Home - News ( United States | United Kingdom | Italy | Germany ) - Football scores

Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/blast__setup_8hpp_source.html below:

NCBI C++ ToolKit: src/algo/blast/api/blast_setup.hpp Source File

:

(d), length(

) {}

()

{

(Size() == 0); }

objects::CSeq_id*

(

index)

= 0;

(objects::CSeq_data::E_Choice coding) = 0;

);

*

) {

[pos] = operator[](pos);

vector<BLAST_SequenceBlk*>* seqblk_vec,

* max_subjlen);

AddSeqLoc(

objects::CSeq_interval & intv,

frame);

Release(

frame);

QueryHasMultipleFrames()

;

UseProteinCoords(

dna_length);

x_VerifyFrame(

frame);

bool IsForward(ENa_strand s)

Contains C++ wrapper classes to structures in algo/blast/core as well as some auxiliary functions to ...

Declares the BLAST exception class.

#define NCBI_XBLAST_EXPORT

NULL operations for other cases.

The structures and functions in blast_options.

EBlastProgramType

Defines the engine's notion of the different applications of the BLAST algorithm.

Definitions of special type used in BLAST.

unsigned int BLAST_GetNumberOfContexts(EBlastProgramType program)

Get the number of contexts for a given program.

Defines BLAST error codes (user errors included)

Encapsulates ALL the BLAST algorithm's options.

Collection of BlastSeqLoc lists for filtering processing.

Defines system exceptions occurred while running BLAST.

Lightweight wrapper around an indexed sequence container.

Lightweight wrapper around sequence data which provides a CSeqVector-like interface to the data.

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...

bool Empty(const CNcbiOstrstream &src)

TSeqPos length

Length of the buffer above (not necessarily sequence length!)

virtual TMaskedQueryRegions GetMaskedRegions(int index)=0

Return the filtered (masked) regions for a sequence.

bool Empty() const

Returns true if the container is empty, else false.

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

Return the filtered (masked) regions for a sequence.

void SetupQueries_OMF(IBlastQuerySource &queries, BlastQueryInfo *qinfo, BLAST_SequenceBlk **seqblk, EBlastProgramType prog, objects::ENa_strand strand_opt, TSearchMessages &messages)

ObjMgr Free version of SetupQueries.

EBlastEncoding

Different types of sequence encodings for sequence retrieval from the BLAST database.

void SetMinusStrand()

For nucleotide sequences this instructs the implementation to convert its representation to be that o...

virtual bool IsFirstOfAPair(int index) const =0

Is this sequence followed by a mate (for mapping short reads)

SBlastSequence GetSequence_OMF(IBlastSeqVector &sv, EBlastEncoding encoding, objects::ENa_strand strand, ESentinelType sentinel, std::string *warnings=0)

Object manager free version of GetSequence.

virtual Uint4 GetGeneticCodeId(int index) const =0

Retrieve the genetic code associated with a sequence.

void SetupSubjects_OMF(IBlastQuerySource &subjects, EBlastProgramType program, vector< BLAST_SequenceBlk * > *seqblk_vec, unsigned int *max_subjlen)

Object manager free version of SetupSubjects.

bool m_TranslateCoords

True if this object's masked regions store DNA coordinates that will later be translated into protein...

CBlastQueryFilteredFrames(CBlastQueryFilteredFrames &f)

Prevent copy construction.

EBlastEncoding GetQueryEncoding(EBlastProgramType program)

Returns the encoding for the sequence data used in BLAST for the query.

map< ETranslationFrame, BlastSeqLoc * > TFrameSet

Frame and BlastSeqLoc* info type.

objects::ENa_strand GetStrand() const

Accessor for the strand currently set.

objects::ENa_strand m_Strand

Maintains the state of the strand currently saved by the implementation of this class.

TSeqPos CalculateSeqBufferLength(TSeqPos sequence_length, EBlastEncoding encoding, objects::ENa_strand strand=objects::eNa_strand_unknown, ESentinelType sentinel=eSentinels) THROWS((CBlastException))

Calculates the length of the buffer to allocate given the desired encoding, strand (if applicable) an...

EBlastProgramType m_Program

The type of search being done.

virtual TSeqPos x_Size() const =0

Method which retrieves the size of the sequence vector, as described in the size() method above.

SBlastSequence(Uint1 *d, TSeqPos l)

Parametrized constructor.

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

Return the CSeq_loc associated with a sequence.

virtual const objects::CSeq_id * GetSeqId(int index) const =0

Return the sequence identifier associated with a sequence.

set< ETranslationFrame > m_Frames

Frames for masked locations.

virtual string GetTitle(int index) const =0

Return the title of a sequence.

virtual void x_SetMinusStrand()=0

Method which does the work for setting the minus strand of the nucleotide sequence data.

TAutoUint1Ptr data

Sequence data.

virtual SBlastSequence GetCompressedPlusStrand()=0

Returns the compressed nucleotide data for the plus strand, still occupying one base per byte.

ESentinelType

Allows specification of whether sentinel bytes should be used or not.

virtual ~IBlastSeqVector()

Our no-op virtual destructor.

objects::ENa_strand BlastSetup_GetStrand(const objects::CSeq_loc &query_seqloc, EBlastProgramType program, objects::ENa_strand strand_option)

Choose between a Seq-loc specified query strand and the strand obtained from the CBlastOptions.

CSeqLocInfo::ETranslationFrame ETranslationFrame

Data type for frame value, however inputs to methods use "int" instead of this type for readability a...

size_t GetNumFrames() const

virtual ~IBlastQuerySource()

Our no-op virtual destructor.

virtual void GetStrandData(objects::ENa_strand strand, unsigned char *buf)

Retrieve strand data in one chunk.

char * BlastFindMatrixPath(const char *matrix_name, Boolean is_prot)

Returns the path to a specified matrix.

virtual objects::ENa_strand GetStrand(int index) const =0

Return strand for a sequence.

unsigned int GetNumberOfContexts(EBlastProgramType p)

Returns the number of contexts for a given BLAST program.

virtual TSeqPos GetLength(int index) const =0

Return the length of a sequence.

virtual SBlastSequence GetBlastSequence(int index, EBlastEncoding encoding, objects::ENa_strand strand, ESentinelType sentinel, std::string *warnings=0) const =0

Return the sequence data for a sequence.

string FindBlastDbPath(const char *dbname, bool is_prot)

Returns the path (including a trailing path separator) to the location where the BLAST database can b...

virtual void SetCoding(objects::CSeq_data::E_Choice coding)=0

Sets the encoding for the sequence data.

EBlastEncoding GetSubjectEncoding(EBlastProgramType program)

Returns the encoding for the sequence data used in BLAST2Sequences for the subject.

void SetPlusStrand()

For nucleotide sequences this instructs the implementation to convert its representation to be that o...

SBlastSequence(TSeqPos buf_len)

Allocates a sequence buffer of the specified length.

SBlastSequence CompressNcbi2na(const SBlastSequence &source)

Compresses the sequence data passed in to the function from 1 base per byte to 4 bases per byte.

SBlastSequence()

Default constructor.

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.

void SetupQueryInfo_OMF(const IBlastQuerySource &queries, EBlastProgramType prog, objects::ENa_strand strand_opt, BlastQueryInfo **qinfo)

ObjMgr Free version of SetupQueryInfo.

virtual int GetSegmentInfo(int index) const =0

Get segment information (for mapping paired short reads)

CBlastQueryFilteredFrames & operator=(CBlastQueryFilteredFrames &f)

Prevent assignment.

TFrameSet m_Seqlocs

Frame and BlastSeqLoc* data.

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

Wrapper around SetupQueries.

TSeqPos size() const

Returns the length of the sequence data (in the case of nucleotides, only one strand)

Uint1 GetSentinelByte(EBlastEncoding encoding) THROWS((CBlastException))

Convenience function to centralize the knowledge of which sentinel bytes we use for supported encodin...

virtual void x_SetPlusStrand()=0

Method which does the work for setting the plus strand of the nucleotide sequence data.

TFrameSet m_SeqlocTails

Frame and tail of BlastSeqLoc* linked list (to speed up appending)

@ eNoSentinels

Do not use sentinel bytes.

@ eSentinels

Use sentinel bytes.

unsigned int TSeqPos

Type for sequence locations and lengths.

#define NCBI_THROW(exception_class, err_code, message)

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

uint8_t Uint1

1-byte (8-bit) unsigned integer

uint32_t Uint4

4-byte (32-bit) unsigned integer

#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.

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

Convert int to string.

ENa_strand

strand of nucleic acid

char * dbname(DBPROCESS *dbproc)

Get name of current database.

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

const CharType(& source)[N]

Uint1 Boolean

bool replacment for C

static SLJIT_INLINE sljit_ins l(sljit_gpr r, sljit_s32 d, sljit_gpr x, sljit_gpr b)

Structure to hold a sequence.

The query related information.

Used to hold a set of positions, mostly used for filtering.

Structure to store sequence data and its length for use in the CORE of BLAST (it's a malloc'ed array ...

voidp calloc(uInt items, uInt size)

RetroSearch is an open source project built by @garambo | Open a GitHub Issue

Search and Browse the WWW like it's 1997 | Search results from DuckDuckGo

HTML: 3.2 | Encoding: UTF-8 | Version: 0.7.4