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NCBI C++ ToolKit: src/algo/cobalt/dist.cpp Source File

align1.

() + (seq2_length - 1 - align2.

()));

second =

(second, seq1_length - 1);

vector<double>& self_score,

num_queries = query_data.size();

vector<TRange> seq_ranges(num_queries);

(

= 0;

< num_queries;

++) {

self_score[

] = 0.0;

seq_ranges[

].SetEmpty();

(

= 0;

< hitlist.

();

++) {

& range1 = seq_ranges[seq1];

& range2 = seq_ranges[seq2];

(

= 0;

< num_queries;

++) {

& range = seq_ranges[

];

(

j = range.

(); j <= range.

(); j++) {

c = query_data[

].GetLetter(j);

score += score_matrix.

[c][c];

self_score[

] = karlin_blk.

* score - karlin_blk.

;

printf(

);

(

= 0;

< num_queries;

++) {

printf(

,

,

seq_ranges[

].GetFrom(), seq_ranges[

].GetTo(),

num_queries = query_data.size();

vector<double> self_score(num_queries);

self_score, karlin_blk);

(

= 0;

< hitlist.

();

++) {

align_score = karlin_blk.

*

(j,k) -= 0.5 * align_score *

(1.0 / self_score[j] + 1.0 / self_score[k]);

(

= 0;

< num_queries;

++) {

(

j = 0; j <

; j++) {

int TOffset

Basic data type for offsets into a sequence.

CDistMethods::TMatrix m_Matrix

Current distance matrix.

void x_GetSelfScores(vector< CSequence > &query_data, CHitList &hitlist, SNCBIFullScoreMatrix &score_matrix, vector< double > &self_score, Blast_KarlinBlk &karlin_blk)

Compute the self-scores of the input sequences.

void ComputeMatrix(vector< CSequence > &query_data, CHitList &hitlist, SNCBIFullScoreMatrix &score_matrix, Blast_KarlinBlk &karlin_blk)

Recompute the distance matrix using new parameters.

An ordered collection of CHit objects.

int Size() const

Retrieve number of hits in list.

CHit * GetHit(int index)

Retrieve a hit from the hitlist.

A generalized representation of a pairwise alignment.

int m_Score

Score of alignment.

int m_SeqIndex1

Numerical identifier for first sequence in alignment.

int m_SeqIndex2

Numerical identifier for second sequence in alignment.

TRange m_SeqRange1

The range of offsets on the first sequence.

TRange m_SeqRange2

The range of offsets on the second sequence.

void Resize(size_t i, size_t j, T val=T())

resize this matrix, filling the empty cells with a known value

void Set(T val)

set all values in the matrix to a known value

static void x_UpdateRanges(TRange &seq1, TRange align1, int seq1_length, TRange align2, int seq2_length)

Update the extent of a sequence that figures into its self score, based upon the sequence ranges of a...

Interface for CDistances class.

static DLIST_TYPE *DLIST_NAME() first(DLIST_LIST_TYPE *list)

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

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

position_type GetLength(void) const

TThisType & Set(position_type from, position_type to)

#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.

TTo GetTo(void) const

Get the To member data.

TFrom GetFrom(void) const

Get the From member data.

Structure to hold the Karlin-Altschul parameters.

double Lambda

Lambda value used in statistics.

double logK

natural log of K value used in statistics

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