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NCBI C++ ToolKit: include/objtools/blast/seqdb_reader/seqdb.hpp Source File

x_GetSeq();

x_RetSeq();

ESeqType2String(ESeqType

);

(_size + 1 > _capacity) {

()

{

_size == 0; }

(num_elements > _capacity) {

(

*) realloc(_data, (num_elements + 1) *

( !reallocation ) {

(

);

_data = (

*) reallocation;

_capacity = num_elements;

reserve(_size + num_elements);

memcpy(&_data[1+ 2*_size], src, num_elements *

(

));

_size += num_elements;

x_reallocate_if_necessary();

use_atlas_lock =

);

(

vector<string> & dbs,

GenerateSearchPath();

GetSeqGI(

oid)

;

GetSeqLengthApprox(

oid)

;

vector<TTaxId> & taxids,

GetTaxIDs(

oid,

persist =

)

;

GetTaxIDs(

oid,

vector<TTaxId> & taxids,

persist =

)

;

GetAllTaxIDs(

oid,

ExtractBlastDefline(

& bioseq);

GetAmbigSeq(

oid,

**

,

nucl_code)

;

GetAmbigSeq(

oid,

end_offset)

;

GetAmbigSeqAlloc(

oid,

GetAmbigPartialSeq(

oid,

RetSequence(

**

)

;

RetAmbigSeq(

**

)

;

list< CRef<CSeq_id> > GetSeqIDs(

oid)

;

GetGis(

oid, vector<TGi> & gis,

=

)

;

GetDate()

;

GetNumSeqs()

;

GetNumSeqsStats()

;

GetNumOIDs()

;

GetTotalLength()

;

GetExactTotalLength();

GetTotalLengthStats()

;

GetVolumeLength()

;

* total_length,

use_approx =

)

;

GetMaxLength()

;

GetMinLength()

;

CheckOrFindOID(

& next_oid)

;

GetNextOIDChunk(

& begin_chunk,

vector<int> & oid_list,

* oid_state =

);

ResetInternalChunkBookmark();

& GetDBNameList()

;

PigToOid(

pig,

& oid)

;

OidToPig(

oid,

& pig)

;

TiToOid(

ti,

& oid)

;

OidToGi(

oid,

& gi)

;

GiToOid(

gi,

& oid)

;

GiToOidwFilterCheck(

gi,

& oid)

;

GiToPig(

gi,

& pig)

;

PigToGi(

pig,

& gi)

;

AccessionToOids(

& acc, vector<int> & oids)

;

AccessionsToOids(

vector<string>& accs, vector<blastdb::TOid>& oids)

;

SeqidToOids(

& seqid, vector<int> & oids)

;

SeqidToOid(

& seqid,

& oid)

;

GetOidAtOffset(

first_seq,

residue)

;

FindVolumePaths(

&

,

vector<string> & paths,

vector<string> * alias_paths =

,

recursive =

,

expand_links =

);

FindVolumePaths(vector<string> & paths,

recursive=

)

;

SetIterationRange(

oid_begin,

oid_end);

GetSequenceAsString(

oid,

GetSequenceAsString(

oid,

ListColumns(vector<string> & titles);

GetColumnId(

& title);

& GetColumnValue(

column_id,

&

);

GetColumnMetaData(

column_id,

& volname);

GetColumnBlob(

col_id,

oid,

& blob);

GetAvailableMaskAlgorithms(vector<int> & algorithms);

GetMaskAlgorithmId(

&algo_name)

;

GetAvailableMaskAlgorithmDescriptions();

vector<int> ValidateMaskAlgorithms(

vector<int>& algorithm_ids);

GetMaskAlgorithmDetails(

algorithm_id,

& program_name,

& algo_opts);

GetMaskAlgorithmDetails(

algorithm_id,

& program_name,

& algo_opts);

vector<int> & algo_ids,

GetMaskData(oid, algo_ids[0], ranges);

GetMaskData(

oid,

TSequenceRanges &ranges);

SetOffsetRanges(

oid,

RemoveOffsetRanges(

oid);

FlushOffsetRangeCache();

SetNumberOfThreads(

num_threads,

force_mt =

);

GetDiskUsage()

;

SetVolsMemBit(

mbit);

TaxIdsToOids(

& tax_ids, vector<blastdb::TOid>& rv)

;

GetTaxIdsForOids(

vector<blastdb::TOid> & oids,

& tax_ids)

;

GetTaxIdsForAccession(

& accs, vector<TTaxId> & taxids);

GetTaxIdsForSeqId(

& seq_id, vector<TTaxId> & taxids);

x_GetDBFilesMetaData(

& disk_bytes,

& cached_bytes, vector<string> & db_files,

& user_path)

;

vector<SSeqDBInitInfo>

(

& path,

& dbtype,

recurse,

include_alias_files =

,

remove_redundant_dbs =

);

m_Length = m_DB->GetSequence(oid, & m_Data);

m_DB->RetSequence(& m_Data);

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

bool GetSeqData(ParserPtr pp, const DataBlk &entry, CBioseq &bioseq, Int4 nodetype, unsigned char *seqconv, Uint1 seq_data_type)

const size_t kResizeFactor

factor by which these arrays are resized

@ eOidRange

Data is a range of contiguous ordinal ids (indices)

`Blob' Class for SeqDB (and WriteDB).

SeqDB ID list for performing boolean set operations.

virtual ~CSeqDBIter()

Destructor.

int m_Length

The length of this OID.

const CSeqDB * m_DB

The CSeqDB object which this object iterates over.

void x_RetSeq()

Release hold on current sequence.

const char * m_Data

The sequence data for this OID.

int GetLength()

Get the length (in base pairs) of the currently held sequence.

int m_OID

The OID this iterator is currently accessing.

void x_GetSeq()

Get data pointer and length for the current sequence.

const char * GetData()

Get the sequence data for the currently held sequence.

int GetOID()

Get the OID of the currently held sequence.

DECLARE_OPERATOR_BOOL(m_Length !=-1)

Returns true if the iterator points to a valid sequence.

CSeqDBSequence(const CSeqDBSequence &)

Prevent copy construct.

const char * GetData()

Get pointer to sequence data.

CRef< CSeqDB > m_DB

The CSeqDB object this sequence is from.

~CSeqDBSequence()

Destructor, returns the sequence.

const char * m_Data

The sequence data for this sequence.

CSeqDBSequence & operator=(const CSeqDBSequence &)

Prevent copy.

int m_Length

The length of this sequence.

CSeqDB::TOID TOID

Defines the type used to select which sequence to get.

CSeqDBSequence(CSeqDB *db, int oid)

Get a hold a database sequence.

int GetLength()

Get sequence length.

int TOID

Sequence type accepted and returned for OID indices.

int TPIG

Sequence type accepted and returned for PIG indices.

static const char * kOidNotFound

String containing the error message in exceptions thrown when a given OID cannot be found.

EOidListType

Indicates how block of OIDs was returned.

ESeqType

Sequence types (eUnknown tries protein, then nucleotide).

void RetSequence(const char **buffer) const

Returns any resources associated with the sequence.

int GetSequence(int oid, const char **buffer) const

Get a pointer to raw sequence data.

ESummaryType

Types of summary information available.

@ eUnfilteredAll

Sum of all sequences, ignoring GI and OID lists and alias files.

@ eFilteredAll

Values from alias files, or summation over all included sequences.

static const char * kBlastDbDateFormat

Format string for the date returned by CSeqDB::GetDate.

class CSeqDBImpl * m_Impl

Implementation details are hidden. (See seqdbimpl.hpp).

TGi TGI

Sequence type accepted and returned for GI indices.

EMmapStrategies

Permitted mmap strategies.

@ eMmap_Normal

Normal, no special behavior (should undo next two options).

@ eMmap_Sequential

Expect sequential page references.

TSeqDBAliasFileValues TAliasFileValues

Import type to allow shorter name.

EMmapFileTypes

File type for which mmap strategy may be set.

@ eMmap_IndexFile

Index files (name ends with ".pin" or ".nin").

set< pair< int, int > > TRangeList

List of sequence offset ranges.

void GetMaskData(int oid, const vector< int > &algo_ids, TSequenceRanges &ranges)

Get masked ranges of a sequence.

static unsigned char depth[2 *(256+1+29)+1]

int GetSeqLength(const CBioseq &bioseq)

static void DLIST_NAME() append(DLIST_LIST_TYPE *list, DLIST_TYPE *item)

static DLIST_TYPE *DLIST_NAME() first(DLIST_LIST_TYPE *list)

static SQLCHAR output[256]

static const char * str(char *buf, int n)

SBlastSequence GetSequence(const objects::CSeq_loc &sl, EBlastEncoding encoding, objects::CScope *scope, objects::ENa_strand strand=objects::eNa_strand_plus, ESentinelType sentinel=eSentinels, std::string *warnings=NULL)

Retrieves a sequence using the object manager.

unsigned int TSeqPos

Type for sequence locations and lengths.

SStrictId_Tax::TId TTaxId

Taxon id type.

#define NCBI_THROW(exception_class, err_code, message)

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

CBeginInfo Begin(C &obj)

Get starting point of object hierarchy.

NCBI_XOBJUTIL_EXPORT string GetTitle(const CBioseq_Handle &hnd, TGetTitleFlags flags=0)

int64_t Int8

8-byte (64-bit) signed integer

uint64_t Uint8

8-byte (64-bit) unsigned integer

CRange< TSeqPos > TSeqRange

typedefs for sequence ranges

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

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

Convert size_t to string.

#define NCBI_XOBJREAD_EXPORT

strategy

Block allocation strategies.

EBlast_filter_program

This defines the possible sequence filtering algorithms to be used in a BLAST database.

char * dbname(DBPROCESS *dbproc)

Get name of current database.

CBioseq_Info & GetBioseq(CTSE_Info &tse, const CBioObjectId &id)

double value_type

The numeric datatype used by the parser.

const struct ncbi::grid::netcache::search::fields::KEY key

USING_SCOPE(objects)

Include definitions from the objects namespace.

CSeqDB::ESeqType ParseMoleculeTypeString(const string &str)

Convert a string to a CSeqDB ESeqType object.

vector< SSeqDBInitInfo > FindBlastDBs(const string &path, const string &dbtype, bool recurse, bool include_alias_files=false, bool remove_redundant_dbs=false)

Find BLAST DBs in the directory specified.

bool DeleteBlastDb(const string &dbpath, CSeqDB::ESeqType seq_type)

Deletes all files associated with a BLAST database.

Defines BlastDb `Blob' class for SeqDB and WriteDB.

Defines exception class and several constants for SeqDB.

ESeqDBAllocType

Certain methods have an "Alloc" version.

EBlastDbVersion

BLAST database version.

Uint4 GetSequenceType(const CBioseq_Handle &bsh)

Return a (corrected) set of flags identifying the sequence type.

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

Structure to represent a range.

TOffsetPair()

Default constructor.

List of sequence offset ranges.

void append(const void *src, size_type num_elements)

Append extra elements at the end.

const_iterator end() const

value_type & operator[](size_type i)

const value_type * const_iterator

const_iterator begin() const

void reserve(size_t num_elements)

Reserves capacity for at least num_elements elements.

void push_back(const value_type &element)

Append extra element at the end.

void x_reallocate_if_necessary()

value_type * get_data() const

Structure to define basic information to initialize a BLAST DB.

string m_BlastDbName

The BLAST DB name.

bool operator<(const SSeqDBInitInfo &rhs) const

operator less to support sorting

CRef< CSeqDB > InitSeqDb() const

Create a new CSeqDB instance from this object.

CSeqDB::ESeqType m_MoleculeType

The molecule type.

SSeqDBInitInfo()

Default constructor.

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