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

fn(name +

+ prot_nucl +

);

list< CRef<CSeq_id> >

(

oid)

;

(

pig,

& oid)

;

(

oid,

* ambig_length)

;

&

)

;

cache_data)

;

);

& str_id,

vector<int> & oids)

;

& have_vol)

match_type =

;

found = L.

(

, match_type);

(! found) && match_type;

* changed)

;

vector<char> & hdr_data)

;

* changed)

;

vector<Int4> & ambchars)

;

**

)

;

* preferred_seq_id);

list< CRef<CSeqdesc> >

* preferred_seq_id);

vector<int> & oids)

;

`Blob' Class for SeqDB (and WriteDB).

CObjectIStreamAsnBinary –.

CNcbiStreamoff TIndx

The type used for file offsets.

void Init(const string &filename)

Initializes a memory map object.

void Clear()

Clears the memory mapobject.

CSeqDBGiIndex(CSeqDBAtlas &atlas, const string &dbname, char prot_nucl)

static bool IndexExists(const string &name, const char prot_nucl)

TGi GetSeqGI(TOid oid, CSeqDBLockHold &locked)

bool HasIdFilters() const

bool FindId(const CSeq_id &id)

Test for existence of a Seq-id by type.

bool FindId(const CSeq_id &id, bool &match_type)

Test for existence of a TI or GI here and report whether the ID was one of those types.

bool HasIdFilters() const

~CSeqDBRangeList()

Destructor.

CSeqDBRangeList()

Constructor.

TRangeList m_Ranges

Range of offsets needed for this sequence.

void SetRanges(const TRangeList &ranges, bool append_ranges, bool cache_data)

Set ranges of the sequence that will be used.

const TRangeList & GetRanges()

Get ranges of sequence offsets that will be used.

static int ImmediateLength()

Sequences shorter than this will not use ranges in any case.

bool IsCached()

Returns true if the sequence data is cached.

bool m_CacheData

True if caching of sequence data is required for this sequence.

set< pair< int, int > > TRangeList

List of sequence offset ranges.

void FlushSequence()

Flush cached sequence data (if any).

void OptimizeGiLists() const

Simplify the GI list configuration.

bool m_HaveColumns

True if we have opened the columns for this volume.

list< CRef< CSeq_id > > GetSeqIDs(int oid) const

Get the Seq-ids associated with a sequence.

int x_GetSequence(int oid, const char **buffer, bool keep, CSeqDBLockHold &locked, bool can_release, SSeqDBSlice *region) const

Get partial sequence data.

CFastMutex m_MtxCachedRange

CRef< CSeqDBIsam > m_IsamGi

Handles translation of GIs to OIDs.

void SeqidToOids(CSeq_id &seqid, vector< int > &oids, CSeqDBLockHold &locked) const

Find OIDs for the specified Seq-id.

Uint8 x_GetSeqResidueOffset(int oid) const

Returns the base-offset of the specified oid.

void x_OpenHashFile(void) const

void x_UnleasePigFile(void) const

int GetAmbigPartialSeq(int oid, char **buffer, int nucl_code, ESeqDBAllocType alloc_type, CSeqDB::TSequenceRanges *partial_ranges, CSeqDB::TSequenceRanges *masks) const

void x_UnleaseTiFile(void) const

CSeqDBAtlas & m_Atlas

The memory management layer.

void AccessionToOids(const string &acc, vector< int > &oids, CSeqDBLockHold &locked) const

Find OIDs for the specified accession or formatted Seq-id.

void GetColumnBlob(int col_id, int oid, CBlastDbBlob &blob, bool keep, CSeqDBLockHold &locked)

Fetch the data blob for the given column and oid.

CRef< CSeqDBHdrFile > m_Hdr

Contains header (defline) information for this volume.

void x_OpenSeqFile(void) const

CSeqDBIntCache< CRef< CSeqdesc > > m_TaxCache

This cache allows CBioseqs to share taxonomic objects.

const string & GetVolName() const

Get the volume name.

void x_OpenTiFile(void) const

int GetAmbigSeq(int oid, char **buffer, int nucl_code, ESeqDBAllocType alloc_type, SSeqDBSlice *region, CSeqDB::TSequenceRanges *masks) const

Get a sequence with ambiguous regions.

vector< CRef< CSeqDBColumn > > m_Columns

Set of columns defined for this volume.

CRef< CSeqDBIdxFile > m_Idx

Metadata plus offsets into the sequence, header, and ambiguity data.

void x_OpenStrFile(void) const

int GetSeqLengthExact(int oid) const

Exact sequence length for nucleotide databases.

void x_StringToOids(const string &acc, ESeqDBIdType id_type, Int8 ident, const string &str_id, bool simplified, vector< int > &oids) const

void OpenSeqFile(CSeqDBLockHold &locked) const

Open sequence file.

int GetColumnId(const string &title, CSeqDBLockHold &locked)

Get an ID number for a given column title.

CRef< CSeqDBIsam > m_IsamStr

Handles translation of strings (accessions) to OIDs.

vector< CRef< CSeqDBGiList > > TGiLists

A set of GI lists.

CSeqDBIntCache< TDeflineCacheItem > m_DeflineCache

Cache of filtered deflines.

int x_GetAmbigSeq(int oid, char **buffer, int nucl_code, ESeqDBAllocType alloc_type, SSeqDBSlice *region, CSeqDB::TSequenceRanges *masks) const

Get a sequence with ambiguous regions.

int m_VolStart

Starting OID of this volume.

int GetNumOIDs() const

Get the number of OIDs for this volume.

map< int, CRef< CSeqDBRangeList > > TRangeCache

Cached/ranged sequence info type.

bool GetGi(int oid, TGi &gi, CSeqDBLockHold &locked) const

Find the GI given an OID.

CRef< CBlast_def_line_set > x_GetHdrAsn1(int oid, bool adjust_oids, bool *changed) const

Get sequence header object.

void GetPigBounds(int &low_id, int &high_id, int &count, CSeqDBLockHold &locked) const

Get PIG Bounds.

void x_FilterHasId(const CSeq_id &id, bool &have_user, bool &have_vol) const

Determine if a user ID list affects this ID, and how.

string m_VolName

The name of this volume.

CTempString x_GetHdrAsn1Binary(int oid) const

Get sequence header binary data.

void FlushOffsetRangeCache()

Flush all offset ranges cached.

CSeqDBVol(CSeqDBAtlas &atlas, const string &name, char prot_nucl, CSeqDBGiList *user_list, CSeqDBNegativeList *neg_list, int vol_start, CSeqDBLockHold &locked)

Constructor.

void GetRawSeqAndAmbig(int oid, const char **buffer, int *seq_length, int *ambig_length) const

Get Raw Sequence and Ambiguity Data.

void x_OpenHdrFile(void) const

bool x_HaveNegativeList(void) const

Returns true if this volume has a negative ID list.

string GetLMDBFileName() const

Get sqlite file name associated with this volume Empty string if version 4.

void ListColumns(set< string > &titles, CSeqDBLockHold &locked)

List the titles of all columns for this volume.

int GetSeqLengthApprox(int oid) const

Approximate sequence length for nucleotide databases.

TRangeCache m_RangeCache

Cached/ranged sequence info.

int m_VolEnd

First OID past end of this volume.

int GetOidMaskType() const

bool x_ListIncludesId(CSeqDBNegativeList &L, const CSeq_id &id) const

Returns true if this ID is not found in the negative ID list.

bool m_SeqFileOpened

True if the volume file has been (at least tried to) opened.

bool GetPig(int oid, int &pig, CSeqDBLockHold &locked) const

Find the PIG given an OID.

int GetSeqLengthProt(int oid) const

Sequence length for protein databases.

CRef< CSeqDBSeqFile > m_Seq

Contains sequence data for this volume.

CRef< CSeqdesc > x_GetAsnDefline(int oid) const

Get sequence header information structures.

string GetTitle() const

Get the volume title.

CRef< CSeqDBGiIndex > m_GiIndex

The GI index file (for fast oid->gi conversion)

CRef< CSeqDBNegativeList > m_NegativeList

The negative ID list, if one exists.

TGiLists m_VolumeGiLists

The volume GI lists, if any exist.

CRef< CSeqDBIsam > m_IsamTi

Handles translation of TI (trace ids) to OIDs.

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

Get sequence data.

CRef< CSeqDBIsam > m_IsamHash

Handles translation of sequence hash value to OIDs.

void UnLease()

Return expendable resources held by this volume.

set< pair< int, int > > TRangeList

List of sequence offset ranges.

list< CRef< CSeqdesc > > x_GetTaxonomy(int oid, TGi preferred_gi, const CSeq_id *preferred_seq_id)

Get taxonomic descriptions of a sequence.

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

Get the sequence data.

void IdsToOids(CSeqDBGiList &gis) const

Translate Gis to Oids for the given vector of Gi/Oid pairs.

CRef< CBlast_def_line_set > x_GetFilteredHeader(int oid, bool *changed) const

Get sequence header information.

char * x_AllocType(size_t length, ESeqDBAllocType alloc_type) const

Allocate memory in one of several ways.

void SetOidMaskType(int oid_masks) const

void x_CheckVersions(const string &acc, vector< int > &oids) const

Check Seq-id versions for special sparse-id support case.

void AttachVolumeGiList(CRef< CSeqDBGiList > gilist) const

Filter this volume using the specified GI list.

bool GiToOid(TGi gi, int &oid, CSeqDBLockHold &locked) const

Find the OID given a GI.

bool x_HaveGiList(void) const

Returns true if this volume has a positive ID list.

TGi GetSeqGI(int oid, CSeqDBLockHold &locked) const

Get the GI of a sequence This method returns the gi of the sequence.

CRef< CSeq_data > GetSeqData(int oid, TSeqPos begin, TSeqPos end, CSeqDBLockHold &locked) const

Fetch data as a CSeq_data object.

void GetGiBounds(TGi &low_id, TGi &high_id, int &count, CSeqDBLockHold &locked) const

Get GI Bounds.

int GetOidAtOffset(int first_seq, Uint8 residue, CSeqDBLockHold &locked) const

Find the OID at a given index into the database.

char GetSeqType() const

Get the sequence type stored in this database.

bool x_HaveIdFilter(void) const

Returns true if this volume has an ID list.

void x_OpenAllColumns(CSeqDBLockHold &locked)

Find all columns for this volume.

CRef< CBioseq > GetBioseq(int oid, TGi pref_gi, const CSeq_id *pref_seq_id, bool seqdata, CSeqDBLockHold &locked)

Get a CBioseq object for this sequence.

int GetMinLength() const

Get the length of the smallest sequence in this volume.

void x_UnleaseStrFile(void) const

CRef< CSeqDBGiList > m_UserGiList

The user ID list, if one exists.

CSeqDBAtlas::TIndx TIndx

Import TIndx definition from the CSeqDBAtlas class.

void x_OpenGiFile(void) const

pair< CRef< CBlast_def_line_set >, bool > TDeflineCacheItem

Filtered defline plus whether binary data needed changes.

CRef< CSeqDBIsam > m_IsamPig

Handles translation of GIs to OIDs.

bool m_IsAA

True if the volume is protein, false for nucleotide.

const map< string, string > & GetColumnMetaData(int col_id, CSeqDBLockHold &locked)

Get all metadata for the specified column.

CRef< CBlast_def_line_set > x_GetTaxDefline(int oid, TGi preferred_gi, const CSeq_id *preferred_seq_id)

Get defline filtered by several criteria.

void x_OpenOidFile(void) const

int GetMaxLength() const

Get the length of the largest sequence in this volume.

bool PigToOid(int pig, int &oid) const

Find the OID given a PIG.

bool TiToOid(Int8 ti, int &oid, CSeqDBLockHold &locked) const

Find the OID given a TI.

void x_OpenPigFile(void) const

void SetMemBit(int mbit) const

Set the MEMB_BIT fitlering for this volume.

void x_GetFilteredBinaryHeader(int oid, vector< char > &hdr_data) const

Get binary sequence header information.

bool x_ListIncludesId(CSeqDBGiList &L, const CSeq_id &id) const

Returns true if this volume's ID list has this Seq-id.

Uint8 GetVolumeLength() const

Get the total length of this volume (in bases).

CRef< CBlast_def_line_set > GetFilteredHeader(int oid, CSeqDBLockHold &locked) const

Get filtered sequence header information.

string GetDate() const

Get the formatting date of the volume.

unsigned GetSequenceHash(int oid)

Get the sequence hash for a given OID.

int m_MemBit

The filtering MEMB_BIT.

void x_UnleaseGiFile(void) const

void SetOffsetRanges(int oid, const TRangeList &offset_ranges, bool append_ranges, bool cache_data) const

Apply a range of offsets to a database sequence.

void GetStringBounds(string &low_id, string &high_id, int &count) const

Get String Bounds.

void HashToOids(unsigned hash, vector< int > &oids, CSeqDBLockHold &locked) const

Get the OIDs for a given sequence hash.

void x_GetAmbChar(int oid, vector< Int4 > &ambchars) const

Get ambiguity information.

char x_GetSeqType() const

Returns 'p' for protein databases, or 'n' for nucleotide.

CTempString implements a light-weight string on top of a storage buffer whose lifetime management is ...

unsigned int TSeqPos

Type for sequence locations and lengths.

#define NON_CONST_ITERATE(Type, Var, Cont)

Non constant version of ITERATE macro.

#define NCBI_THROW(exception_class, err_code, message)

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

virtual bool Exists(void) const

Check existence of file.

bool NotEmpty(void) const THROWS_NONE

Check if CRef 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.

int32_t Int4

4-byte (32-bit) signed integer

int64_t Int8

8-byte (64-bit) signed integer

uint64_t Uint8

8-byte (64-bit) unsigned integer

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

char * dbname(DBPROCESS *dbproc)

Get name of current database.

The SeqDB memory management layer.

Defines database column access classes.

ESeqDBAllocType

Certain methods have an "Alloc" version.

Int4 TOid

Ordinal ID in BLAST databases.

ESeqDBIdType

Various identifier formats used in Id lookup.

This file defines several SeqDB utility functions related to byte order and file system portability.

Defines database volume access classes.

USING_SCOPE(objects)

Import definitions from the objects namespace.

List of sequence offset ranges.

OID-Range type to simplify interfaces.

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