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NCBI C++ ToolKit: include/objtools/alnmgr/aln_stats.hpp Source File

<

_TAlnIdVec>

_TAlnIdVec::TAlnVec

;

_TAlnIdVec::TIdVec

;

(

aln_i = 0; aln_i <

; ++aln_i) {

(

row_i = 0; row_i <

[aln_i].size(); ++row_i) {

it->second.push_back(

(

, aln_i, row_i));

& idx_vec = it->second;

TIdxVec::iterator idx_it = idx_vec.begin();

(idx_it != idx_vec.end()) {

(idx_it == idx_vec.end()) {

idx_vec.push_back(

(

, aln_i, row_i));

aln_it->second;

);

& id_idx = it->second[0];

(

aln_i = 0; aln_i <

; ++aln_i) {

(

aligned_id_idx = 0;

(aligned_id_idx != id_idx &&

( !id_bit_vec[

(aligned_id_idx)] ) {

id_bit_vec[

(aligned_id_idx)] =

;

aligned_ids_vec.push_back

aligned_ids_vec;

rows[aln_i] =

(row_i);

(

id_idx = 0; id_idx <

.size(); ++id_idx) {

it->second.push_back(id_idx);

CAlnStats< TAlnIdMap > TAlnStats

Default implementations for alignment stats.

CAlnStats< TScopeAlnIdMap > TScopeAlnStats

Helper class which collects seq-align statistics: seq-ids participating in alignments and rows,...

TDim GetDimForAln(size_t aln_idx) const

What is the dimension of an alignment?

_TAlnIdVec::TAlnVec TAlnVec

Vector of original seq-aligns.

_TAlnIdVec::TIdVec TIdVec

Vector of ids used in all alignments.

const TIdxVec & GetAnchorIdxVec(void) const

Get vector of id indexes (from IdVec) for potential anchors.

void x_IdentifyPotentialAnchors(void) const

const TIdVec & GetIdVec(void) const

Get vector of all ids from all alignments.

const TIdVec & GetSeqIdsForAln(const CSeq_align &aln) const

Access the vector of seq-ids of a particular alignment.

vector< TRowVec > TRowVecVec

One entry per id (in sync with TIdVec).

const TIdMap & GetAnchorIdMap(void) const

Get map of potential anchor ids.

const TAlnIdVec & m_AlnIdVec

bool IsCanonicalQueryAnchored(void) const

Canonical Query-Anchored: all alignments have 2 or 3 rows and exactly 2 sequences (A and B),...

vector< TDim > TRowVec

Vector, describing how a single id participates in all alignments from TAlnVec.

bool IsCanonicalMultiple(void) const

Canonical Multiple: Single alignment with multiple sequences.

const TIdVec & GetAnchorIdVec(void) const

Get vector of potential anchor ids.

size_t x_AddId(const TAlnSeqIdIRef &id, size_t aln_i, size_t row_i)

vector< TBitVec > TBitVecVec

One entry per id (in sync with TIdVec).

CAlnStats(const TAlnIdVec &aln_id_vec)

Constructor.

size_t GetAlnCount(void) const

How many alignments do we have?

TAlignedIdsMap m_AlignedIdsMap

bool CanBeAnchored(void) const

Check if there are any ids which can be used as anchors for the whole set of alignments.

vector< size_t > TIdxVec

Vector of indexes in TIdVec.

const TRowVecVec & GetRowVecVec(void) const

Get vector describing ids usage in each alignment.

const TIdMap & GetIdMap(void) const

Get map of ids to there indexes in TIdVec.

map< TAlnSeqIdIRef, TIdVec > TAlignedIdsMap

bm::bvector TBitVec

Bitmap where each bit indicates an alignment from TAlnVec.

const TIdVec & GetSeqIdsForAln(size_t aln_idx) const

Access the vector of seq-ids of a particular alignment.

_TAlnIdVec TAlnIdVec

Container with one entry per seq-align using the same indexing as m_AlnVec.

const TIdVec & GetAlignedIds(const TAlnSeqIdIRef &id) const

Get a set of ids that are aligned to a particular id.

map< TAlnSeqIdIRef, TIdxVec, SAlnSeqIdIRefComp > TIdMap

Each id mapped to a vector of indexes in TIdVec.

const TAlnVec & GetAlnVec(void) const

Access the underlying vector of alignments.

void resize(size_type new_size)

Change size of the bvector.

bvector_size_type size_type

container_type::const_iterator const_iterator

container_type::iterator iterator

const_iterator end() const

const_iterator lower_bound(const key_type &key) const

iterator_bool insert(const value_type &val)

container_type::value_type value_type

const_iterator find(const key_type &key) const

Include a standard set of the NCBI C++ Toolkit most basic headers.

bool Empty(const CNcbiOstrstream &src)

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

#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.

unsigned int

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

const struct ncbi::grid::netcache::search::fields::SIZE size

Compressed bitset (entry point to bm.h)

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

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