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NCBI C++ ToolKit: src/app/blast/blast_app_util.cpp Source File

& client_id

,

);

db_args->GetSubjects()));

(verbose_output) {

blast::SDataLoaderConfig

(db_adapter->IsBlastDb() &&

(query_is_protein == db_adapter->IsProtein())) {

vector<string> default_dbs;

(default_dbs.size() &&

(find(default_dbs.begin(), default_dbs.end(),

db_adapter->GetDatabaseName()) == default_dbs.end())) {

oss << db_adapter->GetDatabaseName() <<

<< retval.

;

<<

<< (query_is_protein ?

:

)

<<

);

(

);

is_remote_search,

db_adapter.

();

(is_remote_search) {

is_protein =

(search_db.

()) {

(scope.

()) {

( (subjects = db_args->GetSubjects(scope)) ) {

* bl2seq_legacy = getenv(

);

scope->AddDataLoader(dl);

(is_remote_search ) {

(

<< dl <<

<<

);

(

<< retval <<

<<

<<

);

& client_id

,

num_iters

retval.

(

blast::CExportStrategy(pssm, opts_hndl, search_db, client_id, num_iters));

retval.

(

blast::CExportStrategy(pssm, opts_hndl, search_db, client_id));

retval.

(

blast::CExportStrategy(queries, opts_hndl, search_db, client_id, num_iters));

retval.

(

blast::CExportStrategy(queries, opts_hndl, search_db, client_id));

);

retval.

(

blast::CExportStrategy(queries, opts_hndl,

db_args->GetSubjects(), client_id));

num_iters

)

export_strategy->ExportSearchStrategy_ASN1(

);

length = (*bioseq)->GetInst().GetLength();

retval.push_back(

(sl, subj_scope));

blast::CBlastAppArgs* cmdline_args)

}

( (tbn_args =

(

);

blast::CBlastAppArgs* cmdline_args)

((*itr)->GetId()) {

.Write(**seq_entry);

cmdline_args->SetInputStream(tmpfile);

subject_is_protein,

is_remote_search)

( !is_remote_search ) {

(

);

+= limit +

(

);

+=

(

);

runtime_error(

);

gilist->

(*gi);

gilist->

(*gi);

db_args->

(subject_factory, subj_scope, subject_is_protein);

blast::CBlastAppArgs* cmdline_args,

is_remote_search,

override_subject)

);

cmdline_args->SetOptionsHandle(opts_hndl);

cmdline_args->SetTask(

.GetTask());

* program_string = 0;

(

<< program_string <<

<<

.GetTask());

(program_string);

(override_subject) {

(

<<

);

subject_is_protein, is_remote_search);

cmdline_args->SetBlastDatabaseArgs(db_args);

(override_query) {

(queries->

()) {

cmdline_args->GetQueryOptionsArgs()->SetRange(query_range);

psi_args->SetNumberOfIterations(

.GetPsiNumOfIterations());

*

= cmdline_args->GetImportSearchStrategyStream(args);

is_remote_search =

override_query = (args[

].HasValue() &&

(

<<

);

blast::CBlastAppArgs* cmdline_args,

num_iters

)

*

= cmdline_args->GetExportSearchStrategyStream(args);

cmdline_args->GetBlastDatabaseArgs(),

TSeqIdRanges id_ranges;

( !(*result)->HasAlignments() ) {

subj_range((*aln)->GetSeqRange(kSubjRow));

subj_range.

(

.GetToOpen());

id_ranges[subj].push_back(subj_range);

(TSeqIdRanges, itr, id_ranges) {

(vector<TSeqRange>, range, itr->second) {

ranges.push_back(*range);

(ids.size() == ranges.size());

(

(*name, objects::CRemoteBlastDbDataLoader::kNamePrefix)) {

* pre_fetch_limit_str = getenv(

);

(pre_fetch_limit_str) {

(pre_fetch_limit == 0) {

(pre_fetch_limit == INT_MAX){

(

=0;

<

.GetNumResults();

++) {

(

[

].HasAlignments()) {

num_of_seqs +=

[

].GetSeqAlign()->Size();

(num_of_seqs > pre_fetch_limit) {

vector<TSeqRange> ranges;

(

<< ids.size() <<

);

(

<<

);

pair<double, double>

, k, h;

list<string> failed_db;

(

=0;

< db.size();

++) {

vector<string> dbpath;

path = *dbpath.begin();

);

(path +

);

failed_db.push_back(db[

]);

(!failed_db.empty()) {

all_failed =

(failed_db,

);

prog_str = isRpsblast ?

:

;

= all_failed +

\

+

\

+ prog_str +

;

.setf(ios::skipws);

IOS_BASE::iostate orig_state =

.rdstate();

IOS_BASE::fmtflags orig_flags =

.setf(ios::skipws);

.flags(orig_flags);

.setstate(orig_state);

(

=0;

<

.Size();

++) {

+=

[

] +

;

+ f_str);

filename=

;

.SetRequest_id(

);

db_name.erase(0, off+1);

* mt_query_batch_env = getenv(

);

(mt_query_batch_env) {

(task ==

)

warn =

\

\

(is_db_protein) {

warn += +

;

(

<< warn +

);

warning =

\

;

warning +=

;

warning +=

;

warning +=

;

User-defined methods of the data storage class.

Produce formatted blast output for command line applications.

Data loader implementation that uses the blast databases.

Data loader implementation that uses the blast databases remotely.

void LogCmdOptions(blast::CBlastUsageReport &report, const CBlastAppArgs &args)

void CheckForFreqRatioFile(const string &rps_dbname, CRef< CBlastOptionsHandle > &opt_handle, bool isRpsblast)

static TSeqLocVector s_ConvertBioseqs2TSeqLocVector(const CBlast4_subject::TSequences &subjects)

Converts a list of Bioseqs into a TSeqLocVector.

CRef< blast::CRemoteBlast > InitializeRemoteBlast(CRef< blast::IQueryFactory > queries, CRef< blast::CBlastDatabaseArgs > db_args, CRef< blast::CBlastOptionsHandle > opts_hndl, bool verbose_output, const string &client_id, CRef< objects::CPssmWithParameters > pssm)

Initializes a CRemoteBlast instance for usage by command line BLAST binaries.

blast::SDataLoaderConfig InitializeQueryDataLoaderConfiguration(bool query_is_protein, CRef< blast::CLocalDbAdapter > db_adapter)

Initialize the data loader configuration for the query.

void SaveSearchStrategy(const CArgs &args, blast::CBlastAppArgs *cmdline_args, CRef< blast::IQueryFactory > queries, CRef< blast::CBlastOptionsHandle > opts_hndl, CRef< objects::CPssmWithParameters > pssm, unsigned int num_iters)

Save the search strategy corresponding to the current command line search.

void QueryBatchCleanup()

Clean up formatter scope and release.

static bool s_IsPrefetchFormat(blast::CFormattingArgs::EOutputFormat format_type)

string RegisterOMDataLoader(CRef< CSeqDB > db_handle)

Register the BLAST database data loader using the already initialized CSeqDB object.

static void s_ImportQueries(const CBlast4_queries &queries, CRef< blast::CBlastOptionsHandle > opts_hndl, blast::CBlastAppArgs *cmdline_args)

Import queries into command line arguments object.

CRef< CBlastAncillaryData > ExtractPssmAncillaryData(const CPssmWithParameters &pssm)

Auxiliary function to extract the ancillary data from the PSSM.

string GetSubjectFile(const CArgs &args)

Get name of subject file @parameter args arguments class [in].

bool RecoverSearchStrategy(const CArgs &args, blast::CBlastAppArgs *cmdline_args)

Recover search strategy from input file.

int GetMTByQueriesBatchSize(EProgram p, int num_threads, const string &task)

void MTByQueries_DBSize_Warning(const Int8 length_limit, bool is_db_protein)

static void s_ExportSearchStrategy(CNcbiOstream *out, CRef< blast::IQueryFactory > queries, CRef< blast::CBlastOptionsHandle > options_handle, CRef< blast::CBlastDatabaseArgs > db_args, CRef< objects::CPssmWithParameters > pssm, unsigned int num_iters)

Real implementation of search strategy extraction.

void CheckMTByQueries_QuerySize(EProgram prog, int batch_size)

static bool s_IsUsingRemoteBlastDbDataLoader()

Returns true if the remote BLAST DB data loader is being used.

void PrintErrorArchive(const CArgs &a, const list< CRef< CBlast4_error > > &msg)

Function to print blast archive with only error messages (search failed) to output stream.

static void s_ImportPssm(const CBlast4_queries &queries, CRef< blast::CBlastOptionsHandle > opts_hndl, blast::CBlastAppArgs *cmdline_args)

Import PSSM into the command line arguments object.

void InitializeSubject(CRef< blast::CBlastDatabaseArgs > db_args, CRef< blast::CBlastOptionsHandle > opts_hndl, bool is_remote_search, CRef< blast::CLocalDbAdapter > &db_adapter, CRef< objects::CScope > &scope)

Initializes the subject/database as well as its scope.

string GetCmdlineArgs(const CNcbiArguments &a)

static CRef< blast::CBlastDatabaseArgs > s_ImportSubjects(const CBlast4_subject &subj, bool subject_is_protein)

Import the subject sequences into a CBlastDatabaseArgs object.

void BlastFormatter_PreFetchSequenceData(const blast::CSearchResultSet &results, CRef< CScope > scope, blast::CFormattingArgs::EOutputFormat format_type)

This method optimize the retrieval of sequence data to scope.

void LogBlastOptions(blast::CBlastUsageReport &report, const CBlastOptions &opt)

static void s_ExtractSeqidsAndRanges(const blast::CSearchResultSet &results, CScope::TIds &ids, vector< TSeqRange > &ranges)

Extracts the subject sequence IDs and ranges from the BLAST results.

static void s_ImportSearchStrategy(CNcbiIstream *in, blast::CBlastAppArgs *cmdline_args, bool is_remote_search, bool override_query, bool override_subject)

Imports search strategy, using CImportStrategy.

bool UseXInclude(const CFormattingArgs &f, const string &s)

static CRef< blast::CBlastDatabaseArgs > s_ImportDatabase(const CBlast4_subject &subj, CBlastOptionsBuilder &opts_builder, bool subject_is_protein, bool is_remote_search)

Import the database and return it in a CBlastDatabaseArgs object.

static CRef< blast::CExportStrategy > s_InitializeExportStrategy(CRef< blast::IQueryFactory > queries, CRef< blast::CBlastDatabaseArgs > db_args, CRef< blast::CBlastOptionsHandle > opts_hndl, const string &client_id, CRef< objects::CPssmWithParameters > pssm, unsigned int num_iters)

bool IsIStreamEmpty(CNcbiIstream &in)

static bool s_PreFetchSeqs(const blast::CSearchResultSet &results, blast::CFormattingArgs::EOutputFormat format_type)

void LogQueryInfo(CBlastUsageReport &report, const CBlastInput &q_info)

Utility functions for BLAST command line applications.

ESubjectMaskingType

Define the possible subject masking types.

#define sfree(x)

Safe free a pointer: belongs to a higher level header.

Interface for converting sources of sequence data into blast sequence input.

int GetQueryBatchSize(EProgram program, bool is_ungapped=false, bool remote=false, bool use_default=true, string task="", bool mt_mode=false)

Retrieve the appropriate batch size for the specified task.

Declares the CBlastOptionsBuilder class.

Boolean Blast_SubjectIsProtein(EBlastProgramType p)

Returns true if the subject is protein.

Boolean Blast_ProgramIsNucleotide(EBlastProgramType p)

Boolean Blast_QueryIsProtein(EBlastProgramType p)

Returns true if the query is protein.

EBlastProgramType

Defines the engine's notion of the different applications of the BLAST algorithm.

Declares CBlastScopeSource class to create properly configured CScope objects to invoke the BLAST dat...

EProgram

This enumeration is to evolve into a task/program specific list that specifies sets of default parame...

Int2 BlastNumber2Program(EBlastProgramType number, char **program)

Return string name for program given a number.

const Int4 k_MinBatchSize

Int4 GetBatchSize(Int4 hits=-1)

const Int4 k_MaxBatchSize

CBlast4_get_request_info_request –.

CBlast4_get_search_results_reply –.

Class used to return ancillary data from a blast search, i.e.

Base command line argument class for a generic BLAST command line binary.

CRef< CBlastDatabaseArgs > GetBlastDatabaseArgs() const

Get the BLAST database arguments.

CRef< CFormattingArgs > GetFormattingArgs() const

Get the formatting options.

Argument class to collect database/subject arguments.

static bool HasBeenSet(const CArgs &args)

Auxiliary function to determine if the database/subject sequence has been set.

CRef< CSearchDatabase > GetSearchDatabase() const

Retrieve the search database information.

static const int kSubjectsDataLoaderPriority

The default priority for subjects, should be used for subjects/databases.

void SetSubjects(CRef< IQueryFactory > subjects, CRef< CScope > scope, bool is_protein)

Sets the subject sequences.

void SetSearchDatabase(CRef< CSearchDatabase > search_db)

Set the search database information.

static TRegisterLoaderInfo RegisterInObjectManager(CObjectManager &om, const string &dbname="nr", const EDbType dbtype=eUnknown, bool use_fixed_size_slices=true, CObjectManager::EIsDefault is_default=CObjectManager::eNonDefault, CObjectManager::TPriority priority=CObjectManager::kPriority_NotSet)

static string GetLoaderNameFromArgs(CConstRef< CSeqDB > db_handle)

Defines BLAST error codes (user errors included)

static void PrintArchive(CRef< objects::CBlast4_archive > archive, CNcbiOstream &out)

Auxiliary function to print the BLAST Archive in multiple output formats.

Generalized converter from an abstract source of biological sequence data to collections of blast inp...

Int8 GetNumSeqsProcessed() const

Int8 GetTotalLengthProcessed() const

Class to build CBlastOptionsHandle from blast4 ASN objects.

Encapsulates ALL the BLAST algorithm's options.

Class whose purpose is to create CScope objects which have data loaders added with different prioriti...

void AddDataLoaders(CRef< objects::CScope > scope)

Add the data loader configured in the object to the provided scope.

CRef< objects::CScope > NewScope()

Create a new, properly configured CScope.

void RevokeBlastDbDataLoader()

Removes the BLAST database data loader from the object manager.

void AddParam(EUsageParams p, int val)

FASTA-format output; see also ReadFasta in <objtools/readers/fasta.hpp>

Argument class to collect formatting options, use this to create a CBlastFormat object.

EOutputFormat GetFormattedOutputChoice() const

Get the choice of formatted output.

EOutputFormat

Defines the output formats supported by our command line formatter.

@ eJsonSeqalign

JSON seq-align.

@ eAsnText

ASN.1 text output.

@ eArchiveFormat

BLAST archive format.

@ eAsnBinary

ASN.1 binary output.

Class to return parts of the CBlast4_request, or data associated with a CBlast4_request,...

Defines user input exceptions.

Interface to create a BlastSeqSrc suitable for use in CORE BLAST from a a variety of BLAST database/s...

static bool HasBeenSet(const CArgs &args)

Auxiliary function to determine if the megablast database indexing options have been set.

CNcbiOstrstreamToString class helps convert CNcbiOstrstream to a string Sample usage:

NCBI C++ Object Manager dependant implementation of IQueryFactory.

Handle command line arguments for psiblast binary Programs supported: psiblast, phi-blastn,...

void SetInputPssm(CRef< objects::CPssmWithParameters > pssm)

Set the PSSM from the saved search strategy.

double GetKappaUngapped() const

double GetLambdaUngapped() const

double GetHUngapped() const

API for Remote Blast Requests.

void AddTaxIds(const set< TTaxId > &tax_ids)

void AddGi(TGi gi)

Add a new GI to the list.

static void FindVolumePaths(const string &dbname, ESeqType seqtype, vector< string > &paths, vector< string > *alias_paths=NULL, bool recursive=true, bool expand_links=true)

Find volume paths.

Uint8 GetTotalLength() const

Returns the sum of the lengths of all available sequences.

const string & GetDBNameList() const

Get list of database names.

int GetNumSeqs() const

Returns the number of sequences available.

string GetDate() const

Returns the construction date of the database.

Root class for all serialization exceptions.

Handles command line arguments for Tblastn binary.

void SetInputPssm(CRef< objects::CPssmWithParameters > pssm)

Set the PSSM from the saved search strategy.

const string kArgOutput

Output file name.

const string kArgRemote

Argument to determine whether searches should be run locally or remotely.

const string kArgUseIndex

Flag to force using or not using megablast database index.

const bool kDfltArgUseIndex

Default value for megablast database index flag.

const string kDfltArgQuery

Default value for query sequence input.

const string kArgQuery

Query sequence(s)

const string kArgSubject

Subject input file to search.

@ eNoCompositionBasedStats

Don't use composition based statistics.

std::ofstream out("events_result.xml")

main entry point for tests

const char * kArgOutputFormat

Argument to select formatted output type.

void SetEntrezQueryLimitation(const string &entrez_query)

Mutator for the entrez query.

string GetDatabaseName() const

Accessor for the database name.

void SetCompositionBasedStats(ECompoAdjustModes mode)

double GetEvalueThreshold() const

void SetNegativeGiList(CSeqDBGiList *gilist)

Mutator for the negative gi list.

int GetDbFilteringAlgorithmId()

Get the database filtering algorithm ID.

bool HaveNegativeTaxidList()

Check whether a negative tax id list is specified.

CRef< CSeqDB > GetSeqDb() const

Obtain a reference to the database.

void SetVerbose(EDebugMode verb=eDebug)

Adjust the debugging level.

list< TGi > GetNegativeGiList()

Get the negative GI list.

ESubjectMaskingType GetSubjectMaskingType()

int GetHitlistSize() const

bool HaveGiList()

Check whether a GI list is specified.

CBlastOptions & SetOptions()

Returns a reference to the internal options class which this object is a handle for.

void SetClientId(const string &client_id)

Sets the client ID used by this object to send requests.

list< TTaxId > GetTaxidList()

Get the Tax list.

EBlastProgramType EProgramToEBlastProgramType(EProgram p)

Convert EProgram to EBlastProgramType.

bool HaveEntrezQuery()

Check whether an Entrez query is specified.

list< TTaxId > GetNegativeTaxidList()

Get the negative tax id list.

EBlastProgramType GetProgramType() const

Returns the CORE BLAST notion of program type.

CRef< objects::CBlast4_request > ExtractBlast4Request(CNcbiIstream &in)

Extract a Blast4-request (a.k.a.

bool HasDbFilteringAlgorithmKey()

Check whether a database filtering algorithm key is specified.

const CBlastOptions & GetOptions() const

Return the object which this object is a handle for.

list< TGi > GetGiList()

Get the GI list.

bool HasSubjectMaskingType()

Get Subject Maksing Type (soft/hard)

ECompoAdjustModes GetCompositionBasedStats() const

string Blast_ProgramNameFromType(EBlastProgramType program)

Returns a string program name, given a blast::EBlastProgramType enumeration.

void LoadSequencesToScope(objects::CScope::TIds &ids, vector< TSeqRange > &ranges, CRef< objects::CScope > &scope)

This method retrieve sequence data in bulk to scope @ids seq id list [in] @ranges seq range list [in]...

bool HaveNegativeGiList()

Check whether a negative GI list is specified.

string GetEntrezQuery()

Get the Entrez query.

void SetFilteringAlgorithm(int filt_algorithm_id)

Temporary fix for backwards compatibility with other 6.0 SCs.

string GetDbFilteringAlgorithmKey()

Get the database filtering algorithm key.

bool HasDbFilteringAlgorithmId()

Check whether a database filtering algorithm ID is specified.

EMoleculeType

Molecule of the BLAST database.

void SetGiList(CSeqDBGiList *gilist)

Mutator for the gi list.

@ eNotSupported

Feature not supported.

@ eBlastDbIsNucleotide

nucleotide

@ eBlastDbIsProtein

protein

unsigned int TSeqPos

Type for sequence locations and lengths.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

bool Exist(const string &name) const

Check existence of argument description.

#define ERR_POST(message)

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

TErrCode GetErrCode(void) const

Get error code.

#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)

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

Generic macro to re-throw an exception.

CNcbiOstream & AsOutputFile(EIfExists if_exists, IOS_BASE::openmode mode=IOS_BASE::out)

const string & GetFileName(void) const

Return used file name (generated or given in the constructor).

static char GetPathSeparator(void)

Get path separator symbol specific for the current platform.

@ eIfExists_Throw

You can make call of AsInputFile/AsOutputFile only once, on each following call throws CFileException...

@ eNoRemove

Do not remove file.

static CSeq_id_Handle GetHandle(const CSeq_id &id)

Normal way of getting a handle, works for any seq-id.

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

CBioseq_Handle AddBioseq(CBioseq &bioseq, TPriority pri=kPriority_Default, EExist action=eExist_Throw)

Add bioseq, return bioseq handle.

static CRef< CObjectManager > GetInstance(void)

Return the existing object manager or create one.

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

void GetRegisteredNames(TRegisteredNames &names)

Get names of all registered data loaders.

vector< string > TRegisteredNames

vector< CSeq_id_Handle > TIds

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

int64_t Int8

8-byte (64-bit) signed integer

TThisType & SetToOpen(position_type toOpen)

static TThisType GetEmpty(void)

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

IO_PREFIX::ostream CNcbiOstream

Portable alias for ostream.

IO_PREFIX::istream CNcbiIstream

Portable alias for istream.

IO_PREFIX::streampos CNcbiStreampos

Portable alias for streampos.

static string Int8ToString(Int8 value, TNumToStringFlags flags=0, int base=10)

Convert Int8 to string.

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

Convert string to int.

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 Join(const TContainer &arr, const CTempString &delim)

Join strings using the specified delimiter.

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

Check if a string starts with a specified prefix value.

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

Truncate whitespace in a string.

@ fWithCommas

Use commas as thousands separator.

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

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

strategy

Block allocation strategies.

const TSequences & GetSequences(void) const

Get the variant data.

bool IsSeq_loc_list(void) const

Check if variant Seq_loc_list is selected.

bool IsDatabase(void) const

Check if variant Database is selected.

void SetResults(TResults &value)

Assign a value to Results data member.

const TDatabase & GetDatabase(void) const

Get the variant data.

void SetRequest(TRequest &value)

Assign a value to Request data member.

bool IsPssm(void) const

Check if variant Pssm is selected.

void SetBody(TBody &value)

Assign a value to Body data member.

bool IsSequences(void) const

Check if variant Sequences is selected.

list< CRef< CSeq_loc > > TSeq_loc_list

const TBioseq_set & GetBioseq_set(void) const

Get the variant data.

bool IsBioseq_set(void) const

Check if variant Bioseq_set is selected.

const TSeq_loc_list & GetSeq_loc_list(void) const

Get the variant data.

TMessages & SetMessages(void)

Assign a value to Messages data member.

const TPssm & GetPssm(void) const

Get the variant data.

list< CRef< CBioseq > > TSequences

void SetFrom(TFrom value)

Assign a value to From data member.

bool CanGetPssm(void) const

Check if it is safe to call GetPssm method.

const TPssm & GetPssm(void) const

Get the Pssm member data.

list< CRef< CSeq_align > > Tdata

const TSeq_set & GetSeq_set(void) const

Get the Seq_set member data.

list< CRef< CSeq_entry > > TSeq_set

char * dbname(DBPROCESS *dbproc)

Get name of current database.

std::istream & in(std::istream &in_, double &x_)

double r(size_t dimension_, const Int4 *score_, const double *prob_, double theta_)

double lambda(size_t dimMatrix_, const Int4 *const *scoreMatrix_, const double *q_)

NOTE: This file contains work in progress and the APIs are likely to change, please do not rely on th...

Main argument class for PSI-BLAST application.

Declares the CRemoteBlast class.

Declares the CImportStrategy and CExportStrategy.

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

CRef< objects::CObjectManager > om

vector< SSeqLoc > TSeqLocVector

Vector of sequence locations.

Configuration structure for the CBlastScopeSource.

bool m_UseGenbank

Use the Genbank data loader.

string m_BlastDbName

Name of the BLAST database to use (non-empty if m_UseBlastDbs is true)

void OptimizeForWholeLargeSequenceRetrieval(bool value=true)

Configures the BLAST database data loader to optimize the retrieval of *entire* large sequences.

bool m_UseBlastDbs

Use the BLAST database data loaders.

Structure to represent a single sequence to be fed to BLAST.

Main argument class for TBLASTN application.

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