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

slen = s.

();

extn2(extn, 2, 4);

(extn[1] ==

|| extn[1] ==

) &&

(extn2 ==

|| extn2 ==

|| extn2 ==

)) {

(

= 0;

<

.Size();

++) {

extn_amt = extn ? (extn->

()+1) : 0;

only_two =

;

(one.Empty() || two[0] == delim) {

outp.reserve(two.

() + extn_amt);

outp.reserve(one.Size() + two.

() + 1 + extn_amt);

(outp[outp.size() - 1] != delim) {

(x1 != x2)

(x1 < x2);

(s1 < s2);

linkoutdb_search)

path.reserve(

.size() + 4);

(linkoutdb_search) {

path.append(

);

path.append(

);

path[path.size()-3] = dbtype;

path[path.size()-2] =

;

path[path.size()-1] =

;

* splitter = 0;

(

= 0;

<dbs.size();

++) {

(dbs[

] ==

|| dbs[

] ==

) {

linkoutdb_search =

)

vector<string> roads;

(vector<string>, road, roads) {

path=

)

.GetLength() != (

) -1;

dbtype(

);

(pathology, filename, dbtype,

, access,

);

newlen =

.length() +

.length() + delim.length();

(

.capacity() < newlen) {

(newcap < newlen) {

: m_CurrentOrder(

), m_MaskOpts(0)

lhs.

< rhs.

;

lhs.

< rhs.

;

lhs.

< rhs.

;

lhs.

< rhs.

;

lhs.

< rhs.

;

<

TCompare,

TVector>

already =

;

TCompare compare_less;

(

= 1;

< (

) v.size();

++) {

(compare_less(v[

], v[

-1])) {

(v.begin(), v.end(), compare_less);

);

s_InsureOrder<CSeqDB_SortGiLessThan>(

);

s_InsureOrder<CSeqDB_SortTiLessThan>(

);

s_InsureOrder<CSeqDB_SortSiLessThan>(

);

s_InsureOrder<CSeqDB_SortPigLessThan>(

);

);

oid(0), index(0);

(

*

(

))->GiToOid(gi, oid, index);

(gi, oid, index);

}

(m_gi > gi) {

oid(0), index(0);

(

*

(

))->TiToOid(ti, oid, index);

(ti, oid, index);

}

(m_ti > ti) {

oid(0), index(0);

(

*

(

))->SiToOid(

, oid, index);

}

(

< m_si) {

gis.push_back(itr->gi);

pigs.push_back(itr->pig);

tis.push_back(itr->ti);

sis.push_back(itr->si);

num_gis = (

) (endp - beginp) - 2;

(((endp - beginp) < 2U)

|| (beginp[0] != 0xFFFFFFFFU)

);

gis.reserve(num_gis);

(

* elem = (beginp + 2); elem < endp; ++elem) {

& has_long_ids,

* has_tis =

)

retval =

;

has_long_ids =

;

file_size = fendp - fbeginp;

(file_size == 0) {

);

}

(

((

)(*((

*) fbeginp))) ||

((

)(*((

*) fbeginp)) ==

)) {

}

((file_size >= 8) && ((*fbeginp & 0xFF) == 0xFF)) {

marker = fbeginp[3] & 0xFF;

(marker == 0xFE || marker == 0xFC) {

has_long_ids =

;

(has_tis && (marker == 0xFD || marker == 0xFC)) {

);

=

(

+ list_type +

) +

vector<CSeqDBGiList::SGiOid> & gis,

long_ids =

;

file_size = fendp - fbeginp;

num_gis = bendp - bbeginp - 2;

((bbeginp[0] != 0xFFFFFFFFU)

);

gis.reserve(num_gis);

in_gi_order =

;

* elem = bbeginp + 2;

(elem < bendp) {

gis.push_back(this_gi);

(prev_gi > this_gi) {

in_gi_order =

;

(elem < bendp) {

*in_order = in_gi_order;

(

* elem = (bbeginp + 2); elem < bendp; ++elem) {

gis.reserve((

) (file_size / 7));

list_type(

);

(

* p = fbeginp; p < fendp; p ++) {

vector<CSeqDBGiList::SPigOid> & pigs,

long_ids =

;

file_size = fendp - fbeginp;

num_pigs = (

) (bendp - bbeginp) - 2;

(((bendp - bbeginp) < 2U)

|| (bbeginp[0] != 0xFFFFFFFFU)

);

pigs.reserve(num_pigs);

sorted =

;

* elem = bbeginp + 2;

(elem < bendp) {

pigs.push_back(this_pig);

(prev_pig > this_pig) {

prev_pig = this_pig;

(elem < bendp) {

(

* elem = (bbeginp + 2); elem < bendp; ++elem) {

pigs.reserve((

) (file_size / 7));

list_type(

);

(

* p = fbeginp; p < fendp; p ++) {

pigs.push_back(elem);

long_ids =

;

* bbeginp = (

*) fbeginp;

num_taxids = (bendp - bbeginp) - 2;

taxids.

.clear();

(((bendp - bbeginp) < 2) || (bbeginp[0] != 0xFFFFFFFF)

);

(

* elem = (bbeginp + 2); elem < bendp; ++elem) {

list_type(

);

(

* p = fbeginp; p < fendp; p ++) {

vector<CSeqDBGiList::STiOid> & tis,

long_ids =

;

file_size = fendp - fbeginp;

* bbeginp = (

*) fbeginp;

* bdatap = bbeginp + 2;

num_tis = (

)(bendp-bdatap);

remainder = num_tis % 2;

bad_fmt =

;

(bendp < bdatap) {

((marker != -3 && marker != -4) ||

(num_ids != num_tis) ||

(remainder && long_ids)) {

);

tis.reserve(num_tis);

in_ti_order =

;

* elem = bdatap8;

(elem < bendp8) {

tis.push_back(this_ti);

(prev_ti > this_ti) {

in_ti_order =

;

(elem < bendp8) {

*in_order = in_ti_order;

(

* elem = bdatap8; elem < bendp8; elem ++) {

in_ti_order =

;

* elem = bdatap;

(elem < bendp) {

tis.push_back(this_ti);

(prev_ti > this_ti) {

in_ti_order =

;

(elem < bendp) {

*in_order = in_ti_order;

(

* elem = bdatap; elem < bendp; elem ++) {

tis.reserve(

(file_size / 7));

list_type(

);

(

* p = fbeginp; p < fendp; p ++) {

tis.push_back(elem);

vector<CSeqDBGiList::SSiOid> & sis,

file_size = fendp - fbeginp;

sis.reserve(sis.size() +

(file_size / 7));

* p = fbeginp;

( p < fendp) {

(p< fendp && (*p==

|| *p==

|| *p==

|| *p==

|| *p==

)) ++p;

(p< fendp && *p ==

) {

(p< fendp && *p!=

) ++p;

(p< fendp && *p!=

&& *p!=

&& *p!=

&& *p!=

) ++p;

acc(

, p);

(str_id !=

) {

sis.push_back(str_id);

cerr <<

<< acc

<<

<< endl;

(in_order) *in_order =

;

vector<CSeqDBGiList::SGiOid> & gis,

vector<CSeqDBGiList::STiOid> & tis,

vector<CSeqDBGiList::SSiOid> & sis,

file_size = fendp - fbeginp;

sis.reserve(sis.size() +

(file_size / 7));

* p = fbeginp;

( p < fendp) {

(p< fendp && (*p==

|| *p==

|| *p==

|| *p==

|| *p==

)) ++p;

(p< fendp && *p ==

) {

(p< fendp && *p!=

) ++p;

(p< fendp && *p!=

&& *p!=

&& *p!=

&& *p!=

) ++p;

acc(

, p);

(

== id_type) {

tis.push_back((

) num_id);

(

== id_type) {

cerr <<

<< acc

<<

<< endl;

(in_order) *in_order =

;

* fbeginp = (

*) mfile.

();

* fendp = fbeginp + (

)file_size;

ignore =

;

has_tis =

;

retval = has_tis && retval;

(

& fname, vector<CSeqDBGiList::SGiOid> & gis,

* in_order)

* fbeginp = (

*) mfile.

();

* fendp = fbeginp + file_size;

(

& fname, vector<CSeqDBGiList::STiOid> & tis,

* in_order)

* fbeginp = (

*) mfile.

();

* fendp = fbeginp + file_size;

vector<CSeqDBGiList::STiOid> & tis, vector<CSeqDBGiList::SSiOid> & sis,

* in_order)

*fbeginp = (

*) mfile.

();

*fendp = fbeginp + file_size;

(

& fname, vector<CSeqDBGiList::SPigOid> & pigs,

* in_order)

* fbeginp = (

*) mfile.

();

* fendp = fbeginp + file_size;

* fbeginp = (

*) mfile.

();

* fendp = fbeginp + file_size;

vector<CSeqDBGiList::SGiOid> TPairList;

gis.reserve(pairs.size());

(TPairList, iter, pairs) {

gis.push_back(iter->gi);

*fbeginp = (

*) mfile.

();

*fendp = fbeginp + file_size;

(0), e((

)

.size());

}

(m_gi > gi) {

(0), e((

)

.size());

}

(m_ti > ti) {

match_type =

;

(

, match_type);

(0), e((

)

.size());

m_si =

[m];

}

(m_si >

) {

match_type = (

() > 0) ?

:

;

}

(

.IsGeneral() &&

.GetGeneral().GetDb() ==

) {

match_type = (

() > 0) ?

:

;

& obj =

.GetGeneral().GetTag();

match_type = (

() > 0) ?

:

;

pos = str_id.find(

);

(pos != str_id.npos) {

nover(str_id, 0, pos);

(

.GetGi());

}

(

.IsGeneral() &&

.GetGeneral().GetDb() ==

) {

& obj =

.GetGeneral().GetTag();

(

(str_id))

;

pos = str_id.find(

);

(pos != str_id.npos) {

nover(str_id, 0, pos);

in_order =

;

(

= 0;

< dbs.size();

++) {

(

= 0;

< dbs.size();

++) {

(dbs[

].find(

) != string::npos) {

vector<CTempString> & dbs,

vector<CSeqDB_Substring> subs;

dbs.reserve(subs.size());

(vector<CSeqDB_Substring>, iter, subs) {

dbs.push_back(

);

vector<CSeqDB_Substring> & dbs,

* sp =

.data();

quoted =

;

(

= 0;

<

.size();

++) {

(keep_quote)

++;

}

(ch ==

) {

begin = keep_quote ?

:

+ 1;

(begin <

.size()) {

(gis.begin(), gis.end());

gis_n = (

) gis.size();

(list_i < list_n && gis_i < gis_n) {

(gis.begin(), gis.end());

gis_n = (

) gis.size();

(list_i < list_n && gis_i < gis_n) {

L = neg_gilist.

(list_i);

last_gi = gis[gis_i];

{ gis_i++; }

(gis_i < gis_n && gis[gis_i] == last_gi);

(gis_i < gis_n) {

(ids.begin(), ids.end());

ids.erase(unique(ids.begin(), ids.end()), ids.end());

(ids.begin(), ids.end());

ids.erase(unique(ids.begin(), ids.end()), ids.end());

incl_A = incl_B = incl_AB =

;

((! A_pos) && (! B_pos)) {

result_pos =

;

A_pos = B_pos =

;

((! A_pos) || (! B_pos)) {

result_pos =

;

result_pos = A_pos == B_pos;

incl_AB = A_pos && B_pos;

incl_A = incl_B = incl_AB =

;

incl_AB = (A_pos != B_pos);

incl_A = incl_B = ! incl_AB;

vector<Int8> &

,

vector<Int8> &

,

incl_A(

),

A_i(0), B_i(0);

((A_i <

.size()) && (B_i <

.size())) {

Ax(

[A_i]),

(

[B_i]), target(-1);

included(

);

}

(Ax >

) {

.push_back(target);

(A_i <

.size()) {

.push_back(

[A_i++]);

(B_i <

.size()) {

.push_back(

[B_i++]);

vector<Int4> & ids,

result_pos(

);

vector<Int8> & ids,

result_pos(

);

vector<Uint8> & ids,

result_pos(

);

);

result_pos(

);

);

ids->

(*iter);

(((*iter) >> 32) == 0);

);

ids->

(*iter);

(((*iter) >> 32) == 0);

ids->

(*iter);

: m_Positive (

),

&

)

=

+

+

;

matched =

;

(bestid.

()) {

(dbt.

() ==

) {

(dbt.

() ==

) {

(dbt.

() ==

) {

(objid.

()) {

str_id = objid.

();

found =

;

vbar =

.find(

, pos);

(vbar == string::npos) {

string::npos;

portion(

, pos, vbar - pos);

vbar_prev = vbar;

(

=0; ; ++

, vbar_prev = vbar) {

vbar =

.find(

, vbar_prev + 1);

(vbar == string::npos) {

start_pt =

(vbar_prev + 1);

element(

, start_pt, vbar - start_pt);

string::npos;

(vbar == string::npos) ?

.size() : vbar;

(pos < line.size()) {

(end == string::npos) {

element(line, pos, end - pos);

(invalid_argument &) {

seqids.push_back(

);

! seqids.empty();

num_id = (

)-1;

vector< CRef< CSeq_id > > seqid_set;

list< CRef<CSeq_id> > seqids;

(!seqids.empty() && seqids.front()->IsPdb() &&

acc.find(

) != string::npos) {

str_id = seqids.front()->AsFastaString();

(!seqids.empty() && seqids.front()->IsLocal()) {

( acc.find(

) != string::npos) {

* GNL_DBs[] = {

,

,

,

,

};

db_tag, gnl_id;

** p = GNL_DBs;

(; p && *p; ++p) {

str_id =

+ db_tag +

+ gnl_id;

seqids.front().Reset();

seqids.front() = new_id;

str_id =

+ acc;

simpler(

);

kExtnMol(1, db_is_protein ?

:

);

extn.push_back(kExtnMol +

);

extn.push_back(kExtnMol +

);

extn.push_back(kExtnMol +

);

extn.push_back(kExtnMol +

);

extn.push_back(kExtnMol +

);

extn.push_back(kExtnMol +

);

extn.push_back(kExtnMol +

);

extn.push_back(kExtnMol +

);

extn.push_back(kExtnMol +

);

extn.push_back(kExtnMol +

);

extn.push_back(kExtnMol +

);

vector<string> lmdbs;

extn.insert(extn.end(), lmdbs.begin(), lmdbs.end());

extn.push_back(kExtnMol +

);

extn.push_back(kExtnMol +

);

extn.push_back(kExtnMol +

);

extn.push_back(kExtnMol +

);

extn.push_back(kExtnMol +

);

extn.push_back(kExtnMol +

);

extn.push_back(kExtnMol +

);

extn.push_back(kExtnMol +

);

extn.push_back(kExtnMol +

);

* ext[]={

,

,

,

,

,

,

,

};

kExtnMol(1, db_is_protein ?

:

);

(

** p=ext; *p !=

; p++) {

extn.push_back(kExtnMol + (*p));

kExtnMol(1, db_is_protein ?

:

);

extn = kExtnMol +

;

(

.Which()) {

& dbt =

.GetGeneral();

(db_is_protein ?

:

);

static int GetSeqidlist(CMemoryFile &file, vector< CSeqDBGiList::SSiOid > &idlist, SBlastSeqIdListInfo &list_info)

Get seqidlist from dbv5 seqidlist file.

CIntersectionGiList(CSeqDBGiList &gilist, vector< TGi > &gis)

Construct an intersection of two lists of GIs.

bool DoesFileExist(const string &fname)

Check if file exists.

const string GetSearchPath() const

Get BlastDB search path.

static const string GenerateSearchPath()

Generate search path.

@ eFileErr

Files were missing or contents were incorrect.

CSeqDBFileGiList(const string &fname, EIdType idtype=eGiList)

Build a GI list from a file.

vector< SGiOid > & GetGiList()

Get list of GIs and OIDs.

void AddTi(TTi ti)

Add a new TI to the list.

vector< SGiOid > m_GisOids

Pairs of GIs and OIDs.

int GetNumGis() const

Get the number of GIs in the array.

bool GiToOid(TGi gi, int &oid)

Try to find a GI and return the associated OID.

const SGiOid & GetGiOid(int index) const

Access an element of the array.

vector< SPigOid > m_PigsOids

bool FindSi(const string &si) const

int GetNumSis() const

Get the number of Seq-ids in the array.

bool SiToOid(const string &si, int &oid)

CSeqDBGiList()

Constructor.

bool TiToOid(TTi ti, int &oid)

Try to find a TI and return the associated OID.

bool FindTi(TTi ti) const

Test for existence of a TI.

vector< SPigOid > & GetPigList()

Get list og Pigs and OIDs.

int GetNumTis() const

Get the number of TIs in the array.

vector< STiOid > m_TisOids

Pairs of GIs and OIDs.

vector< STiOid > & GetTiList()

Get list of Tis and OIDs.

SBlastSeqIdListInfo m_ListInfo

ESortOrder

Possible sorting states.

@ eNone

The array is unsorted or the sortedness is unknown.

@ eGi

The array is sorted by GI.

void AddGi(TGi gi)

Add a new GI to the list.

void ReserveGis(size_t n)

Reserve space for GIs.

vector< SSiOid > & GetSiList()

Get list of Seq-ids and OIDs.

void ReserveTis(size_t n)

Reserve space for TIs.

void PreprocessIdsForISAMSiLookup()

Preprocess ids for ISAM string id lookup.

bool FindGi(TGi gi) const

Test for existence of a GI.

void InsureOrder(ESortOrder order)

Sort if necessary to insure order of elements.

vector< SSiOid > m_SisOids

Pairs of Seq-ids and OIDs.

bool FindId(const CSeq_id &id)

Test for existence of a Seq-id by type.

ESortOrder m_CurrentOrder

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

Helper class to allow copy-on-write semantics for CSeqDBIdSet.

const vector< Int8 > & Get() const

Access the Int8 set.

size_t Size() const

Get the number of elements stored here.

vector< Int8 > & Set()

Access the Int8 set.

vector< string > & SetSeqIDs()

Access the string set.

SeqDB ID list for performing boolean set operations.

CRef< CSeqDBIdSet_Vector > m_Ids

Ids stored here.

static void x_SortAndUnique(vector< Int8 > &ids)

Sort and unique the internal set.

void x_BooleanSetOperation(EOperation op, const vector< Int8 > &A, bool A_pos, const vector< Int8 > &B, bool B_pos, vector< Int8 > &result, bool &result_pos)

Compute boolean operation on two vectors.

static void x_SummarizeBooleanOp(EOperation op, bool A_pos, bool B_pos, bool &result_pos, bool &incl_A, bool &incl_B, bool &incl_AB)

Compute inclusion flags for a boolean operation.

CSeqDBIdSet()

Construct a 'blank' CSeqDBIdSet object.

bool m_Positive

True if the current list is positive.

void Negate()

Invert the current list.

bool Blank() const

Check if an ID list is blank.

EIdType

Type of IDs stored here.

EOperation

Types of operations that may be performed on GI lists.

void Compute(EOperation op, const vector< int > &ids, bool positive=true)

Perform a logical operation on a list.

EIdType m_IdType

Id type.

CRef< CSeqDBNegativeList > GetNegativeList()

Retrieve a negative GI list.

CRef< CSeqDBGiList > GetPositiveList()

Retrieve a positive GI list.

void AddSi(const string &si)

Add a new SeqId to the list.

void AddGi(TGi gi)

Add a new GI to the list.

void ReserveGis(size_t n)

Reserve space for GIs.

void AddTi(TTi ti)

Add a new TI to the list.

int GetNumTis() const

Get the number of TIs in the array.

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.

void ReserveTis(size_t n)

Reserve space for TIs.

vector< TTi > m_Tis

TIs to exclude from the SeqDB instance.

TGi GetGi(int index) const

Access an element of the GI array.

vector< string > m_Sis

SeqIds to exclude from the SeqDB instance.

bool FindTi(TTi ti)

Test for existence of a TI.

void PreprocessIdsForISAMSiLookup()

int GetNumGis() const

Get the number of GIs in the array.

bool FindGi(TGi gi)

Test for existence of a GI.

size_t m_LastSortSize

Zero if unsorted, or the size it had after the last sort.

vector< TGi > m_Gis

GIs to exclude from the SeqDB instance.

int GetNumSis() const

Get the number of SeqIds in the array.

void ReserveSis(size_t n)

void InsureOrder()

Sort list if not already sorted.

Check file existence using CSeqDBAtlas.

CSeqDB_AtlasAccessor(CSeqDBAtlas &atlas)

Constructor.

virtual bool DoesFileExist(const string &fname)

Test file existence.

File existence test interface.

virtual ~CSeqDB_FileExistence()

Destructor.

virtual bool DoesFileExist(const string &fname)=0

Check if file exists at fully qualified path.

CSeqDB_Substring FindBaseName() const

Returns the portion of this path containing the base name.

Check file existence using CFile.

virtual bool DoesFileExist(const string &fname)

Test file existence.

CSeqDB_SimpleAccessor()

Constructor.

Compare SGiOid structs by GI.

int operator()(const CSeqDBGiList::SGiOid &lhs, const CSeqDBGiList::SGiOid &rhs)

Test whether lhs is less than (occurs before) rhs.

Compare SGiOid structs by OID.

int operator()(const CSeqDBGiList::SGiOid &lhs, const CSeqDBGiList::SGiOid &rhs)

Test whether lhs is less than (occurs before) rhs.

int operator()(const CSeqDBGiList::SPigOid &lhs, const CSeqDBGiList::SPigOid &rhs)

Test whether lhs is less than (occurs before) rhs.

Compare SSeqIdOid structs by SeqId.

int operator()(const CSeqDBGiList::SSiOid &lhs, const CSeqDBGiList::SSiOid &rhs)

Test whether lhs is less than (occurs before) rhs.

Compare SGiOid structs by GI.

int operator()(const CSeqDBGiList::STiOid &lhs, const CSeqDBGiList::STiOid &rhs)

Test whether lhs is less than (occurs before) rhs.

void GetString(string &s) const

Return the data by assigning it to a string.

int Size() const

Return the length of the string in bytes.

void Clear()

Reset the string to an empty state.

const char * GetEnd() const

Returns a pointer to the end of the string, which is always a pointer to the character past the last ...

void EraseFront(int n)

Disinclude data from the beginning of the string.

void Resize(int n)

Change the length of the string.

const char * GetBegin() const

Returns a pointer to the start of the string.

bool Empty() const

Returns true iff the string is empty.

int FindLastOf(char ch) const

Find last instance of a character in the substring.

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

iterator_bool insert(const value_type &val)

static const char si[8][64]

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

#define GI_FROM(T, value)

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define NON_CONST_ITERATE(Type, Var, Cont)

Non constant version of ITERATE macro.

#define TAX_ID_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.

size_t GetSize(void) const

Get length of the mapped region.

void * GetPtr(void) const

Get pointer to beginning of data.

static char GetPathSeparator(void)

Get path separator symbol specific for the current platform.

const string AsFastaString(void) const

string GetSeqIdString(bool with_version=false) const

Return seqid string with optional version for text seqid type.

void GetLabel(string *label, ELabelType type=eDefault, TLabelFlags flags=fLabel_Default) const

Append a label for this Seq-id to the supplied string.

static SIZE_TYPE ParseFastaIds(CBioseq::TId &ids, const CTempString &s, bool allow_partial_failure=false)

Parse an entire set of |-delimited FASTA-style IDs, appending the results to IDS.

static E_Choice WhichInverseSeqId(const CTempString &SeqIdCode)

Converts a string to a choice, no need to require a member.

static int BestRank(const CRef< CSeq_id > &id)

const CTextseq_id * GetTextseq_Id(void) const

Return embedded CTextseq_id, if any.

@ fLabel_Version

Show the version.

@ fLabel_GeneralDbIsContent

For type general, use the database name as the tag and the (text or numeric) key as the content.

@ eFasta

Tagged ID in NCBI's traditional FASTA style.

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 int CompareNocase(const CTempString s1, SIZE_TYPE pos, SIZE_TYPE n, const char *s2)

Case-insensitive compare of a substring with another string.

static Int8 StringToInt8(const CTempString str, TStringToNumFlags flags=0, int base=10)

Convert string to Int8.

static list< string > & Split(const CTempString str, const CTempString delim, list< string > &arr, TSplitFlags flags=0, vector< SIZE_TYPE > *token_pos=NULL)

Split a string using specified delimiters.

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

Convert int to string.

static string UIntToString(unsigned int value, TNumToStringFlags flags=0, int base=10)

Convert UInt to string.

static bool SplitInTwo(const CTempString str, const CTempString delim, string &str1, string &str2, TSplitFlags flags=0)

Split a string into two pieces using the specified delimiters.

static bool EqualNocase(const CTempString s1, SIZE_TYPE pos, SIZE_TYPE n, const char *s2)

Case-insensitive equality of a substring with another string.

static string TruncateSpaces(const string &str, ETrunc where=eTrunc_Both)

Truncate whitespace in a string.

static string & ToLower(string &str)

Convert string to lower case – string& version.

@ fConvErr_NoThrow

Do not throw an exception on error.

@ fSplit_Tokenize

All delimiters are merged and trimmed, to get non-empty tokens only.

@ eTrunc_Both

Truncate whitespace at both begin and end of string.

C::value_type FindBestChoice(const C &container, F score_func)

Find the best choice (lowest score) for values in a container.

bool IsStr(void) const

Check if variant Str is selected.

const TTag & GetTag(void) const

Get the Tag member data.

bool IsId(void) const

Check if variant Id is selected.

bool CanGetDb(void) const

Check if it is safe to call GetDb method.

bool CanGetTag(void) const

Check if it is safe to call GetTag method.

const TDb & GetDb(void) const

Get the Db member data.

const TStr & GetStr(void) const

Get the variant data.

TId GetId(void) const

Get the variant data.

TGibbsq GetGibbsq(void) const

Get the variant data.

const TName & GetName(void) const

Get the Name member data.

bool CanGetName(void) const

Check if it is safe to call GetName method.

bool IsPrf(void) const

Check if variant Prf is selected.

E_Choice Which(void) const

Which variant is currently selected.

TGi GetGi(void) const

Get the variant data.

TVersion GetVersion(void) const

Get the Version member data.

bool CanGetVersion(void) const

Check if it is safe to call GetVersion method.

E_Choice

Choice variants.

const TLocal & GetLocal(void) const

Get the variant data.

bool CanGetAccession(void) const

Check if it is safe to call GetAccession method.

const TGeneral & GetGeneral(void) const

Get the variant data.

bool IsPir(void) const

Check if variant Pir is selected.

const TAccession & GetAccession(void) const

Get the Accession member data.

@ e_Other

for historical reasons, 'other' = 'refseq'

@ e_Gpipe

Internal NCBI genome pipeline processing ID.

@ e_Tpe

Third Party Annot/Seq EMBL.

@ e_Tpd

Third Party Annot/Seq DDBJ.

@ e_Gibbsq

Geninfo backbone seqid.

@ e_General

for other databases

@ e_Gi

GenInfo Integrated Database.

@ e_not_set

No variant selected.

@ e_Tpg

Third Party Annot/Seq Genbank.

char * dbname(DBPROCESS *dbproc)

Get name of current database.

unsigned int

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

where boath are integers</td > n< td ></td > n</tr > n< tr > n< td > tse</td > n< td > optional</td > n< td > String</td > n< td class=\"description\"> TSE option controls what blob is whole

static void text(MDB_val *v)

constexpr auto sort(_Init &&init)

constexpr auto front(list< Head, As... >, T=T()) noexcept -> Head

const string version

version string

const struct ncbi::grid::netcache::search::fields::SIZE size

Defines unified interface to application:

Defines classes: CDirEntry, CFile, CDir, CSymLink, CMemoryFile, CFileUtil, CFileLock,...

The SeqDB memory management layer.

bool SeqDB_IsBinaryTiList(const string &fname)

Returns true if the file name passed contains a binary TI list.

void SeqDB_ReadPigList(const string &fname, vector< CSeqDBGiList::SPigOid > &pigs, bool *in_order)

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

static bool s_SeqDB_DBExists(const string &dbname, char dbtype, CSeqDB_FileExistence &access, bool linkoutdb_search)

Test whether an index or alias file exists.

void SeqDB_ReadGiList(const string &fname, vector< CSeqDBGiList::SGiOid > &gis, bool *in_order)

Read a text or binary GI list from a file.

void SeqDB_GetLMDBFileExtensions(bool db_is_protein, vector< string > &extn)

Retrieves file extensions for BLAST LMDB files.

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

Read a text SeqID list from an area of memory.

void SeqDB_ReadBinaryGiList(const string &fname, vector< TGi > &gis)

Read a binary-format GI list from a file.

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

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

CSeqDB_Substring SeqDB_RemoveExtn(CSeqDB_Substring s)

Returns a filename minus greedy path.

bool SeqDB_CompareVolume(const string &s1, const string &s2)

Compares two volume file names and determine the volume order.

ESeqDBIdType SeqDB_SimplifySeqid(CSeq_id &bestid, const string *acc, Int8 &num_id, string &str_id, bool &simpler)

Seq-id simplification.

void SeqDB_ReadMemoryMixList(const char *fbeginp, const char *fendp, vector< CSeqDBGiList::SGiOid > &gis, vector< CSeqDBGiList::STiOid > &tis, vector< CSeqDBGiList::SSiOid > &sis, bool *in_order)

Read an ID list (mixed type) from an area of memory.

string SeqDB_FindBlastDBPath(const string &dbname, char dbtype, string *sp, bool exact, CSeqDBAtlas &atlas)

Finds a file in the search path.

string GetBlastSeqIdString(const CSeq_id &seqid, bool version)

Return ID string as stored in lmdb.

void SeqDB_ReadMixList(const string &fname, vector< CSeqDBGiList::SGiOid > &gis, vector< CSeqDBGiList::STiOid > &tis, vector< CSeqDBGiList::SSiOid > &sis, bool *in_order)

Read a text SeqId list from a file.

static string s_SeqDB_FindBlastDBPath(const string &dbname, char dbtype, string *sp, bool exact, CSeqDB_FileExistence &access, const string path="")

void SeqDB_SplitQuoted(const string &dbname, vector< CTempString > &dbs, bool keep_quote)

Split a (possibly) quoted list of database names into pieces.

int s_ReadDigit(const char d, const string &list_type)

static string s_SeqDB_TryPaths(const string &blast_paths, const string &dbname, char dbtype, bool exact, CSeqDB_FileExistence &access, bool linkoutdb_search=false)

Search for a file in a provided set of paths.

CSeqDB_Substring SeqDB_RemoveFileName(CSeqDB_Substring s)

Returns a path minus filename.

static string s_GetPathSplitter()

Returns the character used to seperate path components in the current operating system or platform.

void SeqDB_GetFileExtensions(bool db_is_protein, vector< string > &extn, EBlastDbVersion dbver)

Retrieves a list of all supported file extensions for BLAST databases.

bool IsStringId(const CSeq_id &id)

Determine if id is srting id.

void SeqDB_JoinDelim(string &a, const string &b, const string &delim)

Join two strings with a delimiter.

ESeqDBIdType SeqDB_SimplifyAccession(const string &acc, Int8 &num_id, string &str_id, bool &simpler)

String id simplification.

static bool s_SeqDB_ParseSeqIDs(const string &line, vector< CRef< CSeq_id > > &seqids)

Parse string into a sequence of Seq-id objects.

bool SeqDB_IsBinaryGiList(const string &fname)

Read a text or binary SeqId list from a file.

void s_InsureOrder(TVector &v)

void SeqDB_FileIntegrityAssert(const string &file, int line, const string &text)

Report file corruption by throwing an eFile CSeqDBException.

CSeqDB_Substring SeqDB_RemoveDirName(CSeqDB_Substring s)

Returns a filename minus greedy path.

void SeqDB_ReadTaxIdList(const string &fname, CSeqDBGiList::STaxIdsOids &taxids)

void SeqDB_ReadSiList(const string &fname, vector< CSeqDBGiList::SSiOid > &sis, bool *in_order, SBlastSeqIdListInfo &db_info)

Read a text SeqId list from a file.

const string SeqDB_GetOidMaskFileExt(bool db_is_protein, EOidMaskType t)

string SeqDB_ResolveDbPathForLinkoutDB(const string &filename)

Resolve a file path using SeqDB's path algorithms.

void SeqDB_ReadMemoryTaxIdList(const char *fbeginp, const char *fendp, CSeqDBGiList::STaxIdsOids &taxids)

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

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

void SeqDB_CombineAndQuote(const vector< string > &dbs, string &dbname)

Combine and quote list of database names.

string SeqDB_MakeOSPath(const string &dbs)

Return path with delimiters changed to platform preferred kind.

void SeqDB_ReadTiList(const string &fname, vector< CSeqDBGiList::STiOid > &tis, bool *in_order)

Read a text or binary TI list from a file.

static bool s_SeqDB_IsBinaryNumericList(const char *fbeginp, const char *fendp, bool &has_long_ids, bool *has_tis=NULL)

This function determines whether a file is a valid binary GI/TI file.

string SeqDB_ResolveDbPath(const string &filename)

Resolve a file path using SeqDB's path algorithms.

string SeqDB_ResolveDbPathNoExtension(const string &filename, char dbtype)

Resolve a file path using SeqDB's path algorithms.

void SeqDB_GetMetadataFileExtension(bool db_is_protein, string &extn)

bool SeqDB_SplitString(CSeqDB_Substring &buffer, CSeqDB_Substring &front, char delim)

Parse a prefix from a substring.

static bool s_ContainsBinaryNumericIdList(const string &fname, CSeqDBFileGiList::EIdType type)

static size_t s_SeqDB_EndOfFastaID(const string &str, size_t pos)

Find the end of a single element in a Seq-id set.

void SeqDB_CombinePath(const CSeqDB_Substring &one, const CSeqDB_Substring &two, const CSeqDB_Substring *extn, string &outp)

Combine a filesystem path and file name.

const string kSeqDBGroupAliasFileName("index.alx")

void SeqDB_ConvertOSPath(string &dbs)

Change path delimiters to platform preferred kind in-place.

Defines exception class and several constants for SeqDB.

EBlastDbVersion

BLAST database version.

ESeqDBIdType

Various identifier formats used in Id lookup.

@ eStringId

Each PIG identifier refers to exactly one protein sequence.

@ eTiId

Genomic ID is a relatively stable numeric identifier for sequences.

@ ePigId

Trace ID is a numeric identifier for Trace sequences.

@ eOID

Lookup from sequence hash values to OIDs.

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

void SeqDB_ThrowException(CSeqDBException::EErrCode code, const string &msg)

Thow a SeqDB exception; this is seperated into a function primarily to allow a breakpoint to be set.

T SeqDB_GetStdOrd(const T *stdord_obj)

Read a network order integer value.

void s_SeqDB_QuickAssign(string &dst, const char *bp, const char *ep)

Higher Performance String Assignment.

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

Structure that holds GI,OID pairs.

TGi gi

The GI or 0 if unknown.

int oid

The OID or -1 if unknown.

TPig pig

The PIG or 0 if unknown.

Structure that holds Seq-id,OID pairs.

string si

The String-id or "" if unknown.

vector< blastdb::TOid > oids

Structure that holds TI,OID pairs.

TTi ti

The TI or 0 if unknown.

Blast DB v5 seqid list info.

vector< CRef< CSeq_id > > TIdList

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