RetroSearch Browse

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

Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/seqdbgilistset_8cpp_source.html below:

NCBI C++ ToolKit: src/objtools/blast/seqdb_reader/seqdbgilistset.cpp Source File

99 const char

* fendp = fbeginp + file_size;

102 bool

in_order =

false

;

150

vector<string> tmplist;

151

tmplist.reserve(idlist.size());

152 for

(

unsigned int i

=0;

< idlist.size();

++) {

155 if

(seqid.

IsGi

()) {

161

tmplist.push_back(

id

);

172 if

(tmplist.size() == 0) {

176 sort

(tmplist.begin(), tmplist.end());

177

vector<string>::iterator it = unique (tmplist.begin(), tmplist.end());

178

tmplist.resize(distance(tmplist.begin(),it));

180

idlist.swap(tmplist);

186

newInfo.

is_v4

false

;

189

vector<string> idlist;

198

newInfo.

is_v4

false

;

201

vector<string> idlist = user_list->

GetSiList

();

210 "please run blastdb_aliastool -seqid_file_in <INPUT_FILE_NAME> "

211 "-seqid_file_out <OUT_FILE_NAME> and use <OUT_FILE_NAME> as the argument to -seqidlist"

);

217 "Seqidlist is not in BLAST db v4 format"

);

222 ERR_POST

(

Warning

"Seqidlist file db info does not match input db"

);

248

vector<blastdb::TOid> oids;

251 for

(

unsigned int i

=0;

< accs.size();

++) {

271

vector<TIndexCount> OidsPerVolume;

278

TIndexCount vol_oids;

279

vol_oids.m_Index =

;

282

OidsPerVolume.push_back(vol_oids);

291 std::sort

(OidsPerVolume.begin(), OidsPerVolume.end());

293 for

(

int i

= 0;

< (

int

)OidsPerVolume.size();

++) {

294 int

vol_idx = OidsPerVolume[

].m_Index;

355 for

(

int

v = 0; v < volset.

GetNumVols

(); v++) {

361 for

(

int

o=0; o < pigs.

GetNumPigs

(); o++) {

363 if

(pig.

oid

!= -1) {

364

exclude_oid_list.push_back(pig.

oid

);

386

m_UserList (user_list),

387

m_NegativeList (neg_list)

414 if

(gilist.

Empty

()) {

425

map_ref[filename.

GetPathS

()] = gilist;

482 int

source_num =

source

.GetNumGis();

485 int

source_index = 0;

486 int

target_index = 0;

488 while

(source_index < source_num && target_index < target_num) {

489 TGi

source_gi =

source

.GetGiOid(source_index).gi;

494 if

(source_gi == target_gi) {

500

}

else if

(source_gi > target_gi) {

505 int test

= target_index + jump;

508

target_index =

test

;

510 test

= target_index + jump;

517 int test

= source_index + jump;

519 while

(

test

< source_num &&

source

.GetGiOid(

test

).gi < target_gi) {

520

source_index =

test

;

522 test

= source_index + jump;

536 int

source_num =

source

.GetNumTis();

539 int

source_index = 0;

540 int

target_index = 0;

542 while

(source_index < source_num && target_index < target_num) {

543 TTi

source_ti =

source

.GetTiOid(source_index).ti;

548 if

(source_ti == target_ti) {

551 source

.GetTiOid(source_index).oid);

556

}

else if

(source_ti > target_ti) {

561 int test

= target_index + jump;

563 while

(

test

< target_num &&

566

target_index =

test

;

568 test

= target_index + jump;

575 int test

= source_index + jump;

577 while

(

test

< source_num &&

580

source_index =

test

;

582 test

= source_index + jump;

bool GetFileSizeL(const string &fname, TIndx &length)

Get size of a file.

CNcbiStreamoff TIndx

The type used for file offsets.

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

Get a pointer to the specified offset.

void Clear()

Clears the memory mapobject.

EGiListType

Gilist types.

TNodeListMap m_GINodeListMap

Map of filenames to alias node specified GI lists.

void x_ResolveNegativeList(CSeqDBAtlas &atlas, const CSeqDBVolSet &volset, CRef< CSeqDBNegativeList > neg_list, CSeqDBLockHold &locked, const CSeqDBLMDBSet &lmdb_set)

void x_ResolvePositiveList(CSeqDBAtlas &atlas, const CSeqDBVolSet &volset, CRef< CSeqDBGiList > user_list, CSeqDBLockHold &locked, const CSeqDBLMDBSet &lmdb_set)

CSeqDBGiListSet(CSeqDBAtlas &atlas, const CSeqDBVolSet &vol_set, TListRef user_list, TNegativeRef neg_list, CSeqDBLockHold &locked, const CSeqDBLMDBSet &lmdb_set)

Constructor.

TListRef m_UserList

User-specified GI list.

TNodeListMap m_SINodeListMap

Map of filenames to alias node specified SI lists.

TNegativeRef m_NegativeList

User-specified Negative GI list.

void x_TranslateFromUserList(CSeqDBGiList &gilist)

Translate a volume gilist from the user gilist.

CSeqDBAtlas & m_Atlas

Memory management layer object.

TNodeListMap m_TINodeListMap

Map of filenames to alias node specified TI lists.

void x_TranslateTisFromUserList(CSeqDBGiList &gilist)

Translate a volume gilists's TIs from the user gilist's TIs.

void x_TranslateGisFromUserList(CSeqDBGiList &gilist)

Translate a volume gilists's GIs from the user gilist's GIs.

TListRef GetNodeIdList(const CSeqDB_Path &filename, const CSeqDBVol *volp, EGiListType list_type, CSeqDBLockHold &locked)

Get a reference to a named GI list.

vector< SGiOid > m_GisOids

Pairs of GIs and OIDs.

int GetNumGis() const

Get the number of GIs in the array.

const SGiOid & GetGiOid(int index) const

Access an element of the array.

vector< SPigOid > m_PigsOids

int GetNumSis() const

Get the number of Seq-ids in the array.

const SPigOid & GetPigOid(int index) const

int GetNumTis() const

Get the number of TIs in the array.

vector< STiOid > m_TisOids

Pairs of GIs and OIDs.

void SetSiTranslation(int index, int oid)

Specify the correct OID for a Seq-id.

void SetSiList(const vector< string > &new_list)

void SetTiTranslation(int index, int oid)

Specify the correct OID for a TI.

void GetSiList(vector< string > &sis) const

TODO Get the seqid list?

void SetListInfo(const SBlastSeqIdListInfo &list_info)

TODO Reserve space for seqids?

@ eGi

The array is sorted by GI.

vector< blastdb::TOid > & SetOidsForTaxIdsList()

bool NotEmpty() const

Return true if there are elements present.

const SBlastSeqIdListInfo & GetListInfo()

set< TTaxId > & GetTaxIdsList()

void ReservePigs(size_t n)

void PreprocessIdsForISAMSiLookup()

Preprocess ids for ISAM string id lookup.

const STiOid & GetTiOid(int index) const

Access an element of the array.

void SetGiTranslation(int index, int oid)

Specify the correct OID for a GI.

void InsureOrder(ESortOrder order)

Sort if necessary to insure order of elements.

vector< SSiOid > m_SisOids

Pairs of Seq-ids and OIDs.

ESortOrder m_CurrentOrder

Indicates the current sort order, if any, of this container.

void NegativeTaxIdsToOids(set< TTaxId > &tax_ids, vector< blastdb::TOid > &rv) const

void NegativeSeqIdsToOids(const vector< string > &ids, vector< blastdb::TOid > &rv) const

void AccessionsToOids(const vector< string > &accs, vector< TOid > &oids) const

bool IsBlastDBVersion5() const

void TaxIdsToOids(set< TTaxId > &tax_ids, vector< blastdb::TOid > &rv) const

const vector< string > & GetSiList()

const SBlastSeqIdListInfo & GetListInfo()

int GetNumTis() const

Get the number of TIs in the array.

bool NotEmpty() const

Return true if there are elements present.

void SetSiList(const vector< string > &new_list)

void PreprocessIdsForISAMSiLookup()

int GetNumGis() const

Get the number of GIs in the array.

const vector< TPig > & GetPigList()

void SetListInfo(const SBlastSeqIdListInfo &list_info)

vector< blastdb::TOid > & SetExcludedOids()

int GetNumSis() const

Get the number of SeqIds in the array.

set< TTaxId > & GetTaxIdsList()

CSeqDBMemReg m_VectorMemory

Memory associated with the m_GisOids vector.

virtual ~CSeqDBNodeFileIdList()

Destructor.

CSeqDBNodeFileIdList(CSeqDBAtlas &atlas, const CSeqDB_Path &fname, CSeqDBGiListSet::EGiListType list_type, CSeqDBLockHold &locked)

Build a GI,TI, or SI list from a memory mapped file.

int OIDStart() const

Get the starting OID in this volume's range.

int OIDEnd() const

Get the ending OID in this volume's range.

CSeqDBVol * Vol()

Get a pointer to the underlying volume object.

const CSeqDBVolEntry * GetVolEntry(int i) const

Find a volume entry by index.

Uint8 GetVolumeSetLength() const

Find total volume length for all volumes.

int GetNumVols() const

Get the number of volumes.

void IdsToOids(CSeqDBGiList &gis) const

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

void AttachVolumeGiList(CRef< CSeqDBGiList > gilist) const

Filter this volume using the specified GI list.

const string & GetPathS() const

Get the path as a string.

#define test(a, b, c, d, e)

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define ERR_POST(message)

Error posting with file, line number information but without error codes.

#define NCBI_THROW(exception_class, err_code, message)

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

const string & GetMsg(void) const

Get message string.

void Warning(CExceptionArgs_Base &args)

const string AsFastaString(void) const

string GetSeqIdString(bool with_version=false) const

Return seqid string with optional version for text seqid type.

@ fParse_RawText

Try to ID raw non-numeric accessions.

@ fParse_PartialOK

Warn rather than throwing an exception when a FASTA-style ID set contains unparsable portions,...

@ fParse_AnyLocal

Treat otherwise unidentified strings as local accessions as long as they don't resemble FASTA-style I...

void Reset(void)

Reset reference object.

bool NotEmpty(void) const THROWS_NONE

Check if CRef is not empty â pointing to an object and has a non-null value.

bool Empty(void) const THROWS_NONE

Check if CRef is empty â not pointing to any object, which means having a null value.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

bool IsPrf(void) const

Check if variant Prf is selected.

bool IsGi(void) const

Check if variant Gi is selected.

bool IsPir(void) const

Check if variant Pir is selected.

unsigned int

A callback function used to compare two keys in a database.

constexpr auto sort(_Init &&init)

const CharType(& source)[N]

void SeqDB_ReadMemorySiList(const char *fbeginp, const char *fendp, vector< CSeqDBGiList::SSiOid > &sis, bool *in_order=0)

Read a text SeqID list from an area of memory.

void SeqDB_ReadMemoryGiList(const char *fbeginp, const char *fendp, vector< CSeqDBGiList::SGiOid > &gis, bool *in_order=0)

Read a text or binary GI list from an area of memory.

void SeqDB_ReadMemoryTiList(const char *fbeginp, const char *fendp, vector< CSeqDBGiList::STiOid > &tis, bool *in_order=0)

Read a text or binary TI list from an area of memory.

void SeqDB_ReadMemoryPigList(const char *fbeginp, const char *fendp, vector< CSeqDBGiList::SPigOid > &pigs, bool *in_order=0)

void s_ProcessSeqIDsForV5(vector< string > &idlist)

bool s_VerifySeqidlist(const SBlastSeqIdListInfo &list_info, const CSeqDBVolSet &volset, const CSeqDBLMDBSet &lmdb_set)

void s_ProcessNegativeSeqIDsForV5(CRef< CSeqDBNegativeList > &user_list)

void s_ProcessPositiveSeqIDsForV5(CRef< CSeqDBGiList > &user_list)

TGi gi

The GI or 0 if unknown.

int oid

The OID or -1 if unknown.

int oid

The OID or -1 if unknown.

int oid

The OID or -1 if unknown.

TTi ti

The TI or 0 if unknown.

Blast DB v5 seqid list info.

Defines a pair of integers and a sort order.

bool operator<(const SSeqDB_IndexCountPair &rhs) const

Less than operator, where elements with larger allows sorting.

int m_Index

Index of the volume in the volume set.

int m_Count

Number of OIDs associated with this volume.

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