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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/build__db_8cpp_source.html below:

NCBI C++ ToolKit: src/objtools/blast/seqdb_writer/build_db.cpp Source File

have_seqid =

;

have_gi =

;

<<

<< seqid->AsFastaString()

<<

<<

->AsFastaString() << endl;

<<

<<

<< seqid->AsFastaString()

<<

->GetGi() << endl;

}

((! have_seqid) && (id->

() == seqid->Which())) {

<<

<< seqid->AsFastaString()

<<

<<

->AsFastaString() <<

<< endl;

<<

seqid.

(

*

(

.GetPointer()));

(vector<string>,

, ids) {

specific =

;

<<

<< *

<<

<< endl;

<<

<< gi << endl;

found(

),

(

);

(vector<int>, oid, oids) {

pos =

.find(acc);

(pos != string::npos) {

endpos = pos + acc.size();

start_okay = (pos == 0 ||

[pos-1] ==

);

end_okay = ((endpos ==

.size()) ||

(

[endpos] ==

||

[endpos] ==

));

(start_okay && end_okay) {

(

|| (! found)) {

<<

<<

<<

<<

<<

<< endl;

((! bs->CanGetInst()) || bs->GetInst().CanGetSeq_data() ||

! bs->GetInst().CanGetExt() || ! bs->GetInst().GetExt().IsDelta()) {

(bs->GetInst().CanGetMol() &&

oss <<

->AsFastaString() <<

;

& dext = bs->GetInst().GetExt().GetDelta();

list< CRef< CDelta_seq > >

;

(bs->GetInst().CanGetLength()) {

seq8na.reserve(bs->GetInst().GetLength());

(((**item).IsLoc()) && ((**item).GetLoc().IsNull())) {

seq8na.append(1, 0x0f);

);

);

length = seq8na.size();

bs2->

() = bs->GetId();

(bs->IsSetDescr()) {

inst->

().SetNcbi4na().Set().swap(seq4na);

(bs->IsSetAnnot()) {

);

headers->RemoveGIs();

gis.push_back((*id)->GetGi());

objects::CSeqVector * sv,

(bs->GetInst().CanGetSeq_data())

list< CRef<CSeq_id> > & ids = bs->GetId();

<<

<< seqid.AsFastaString() << endl

<< e.

() << endl;

<<

<< seqid.AsFastaString() << endl;

<<

<< seqid.AsFastaString() << endl;

found_all =

;

(

= 0;

< num_gis;

++) {

<<

<< endl;

<<

<< endl;

(

= 0;

< num_seqids;

++) {

<< gi_list.

<

>(

);

<<

<< endl;

acc = gi_list.

<

>(

);

<<

<< endl;

<<

<<

<<

<<

<<

<< endl;

success =

;

(

= 0;

< num_gis;

++) {

<<

<< endl;

<<

<< endl;

(

= 0;

< num_seqids;

++) {

<< gi_list.

<

>(

)

<<

<< endl;

<< gi_list.

<

>(

)

<<

<< endl;

<<

<< unresolved <<

<< endl;

: m_FastaReader(

)

TFlags

= (TFlags) iflags;

(!

.empty()) {

(

exception&) {}

kKeyword(

);

pos(

);

(start !=

&& end !=

) {

start += kKeyword.size();

pos =

(e.what()).substr(start, end-start);

= e.GetMsg();

extra_string(

);

.erase(0, extra_string.size());

bioseq_id(

);

list< CRef<CSeq_id> > & ids = bs->

();

skip_this =

;

(list<

>::const_iterator it = ids.begin(); it != ids.end(); it++ ){

( it->NotEmpty() ){

(

== CSeq_id::EAccessionInfo::eAcc_gi ){

check_gi = (*it)->GetGi();

( check_gi > max_gi32_val )

<<

<< check_gi <<

<< 0xFFFFFFFF<< endl;

(! ids.empty() && ids.front().NotEmpty()) {

bioseq_id.assign(ids.front()->AsFastaString());

(

& it: bss->

()) {

(!it->IsLocal() && !it->IsGi() &&

= it->GetSeqIdString(

);

+ bioseq_id);

<<

<< bioseq_id

<<

<< endl;

<<

<< bioseq_id

<<

<<

<<

<<

<<

<< endl;

vector<string> all_names;

(

= 0;

< (

) all_names.size();

++) {

name = all_names[

];

(name ==

) {

(StringPairMap, iter, meta) {

in2out[in_id] = out_id;

vector<CTempString> column_blobs;

vector<int> column_ids;

(column_blobs.size() == column_ids.size());

(sequence.

()) {

);

);

(deflines.

()) {

);

(

= 0;

< (

)column_ids.size();

++) {

in_id = column_ids[

];

(in_id == mask_id)

;

(column_blobs[

].

() == 0)

out_id = in2out[in_id];

list< CRef<CSeq_id> > & ids = (*defline)->GetSeqid();

((*id)->IsGi()) {

gis.push_back((*id)->GetGi());

(!rng.

()) {

mask_data.insert(mask_data.end(), rng.begin(), rng.end());

(!mask_data.

()) {

<<

<<

<<

<<

<<

<< endl;

(dir_name.empty()) {

(

+ d.

() +

);

(

+

& title,

scan_bioseq_4_cfastareader_usrobj)

: m_IsProtein (is_protein),

m_KeepLinks (

),

m_KeepMbits (

),

m_KeepLeafs (

),

m_LogFile (*logfile),

m_UseRemote (

),

m_Verbose (

),

m_LongIDs (long_seqids),

m_FoundMatchingMasks(

),

m_SkipCopyingGis(

),

m_SkipLargeGis(

),

m_ScanBioseq4CFastaReaderUsrObjct(scan_bioseq_4_cfastareader_usrobj)

<<

<<

<< output_dbname << endl;

<<

<< title << endl;

mol_type(is_protein ?

:

);

<<

<< mol_type << endl;

<<

<< mol_type

<<

<< output_dbname << endl;

& title,

scan_bioseq_4_cfastareader_usrobj)

: m_IsProtein (is_protein),

m_KeepLinks (

),

m_KeepMbits (

),

m_KeepLeafs (

),

m_LogFile (*logfile),

m_UseRemote (

),

m_Verbose (

),

m_ParseIDs (parse_seqids),

m_LongIDs (long_seqids),

m_FoundMatchingMasks(

),

m_SkipCopyingGis(

),

m_SkipLargeGis(

),

m_ScanBioseq4CFastaReaderUsrObjct(scan_bioseq_4_cfastareader_usrobj)

<<

<<

<< output_dbname << endl;

<<

<< title << endl;

mol_type(is_protein ?

:

);

<<

<< mol_type << endl;

<<

<< mol_type

<<

<< output_dbname << endl;

scan_bioseq_4_cfastareader_usrobj));

(

<<

<<

<<

);

(

<<

);

<<

<< (keep_links ?

:

) << endl;

<<

<< (keep_mbits ?

:

) << endl;

<<

<< (keep_taxids ?

:

) << endl;

success =

(ids);

success = success && success2;

<<

<<

<<

<< endl;

success =

;

(this_oid != -1) {

(seen_it.

(this_oid) == seen_it.

()) {

seen_it[this_oid] = this_gi;

<<

<< seen_it[this_oid]

success =

;

(success ==

)

}

(exception& e) {

success =

;

vector<string> vols;

vector<string> files;

(vols.empty() == files.empty());

(vector<string>, iterf, files) {

(

<< *iterf);

(close_exception) {

close_exception->

());

objects::CBlast_def_line& defline,

vector<string>& keys

found =

;

(!

->empty()) {

(item != leafs.

()) {

taxids.

(item->second.begin(), item->second.end());

defline.SetLeafTaxIds(tv);

defline.SetLeafTaxIds(tv);

vector<string> & keys)

found =

;

(item != bitmap.

()) {

|= item->second;

list<int> & linkv = (is_memb

? defline.SetMemberships()

: defline.SetLinks());

(linkv.empty()) {

linkv.push_back(

);

linkv.front() |=

;

defline.ResetMemberships();

defline.ResetLinks();

vector<string> keys;

& options,

& name)

& description,

& options)

static CConstRef< CBioseq > s_FixBioseqDeltas(CConstRef< objects::CBioseq > bs)

static void s_SetDeflineLeafs(objects::CBlast_def_line &defline, TIdToLeafs &leafs, bool keep_old, vector< string > &keys)

static void s_SetDeflineBits(objects::CBlast_def_line &defline, TIdToBits &bitmap, bool keep_old, bool is_memb, vector< string > &keys)

Code to build a database given various sources of sequence data.

TSeqPos GetLength(void) const

`Blob' Class for SeqDB (and WriteDB).

void WriteRaw(const char *begin, int size)

Write raw data to the blob (moving the write pointer).

void Clear()

Clear all owned data and reference an empty string.

Implementation of ILineReader for IReader.

bool AddSequences(IBioseqSource &src, bool add_pig=false)

Add sequences from an IBioseqSource object.

bool m_IsProtein

True for a protein database, false for nucleotide.

bool AddFasta(CNcbiIstream &fasta_file)

Add sequences from a file containing FASTA data.

int m_DeflineCount

Define count.

bool m_KeepLinks

True to keep linkout bits from source dbs, false to discard.

bool m_SkipLargeGis

If set to true, skip GIs with value > 0x7FFFFFFF.

TIdToBits m_Id2Links

Table of linkout bits to apply to sequences.

bool m_FoundMatchingMasks

If true, there were sequences whose IDs matched those in the provided masking locations (via SetMaskD...

static void CreateDirectories(const string &dbname)

Create Directory for blast db.

bool x_ReportUnresolvedIds(const CInputGiList &gi_list) const

Write log messages for any unresolved IDs.

bool m_UseRemote

Whether to use remote resolution and sequence fetching.

void x_EditHeaders(CRef< objects::CBlast_def_line_set > headers)

Modify deflines with linkout and membership bits and taxids.

objects::CScope & x_GetScope()

Get a scope for remote loading of objects.

void SetMaskDataSource(IMaskDataSource &ranges)

Specify an object mapping Seq-id to subject masking data.

void SetMembBits(const TLinkoutMap &membbits, bool keep_mbits)

Specify a membership bit lookup object.

bool m_ParseIDs

If true, string IDs found in FASTA input will be parsed as Seq-ids.

int RegisterMaskingAlgorithm(EBlast_filter_program program, const string &options, const string &name="")

Define a masking algorithm.

int m_OIDCount

Number of OIDs stored in this database.

void SetSourceDb(const string &src_db_name)

Specify source database(s) via the database name(s).

bool m_ScanBioseq4CFastaReaderUsrObjct

bool m_KeepMbits

True to keep membership bits from source dbs, false to discard.

CRef< CTaxIdSet > m_Taxids

Set of TaxIDs configured to apply to sequences.

CRef< objects::CScope > m_Scope

Sequence scope, used for remote fetching.

CRef< objects::CObjectManager > m_ObjMgr

Object manager, used for remote fetching.

ostream & m_LogFile

Logfile.

bool m_Verbose

If true, more detailed log messages will be produced.

bool m_KeepLeafs

True to keep leaf taxids from source dbs, false to discard.

bool x_EndBuild(bool erase, const CException *close_exception)

bool m_SkipCopyingGis

If set to true, when copying BLASTDBs, skip the GIs.

CRef< CWriteDB > m_OutputDb

Database being produced here.

CRef< CSeqDBExpert > m_SourceDb

Database for duplicating sequences locally (-sourcedb option.)

void SetTaxids(CTaxIdSet &taxids)

Specify a mapping of sequence ids to taxonomic ids.

CRef< CInputGiList > x_ResolveGis(const vector< string > &ids)

Resolve various input IDs (as strings) to GIs.

void x_SetLinkAndMbit(CRef< objects::CBlast_def_line_set > headers)

Store linkout (now deprecated) and membership bits in provided headers.

CRef< IMaskDataSource > m_MaskData

Subject masking data.

bool x_EditAndAddBioseq(CConstRef< objects::CBioseq > bs, objects::CSeqVector *sv, bool add_pig=false)

Modify a Bioseq as needed and add it to the database.

bool m_LongIDs

If true, use long sequence ids (database|accession)

bool Build(const vector< string > &ids, CNcbiIstream *fasta_file)

Build the database.

void x_AddOneRemoteSequence(const objects::CSeq_id &seqid, bool &found, bool &error)

Fetch a sequence from the remote service and add it to the db.

void x_AddMasksForSeqId(const list< CRef< CSeq_id > > &ids)

Add the masks for the Seq-id(s) (usually just one) to the database being created.

TIdToLeafs m_Id2Leafs

Table of leaf taxids to apply to sequences.

void x_ResolveRemoteId(CRef< objects::CSeq_id > &seqid, TGi &gi)

Resolve an ID remotely.

void x_DupLocal()

Duplicate IDs from local databases.

TIdToBits m_Id2Mbits

Table of membership bits to apply to sequences.

bool x_ResolveFromSource(const string &acc, CRef< objects::CSeq_id > &id)

Determine if this string ID can be found in the source database.

void StartBuild()

Start building a new database.

bool EndBuild(bool erase=false)

Finish building a new database.

void SetLinkouts(const TLinkoutMap &linkouts, bool keep_links)

Specify a linkout bit lookup object.

void SetMaxFileSize(Uint8 max_file_size)

Set the maximum size of database component files.

void x_AddPig(CRef< objects::CBlast_def_line_set > headers)

Add pig if id can be extracted from the deflines.

bool AddIds(const vector< string > &ids)

Add the specified sequences from the source database.

void SetMaskLetters(const string &mask_letters)

Specify letters to mask out of protein sequence data.

bool x_AddRemoteSequences(CInputGiList &gi_list)

Duplicate IDs from local databases.

CBuildDatabase(const string &dbname, const string &title, bool is_protein, CWriteDB::TIndexType indexing, bool use_gi_mask, ostream *logfile, bool long_seqids=false, EBlastDbVersion dbver=eBDB_Version4, bool limit_defline=false, Uint8 oid_masks=EOidMaskType::fNone, bool scan_bioseq_4_cfastareader_usrobj=true)

Constructor.

void SetLeafTaxIds(const TIdToLeafs &taxids, bool keep_taxids)

Specify a leaf-taxids object.

CFastaBioseqSource(CNcbiIstream &fasta_file, bool is_protein, bool parse_ids, bool long_ids)

virtual CConstRef< CBioseq > GetNext()

Get a Bioseq object if there are any more to get.

CFastaReader * m_FastaReader

CRef< ILineReader > m_LineReader

Base class for reading FASTA sequences.

Gi List for database construction.

void AppendSi(const string &si, int oid=-1)

Append a Seq-id.

void AppendGi(TGi gi, int oid=-1)

Append a GI.

Thrown on an attempt to access wrong choice variant.

This represents a set of masks for a given sequence.

bool empty() const

Redefine empty to mean no elements or none of its elements being empty.

static CNcbiApplication * Instance(void)

Singleton method.

CNcbiOstrstreamToString class helps convert CNcbiOstrstream to a string Sample usage:

static SIZE_TYPE Convert(const CTempString &src, TCoding src_coding, TSeqPos pos, TSeqPos length, string &dst, TCoding dst_coding)

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

Raw Sequence and Ambiguity Data.

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 SSiOid & GetSiOid(int index) const

Access an element of the array.

T GetKey(int index) const

const string & GetDBNameList() const

Get list of database names.

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

Gets a list of sequence identifiers.

ESeqType GetSequenceType() const

Returns the type of database opened - protein or nucleotide.

string GetTitle() const

Returns the database title.

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

Translate an Accession to a list of OIDs.

bool CheckOrFindOID(int &next_oid) const

Find an included OID, incrementing next_oid if necessary.

string GetDate() const

Returns the construction date of the database.

CRef< CBlast_def_line_set > GetHdr(int oid) const

Get the ASN.1 header for the sequence.

@Seq_descr.hpp User-defined methods of the data storage class.

void FixTaxId(CRef< objects::CBlast_def_line_set > deflines)

Check that each defline has the specified taxid; if not, replace the defline and set the taxid.

bool HasEverFixedId() const

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

int CreateUserColumn(const string &title)

Set up a user-defined CWriteDB column.

void SetMaxFileSize(Uint8 sz)

Set maximum size for output files.

@ eProtein

Protein database.

@ eNucleotide

Nucleotide database.

int RegisterMaskAlgorithm(EBlast_filter_program program, const string &options=string(), const string &name=string())

Register a type of filtering data found in this database.

void AddColumnMetaData(int col_id, const string &key, const string &value)

Add meta data to a user-defined column.

int FindColumn(const string &title) const

Find an existing column.

void ListFiles(vector< string > &files)

List Filenames.

CBlastDbBlob & SetBlobData(int column_id)

Add blob data to a user-defined column.

void SetMaskData(const CMaskedRangesVector &ranges, const vector< TGi > &gis)

Set filtering data for a sequence.

void SetPig(int pig)

Set the PIG to be used for the sequence.

void AddSequence(const CBioseq &bs)

Add a sequence as a CBioseq.

EIndexType

Whether and what kind of indices to build.

@ eDefault

Like eFullIndex but also build a numeric Trace ID index.

@ eSparseIndex

Use only simple accessions in the string index.

void SetMaskedLetters(const string &masked)

Set letters that should not be used in sequences.

void ListVolumes(vector< string > &vols)

List Volumes.

int TIndexType

Bitwise OR of "EIndexType".

static CRef< CBlast_def_line_set > ExtractBioseqDeflines(const CBioseq &bs, bool parse_ids=true, bool long_ids=false, bool scan_bioseq_4_cfastareader_usrobj=false)

Extract Deflines From Bioseq.

void SetDeflines(const CBlast_def_line_set &deflines)

Set the deflines to be used for the sequence.

void Close()

Close the Database.

Interface to a source of Bioseq objects.

virtual CConstRef< objects::CBioseq > GetNext()=0

Get a Bioseq object if there are any more to get.

@ eProblem_ModifierFoundButNoneExpected

@ eProblem_TooManyAmbiguousResidues

An interface providing lookups of mask-data by Seq-id.

virtual CMaskedRangesVector & GetRanges(const list< CRef< CSeq_id > > &id)=0

Get ranges of masking data for the given Seq-ids.

Interface to a source of raw sequence data.

virtual const map< string, string > & GetColumnMetaData(int id)=0

Get metadata for the column with the specified Column ID.

virtual bool GetNext(CTempString &sequence, CTempString &ambiguities, CRef< objects::CBlast_def_line_set > &deflines, vector< SBlastDbMaskData > &mask_ranges, vector< int > &column_ids, vector< CTempString > &column_blobs)=0

Get a raw sequence.

virtual void GetColumnNames(vector< string > &names)=0

Get the names of all columns defined by this sequence source.

virtual int GetColumnId(const string &name)=0

Get the column ID for a column mentioned by name.

container_type::iterator iterator

const_iterator end() const

const_iterator find(const key_type &key) const

iterator_bool insert(const value_type &val)

const_iterator begin() const

const_iterator end() const

Operators to edit gaps in sequences.

const CNcbiRegistry & GetConfig(void) const

Get the application's cached configuration parameters (read-only).

#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 ERR_POST(message)

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

void Error(CExceptionArgs_Base &args)

#define NCBI_EXCEPTION_VAR(name, exception_class, err_code, message)

Create an instance of the exception to be thrown later.

#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.

virtual const char * what(void) const noexcept

Standard report (includes full backlog).

#define NCBI_RETHROW(prev_exception, exception_class, err_code, message)

Generic macro to re-throw an exception.

static string CreateAbsolutePath(const string &path, ERelativeToWhat rtw=eRelativeToCwd)

Get an absolute path from some, possibly relative, path.

string GetDir(EIfEmptyPath mode=eIfEmptyPath_Current) const

Get the directory component for this directory entry.

bool CreatePath(TCreateFlags flags=fCreate_Default) const

Create the directory path recursively possibly more than one at a time.

virtual bool Remove(TRemoveFlags flags=eRecursive) const

Remove a directory entry.

bool CheckAccess(TMode access_mode) const

Check access rights.

virtual bool Exists(void) const

Check if directory "dirname" exists.

string GetName(void) const

Get the base entry name with extension (if any).

@ eIfEmptyPath_Empty

Return empty string.

@ fWrite

Write permission.

#define MSerial_AsnText

I/O stream manipulators –.

virtual CRef< CSeq_entry > ReadOneSeq(ILineErrorListener *pMessageListener=nullptr)

Read a single effective sequence, which may turn out to be a segmented set.

EFlags

Note on fAllSeqIds: some databases (notably nr) have merged identical sequences, joining their deflin...

virtual bool AtEOF(void) const =0

Indicates (negatively) whether there is any more input.

void SetMaxIDLength(Uint4 max_len)

If this is set, an exception will be thrown if a Sequence ID exceeds the given length.

void IgnoreProblem(ILineError::EProblem problem)

@ fNoParseID

Generate an ID (whole defline -> title)

@ fQuickIDCheck

Just check local IDs' first characters.

@ fRequireID

Reject deflines that lack IDs.

@ fDisableNoResidues

If no residues found do not raise an error.

@ fForceType

Force specified type regardless of accession.

@ fParseRawID

Try to identify raw accessions.

@ fAssumeNuc

Assume nucs unless accns indicate otherwise.

@ fParseGaps

Make a delta sequence if gaps found.

@ fAssumeProt

Assume prots unless accns indicate otherwise.

const string AsFastaString(void) const

EAccessionInfo

For IdentifyAccession (below)

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

const CTextseq_id * GetTextseq_Id(void) const

Return embedded CTextseq_id, if any.

static CRef< CObjectManager > GetInstance(void)

Return the existing object manager or create one.

vector< CSeq_id_Handle > TIds

CConstRef< CBioseq > GetCompleteBioseq(void) const

Get the complete bioseq.

TBioseqStateFlags GetState(void) const

Get state of the bioseq.

bool Empty(void) const THROWS_NONE

Check if CConstRef is empty – not pointing to any object which means having a null value.

void Reset(void)

Reset reference object.

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 NotEmpty(void) const THROWS_NONE

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

TObjectType * GetNonNullPointer(void) const

Get pointer value and throw a null pointer exception if pointer is null.

bool Empty(void) const THROWS_NONE

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

uint64_t Uint8

8-byte (64-bit) unsigned integer

virtual const string & Get(const string &section, const string &name, TFlags flags=0) const

Get the parameter value.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

IO_PREFIX::istream CNcbiIstream

Portable alias for istream.

NCBI_NS_STD::string::size_type SIZE_TYPE

static SIZE_TYPE Find(const CTempString str, const CTempString pattern, ECase use_case=eCase, EDirection direction=eForwardSearch, SIZE_TYPE occurrence=0)

Find the pattern in the string.

const char * data(void) const

Return a pointer to the array represented.

bool empty(void) const

Return true if the represented string is empty (i.e., the length is zero)

static bool StartsWith(const CTempString str, const CTempString start, ECase use_case=eCase)

Check if a string starts with a specified prefix value.

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

Convert string to unsigned int.

size_type size(void) const

Return the length of the represented array.

double Elapsed(void) const

Return time elapsed since first Start() or last Restart() call (in seconds).

string AsString(const CTimeFormat &format=kEmptyStr, TSeconds out_tz=eCurrentTimeZone) const

Transform time to string.

@ eCurrent

Use current time. See also CCurrentTime.

@ eStart

Start timer immediately after creating.

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

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

static const char label[]

EBlast_filter_program

This defines the possible sequence filtering algorithms to be used in a BLAST database.

bool IsSetOther_info(void) const

In proteins this stores the PIG, in nucleotides this stores the "origin GIs" (if one sequence is desc...

const Tdata & Get(void) const

Get the member data.

list< CRef< CBlast_def_line > > Tdata

const TOther_info & GetOther_info(void) const

Get the Other_info member data.

E_Choice Which(void) const

Which variant is currently selected.

bool IsGi(void) const

Check if variant Gi is selected.

bool IsSetVersion(void) const

Check if a value has been assigned to Version data member.

const TSeq & GetSeq(void) const

Get the variant data.

bool IsSeq(void) const

Check if variant Seq is selected.

TId & SetId(void)

Assign a value to Id data member.

TAnnot & SetAnnot(void)

Assign a value to Annot data member.

const TId & GetId(void) const

Get the Id member data.

bool IsNcbi4na(void) const

Check if variant Ncbi4na is selected.

TLength GetLength(void) const

Get the Length member data.

bool CanGetLength(void) const

Check if it is safe to call GetLength method.

void SetInst(TInst &value)

Assign a value to Inst data member.

bool CanGetId(void) const

Check if it is safe to call GetId method.

void SetDescr(TDescr &value)

Assign a value to Descr data member.

const TNcbi4na & GetNcbi4na(void) const

Get the variant data.

void SetRepr(TRepr value)

Assign a value to Repr data member.

bool CanGetSeq_data(void) const

Check if it is safe to call GetSeq_data method.

const TNcbi2na & GetNcbi2na(void) const

Get the variant data.

const Tdata & Get(void) const

Get the member data.

void SetLength(TLength value)

Assign a value to Length data member.

bool IsGap(void) const

Check if variant Gap is selected.

void SetSeq_data(TSeq_data &value)

Assign a value to Seq_data data member.

bool IsNcbi2na(void) const

Check if variant Ncbi2na is selected.

const TSeq_data & GetSeq_data(void) const

Get the Seq_data member data.

void SetMol(TMol value)

Assign a value to Mol data member.

@ eRepr_raw

continuous sequence

@ eMol_na

just a nucleic acid

@ e_Literal

a piece of sequence

char * dbname(DBPROCESS *dbproc)

Get name of current database.

unsigned int

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

bool CheckAccession(const string &acc, TGi &gi, CRef< objects::CSeq_id > &seqid, bool &specific)

void GetDeflineKeys(const objects::CBlast_def_line &defline, vector< string > &keys)

Get all keys for a defline.

void MapToLMBits(const TLinkoutMap &gilist, TIdToBits &gi2links)

Read a set of GI lists, each a vector of strings, and combine the bits into the resulting linkbits ma...

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

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

const GenericPointer< typename T::ValueType > T2 value

Defines unified interface to application:

CSeqDB::ESeqType ParseMoleculeTypeString(const string &str)

Convert a string to a CSeqDB ESeqType object.

bool DeleteBlastDb(const string &dbpath, CSeqDB::ESeqType seq_type)

Deletes all files associated with a BLAST database.

EBlastDbVersion

BLAST database version.

Defines `expert' version of CSeqDB interfaces.

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

TGi gi

The GI or 0 if unknown.

int oid

The OID or -1 if unknown.

int oid

The OID or -1 if unknown.

static bool ambig(char c)

Defines BLAST database construction classes.

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