacaa)

TMol GetSequenceType(void) const

void Reset(void)

Reset reference object.

uint8_t Uint1

1-byte (8-bit) unsigned integer

int16_t Int2

2-byte (16-bit) signed integer

int32_t Int4

4-byte (32-bit) signed integer

uint32_t Uint4

4-byte (32-bit) unsigned integer

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

static enable_if< is_arithmetic< TNumeric >::value||is_convertible< TNumeric, Int8 >::value, string >::type NumericToString(TNumeric value, TNumToStringFlags flags=0, int base=10)

Convert numeric value to string.

TTo GetTo(void) const

Get the To member data.

TFrom GetFrom(void) const

Get the From member data.

void SetType(TType &value)

Assign a value to Type data member.

void SetData(TData &value)

Assign a value to Data data member.

const TDenseg & GetDenseg(void) const

Get the variant data.

TId & SetId(void)

Assign a value to Id data member.

TScore & SetScore(void)

Assign a value to Score data member.

E_Choice Which(void) const

Which variant is currently selected.

list< CRef< CStd_seg > > TStd

bool IsSetExt(void) const

extra info Check if a value has been assigned to Ext data member.

static string SelectionName(E_Choice index)

Retrieve selection name (for diagnostic purposes).

void SetSegs(TSegs &value)

Assign a value to Segs data member.

TProduct_type GetProduct_type(void) const

Get the Product_type member data.

list< CRef< CUser_object > > TExt

bool IsSparse(void) const

Check if variant Sparse is selected.

const TSpliced & GetSpliced(void) const

Get the variant data.

bool CanGetSegs(void) const

Check if it is safe to call GetSegs method.

TExt & SetExt(void)

Assign a value to Ext data member.

list< CRef< CSpliced_exon > > TExons

const TExons & GetExons(void) const

Get the Exons member data.

bool IsStd(void) const

Check if variant Std is selected.

bool IsDisc(void) const

Check if variant Disc is selected.

const TExt & GetExt(void) const

Get the Ext member data.

bool IsSpliced(void) const

Check if variant Spliced is selected.

TNumseg GetNumseg(void) const

Get the Numseg member data.

list< CRef< CSeq_align > > Tdata

TBounds & SetBounds(void)

Assign a value to Bounds data member.

const TSegs & GetSegs(void) const

Get the Segs member data.

bool IsDenseg(void) const

Check if variant Denseg is selected.

ENa_strand

strand of nucleic acid

EMol

molecule class in living organism

unsigned int

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

#define NCBIMATH_LN2

Natural log(2)

#define TRUE

bool replacment for C indicating true.

double r(size_t dimension_, const Int4 *score_, const double *prob_, double theta_)

static int match(PCRE2_SPTR start_eptr, PCRE2_SPTR start_ecode, uint16_t top_bracket, PCRE2_SIZE frame_size, pcre2_match_data *match_data, match_block *mb)

static void s_RecordMatch(size_t match, string &BTOP, string &flipped_BTOP)

void s_CleanSeqAlign(CSeq_align &align)

static pair< string, string > s_ComputeTraceback(CScope &scope, const CSeq_align &align)

static const unsigned char reverse_4na[16]

#define row(bind, expected)

Boolean round_down

Score must be rounded down to nearest even score if odd.

char * name

name of scoring matrix.

Int4 penalty

penalty for mismatch in blastn.

SBlastScoreMatrix * matrix

scoring matrix data

Blast_KarlinBlk * kbp_ideal

Ideal values (for query with average database composition).

Blast_KarlinBlk ** kbp_gap_std

K-A parameters for std (not position-based) alignments.

Int4 reward

reward for match in blastn.

Scoring options block Used to produce the BlastScoreBlk structure This structure may be needed for lo...

Structure to hold the Karlin-Altschul parameters.

double Lambda

Lambda value used in statistics.

double logK

natural log of K value used in statistics

int ** data

actual scoring matrix data, stored in row-major form

RetroSearch is an open source project built by @garambo | Open a GitHub Issue

Search and Browse the WWW like it's 1997 | Search results from DuckDuckGo

HTML: 3.2 | Encoding: UTF-8 | Version: 0.7.4