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NCBI C++ ToolKit: include/algo/blast/api/magicblast.hpp Source File

x_Validate(

);

btop_splice_signals);

query_length = 0,

mate_length = 0);

query_length = 0);

(

)

{

(m_FirstInfo & fUnaligned) == 0;}

(

)

{

(m_LastInfo & fUnaligned) == 0;}

SortAlignments(EOrdering order);

x_SetInfo(

first_length,

(

num) {m_Results.reserve(num);}

{m_Results.push_back(element);}

#define NCBI_XBLAST_EXPORT

NULL operations for other cases.

Definition of classes which constitute the results of running a BLAST search.

Results of Magic-BLAST mapping.

Magic-BLAST results for a single query/read or a pair of reads.

Class that supports setting the number of threads to use with a given algorithm.

Source of query sequence data for BLAST Provides an interface for search classes to retrieve sequence...

Collection of masked regions for a single query sequence.

typedef for the messages for an entire BLAST search, which could be comprised of multiple query seque...

vector< CRef< CMagicBlastResults > > m_Results

CMagicBlast(const CMagicBlast &rhs)

Prohibit copy constructor.

~CMagicBlast()

Destructor.

CRef< CLocalDbAdapter > m_LocalDbAdapter

Reference to a BLAST subject/database object.

bool m_Concordant

True if results are concordant pair.

CRef< IQueryFactory > m_Queries

Queries.

size_type size() const

Get number of results, provided to facilitate STL-style iteration.

bool LastAligned(void) const

Is the mate aligned.

bool m_Paired

True if results are for paired reads.

CRef< SInternalData > m_InternalData

Internal data strctures.

vector< value_type >::size_type size_type

size_type type definition

const CSeq_id & GetFirstId(void) const

Get sequence id of the first segment of a paired read.

CMagicBlast & operator=(const CMagicBlast &rhs)

Prohibit assignment operator.

void push_back(CMagicBlastResultSet::value_type &element)

Add results to the end of the container.

CConstRef< CSeq_align_set > GetSeqAlign(void) const

Get alignments.

bool IsConcordant(void) const

Are an aligned pair concordant?

TSearchMessages m_Messages

Warning and error messages.

void clear()

Clear all results.

bool FirstAligned(void) const

Is the query aligned.

const_iterator end() const

Returns const iterator to the end of the container.

const_iterator begin() const

Returns const iteartor to the beginning of the container, provided to facilitate STL-style iteartion.

CConstRef< CSeq_id > m_QueryId

Query id.

bool empty() const

Is the container empty.

iterator end()

Returns iterator to the end of the container.

bool m_BtopSpliceSignals

Should BTOP strings be formatted with splice signals.

CMagicBlastResultSet & operator=(const CMagicBlastResultSet &)

TSearchMessages GetSearchMessages(void) const

bool IsPaired(void) const

Are alignments computed for paired reads.

void reserve(size_t num)

Reserve memory for a number of result elemetns.

CConstRef< CSeq_id > m_MateId

Mate id if results are for paired reads.

TResultsInfo GetLastInfo(void) const

Get alignment flags for the mate.

CMagicBlastResultSet(const CMagicBlastResultSet &)

TResultsInfo GetFirstInfo(void) const

Get alignment flags for the query.

CRef< CMagicBlastResults > value_type

data type contained by this container

iterator begin()

Returns iterator to the beginning of the container.

TResultsInfo m_FirstInfo

Alignment flags for the query.

vector< value_type >::iterator iterator

iterator type definition

const CSeq_id & GetQueryId(void) const

Get query sequence id.

CMagicBlastResultSet(void)

Create an empty results set.

CRef< CSeq_align_set > m_Aligns

Alignments for a single or a pair of reads.

CRef< CSeq_align_set > SetSeqAlign(void)

Get non-const alignments.

CRef< CBlastPrelimSearch > m_PrelimSearch

Object that runs BLAST search.

vector< value_type >::const_iterator const_iterator

const_iterator type definition

CRef< CBlastOptions > m_Options

Options to configure the search.

const CSeq_id & GetLastId(void) const

Get sequence id of the last sequence of a paired read.

TResultsInfo m_LastInfo

Alignment flags for the mate.

#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 Run(void)

Enter the main loop.

Declares class which provides internal BLAST database representations to the internal BLAST APIs.

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

NOTE: This file contains work in progress and the APIs are likely to change, please do not rely on th...

NOTE: This file contains work in progress and the APIs are likely to change, please do not rely on th...

NOTE: This file contains work in progress and the APIs are likely to change, please do not rely on th...

Structure that contains BLAST mapping results.

The query related information.

A chain of HSPs: spliced alignment.

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