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

<

T>

( (gi_index < gis_size)

( (gi_index + jump < gis_size)

&& (gis.

<

>(gi_index + jump) <

)) {

( (gi_index < gis_size)

<

T>

( (index < num_keys)

&& (keys[index] <= target)) {

( (index + jump < num_keys)

&& (keys[index + jump] <= target)) {

<

T>

( (gi_index < gis_size)

x_IdentToOid(pig, oid);

x_IdentToOid(

, oid);

IdsToOids(

vol_start,

IdsToOids(

vol_start,

StringToOids(

& acc,

& version_check);

HashToOids(

,

vector<TOid> & oids);

GetIdBounds(

& low_id,

GetIdBounds(

& low_id,

IndexExists(

&

,

: m_IsSet(

), m_NKey(-1)

(m_IsSet && (ident < m_NKey));

(m_IsSet && (ident < m_SKey));

(m_IsSet && (ident > m_NKey));

(m_IsSet && (ident > m_SKey));

vector<TIndx> & offs)

* keydatap = lease.

(m_KeySampleOffset);

(

index=0; index < m_NumSamples; ++index) {

keys.push_back(

(x_GetNumericKey(keydatap)));

offs.push_back(index * m_PageSize * m_TermSize);

keydatap += m_TermSize;

offs.push_back(m_NumTerms * m_TermSize);

(

index=0; index < num_keys; ++index) {

keys.push_back(

(x_GetNumericKey(keydatap)));

vals.push_back(x_GetNumericData(keydatap));

keydatap += m_TermSize;

gilist_size = gis.

<

>();

(! gilist_size)

;

(m_Initialized ==

) {

);

vector<T> sample_keys;

vector<TIndx> page_offs;

sample_keys.reserve(m_NumSamples);

page_offs.reserve(m_NumSamples + 1);

keys.reserve(m_PageSize);

vals.reserve(m_PageSize);

x_LoadIndex(m_IndexLease, sample_keys, page_offs);

gilist_index = 0;

sample_index = 0;

((gilist_index < gilist_size) && (sample_index < m_NumSamples)) {

s_AdvanceGiList<T>(gis, gilist_index, gilist_size,

sample_keys[sample_index]);

(gilist_index >= gilist_size)

;

s_AdvanceKeyList<T>(sample_keys, sample_index, m_NumSamples,

gis.

<

>(gilist_index));

num_keys = m_PageSize;

(sample_index + 1 == m_NumSamples) {

num_keys = m_NumTerms - sample_index * m_PageSize;

x_LoadData(m_DataLease, keys, vals, num_keys, page_offs[sample_index]);

((gilist_index < gilist_size) && (index < num_keys)) {

s_AdvanceKeyList<T>(keys, index, num_keys,

gis.

<

>(gilist_index));

s_SetTranslation<T>(gis, gilist_index, gilist_size,

keys[index], vals[index] + vol_start);

(index >= num_keys)

;

s_AdvanceGiList<T>(gis, gilist_index, gilist_size, keys[index]);

s_SetTranslation<T>(gis, gilist_index, gilist_size,

keys[index], vals[index] + vol_start);

x_IdentToOid(

,

x_SearchIndexNumeric(

Number,

x_SearchNegativeMulti(

vol_start,

x_SearchNegativeMultiSeq(

vol_start,

x_SearchDataNumeric(

Number,

x_NumericSearch(

Number,

x_StringSearch(

& term_in,

vector<string> & term_out,

vector<string> & value_out,

vector<TIndx> & index_out);

x_InitSearch(

);

x_GetPageNumElements(

SampleNum,

x_SparseStringToOids(

& acc,

x_DiffCharLease(

& term_in,

x_DiffChar(

& term_in,

x_ExtractData(

* key_start,

* entry_end,

vector<string> & key_out,

vector<string> & data_out);

x_GetIndexKeyOffset(

sample_offset,

x_GetIndexString(

key_offset,

x_DiffSample(

& term_in,

x_ExtractAllData(

& term_in,

vector<TIndx> & indices_out,

vector<string> & keys_out,

vector<string> & data_out);

x_ExtractPageData(

& term_in,

vector<TIndx> & indices_out,

vector<string> & keys_out,

vector<string> & data_out);

x_LoadPage(

SampleNum1,

** beginp,

** endp);

x_MapDataPage(

sample_index,

** data_page_begin);

x_GetDataElement(

* dpage,

x_GetDataElement(

* dpage,

x_FindIndexBounds();

x_OutOfBounds(

);

x_OutOfBounds(

);

(

= 0;

< s.size();

++) {

? ids.

(index)

(ids.

(index));

x_MakeFilenames(

&

,

& index_name,

& data_name);

* keydatap = begin;

* key_begin = keydatap;

(*keydatap != 0x02) ++keydatap;

key_begin = ++keydatap;

(*keydatap != 0x0a) ++keydatap;

* keydatap = 0;

(key_in < key_out) {

}

(key_in > key_out) {

* keydatap = 0;

CSeqDBIsam::x_LoadIndex<TGi>(

vector<TIndx> & offs

CSeqDBIsam::x_LoadData<TGi>(

(

index=0; index < num_keys; ++index) {

<>

vector<string> & keys,

vector<TIndx> & offs)

* keydatap = (

*) lease.

(offset_begin) - 1;

* key_begin = ++ keydatap;

(*keydatap != 0x02) ++keydatap;

keys.push_back(

(key_begin, keydatap));

<>

vector<string> & keys,

* keydatap = (

*) lease.

(begin) - 1;

(

index=0; index < num_keys; ++index) {

* key_begin = ++keydatap;

(*keydatap != 0x02) ++keydatap;

keys.push_back(

(key_begin, keydatap));

key_begin = ++keydatap;

(*keydatap != 0x0a) ++keydatap;

found =

;

((index < ids_size) && (

(ids, index, use_tis) <

)) {

((index + jump) < ids_size &&

(ids, index + jump, use_tis) <

) {

((index < ids_size) && (

(ids,index,use_tis) ==

)) {

found =

;

((index < ids_size) && (

(ids, index) <

)) {

((index + jump) < ids_size &&

((index < ids_size) && (

(ids,index) ==

)) {

** data_page_begin)

CNcbiStreamoff TIndx

The type used for file offsets.

const char * GetFileDataPtr(const string &fname, TIndx offset)

Get a pointer to the specified offset.

bool IsValueSet(int index) const

T GetKey(int index) const

void SetValue(int index, int oid)

@ eGi

The array is sorted by GI.

void InsureOrder(ESortOrder order)

Sort if necessary to insure order of elements.

Stores a key for an ISAM file.

bool OutsideLastBound(Int8 ident)

Returns true if the provided integer compares as higher than the assigned upper boundary for this ISA...

string m_SKey

The key, if it is a string.

bool IsSet()

Returns true if this object has an assigned value.

string GetString() const

Fetch the numeric value of this object.

void SetString(const string &ident)

Fetch the string value of this object.

Int8 m_NKey

The key, if it is a number.

void SetNumeric(Int8 ident)

Assign a numeric value to this object.

Int8 GetNumeric() const

Fetch the numeric value of this object.

bool m_IsSet

True if this object has an assigned value.

bool OutsideLastBound(const string &ident)

Returns true if the provided string compares as lower than the assigned upper boundary for this ISAM ...

bool OutsideFirstBound(Int8 ident)

Returns true if the provided integer compares as lower than the assigned lower boundary for this ISAM...

bool OutsideFirstBound(const string &ident)

Returns true if the provided string compares as lower than the assigned lower boundary for this ISAM ...

Int4 m_LastOffset

First and last offset's of last page.

bool IdToOid(Int8 id, TOid &oid)

GI or TI translation.

EIsamDbType

Types of database this class can access.

CSeqDBGiList::SGiOid TGiOid

Import the type representing one GI, OID association.

CSeqDBFileMemMap m_DataLease

A persistent lease on the ISAM data file.

TIndx m_IndexFileLength

The length of the ISAM index file.

bool m_LongId

Use Uint8 for the key.

int x_GetPageNumElements(Int4 SampleNum, Int4 *Start)

Determine the number of elements in the data page.

Int8 TId

Type large enough to hold any numerical ID.

ESeqDBIdType m_IdentType

The type of identifier this class uses.

SIsamKey m_LastKey

Last volume key.

static string x_GetId(CSeqDBNegativeList &ids, int index)

void x_TranslateGiList(int vol_start, CSeqDBGiList &gis)

GiList Translation.

Int4 m_IdxOption

Options set by upper layer.

void x_LoadData(CSeqDBFileMemMap &lease, vector< T > &keys, vector< int > &vals, int num_keys, TIndx begin)

Load and extract a data page into array at once.

void x_LoadStringData(const char *begin, string &key, int &data)

Int8 TTi

PIG identifiers for numeric indices over protein volumes.

void x_GetNumericSample(CSeqDBFileMemMap &index_lease, int index, Int8 &key_out, int &data_out)

Get a sample key value from a numeric index.

void x_GetDataElement(const void *dpage, int index, Int8 &key, int &data)

Get a particular data element from a data page.

Int4 m_NumSamples

Number of terms in ISAM index.

int x_TestNumericSample(CSeqDBFileMemMap &index_lease, int index, Int8 key_in, Int8 &key_out, int &data_out)

Test a sample key value from a numeric index.

EErrorCode

Exit conditions occurring in this code.

bool PigToOid(TPig pig, TOid &oid)

PIG translation.

Uint8 x_GetNumericKey(const void *p)

void x_LoadIndex(CSeqDBFileMemMap &lease, vector< T > &keys, vector< TIndx > &offs)

Load and extract all index samples into array at once.

Int4 m_NumTerms

Number of terms in database.

int TOid

This class works with OIDs relative to a specific volume.

bool m_Initialized

Flag indicating whether initialization has been done.

bool SeqidToOid(const string &acc, TOid &oid)

Seq-id translation.

static void x_Lower(string &s)

Converts a string to lower case.

Int4 m_PageSize

Page size of ISAM index.

TIndx m_DataFileLength

The length of the ISAM data file.

int m_Type

The format type of database files found (eNumeric or eString).

bool m_TestNonUnique

Check if data for String ISAM sorted.

TIndx m_KeySampleOffset

Offset of samples in index file.

Int4 m_FirstOffset

First and last offset's of last page.

char * m_FileStart

Pointer to index file if no memmap.

SIsamKey m_FirstKey

First volume key.

static Int8 x_GetId(CSeqDBNegativeList &ids, int index, bool use_tis)

Fetch a GI or TI from a GI list.

void x_MapDataPage(int sample_index, int &start, int &num_elements, const void **data_page_begin)

Map a data page.

CSeqDBAtlas::TIndx TIndx

Type which is large enough to span the bytes of an ISAM file.

int x_GetNumericData(const void *p)

bool x_FindInNegativeList(CSeqDBNegativeList &ids, int &index, Int8 key, bool use_tis)

Find ID in the negative GI list using PBS.

Int4 m_MaxLineSize

Maximum string length in the database.

string m_DataFname

The filename of the ISAM data file.

string m_IndexFname

The filename of the ISAM index file.

int m_TermSize

size of the numeric key-data pair

CSeqDBFileMemMap m_IndexLease

A persistent lease on the ISAM index file.

CSeqDBAtlas & m_Atlas

The memory management layer.

TGi GetGi(int index) const

Access an element of the GI array.

TTi GetTi(int index) const

Access an element of the TI array.

const string GetSi(int index) const

Access an element of the SeqId array.

#define GI_FROM(T, value)

#define NCBI_THROW(exception_class, err_code, message)

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

int32_t Int4

4-byte (32-bit) signed integer

uint32_t Uint4

4-byte (32-bit) unsigned 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.

static unsigned int StringToUInt(const CTempString str, TStringToNumFlags flags=0, int base=10)

Convert string to unsigned int.

#define NCBI_XOBJREAD_EXPORT

char * dbname(DBPROCESS *dbproc)

Get name of current database.

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

const GenericPointer< typename T::ValueType > T2 value

Int4 TOid

Ordinal ID in BLAST databases.

ESeqDBIdType

Various identifier formats used in Id lookup.

@ eTiId

Genomic ID is a relatively stable numeric identifier for sequences.

@ ePigId

Trace ID is a numeric identifier for Trace sequences.

CSeqDBAtlas::TIndx TIndx

Index file.

File access objects for CSeqDB.

T SeqDB_GetStdOrd(const T *stdord_obj)

Read a network order integer value.

USING_SCOPE(objects)

Bring the object directory definitions into this scope.

static void s_AdvanceKeyList(const vector< T > &keys, int &index, int num_keys, const T &target)

static void s_AdvanceGiList(CSeqDBGiList &gis, int &gi_index, int gis_size, const T &key)

static void s_SetTranslation(CSeqDBGiList &gis, int &gi_index, int gis_size, const T &key, int value)

Structure that holds GI,OID pairs.

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