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

::

(

seq1_index,

seq2_index,

score,

: m_SeqIndex1(seq1_index), m_SeqIndex2(seq2_index),

m_Score(score), m_EditScript(denseg)

len1 = 0, len2 = 0;

(starts[2*

] >= 0)

(starts[2*

+1] >= 0)

m_SeqRange1 =

(starts[0], starts[0] + len1 - 1);

m_SeqRange2 =

(starts[1], starts[1] + len2 - 1);

(

seq1_index,

seq2_index,

score,

: m_SeqIndex1(seq1_index), m_SeqIndex2(seq2_index),

m_Score(score), m_EditScript(dendiag)

m_SeqRange1 =

(starts[0], starts[0] +

- 1);

m_SeqRange2 =

(starts[1], starts[1] +

- 1);

target_off = seq_range2.

();

seq_range1.

(new_off.first);

new_seq_range2.

(new_off.second);

tback_range.

(new_tback);

target_off = seq_range2.

();

seq_range1.

(new_off.first);

new_seq_range2.

(new_off.second);

tback_range.

(new_tback);

target_off = seq_range1.

();

new_seq_range1.

(new_off.first);

seq_range2.

(new_off.second);

tback_range.

(new_tback);

target_off = seq_range1.

();

new_seq_range1.

(new_off.first);

seq_range2.

(new_off.second);

tback_range.

(new_tback);

(

->m_SeqRange1.GetFrom() <

->m_SeqRange1.GetFrom())

(

->m_SeqRange1.GetFrom() >

->m_SeqRange1.GetFrom())

(

->m_SeqRange1.GetTo() <

->m_SeqRange1.GetTo());

num_subhits = subhits.size();

(

= 0;

< num_subhits - 1;

++) {

*hit1 = subhits[

];

(

j =

+ 1; j < num_subhits; j++) {

*hit2 = subhits[j];

subhits[j]; subhits[j] = 0;

subhits[

]; subhits[

] = 0;

(

= 0;

< num_subhits;

++) {

(subhits[

] != 0)

subhits[j++] = subhits[

];

(

= 0;

< num_subhits - 1;

++) {

new_s_range1, tback_range1);

seq1, seq2_pssm, gap_open, gap_extend);

new_s_range2, tback_range2);

seq1, seq2_pssm, gap_open, gap_extend);

printf(

,

printf(

,

new_q_range2, new_s_range2, score2,

new_q_range1, new_s_range1, score1,

Interface for CHit class, used to encapsulate operations involving pairwise alignments.

int TOffset

Basic data type for offsets into a sequence.

CLocalRange< TOffset > TRange

define for the fundamental building block of sequence ranges

pair< TOffset, TOffset > TOffsetPair

Basic type specifying a range on a sequence.

void VerifyScript(TRange seq1_range, TRange seq2_range)

Validate that the alignment described by the CEditScript has the same size for each sequence as the i...

int GetScore(TRange tback_range, TOffsetPair start_offsets, CSequence &seq1, int **seq2_pssm, int gap_open, int gap_extend)

Compute the score associated with (a portion of) an alignment Assumes that seq1 is a sequence and tha...

void FindOffsetFromSeq2(TOffsetPair start_offsets, TOffsetPair &new_offsets, TOffset seq2_target, TOffset &new_tback, bool go_past_seq1_gap)

Given a subject offset, find the corresponding query offset.

void FindOffsetFromSeq1(TOffsetPair start_offsets, TOffsetPair &new_offsets, TOffset seq1_target, TOffset &new_tback, bool go_past_seq2_gap)

Given a query offset, find the corresponding subject offset.

CEditScript MakeEditScript(TRange tback_range)

Return an edit script corresponding to a subset of the complete traceback available.

A generalized representation of a pairwise alignment.

void GetRangeFromSeq1(TRange seq_range1, TRange &new_seq_range1, TRange &seq_range2, TRange &traceback_range)

Retrieve the seq2 range corresponding to a specified seq1 range.

TSubHit & GetSubHit()

Retrieve a list of subhits.

vector< CHit * > m_SubHit

Subhits for this alignment.

void VerifyHit()

Perform basic integrity checks on a CHit.

void ResolveSubHitConflicts(CSequence &seq1, int **seq2_pssm, CNWAligner::TScore gap_open, CNWAligner::TScore gap_extend)

If pairs of subhits have overlapping ranges, either delete one or change one so that the overlap is a...

CEditScript m_EditScript

Traceback for this alignment.

CHit * Clone()

Produce an independent copy of a CHit.

void InsertSubHit(CHit *hit)

Add a to a CHit's list of subhits.

void GetRangeFromSeq2(TRange seq_range2, TRange &seq_range1, TRange &new_seq_range2, TRange &traceback_range)

Retrieve the seq1 range corresponding to a specified seq2 range.

void AddUpSubHits()

Sum the score of all subhits, and make the sequence ranges the union of the ranges of all subhits.

int m_Score

Score of alignment.

CEditScript & GetEditScript()

Retrieve the traceback associated with a CHit.

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.

bool HasSubHits()

Query if a CHit has a hierarchy of subhits available.

vector< CHit * > TSubHit

Hits can be grouped hierarchically.

bool StrictlyBelow(const TThisType &r)

Test whether 'this' represents a sequence range strictly less than a given sequence range.

bool Contains(const TThisType &r)

Test whether 'this' completely envelops a given sequence range.

Class for representing protein sequences.

#define NON_CONST_ITERATE(Type, Var, Cont)

Non constant version of ITERATE macro.

TThisType & CombineWith(const TThisType &r)

#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.

void SetFrom(TFrom value)

Assign a value to From data member.

TTo GetTo(void) const

Get the To member data.

TFrom GetFrom(void) const

Get the From member data.

void SetTo(TTo value)

Assign a value to To data member.

TLen GetLen(void) const

Get the Len member data.

vector< TSignedSeqPos > TStarts

vector< TSeqPos > TStarts

TDim GetDim(void) const

Get the Dim member data.

const TStarts & GetStarts(void) const

Get the Starts member data.

unsigned int

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

static void x_RemoveEnvelopedSubHits(CHit::TSubHit &subhits)

Delete any hits from a list that are contained within higher-scoring hits.

constexpr auto sort(_Init &&init)

callback used for sorting HSP lists

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

functor that implements hit comparison

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