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NCBI C++ ToolKit: src/algo/blast/api/objmgrfree_query_data.cpp Source File

GetNumQueries();

: m_Options(options), m_BioseqSet(bioseq_set)

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retval.push_back(sl);

: m_ClientBioseqSet(bioseq_set)

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+

+

+

Declares the BLAST exception class.

Declares class to encapsulate all BLAST options.

Boolean Blast_QueryIsProtein(EBlastProgramType p)

Returns true if the query is protein.

Internal auxiliary setup classes/functions for C++ BLAST APIs.

Defines BLAST error codes (user errors included)

Encapsulates ALL the BLAST algorithm's options.

Implements the IBlastQuerySource interface using a CBioseq_set as data source.

Template class for iteration on objects of class C (non-medifiable version)

Provides access (not ownership) to the C structures used to configure local BLAST search class implem...

int GetSeqLength(const CBioseq &bioseq)

CRef< IBlastQuerySource > m_QuerySource

CRef< CBioseq_set > x_BioseqSetFromBioseq(const CBioseq &bioseq)

Auxiliary function to convert a CBioseq into a CRef<CBioseq_set>

BlastQueryInfo * Get() const

virtual CConstRef< objects::CSeq_loc > GetSeqLoc(int index) const

Return the CSeq_loc associated with a sequence.

TSearchMessages m_Messages

Error/warning messages are stored here.

CConstRef< objects::CBioseq_set > m_Bioseqs

virtual size_t GetNumQueries()

Get the number of queries.

CConstRef< CBioseq_set > m_ClientBioseqSet

Queries, expressed as a CBioseq_set.

static IRemoteQueryData::TSeqLocs s_ConstBioseqSetToSeqLocs(CConstRef< CBioseq_set > bioseq_set)

Convert a constant reference to a Bioseq-set to IRemoteQueryData::TSeqLocs.

virtual CConstRef< objects::CSeq_loc > GetSeqLoc(int index) const =0

Return the CSeq_loc associated with a sequence.

CConstRef< CBioseq_set > m_BioseqSet

list< CRef< objects::CSeq_loc > > TSeqLocs

Type definition for CSeq_loc set used as queries in the BLAST remote search class.

virtual CRef< CBioseq_set > GetBioseqSet()

Accessor for the CBioseq_set.

CObjMgrFree_LocalQueryData(CConstRef< CBioseq_set > bioseq_set, const CBlastOptions *options)

EBlastProgramType GetProgramType() const

Returns the CORE BLAST notion of program type.

TSeqLocs m_SeqLocs

Data member to cache the TSeqLocs.

virtual size_t GetSeqLength(size_t index)

Get the length of the sequence indicated by index.

BLAST_SequenceBlk * Get() const

CRef< ILocalQueryData > x_MakeLocalQueryData(const CBlastOptions *opts)

factory method to create an ILocalQueryData, only called if the data members above are not set

CRef< IRemoteQueryData > x_MakeRemoteQueryData()

factory method to create an IRemoteQueryData, only called if the data members above are not set

CObjMgrFree_RemoteQueryData(CConstRef< CBioseq_set > bioseq_set)

Construct query data from a CBioseq_set.

virtual TSeqLocs GetSeqLocs()

Accessor for the TSeqLocs.

virtual TSeqPos GetLength(int index) const =0

Return the length of a sequence.

CRef< objects::CBioseq_set > m_Bioseqs

Data member to cache the CBioseq_set.

void Reset(BLAST_SequenceBlk *p=NULL)

const CBlastOptions * m_Options

CObjMgrFree_QueryFactory(CConstRef< objects::CBioseq > bioseq)

Parametrized constructor taking a single Bioseq.

void Reset(BlastQueryInfo *p=NULL)

BlastQueryInfo * SafeSetupQueryInfo(const IBlastQuerySource &queries, const CBlastOptions *options)

Wrapper around SetupQueryInfo.

virtual TSeqPos Size() const =0

Return the number of elements in the sequence container.

CBLAST_SequenceBlk m_SeqBlk

Data member to cache the BLAST_SequenceBlk.

BLAST_SequenceBlk * SafeSetupQueries(IBlastQuerySource &queries, const CBlastOptions *options, BlastQueryInfo *query_info, TSearchMessages &messages)

Wrapper around SetupQueries.

CBlastQueryInfo m_QueryInfo

Data member to cache the BlastQueryInfo.

virtual BlastQueryInfo * GetQueryInfo()

Accessor for the BlastQueryInfo structure.

virtual CConstRef< CSeq_loc > GetSeq_loc(size_t index)

Get the Seq_loc for the sequence indicated by index.

virtual TSeqPos Size() const

Return the number of elements in the sequence container.

virtual BLAST_SequenceBlk * GetSequenceBlk()

Accessor for the BLAST_SequenceBlk structure.

unsigned int TSeqPos

Type for sequence locations and lengths.

#define NCBI_CURRENT_FUNCTION

Get current function name.

#define NCBI_THROW(exception_class, err_code, message)

Generic macro to throw an exception, given the exception class, error code and message string.

CConstBeginInfo ConstBegin(const C &obj)

Get starting point of non-modifiable object hierarchy.

void Reset(void)

Reset reference object.

bool NotEmpty(void) const THROWS_NONE

Check if CConstRef is not empty – pointing to an object and has a non-null value.

bool Empty(void) const THROWS_NONE

Check if CRef is empty – not pointing to any object, which means having a null value.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define USING_SCOPE(ns)

Use the specified namespace.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define BEGIN_SCOPE(ns)

Define a new scope.

TSeq & SetSeq(void)

Select the variant.

TSeq_set & SetSeq_set(void)

Assign a value to Seq_set data member.

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

Structure to hold a sequence.

The query related information.

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