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

Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/blast__formatter_8cpp_source.html below:

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

arg_desc->SetUsageContext(

().GetProgramBasename(),

arg_desc->SetCurrentGroup(

);

arg_desc->AddOptionalKey(

,

,

,

arg_desc->AddOptionalKey(

,

,

,

arg_desc->SetCurrentGroup(

);

arg_desc->AddDefaultKey(

,

,

,

arg_desc->SetCurrentGroup(

);

,

);

arg_desc->SetCurrentGroup(

);

first_time =

;

(seqloc, scope);

runtime_error(

);

( !seq_entry.

() ) {

runtime_error(

);

(b4_queries->

()) {

( !(*seqloc)->GetId()->IsLocal() );

list<CRef<CBioseq> > subjects =

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

retval.push_back(

(sl, subj_scope));

retval.push_back(

(*sl, subj_scope));

isRemote =

;

db_adapter.

();

(scope.

()) {

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

* bl2seq_legacy = getenv(

);

kGenbankLoaderPriority = 99;

scope->AddDataLoader(genbank_loader, kGenbankLoaderPriority);

(

<<

);

& kRid = args[

].HasValue()

);

filtering_algorithm = -1;

db_args->

(subject_factory, subj_scope,

(!kRid.empty() || isRemoteLoader),

==

,

isPsiBlast = (

==

);

);

);

kRid = args[

].AsString();

cerr <<

<< kRid <<

<< endl;

cerr <<

<< kRid <<

<< endl;

cerr <<

<< kRid <<

<< endl;

(args[

].

()) {

(

argc,

* argv[]

)

Declares singleton objects to store the version and reference for the BLAST engine.

Produce formatted blast output for command line applications.

Data loader implementation that uses the blast databases remotely.

string RegisterOMDataLoader(CRef< CSeqDB > db_handle)

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

string GetCmdlineArgs(const CNcbiArguments &a)

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.

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

Utility functions for BLAST command line applications.

#define CATCH_ALL(exit_code)

Standard catch statement for all BLAST command line programs.

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

#define EXIT_CODE__UNKNOWN_RID

static TSeqLocVector s_ConvertSubjects2TSeqLocVector(CRef< CRemoteBlast > remote_blast)

Extracts the subject sequence data from remote_blast into a TSeqLocVector.

#define EXIT_CODE__SEARCH_PENDING

int main(int argc, const char *argv[])

#define EXIT_CODE__SEARCH_FAILED

Auxiliary classes/functions for BLAST input library.

bool HasRawSequenceData(const objects::CBioseq &bioseq)

Returns true if the Bioseq passed as argument has the full, raw sequence data in its Seq-inst field.

Boolean Blast_SubjectIsProtein(EBlastProgramType p)

Returns true if the subject is protein.

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.

const CSeq_id * GetFirstId() const

bool IsProtein() const

Returns true if the database is protein.

size_t GetNumQueries() const

Retrieve the number of queries in this object.

Argument class to collect database/subject arguments.

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.

@ eNucleotide

nucleotide database

@ eProtein

protein database

Defines BLAST error codes (user errors included)

This class formats the BLAST results for command line applications.

void SetHitsSortOption(int hitsSortOption)

void SetHspsSortOption(int hspsSortOption)

void PrintOneResultSet(const blast::CSearchResults &results, CConstRef< blast::CBlastQueryVector > queries, unsigned int itr_num=numeric_limits< unsigned int >::max(), blast::CPsiBlastIterationState::TSeqIds prev_seqids=blast::CPsiBlastIterationState::TSeqIds(), bool is_deltablast_domain_result=false)

Print all alignment information for a single query sequence along with any errors or warnings (errors...

void SetCustomDelimiter(string customDelim)

void PrintEpilog(const blast::CBlastOptions &options)

Print the footer of the blast report.

void SetBaseFile(string base)

For use by XML2 only.

void SetLineLength(size_t len)

Set Alignment Length.

void WriteArchive(blast::IQueryFactory &queries, blast::CBlastOptionsHandle &options_handle, const blast::CSearchResultSet &results, unsigned int num_iters=0, const list< CRef< objects::CBlast4_error > > &msg=list< CRef< objects::CBlast4_error > >())

Writes out the query and results as an "archive" format.

void PrintProlog()

Print the header of the blast report.

bool m_LoadFromArchive

Tracks whether results come from an archive file.

virtual int Run()

@inheritDoc

virtual void Init()

@inheritDoc

CRef< CRemoteBlast > m_RmtBlast

Our link to the NCBI BLAST service.

CBlastUsageReport m_UsageReport

CRef< CBlastQueryVector > x_ExtractQueries(bool query_is_protein)

Extracts the queries to be formatted.

int PrintFormattedOutput(void)

Prints the BLAST formatted output.

CRef< CBlastScopeSource > m_QueryScopeSource

The source of CScope objects for queries.

SSeqLoc x_QueryBioseqToSSeqLoc(const CBioseq &bioseq, CRef< CScope > scope)

Package a scope and Seq-loc into a SSeqLoc from a Bioseq.

CBlastFormatterApp()

@inheritDoc

CRef< CBlastSearchQuery > x_BuildQueryFromPssm(const CPssmWithParameters &pssm)

Build the query from a PSSM.

Encapsulates ALL the BLAST algorithm's options.

void AddQuery(CRef< CBlastSearchQuery > q)

Add a query to the set.

CRef< objects::CScope > GetScope(size_type i) const

Get the scope containing a query by index.

size_type size() const

Identical to Size, provided to facilitate STL-style iteration.

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 AddParam(EUsageParams p, int val)

Keeps track of the version of the BLAST engine in the NCBI C++ toolkit.

Argument class to collect debugging options.

bool ProduceDebugRemoteOutput() const

Return whether debug (verbose) output should be produced on remote searches (only available when comp...

virtual void ExtractAlgorithmOptions(const CArgs &cmd_line_args, CBlastOptions &options)

Interface method,.

bool ProduceDebugOutput() const

Return whether debug (verbose) output should be produced (only available when compiled with _DEBUG)

virtual void SetArgumentDescriptions(CArgDescriptions &arg_desc)

Interface method,.

void DebugDumpText(ostream &out, const string &bundle, unsigned int depth) const

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

int GetHitsSortOption() const

virtual bool ArchiveFormatRequested(const CArgs &args) const

virtual void SetArgumentDescriptions(CArgDescriptions &arg_desc)

Interface method,.

string GetCustomOutputFormatSpec() const

Retrieve for string that specifies the custom output format for tabular and comma-separated value.

EOutputFormat GetFormattedOutputChoice() const

Get the choice of formatted output.

virtual void ExtractAlgorithmOptions(const CArgs &args, CBlastOptions &opts)

Interface method,.

@ eXml2_S

XML2 single file.

@ eJson_S

JSON2 single file.

int GetHspsSortOption() const

TSeqPos GetNumAlignments() const

Number of alignments to show in traditional BLAST output.

bool ShowGis() const

Display the NCBI GIs in formatted output?

TSeqPos GetNumDescriptions() const

Number of one-line descriptions to show in traditional BLAST output.

size_t GetLineLength() const

bool DisplayHtmlOutput() const

Display HTML output?

string GetCustomDelimiter()

static TRegisterLoaderInfo RegisterInObjectManager(CObjectManager &om, CReader *reader=0, CObjectManager::EIsDefault is_default=CObjectManager::eDefault, CObjectManager::TPriority priority=CObjectManager::kPriority_NotSet)

Defines user input exceptions.

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

NCBI C++ Object Manager dependant implementation of IQueryFactory.

const CSeq_entry & GetQuery() const

Retrieve the query sequence.

bool HasQuery() const

Has this PSSM a query in it?

void SetPreopenConnection(bool preopen=true)

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)

API for Remote Blast Requests.

Search Results for All Queries.

void AddTaxIds(const set< TTaxId > &tax_ids)

Root class for all serialization exceptions.

Template class for iteration on objects of class C (non-medifiable version)

const string kArgOutput

Output file name.

const string kArgArchive

Argument to blast_formatter to request BLAST archive file name.

const string kTask

Task to perform.

const string kArgParseDeflines

Argument to specify if the query and subject sequences defline should be parsed.

const string kArgRid

Argument to blast_formatter to request RID.

void Print(const CCompactSAMApplication::AlignInfo &ai)

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

main entry point for tests

bool LoadFromArchive()

Loads next chunk of archive from file.

CRef< CBlastOptionsHandle > GetSearchOptions()

Get the search options used for this search.

string GetDatabaseName() const

Accessor for the database name.

CRef< objects::CPssmWithParameters > GetPSSM(void)

Get the PSSM produced by the search.

int GetDbGeneticCode() const

void SetNegativeGiList(CSeqDBGiList *gilist)

Mutator for the negative gi list.

string GetErrors(void)

This returns a string containing any errors that were produced by the search.

set< TTaxId > & GetNegativeTaxidList()

CRef< CSeqDB > GetSeqDb() const

Obtain a reference to the database.

ESearchStatus CheckStatus()

Returns the status of a previously submitted search/RID.

void SetVerbose(EDebugMode verb=eDebug)

Adjust the debugging level.

string GetTask() const

Returns the task used to create the remote search (if any)

bool IsProtein() const

Determine whether this database contains protein sequences or not.

CBlastOptions & SetOptions()

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

CRef< objects::CBlast4_queries > GetQueries()

Get the queries used for this search.

EBlastProgramType GetProgramType() const

Returns the CORE BLAST notion of program type.

int GetQueryGeneticCode() const

CRef< objects::CBlast4_database > GetDatabases()

Get the database used by the search.

bool GetSumStatisticsMode() const

Sum statistics options.

CRef< CSearchResultSet > GetResultSet()

Submit the search (if necessary) and return the results.

bool GetMBIndexLoaded() const

string Blast_ProgramNameFromType(EBlastProgramType program)

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

CBlast4_subject::TSeq_loc_list GetSubjectSeqLocs()

set< TTaxId > & GetTaxidList()

bool IsErrMsgArchive(void)

Int4 GetDbFilteringAlgorithmId() const

Returns the filtering algorithm ID used in the database.

list< CRef< objects::CBioseq > > GetSubjectSequences()

Returns subject sequences if "bl2seq" mode used.

const char * GetMatrixName() const

bool IsDbSearch()

Return values states whether GetDatabases or GetSubjectSequences call should be used.

unsigned int GetPsiNumberOfIterations(void)

void SetGiList(CSeqDBGiList *gilist)

Mutator for the gi list.

@ eInvalidArgument

Invalid argument to some function/method (could be programmer error - prefer assertions in those case...

@ eStatus_Failed

Completed but failed, call GetErrors/GetErrorVector()

@ eStatus_Pending

Not completed yet.

@ eStatus_Unknown

Never submitted or purged from the system.

@ eStatus_Done

Completed successfully.

@ eBlastDbIsNucleotide

nucleotide

@ eBlastDbIsProtein

protein

void SetFullVersion(CRef< CVersionAPI > version)

Set version data for the program.

void HideStdArgs(THideStdArgs hide_mask)

Set the hide mask for the Hide Std Flags.

unsigned int TSeqPos

Type for sequence locations and lengths.

virtual const CArgs & GetArgs(void) const

Get parsed command line arguments.

int AppMain(int argc, const char *const *argv, const char *const *envp=0, EAppDiagStream diag=eDS_Default, const char *conf=NcbiEmptyCStr, const string &name=NcbiEmptyString)

Main function (entry point) for the NCBI application.

CVersionInfo GetVersion(void) const

Get the program version information.

virtual void SetupArgDescriptions(CArgDescriptions *arg_desc)

Setup the command line argument descriptions.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

const CNcbiArguments & GetArguments(void) const

Get the application's cached unprocessed command-line arguments.

@ fHideXmlHelp

Hide XML help description.

@ fHideLogfile

Hide log file description.

@ fHideFullVersion

Hide full version description.

@ fHideDryRun

Hide dryrun description.

@ fHideConffile

Hide configuration file description.

@ eExcludes

One argument excludes another.

@ eInputFile

Name of file (must exist and be readable)

@ eString

An arbitrary string.

@ eOutputFile

Name of file (must be writable)

EDiagSev SetDiagPostLevel(EDiagSev post_sev=eDiag_Error)

Set the threshold severity for posting the messages.

#define LOG_POST(message)

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

@ eDiag_Warning

Warning message.

@ eDiag_Critical

Critical error message.

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.

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

Generic macro to re-throw an exception.

void Info(CExceptionArgs_Base &args)

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

CConstBeginInfo ConstBegin(const C &obj)

Get starting point of non-modifiable object hierarchy.

TLoader * GetLoader(void) const

Get pointer to the loader.

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.

void AddScope(CScope &scope, TPriority pri=kPriority_Default)

Add the scope's datasources as a single group with the given priority All data sources (data loaders ...

TObjectType * GetPointer(void) THROWS_NONE

Get pointer,.

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.

bool IsEnabled(void)

Indicates whether application usage statistics collection is enabled for a current reporter instance.

IO_PREFIX::ostream CNcbiOstream

Portable alias for ostream.

IO_PREFIX::istream CNcbiIstream

Portable alias for istream.

double Elapsed(void) const

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

void Start(void)

Start the timer.

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

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

bool IsSeq_loc_list(void) const

Check if variant Seq_loc_list is selected.

const TName & GetName(void) const

Get the Name member data.

bool IsPssm(void) const

Check if variant Pssm 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.

const TPssm & GetPssm(void) const

Get the variant data.

list< CRef< CSeq_loc > > TSeq_loc_list

const TSeq & GetSeq(void) const

Get the variant data.

bool IsSeq(void) const

Check if variant Seq is selected.

const string version

version string

Defines the CNcbiApplication and CAppException classes for creating NCBI applications.

NCBI C++ stream class wrappers for triggering between "new" and "old" C++ stream libraries.

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

Declares the CRemoteBlast class.

vector< SSeqLoc > TSeqLocVector

Vector of sequence locations.

Configuration structure for the CBlastScopeSource.

void OptimizeForWholeLargeSequenceRetrieval(bool value=true)

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

@ eUseNoDataLoaders

Do not add any data loaders.

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

CConstRef< objects::CSeq_loc > seqloc

Seq-loc describing the sequence to use as query/subject to BLAST The types of Seq-loc currently suppo...

CRef< objects::CScope > scope

Scope where the sequence referenced can be found by the toolkit's object manager.

RetroSearch is an open source project built by @garambo | Open a GitHub Issue

Search and Browse the WWW like it's 1997 | Search results from DuckDuckGo

HTML: 3.2 | Encoding: UTF-8 | Version: 0.7.4