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

( volset, filters, gi_list, neg_list, locked, lmdb_set);

(

(volset, filters, lmdb_set, f_bits, gi_list, neg_list)) {

vol_end = vol.

();

vols =

(ft->

().size());

(

j = 1; j < vols; j++) {

volume_map->

(*sub_bits,

);

(

.GetType()) {

check_file(path_str);

(!check_file.

()) {

(j = 0; j < gis.

(); j++) {

gilist_oids->

(oid);

(j = 0; j < gis.

(); j++) {

gilist_oids->

(oid);

(j = 0; j < gis.

(); j++) {

gilist_oids->

(oid);

gilist_oids->

(oid);

(oids_tax.size()) {

(

k = 0; k < oids_tax.size(); k++) {

taxlist_oids->

(oids_tax[k]);

vector<blastdb::TOid> & excluded_oids = nlist.

();

(

=0;

< excluded_oids.size();

++) {

(

oid = 0; oid <

; oid++) {

(

= 0;

< num_gis;

++) {

(oid != prev_oid) {

((oid >= oid_start) && (oid < oid_end)) {

(

= 0;

< num_tis;

++) {

(oid != prev_oid) {

((oid >= oid_start) && (oid < oid_end)) {

(

= 0;

< num_sis;

++) {

(oid != prev_oid) {

((oid >= oid_start) && (oid < oid_end)) {

bitend = bitmap + (((num_oids + 31) / 32) * 4);

(

oid = vol_end; bitset->

(oid); oid++) {

vector<const CSeqDBVolEntry * > & excluded_vols,

vector<bool> vol_included(num_vol,

);

excluded_vols.clear();

(

=0;

< num_vol;

++) {

(std::find(vol_basenames.begin(), vol_basenames.end(), vol->

()) != vol_basenames.end()) {

(

= 0;

< excluded_vols.size();

++) {

(

& name,

& vn, vector<string> & fnames, vector<vector<string> > & fnames_vols)

(; j < fnames.size(); j++) {

(fnames[j] == name) {

fnames_vols[j].push_back(vn);

( fnames.size() == j) {

vector<string> p(1,vn);

fnames.push_back(name);

fnames_vols.push_back(p);

(seq_id1.

(seq_id2)) {

vector<vector<string> > & fnames_vols,

(fnames.size() == 0) {

vector<string> user_accs;

vector<string> neg_user_accs;

((!neg_user_list.

()) && (neg_user_list->

() > 0)) {

neg_user_accs = neg_user_list->

();

(neg_user_accs.begin(), neg_user_accs.end());

(

k=0; k < fnames.size(); k++) {

vector<const CSeqDBVolEntry * > excluded_vols;

vector<blastdb::TOid> oids;

(accs.size() == 0){

((user_accs.size() > 0) || (neg_user_accs.size() > 0)){

(user_accs.size() > 0) {

vector<string> common;

common.resize(accs.size());

vector<string>::iterator itr = set_intersection(accs.begin(), accs.end(),

user_accs.begin(), user_accs.end(), common.begin(),

);

common.resize(itr-common.begin());

(common.size() == 0){

(neg_user_accs.size() > 0) {

vector<string> difference;

difference.resize(accs.size());

vector<string>::iterator itr = set_difference(accs.begin(), accs.end(),

neg_user_accs.begin(), neg_user_accs.end(), difference.begin(),

);

difference.resize(itr-difference.begin());

(difference.size() == 0){

(accs, difference);

(

=0;

< accs.size();

++) {

(excluded_vols.size() != 0) {

filter_bit.

(oids[

]);

vector<vector<string> > & fnames_vols,

(fnames.size() == 0) {

(

k=0; k < fnames.size(); k++) {

vector<const CSeqDBVolEntry * > excluded_vols;

vector<blastdb::TOid> oids;

(taxids.

() == 0){

(user_taxids.

() > 0){

vector<TTaxId> common;

common.resize(taxids.

());

vector<TTaxId>::iterator itr = set_intersection(taxids.

(), taxids.

(),

user_taxids.

(), user_taxids.

(), common.begin());

common.resize(itr-common.begin());

( common.size() == 0) {

taxids.

(common.begin(), common.end());

(neg_user_taxids.

() > 0) {

vector<TTaxId> difference;

difference.resize(taxids.

());

vector<TTaxId>::iterator itr = set_difference(taxids.

(), taxids.

(),

neg_user_taxids.

(), neg_user_taxids.

(), difference.begin());

difference.resize(itr-difference.begin());

(difference.size() == 0){

taxids.

(difference.begin(), difference.end());

(

=0;

< oids.size();

++) {

(excluded_vols.size() != 0) {

filter_bit.

(oids[

]);

vector<string> seqid_fnames;

vector<string> taxid_fnames;

vector< vector<string> > seqid_fnames_vols;

vector< vector<string> > taxid_fnames_vols;

name = (*itr)->GetPath().GetPathS();

(seqid_fnames.size() > 0) {

lmdb_set, volset, filter_bit);

(taxid_fnames.size() > 0) {

lmdb_set, volset, filter_bit);

((seqid_fnames.size() + taxid_fnames.size()) > 0 ?

:

);

ncbi::TMaskedQueryRegions mask

void SetFrame(const string &frame)

void Log(const string &name, const char *value, CDebugDumpFormatter::EValueType type=CDebugDumpFormatter::eValue, const string &comment=kEmptyStr)

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

Get a pointer to the specified offset.

void Init(const string &filename)

Initializes a memory map object.

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

Get a reference to a named GI list.

int GetNumGis() const

Get the number of GIs in the array.

const SGiOid & GetGiOid(int index) const

Access an element of the array.

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.

const SSiOid & GetSiOid(int index) const

Access an element of the array.

void GetSiList(vector< string > &sis) const

TODO Get the seqid list?

const vector< blastdb::TOid > & GetOidsForTaxIdsList()

set< TTaxId > & GetTaxIdsList()

const STiOid & GetTiOid(int index) const

Access an element of the array.

bool Empty() const

Return false if there are elements present.

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()

int GetNumTis() const

Get the number of TIs in the array.

bool GetOidStatus(int oid)

Get the inclusion status of an OID.

int GetNumGis() const

Get the number of GIs in the array.

const vector< blastdb::TOid > & GetExcludedOids()

int GetNumSis() const

Get the number of SeqIds in the array.

set< TTaxId > & GetTaxIdsList()

int GetNumOids()

Get the size of the OID array.

CSeqDBOIDList(CSeqDBAtlas &atlas, const CSeqDBVolSet &volumes, CSeqDB_FilterTree &filters, CRef< CSeqDBGiList > &gi_list, CRef< CSeqDBNegativeList > &neg_list, CSeqDBLockHold &locked, const CSeqDBLMDBSet &lmdb_set)

Constructor.

CRef< CSeqDB_BitSet > x_IdsToBitSet(const CSeqDBGiList &ids, int vol_start, int vol_end)

Load an ID (GI or TI) list file into a bitset object.

bool x_IsSet(TOID oid) const

Check if a bit is set.

void DebugDump(CDebugDumpContext ddc, unsigned int depth) const

Dump debug information for this object.

void x_Setup(const CSeqDBVolSet &volset, CSeqDB_FilterTree &filters, CRef< CSeqDBGiList > &gi_list, CRef< CSeqDBNegativeList > &neg_list, CSeqDBLockHold &locked, const CSeqDBLMDBSet &lmdb_set)

Build an oid mask in memory.

void x_ClearBitRange(int oid_start, int oid_end)

Clear all bits in a range.

CRef< CSeqDB_BitSet > x_GetOidMask(const CSeqDB_Path &fn, int vol_start, int vol_end)

Load the named OID mask file into a bitset object.

void x_ApplyUserGiList(CSeqDBGiList &gis)

Apply a user GI list to a volume.

void x_ApplyNegativeList(CSeqDBNegativeList &neg, bool is_v5)

Apply a negative user GI list to a volume.

~CSeqDBOIDList()

Destructor.

CSeqDBAtlas & m_Atlas

The memory management layer object.

CRef< CSeqDB_BitSet > x_ComputeFilters(const CSeqDB_FilterTree &ft, const CSeqDBVolEntry &vol, CSeqDBGiListSet &gis, CSeqDBLockHold &locked, bool isBlastDBv5)

Compute the oid mask bitset for a database volume.

const unsigned char TCUC

Shorthand type to clarify code that iterates over memory.

CRef< CSeqDB_BitSet > m_AllBits

An OID bit set covering all volumes.

int m_NumOIDs

The total number of OIDs represented in the bit set.

TIndx GetFileLength() const

Get the length of the file.

TIndx ReadSwapped(CSeqDBFileMemMap &lease, TIndx offset, Uint4 *value) const

Read a four byte numerical object from the file.

bool Open(const CSeqDB_Path &name)

MMap or Open a file.

const char * GetFileDataPtr(CSeqDBFileMemMap &lease, TIndx start, TIndx end) const

Get a pointer to a section of the 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.

const CSeqDBVol * GetVol(int i) const

Find a volume by index.

int GetNumVols() const

Get the number of volumes.

int GetNumOIDs() const

Get the size of the OID range.

const string & GetVolName() const

Get the volume name.

void SetOidMaskType(int oid_masks) const

void AttachVolumeGiList(CRef< CSeqDBGiList > gilist) const

Filter this volume using the specified GI list.

char GetSeqType() const

Get the sequence type stored in this database.

void SetMemBit(int mbit) const

Set the MEMB_BIT fitlering for this volume.

Something else yet again etc.

@ eTaxIdList

Taxonomay Id List.

@ eOidRange

OID Range [start, end).

@ eAllSet

All OIDs are set.

@ eAllClear

All OIDs are clear.

void IntersectWith(CSeqDB_BitSet &other, bool consume)

This bitset is assigned to the intersection of it and another.

void UnionWith(CSeqDB_BitSet &other, bool consume)

This bitset is assigned to the union of it and another.

void Normalize()

If this is a special case bitset, convert it to a normal one.

void ClearBit(size_t index)

Clear the specified bit (to false).

bool CheckOrFindBit(size_t &index) const

Check if a bit is true or find the next bit that is.

void AssignBitRange(size_t start, size_t end, bool value)

Store the provided value in a range of bits.

void SetBit(size_t index)

Set the specified bit (to true).

Tree of nodes describing filtering of database sequences.

bool HasFilter() const

Check whether this tree represents any volume filtering.

const vector< CRef< CSeqDB_FilterTree > > & GetNodes() const

Get child nodes attached to this node.

vector< CRef< CSeqDB_AliasMask > > TFilters

Type used to store lists of filters found here.

const TFilters & GetFilters() const

Get filters from this node.

const vector< CSeqDB_BasePath > & GetVolumes() const

Get volumes attached to this node.

CRef< CSeqDB_FilterTree > Specialize(string volname) const

Specialized this tree for the indicated volume.

const string & GetPathS() const

Get the path as a string.

iterator_bool insert(const value_type &val)

const_iterator begin() const

const_iterator end() const

The NCBI C++ standard methods for dealing with std::string.

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

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

void swap(NCBI_NS_NCBI::pair_base_member< T1, T2 > &pair1, NCBI_NS_NCBI::pair_base_member< T1, T2 > &pair2)

#define LOG_POST(message)

This macro is deprecated and it's strongly recomended to move in all projects (except tests) to macro...

#define NCBI_THROW(exception_class, err_code, message)

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

void Info(CExceptionArgs_Base &args)

virtual bool Exists(void) const

Check existence of file.

bool Match(const CSeq_id &sid2) const

Match() - TRUE if SeqIds are equivalent.

@ fParse_ValidLocal

Treat otherwise unidentified strings as raw accessions, provided that they pass rudimentary validatio...

virtual void DebugDump(CDebugDumpContext ddc, unsigned int depth) const

Define method for dumping debug information.

void Reset(void)

Reset reference object.

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

uint32_t Uint4

4-byte (32-bit) unsigned integer

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

constexpr auto sort(_Init &&init)

const blastdb::TOid kSeqDBEntryNotFound

Int4 TOid

Ordinal ID in BLAST databases.

const string SeqDB_GetOidMaskFileExt(bool db_is_protein, EOidMaskType t)

File access objects for CSeqDB.

Implementation for some assorted ID list filtering code.

void s_AddFilterFile(string &name, const string &vn, vector< string > &fnames, vector< vector< string > > &fnames_vols)

void s_GetFilteredOidRange(const CSeqDBVolSet &volset, const vector< string > &vol_basenames, vector< const CSeqDBVolEntry * > &excluded_vols, CRef< CSeqDBGiList > &si_list)

void s_ProcessTaxIdFilters(const vector< string > &fnames, vector< vector< string > > &fnames_vols, CRef< CSeqDBGiList > user_list, CRef< CSeqDBNegativeList > neg_user_list, const CSeqDBLMDBSet &lmdb_set, const CSeqDBVolSet &volset, CSeqDB_BitSet &filter_bit)

void s_ProcessSeqIdFilters(const vector< string > &fnames, vector< vector< string > > &fnames_vols, CRef< CSeqDBGiList > user_list, CRef< CSeqDBNegativeList > neg_user_list, const CSeqDBLMDBSet &lmdb_set, const CSeqDBVolSet &volset, CSeqDB_BitSet &filter_bit)

bool s_IsOidInFilteredVol(blastdb::TOid oid, vector< const CSeqDBVolEntry * > &excluded_vols)

bool s_CompareSeqId(const string &id1, const string &id2)

The SeqDB oid filtering layer.

static const sljit_gpr r2

int oid

The OID or -1 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.

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