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NCBI C++ ToolKit: src/objtools/alnmgr/alnmatch.cpp Source File

TCalcScoreMethod calc_score)

m_AlnMixSequences(sequences),

m_Seqs(m_AlnMixSequences->m_Seqs),

x_CalculateScore(calc_score),

m_ContainsAA(m_AlnMixSequences->m_ContainsAA),

m_ContainsNA(m_AlnMixSequences->m_ContainsNA)

match1->m_Score > match2->m_Score;

match1->m_ChainScore == match2->m_ChainScore &&

match1->m_Score > match2->m_Score ||

match1->m_ChainScore > match2->m_ChainScore;

total_aln_score = 0;

prev_matches_size =

.size();

single_chunk =

;

((start1 = ds.

()[seg_off + row1]) >= 0) {

* aln_seq1 = ds_seq[row1].GetNonNullPointer();

row2 < ds.

(); row2++) {

((start2 = ds.

()[seg_off + row2]) >= 0) {

single_chunk =

;

first_non_gapped_row_found = row1;

* aln_seq2 = ds_seq[row2].GetNonNullPointer();

total_aln_score += score;

);

(row1 == first_non_gapped_row_found) {

->m_AlnSeq1 = ds_seq[row1];

->m_MatchIter1 =

->m_AlnSeq1->m_MatchList.end();

->m_Start1 = start1;

->m_AlnSeq2 = ds_seq[row2];

->m_MatchIter2 =

->m_AlnSeq2->m_MatchList.end();

->m_Start2 = start2;

->m_StrandsDiffer =

;

->m_StrandsDiffer =

;

->m_Score = score;

->m_AlnSeq1 = ds_seq[row1];

->m_MatchIter1 =

->m_AlnSeq1->m_MatchList.end();

->m_Start1 = start1;

->m_AlnSeq2 = 0;

->m_Start2 = 0;

->m_StrandsDiffer =

;

new_maches_size =

.size() - prev_matches_size;

((*match_i)->IsGood());

(*match_i)-> m_ChainScore = total_aln_score;

( !(--new_maches_size) ) {

(

= 0;

< ds_seq.size();

++) {

ds_seq[

]->m_ChainScore += total_aln_score;

CDense_seg::TNumseg TNumseg

vector< CRef< CAlnMixMatch > > TMatches

TCalcScoreMethod x_CalculateScore

void Add(const CDense_seg &ds, TAddFlags flags=0)

"Add" a Dense-seg to the existing matches.

static bool x_CompareChainScores(const CRef< CAlnMixMatch > &match1, const CRef< CAlnMixMatch > &match2)

void SortByScore()

Modifying algorithms.

static bool x_CompareScores(const CRef< CAlnMixMatch > &match1, const CRef< CAlnMixMatch > &match2)

CAlnMixMatches(CRef< CAlnMixSequences > &sequences, TCalcScoreMethod calc_score=0)

Constructor.

CRef< CAlnMixSequences > m_AlnMixSequences

void GetSeqString(string &s, TSeqPos start, TSeqPos len, bool positive_strand=true)

map< const CDense_seg *, vector< CRef< CAlnMixSeq > > > m_DsSeq

unsigned int TSeqPos

Type for sequence locations and lengths.

int TSignedSeqPos

Type for signed sequence position.

#define NON_CONST_REVERSE_ITERATE(Type, Var, Cont)

Non constant version of REVERSE_ITERATE macro.

#define NCBI_THROW(exception_class, err_code, message)

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

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

const TStarts & GetStarts(void) const

Get the Starts member data.

const TLens & GetLens(void) const

Get the Lens member data.

TDim GetDim(void) const

Get the Dim member data.

TNumseg GetNumseg(void) const

Get the Numseg member data.

const TStrands & GetStrands(void) const

Get the Strands member data.

ENa_strand

strand of nucleic acid

unsigned int

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

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)

#define row(bind, expected)

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