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NCBI C++ ToolKit: src/algo/winmask/win_mask_dup_table.cpp Source File

{

.push_back( loc ); }

objects::CSeqVector & seq_data );

{

rhs < lhs; }

{

!(lhs < rhs) && !(rhs < lhs); }

objects::CSeqVector & seq_data )

next_offset( 0 );

data_len( seq_data.size() );

next_offset = (next_offset <= data_len) ? 0 : next_offset - data_len;

string::size_type new_offset,

new_count = 1 )

string::size_type subject_offset,

string::size_type s_off,

string::size_type q_off );

string::size_type s_off,

string::size_type q_off )

query_id(

.

( queryseq ) );

<<

<<

<<

<< query_id <<

result_list_type::const_iterator r_iterator;

( riter != rend )

riter->s_offset +

, riter->loc.offset );

string::size_type subject_offset,

result_list_type::const_iterator r_iterator;

do_swap( iter == end ?

:

);

( iter == end )

riter->s_offset +

, riter->loc.offset );

( *iter < riter->loc )

( *iter > riter->loc )

riter->s_offset +

, riter->loc.offset );

( riter != rend && riter->loc == *iter )

( subject_offset > riter->s_offset +

riter->s_offset +

, riter->loc.offset );

= riter->count + 1;

subject_offset,

) );

GetIdString(

& entry )

& infmt,

( input_iterator

(

.begin() );

!=

.end(); ++

)

track( index, seqnum,

, sample->

(), sample->

() );

Base class for sets of seq_id representations used with -ids and -exclude-ids options.

Function iterating over bioseqs in input.

static bool consider(const objects::CBioseq_Handle &bsh, const CIdSet *ids, const CIdSet *exclude_ids)

Check if the given bioseq should be considered for processing.

loc_list_type::const_iterator iterator

vector< sample_loc > loc_list_type

const iterator begin() const

\name Location traversal.

const iterator end() const

void add_loc(const sample_loc &loc)

sample::iterator iterator

sample_set_type sample_set

void add_loc(const string &sample, const sample_loc &loc)

void add_seq_info(const string &seq_id, const objects::CSeqVector &seq_data)

seq_id_list_type seq_id_list

vector< string > seq_id_list_type

const string seqid(Uint4 seqnum) const

map< string, sample > sample_set_type

const sample * operator[](const string &index) const

container_type::const_iterator const_iterator

const_iterator end() const

const_iterator find(const key_type &key) const

result_list_type main_list

const dup_lookup_table & table

dup_lookup_table::sample_loc sample_loc

void operator()(const string &index, Uint4 seqnum, string::size_type subject_offset, iterator start, iterator end)

vector< result > result_list_type

dup_lookup_table::iterator iterator

const string & subject_id

tracker(const dup_lookup_table &the_table, const string &the_subject_id)

result_list_type aux_list

void report_match(Uint4 queryseq, Uint4 match_count, string::size_type s_off, string::size_type q_off)

unsigned int TSeqPos

Type for sequence locations and lengths.

#define LOG_POST(message)

This macro is deprecated and it's strongly recomended to move in all projects (except tests) to macro...

void Warning(CExceptionArgs_Base &args)

void GetLabel(string *label, ELabelType type=eDefault, TLabelFlags flags=fLabel_Default) const

Append a label for this Seq-id to the supplied string.

const CSeq_id & GetId(const CSeq_loc &loc, CScope *scope)

If all CSeq_ids embedded in CSeq_loc refer to the same CBioseq, returns the first CSeq_id found,...

@ eGetId_Best

return the "best" gi (uses FindBestScore(), with CSeq_id::CalculateScore() as the score function

static CRef< CObjectManager > GetInstance(void)

Return the existing object manager or create one.

TSeqPos GetBioseqLength(void) const

CSeqVector GetSeqVector(EVectorCoding coding, ENa_strand strand=eNa_strand_plus) const

Get sequence: Iupacna or Iupacaa if use_iupac_coding is true.

@ eCoding_Iupac

Set coding to printable coding (Iupacna or Iupacaa)

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.

const TSeq & GetSeq(void) const

Get the variant data.

<!DOCTYPE HTML >< html > n< header > n< title > PubSeq Gateway Help Page</title > n< style > n table

NCBI C++ stream class wrappers for triggering between "new" and "old" C++ stream libraries.

Defines Limits for the types used in NCBI C/C++ toolkit.

CRef< objects::CObjectManager > om

sample_loc(size_t new_seqnum, Uint4 new_offset)

result(const sample_loc &newloc, string::size_type new_offset, Uint4 new_count=1)

string::size_type s_offset

bool operator==(const dup_lookup_table::sample_loc &lhs, const dup_lookup_table::sample_loc &rhs)

void CheckDuplicates(const vector< string > &input, const string &infmt, const CWinMaskUtil::CIdSet *ids, const CWinMaskUtil::CIdSet *exclude_ids)

Check for possibly duplicate sequences in the input.

const Uint4 MIN_SEQ_LENGTH

bool operator>(const dup_lookup_table::sample_loc &lhs, const dup_lookup_table::sample_loc &rhs)

bool operator<(const dup_lookup_table::sample_loc &lhs, const dup_lookup_table::sample_loc &rhs)

const Uint4 MAX_OFFSET_ERROR

const Uint4 MIN_MATCH_COUNT

const Uint4 SAMPLE_LENGTH

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