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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/query__data_8cpp_source.html below:

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

all_contexts_valid =

;

i <= query_info->last_context;

all_contexts_valid =

;

all_contexts_valid;

found_valid_query =

;

found_valid_query =

;

found_valid_query;

Defines BLAST error codes (user errors included)

Encapsulates ALL the BLAST algorithm's options.

Class for the messages for an individual query sequence.

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

void GetMessages(TSearchMessages &messages) const

Retrieve all error/warning messages.

size_t m_SumOfSequenceLengths

virtual CRef< ILocalQueryData > x_MakeLocalQueryData(const CBlastOptions *opts)=0

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

TSearchMessages m_Messages

Error/warning messages are stored here.

bool IsValidQuery(size_t index)

Determine if a given query sequence is valid or not.

CRef< ILocalQueryData > MakeLocalQueryData(const CBlastOptions *opts)

Creates and caches an ILocalQueryData.

virtual CRef< IRemoteQueryData > x_MakeRemoteQueryData()=0

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

bool IsAtLeastOneQueryValid()

Determine if at least one query sequence is valid or not.

virtual BlastQueryInfo * GetQueryInfo()=0

Accessor for the BlastQueryInfo structure.

CRef< ILocalQueryData > m_LocalQueryData

void FlushSequenceData()

Frees the cached sequence data structure (as this is usually the larger data structure).

CRef< IRemoteQueryData > m_RemoteQueryData

virtual size_t GetNumQueries()=0

Get the number of queries.

CRef< IRemoteQueryData > MakeRemoteQueryData()

Creates and caches an IRemoteQueryData.

void Reset(BLAST_SequenceBlk *p=NULL)

void x_ValidateIndex(size_t index)

void GetQueryMessages(size_t index, TQueryMessages &qmsgs)

Retrieve error/warning messages for a specific query.

virtual size_t GetSeqLength(size_t index)=0

Get the length of the sequence indicated by index.

CBLAST_SequenceBlk m_SeqBlk

Data member to cache the BLAST_SequenceBlk.

size_t GetSumOfSequenceLengths()

Compute the sum of all the sequence's lengths.

void Reset(void)

Reset reference object.

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.

static string SizetToString(size_t value, TNumToStringFlags flags=0, int base=10)

Convert size_t to string.

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

Boolean is_valid

Determine if this context is valid or not.

Int4 query_index

Index of query (same for all frames)

The query related information.

Int4 first_context

Index of the first element of the context array.

BlastContextInfo * contexts

Information per context.

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