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NCBI C++ ToolKit: include/algo/blast/blastinput/blast_args.hpp Source File

ExtractAlgorithmOptions(

& cmd_line_args,

m_GzipEnabled(

),

m_SRAaccessionEnabled(

),

m_UnalignedOutputStream(0) {};

{

m_UnalignedOutputStream;}

& program_description);

& default_task);

show_perc_identity =

,

is_tblastx =

,

is_igblast =

,

suppress_sum_stats =

)

: m_QueryIsProtein(query_is_protein), m_IsRpsBlast(is_rpsblast),

m_ShowPercentIdentity(show_perc_identity), m_IsTblastx(is_tblastx),

m_IsIgBlast(is_igblast), m_SuppressSumStats(suppress_sum_stats),

m_IsBlastn(

){}

filter_by_default =

)

: m_QueryIsProtein(query_is_protein),

m_FilterByDefault(filter_by_default) {}

x_TokenizeFilteringArgs(

& filtering_args,

vector<string>&

)

;

& default_option

& zero_option_descr =

)

: m_Is2and3Supported(is_2and3supported),

m_DefaultOpt(default_option),

m_ZeroOptDescr(zero_option_descr) {}

: m_QueryIsProtein(query_is_protein) {}

is_deltablast =

)

: m_DbTarget(db_target), m_NumIterations(1),

m_CheckPointOutput(0), m_AsciiMatrixOutput(0),

m_IsDeltaBlast(is_deltablast),

m_SaveLastPssm(

)

m_NumIterations;

m_NumIterations = num_iters;

m_CheckPointOutput !=

;

m_CheckPointOutput ? m_CheckPointOutput->GetStream() :

;

m_AsciiMatrixOutput !=

;

m_AsciiMatrixOutput ? m_AsciiMatrixOutput->GetStream() :

;

m_SaveLastPssm;

save_ascii_pssm,

msa_master_idx,

ignore_pssm_tmpl_seq);

(

) : m_JDistance(0.10), m_MinHits(0), m_CandidateSeqs(1000) {}

{

m_DomainDb;}

m_QueryCannotBeNucl(query_cannot_be_nucl)

m_InputFormat(eFasta),

m_MateInputStream(

),

m_EnableSraCache(

)

{

m_InputFormat;}

{

m_SraAccessions;}

kSubjectsDataLoaderPriority = 10;

HasBeenSet(

& args);

is_rpsblast =

,

is_igblast =

,

is_mapper =

,

is_kblast =

);

m_SupportsDatabaseMasking =

;

m_SearchDb.Empty() ?

: m_SearchDb->GetDatabaseName();

m_SearchDb = search_db;

m_Subjects = subjects;

m_IsProtein = is_protein;

(m_Subjects && scope) {

scope->AddScope(*

, kSubjectsDataLoaderPriority);

m_SupportIPGFiltering =

;

eQueryAnchoredIdentities,

eQueryAnchoredNoIdentities,

eFlatQueryAnchoredIdentities,

eIsVDB_SAM = eIsVDB | eIsSAM,

eIsAirrRearrangement = 0x04

m_NumDescriptions(0), m_NumAlignments(0),

m_DfltNumDescriptions(0), m_DfltNumAlignments(0),

m_IsIgBlast(isIgblast),

m_FormatFlags(flag),

m_HitsSortOption(-1),

m_HspsSortOption(-1)

m_DfltNumAlignments = m_DfltNumDescriptions = 10;

ParseFormattingString(

& args,

& custom_fmt_spec,

& custom_delim)

;

m_OutputFormat;

m_OutputFormat == eXml ||

m_OutputFormat == eAsnText ||

m_OutputFormat == eAsnBinary ||

m_OutputFormat == eXml2 ||

m_OutputFormat == eJson ||

m_OutputFormat == eXml2_S ||

m_OutputFormat == eJson_S ||

m_OutputFormat == eJsonSeqalign ||

m_OutputFormat == eSAM;

m_NumDescriptions;

m_NumAlignments;

m_CustomOutputFormatSpec;

ArchiveFormatRequested(

& args)

;

m_LineLength;

m_HitsSortOption;

m_HspsSortOption;

m_TrimReadIds(

),

m_PrintUnaligned(

),

m_NoDiscordant(

),

m_OnlyStrandSpecific(

),

m_PrintMdTag(

),

m_UnalignedOutputFormat(eSAM)

{

m_UnalignedOutputFormat;}

m_NumThreads(default_num_threads), m_MTMode(mt_mode)

m_MTMode = eNotSupported;

x_ExtractAlgorithmOptions(

& args);

HasBeenSet(

& args);

SetTask(

& task);

m_OptsHandle = opts_hndl;

m_BlastDbArgs;

m_BlastDbArgs = args;

m_QueryOptsArgs;

m_FormattingArgs;

m_MTArgs->GetNumThreads();

m_MTArgs->GetMTMode();

m_StdCmdLineArgs->SetInputStream(

);

m_SearchStrategyArgs->GetImportStream(args);

m_SearchStrategyArgs->GetExportStream(args);

m_RemoteArgs->ExecuteRemotely();

m_DebugArgs->ProduceDebugRemoteOutput();

m_DebugArgs->ProduceDebugOutput();

( !m_ClientId.empty() );

& args) = 0;

& task);

x_IssueWarningsForIgnoredOptions(

& args);

static CRef< CScope > m_Scope

User-defined methods of the data storage class.

CArgDescriptions * SetUpCommandLineArguments(TBlastCmdLineArgs &args)

Create a CArgDescriptions object and invoke SetArgumentDescriptions for each of the TBlastCmdLineArgs...

vector< CRef< IBlastCmdLineArgs > > TBlastCmdLineArgs

Type definition of a container of IBlastCmdLineArgs.

Auxiliary classes/functions for BLAST input library.

Declares class to encapsulate all BLAST options.

Declares the CBlastOptionsHandle and CBlastOptionsFactory classes.

EBlastProgramType

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

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

CRef< CRemoteArgs > m_RemoteArgs

remote vs. local execution options

string GetTask() const

Get the task for this object.

void SetOptionsHandle(CRef< CBlastOptionsHandle > opts_hndl)

Setter for the BLAST options handle, this is used if the options are recovered from a saved BLAST sea...

CRef< CBlastOptionsHandle > m_OptsHandle

The BLAST options handle, only non-NULL if assigned via SetOptionsHandle, i.e.

CRef< CQueryOptionsArgs > m_QueryOptsArgs

query options object

size_t GetNumThreads() const

Get the number of threads to spawn.

virtual int GetQueryBatchSize() const =0

Get the query batch size.

CRef< CBlastDatabaseArgs > m_BlastDbArgs

database/subject object

virtual CRef< CBlastOptionsHandle > x_CreateOptionsHandle(CBlastOptions::EAPILocality locality, const CArgs &args)=0

Create the options handle based on the command line arguments.

CRef< CSearchStrategyArgs > m_SearchStrategyArgs

arguments for dealing with search strategies

string m_Task

Task specified in the command line.

CRef< CDebugArgs > m_DebugArgs

Debugging arguments.

CRef< CBlastDatabaseArgs > GetBlastDatabaseArgs() const

Get the BLAST database arguments.

CNcbiIstream * GetImportSearchStrategyStream(const CArgs &args)

Get the input stream for the search strategy.

virtual ~CBlastAppArgs()

Our virtual destructor.

void SetInputStream(CRef< CTmpFile > input_file)

Set the input stream to a temporary input file (needed when importing a search strategy)

CRef< CMTArgs > m_MTArgs

multi-threaded options

CRef< CFormattingArgs > m_FormattingArgs

formatting options

bool ExecuteRemotely() const

Determine whether the search should be executed remotely or not.

bool ProduceDebugRemoteOutput() const

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

bool m_IsUngapped

Is this application being run ungapped.

CRef< CQueryOptionsArgs > GetQueryOptionsArgs() const

Get the options for the query sequence(s)

string GetClientId() const

Retrieve the client ID for remote requests.

TBlastCmdLineArgs m_Args

Set of command line argument objects.

void SetBlastDatabaseArgs(CRef< CBlastDatabaseArgs > args)

Set the BLAST database arguments.

CRef< CFormattingArgs > GetFormattingArgs() const

Get the formatting options.

CNcbiOstream * GetExportSearchStrategyStream(const CArgs &args)

Get the output stream for the search strategy.

bool ProduceDebugOutput() const

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

CRef< CStdCmdLineArgs > m_StdCmdLineArgs

standard command line arguments class

CRef< CHspFilteringArgs > m_HspFilteringArgs

HSP filtering arguments.

string m_ClientId

Client ID used for remote BLAST submissions, must be populated by subclasses.

Argument class to collect database/subject arguments.

CRef< objects::CScope > m_Scope

CScope object in which all subject sequences read are kept.

bool m_IsMapper

true for short read mapper

CRef< CSearchDatabase > GetSearchDatabase() const

Retrieve the search database information.

bool IsProtein() const

Is the database/subject protein?

bool m_SupportsDatabaseMasking

true if it's supported

static const int kSubjectsDataLoaderPriority

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

void SetIPGFilteringSupport(bool val)

bool m_IsProtein

Is the database/subject(s) protein?

bool m_RequestMoleculeType

Determines whether the database's molecule type should be requested in the command line,...

bool m_IsIgBlast

true if the search is Ig-BLAST

CRef< IQueryFactory > m_Subjects

The subject sequences.

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

Sets the subject sequences.

bool m_IsRpsBlast

true if the search is RPS-BLAST

CRef< IQueryFactory > GetSubjects(objects::CScope *scope=NULL)

Retrieve subject sequences, if provided.

CRef< CSearchDatabase > m_SearchDb

Description of the BLAST database.

CSearchDatabase::EMoleculeType EMoleculeType

alias for the database molecule type

bool m_SupportIPGFiltering

true if IPG filtering is supported

void SetSearchDatabase(CRef< CSearchDatabase > search_db)

Set the search database information.

void SetDatabaseMaskingSupport(bool val)

Turns on/off database masking support.

bool m_IsKBlast

true for Kblastp

string GetDatabaseName() const

Get the BLAST database name.

Encapsulates ALL the BLAST algorithm's options.

EAPILocality

Enumerates the possible contexts in which objects of this type can be used.

Argument class for collecting composition based statistics options.

bool m_Is2and3Supported

Are options 2 and 3 supported.

CCompositionBasedStatsArgs(bool is_2and3supported=true, const string &default_option=kDfltArgCompBasedStats, const string &zero_option_descr="")

Constructor.

string m_ZeroOptDescr

Non standard description for option zero.

string m_DefaultOpt

Default option.

Argument class to collect debugging options.

bool ProduceDebugRemoteOutput() const

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

CDebugArgs()

Default constructor.

bool m_DebugOutput

Should debugging (verbose) output be printed.

bool m_RmtDebugOutput

Should debugging (verbose) output be printed for remote BLAST.

bool ProduceDebugOutput() const

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

Argument class to collect options specific to DELTA-BLAST.

CDeltaBlastArgs & operator=(const CDeltaBlastArgs &rhs)

Prohibit assignment operator.

CDeltaBlastArgs(void)

Constructor.

CRef< CSearchDatabase > m_DomainDb

Conserved Domain Database.

virtual ~CDeltaBlastArgs()

Our virtual destructor.

CRef< CSearchDatabase > GetDomainDatabase(void)

Get domain database.

CDeltaBlastArgs(const CDeltaBlastArgs &rhs)

Prohibit copy constructor.

bool m_ShowDomainHits

Is printing CDD hits requested.

bool GetShowDomainHits(void) const

Get show domain hits option value.

Argument class to retrieve discontiguous megablast arguments.

Argument class for collecting filtering options.

CFilteringArgs(bool query_is_protein=true, bool filter_by_default=true)

Constructor.

bool m_QueryIsProtein

true if the query is protein

bool m_FilterByDefault

Should filtering be applied by default?

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

TSeqPos m_NumDescriptions

Number of 1-line descr. to show.

TSeqPos m_DfltNumDescriptions

Default value for num descriptions.

int GetHitsSortOption() const

bool HasStructuredOutputFormat() const

Returns true if the desired output format is structured (needed to determine whether to print or not ...

CFormattingArgs(bool isIgblast=false, EFormatFlags flag=eDefaultFlag)

Default constructor.

TSeqPos m_NumAlignments

Number of alignments to show.

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.

EFormatFlags m_FormatFlags

EOutputFormat

Defines the output formats supported by our command line formatter.

@ eJsonSeqalign

JSON seq-align.

@ eTabular

Tabular output.

@ eCommaSeparatedValues

Comma-separated values.

@ eCommaSeparatedValuesWithHeader

Comma-separated values with a header.

@ eAsnText

ASN.1 text output.

@ eArchiveFormat

BLAST archive format.

@ eAirrRearrangement

igblast AIRR rearrangement, 19

@ eXml2_S

XML2 single file.

@ eJson_S

JSON2 single file.

@ eFasta

unaligned reads in magicblast

@ eAsnBinary

ASN.1 binary output.

@ eFlatQueryAnchoredNoIdentities

@ eTabularWithComments

Tabular output with comments.

bool m_IsIgBlast

IgBlast has a different default num_alignments.

int GetHspsSortOption() const

string m_CustomOutputFormatSpec

The format specification for custom output, e.g.

EOutputFormat m_OutputFormat

Choice of formatting output.

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?

TSeqPos m_DfltNumAlignments

Default value for num alignments.

string GetCustomDelimiter()

bool m_ShowGis

Display NCBI GIs?

bool m_Html

Display HTML output?

Argument class to collect the frame shift penalty for out-of-frame searches.

Argument class to retrieve the gap trigger option.

bool m_QueryIsProtein

true if the query is protein

CGapTriggerArgs(bool query_is_protein)

Constructor.

Argument class for collecting gapped options.

Argument class for general search BLAST algorithm options: evalue, gap penalties, query filter string...

bool m_QueryIsProtein

true if the query is protein

bool m_IsRpsBlast

true if the search is RPS-BLAST

bool m_IsIgBlast

true if the search is igblast

bool m_IsTblastx

true if the search is tblastx

bool m_ShowPercentIdentity

true if the percent identity option should be shown

CGenericSearchArgs(bool query_is_protein=true, bool is_rpsblast=false, bool show_perc_identity=false, bool is_tblastx=false, bool is_igblast=false, bool suppress_sum_stats=false)

Constructor.

bool m_SuppressSumStats

true if search is blastn or blastp

Argument class to collect the genetic code for all queries/subjects.

CGeneticCodeArgs(ETarget t)

Constructor.

ETarget m_Target

Genetic code target.

ETarget

Enumeration defining which sequences the genetic code applies to.

@ eQuery

Query genetic code.

Argument class to retrieve options for filtering HSPs (e.g.

Argument class to collect options specific to igBLAST.

CRef< CIgBlastOptions > m_IgOptions

Igblast options to fill.

bool m_IsProtein

Is this a protein search?

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

CRef< CIgBlastOptions > GetIgBlastOptions()

CIgBlastArgs(bool is_protein)

CRef< objects::CScope > m_Scope

scope to get sequences

Argument class to collect options specific to KBLASTP.

virtual ~CKBlastpArgs()

Our virtual destructor.

double m_JDistance

Jaccard distance.

int m_CandidateSeqs

Number of candidate sequences to try BLAST on.

CKBlastpArgs(const CKBlastpArgs &rhs)

Prohibit copy constructor.

CKBlastpArgs & operator=(const CKBlastpArgs &rhs)

Prohibit assignment operator.

CKBlastpArgs(void)

Constructor.

int GetMinHits(void)

Get the minimum number of LSH matches.

int m_MinHits

Minimum number of hits in LSH phase.

string m_DbIndex

Database/index.

int GetCandidateSeqs(void)

Number of candidate sequences to attempt with BLASTP.

string GetDatabase(void)

The database.

double GetJaccardDistance(void)

Get the Jaccard distance.

Argument class for collecting the largest intron size.

Argument class to collect multi-threaded arguments.

size_t GetNumThreads() const

Get the number of threads to spawn.

size_t m_NumThreads

Number of threads to spawn.

CMTArgs(size_t default_num_threads=CThreadable::kMinNumThreads, EMTMode mt_mode=eNotSupported)

Default Constructor.

Formatting args for magicblast advertising only SAM and fast tabular formats.

bool TrimReadIds(void) const

Should read ids be in SAM format be trimmed of .1 and .2 endings for paired mapping.

const string & GetUserTag(void) const

Get a user tag added to each alignment.

bool SelectRevOnly(void) const

Specify rev-only strands.

bool SelectFwdRev(void) const

Specify fwd/ref strands.

CMapperFormattingArgs(void)

EOutputFormat m_UnalignedOutputFormat

bool SelectFwdOnly(void) const

Specify fwd-only strands.

EOutputFormat GetUnalignedOutputFormat(void) const

Get format choice for unaligned reads.

bool SelectRevFwd(void) const

Specify rev/fwd strands.

bool SelectOnlyStrandSpecific(void) const

Specify only-strand-specific.

virtual bool ArchiveFormatRequested(const CArgs &) const

bool PrintMdTag(void) const

Should MD tag be included in SAM report.

bool NoDiscordant(void) const

Should non-concordant pairs be filtered out of report.

bool m_OnlyStrandSpecific

bool PrintUnaligned(void) const

Should unaligned reads be reported.

Argument class to collect query options for BLAST Mapper.

bool IsSraCacheEnabled(void) const

Is SRA caching in local files enabled (see File Caching at https://github.com/ncbi/sra-tools/wiki/Too...

const vector< string > & GetSraAccessions(void) const

Get a list of SRA accessions.

bool HasMateInputStream(void) const

Does the mate input stream exits.

CMapperQueryOptionsArgs(void)

EInputFormat GetInputFormat(void) const

Are queries provided in Fastc format.

CNcbiIstream * m_MateInputStream

EInputFormat m_InputFormat

bool IsPaired(void) const

Are query sequences paired.

EInputFormat

Input formats.

vector< string > m_SraAccessions

unique_ptr< CDecompressIStream > m_DecompressIStream

CNcbiIstream * GetMateInputStream(void) const

Get input stream for query mates.

Argument class to retrieve and set the scoring matrix name BLAST algorithm option.

Argument class to retrieve megablast database indexing options.

Defines values for match and mismatch in nucleotide comparisons as well as non-greedy extension.

Argument class to retrieve and set the off-diagonal range used in 2-hit algorithm.

Argument class to collect options specific to PHI-BLAST.

Argument class to populate an application's name and description.

string m_ProgDesc

Application's description.

string m_ProgName

Application's name.

Argument class to collect options specific to PSI-BLAST.

CPsiBlastArgs(ETargetDatabase db_target=eProteinDb, bool is_deltablast=false)

Constructor.

CPsiBlastArgs & operator=(const CPsiBlastArgs &rhs)

Prohibit assignment operator.

size_t GetNumberOfIterations() const

Retrieve the number of iterations to perform.

virtual ~CPsiBlastArgs()

Our virtual destructor.

bool RequiresAsciiPssmOutput() const

Returns true if ASCII PSSM is required to be printed.

bool m_SaveLastPssm

Save PSSM after the last database search.

CNcbiOstream * GetCheckPointOutputStream()

Get the checkpoint file output stream.

CRef< CAutoOutputFileReset > m_AsciiMatrixOutput

ASCII matrix output file.

bool m_IsDeltaBlast

Are the aruments set up for Delta Blast.

ETargetDatabase

Enumeration to determine the molecule type of the database.

@ eProteinDb

Traditional, iterated PSI-BLAST.

void SetNumberOfIterations(unsigned int num_iters)

Retrieve the number of iterations to perform.

CNcbiOstream * GetAsciiMatrixOutputStream()

Get the ASCII matrix output stream.

bool RequiresCheckPointOutput() const

Returns true if checkpoint PSSM is required to be printed.

CRef< CAutoOutputFileReset > m_CheckPointOutput

checkpoint output file

CPsiBlastArgs(const CPsiBlastArgs &rhs)

Prohibit copy constructor.

bool GetSaveLastPssm(void) const

Should the PSSM after the last database search be saved.

ETargetDatabase m_DbTarget

Molecule of the database.

void SetSaveLastPssm(bool b)

Set the on/off switch for saving PSSM after the last database search.

CRef< objects::CPssmWithParameters > m_Pssm

PSSM.

size_t m_NumIterations

number of iterations to perform

CRef< objects::CPssmWithParameters > GetInputPssm() const

Get the PSSM read from checkpoint file.

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

Set the PSSM read from saved search strategy.

Argument class to collect PSSM engine options.

bool m_IsDeltaBlast

Are these arumnets for Delta Blast.

CPssmEngineArgs(bool is_deltablast=false)

Constructor.

Argument class to collect query options.

bool m_UseLCaseMask

use lowercase masking in FASTA input

objects::ENa_strand GetStrand() const

Get strand to search in query sequence(s)

void SetRange(const TSeqRange &range)

Set query sequence range restriction.

bool GetParseDeflines() const

Should the defline be parsed?

bool QueryIsProtein() const

Is the query sequence protein?

CQueryOptionsArgs(bool query_cannot_be_nucl=false)

Constructor.

objects::ENa_strand m_Strand

Strand(s) to search.

TSeqRange m_Range

range to restrict the query sequence(s)

bool m_ParseDeflines

Should the deflines be parsed?

bool m_QueryCannotBeNucl

only false for blast[xn], and tblastx true in case of PSI-BLAST

TSeqRange GetRange() const

Get query sequence range restriction.

bool UseLowercaseMasks() const

Use lowercase masking in FASTA input?

RMH: Argument class to retrieve and set the options specific to the RMBlastN algorithm.

Argument class to collect remote vs. local execution.

bool m_IsRemote

Should the search be executed remotely?

CRemoteArgs()

Default constructor.

bool ExecuteRemotely() const

Return whether the search should be executed remotely or not.

Argument class to import/export the search strategy.

Argument class to retrieve input and output streams for a command line program.

bool m_GzipEnabled

If true input file will be decompressed with gzip if filename ends with ".gz".

CNcbiOstream * GetUnalignedOutputStream() const

Get output stream for unaligned sequences/reads (for magicblast)

unique_ptr< CDecompressIStream > m_DecompressIStream

CRef< CTmpFile > m_QueryTmpInputFile

ASN.1 specification of query sequences when read from a saved search strategy.

void SetGzipEnabled(bool g)

Set automatic decompression of the input file is file name is recognized.

unique_ptr< CCompressOStream > m_CompressOStream

CNcbiOstream * m_OutputStream

Application's output stream.

CNcbiIstream * m_InputStream

Application's input stream.

bool m_SRAaccessionEnabled

If true, option to specify SRA runs will be presented as possible query input.

bool HasUnalignedOutputStream(void) const

Is there a separate output stream for unaligned sequences/reads (for magicblast)

CNcbiOstream * m_UnalignedOutputStream

Output stream to report unaligned sequences/reads.

void SetSRAaccessionEnabled(bool g)

enables sra accession flag

unique_ptr< CCompressOStream > m_UnalignedCompressOStream

CStdCmdLineArgs()

Default constructor.

Argument class to specify the supported tasks a given program.

const set< string > m_SupportedTasks

Set of supported tasks by this command line argument.

string m_DefaultTask

Default task for this command line argument.

Argument class to retrieve and set the window size BLAST algorithm option.

Argument class to retrieve and set the word threshold BLAST algorithm option.

BLAST Command line arguments design The idea is to have several small objects (subclasses of IBlastCm...

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

Extracts BLAST algorithmic options from the command line arguments into the CBlastOptions object.

virtual void SetArgumentDescriptions(CArgDescriptions &arg_desc)=0

Sets the command line descriptions in the CArgDescriptions object relevant to the subclass.

virtual ~IBlastCmdLineArgs()

Our virtual destructor.

Constant declarations for command line arguments for BLAST programs.

const bool kDfltArgParseDeflines

Default argument to specify whether sequences deflines should be parsed.

const bool kDfltArgUseLCaseMasking

Default argument to specify whether lowercase masking should be used.

const string kDfltArgCompBasedStats

Default argument for composition based statistics.

Include a standard set of the NCBI C++ Toolkit most basic headers.

const size_t kDfltArgNumDescriptions

Default number of one-line descriptions to display in the traditional BLAST report.

const size_t kDfltArgNumAlignments

Default number of alignments to display in the traditional BLAST report.

const size_t kDfltLineLength

static SQLCHAR output[256]

bool IsProtein() const

Determine whether this database contains protein sequences or not.

EMoleculeType

Molecule of the BLAST database.

unsigned int TSeqPos

Type for sequence locations and lengths.

bool NotEmpty(void) const THROWS_NONE

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

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define BEGIN_SCOPE(ns)

Define a new scope.

IO_PREFIX::ostream CNcbiOstream

Portable alias for ostream.

IO_PREFIX::istream CNcbiIstream

Portable alias for istream.

#define NCBI_BLASTINPUT_EXPORT

ENa_strand

strand of nucleic acid

Declares CIgBlast, the C++ API for the IG-BLAST engine.

Defines command line argument related classes.

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

C++ I/O stream wrappers to compress/decompress data on-the-fly.

int g(Seg_Gsm *spe, Seq_Mtf *psm, Thd_Gsm *tdg)

Uniform BLAST Search Interface.

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