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NCBI C++ ToolKit: src/algo/blast/blastinput/blast_args.cpp Source File

& program_desc)

: m_ProgName(program_name), m_ProgDesc(program_desc)

& default_task)

: m_SupportedTasks(supported_tasks), m_DefaultTask(default_task)

arg_desc.

(

,

,

,

=

;

+=

;

,

,

?

:

;

,

,

,

,

,

,

,

,

,

gap_open=0, gap_extend=0;

(args[

].AsString().c_str(), &gap_open, &gap_extend);

.Set(

,

);

,

,

,

,

,

vector<string>&

)

(

.size() != 3) {

);

vector<string> tokens;

);

(

);

(filter_dbs > 1) {

,

,

,

,

,

word_threshold =

(threshold);

}

(program ==

&&

threshold = -1;

(threshold != -1) {

,

,

,

,

,

,

,

allowed_values.

(16);

allowed_values.

(18);

allowed_values.

(21);

;

:

;

legend = (

)

+

+

+

+ one_opt_insrt +

,

& comp_stat_string,

smith_waterman_value,

(comp_stat_string[0]) {

:

:

:

:

:

:

:

);

(comp_stat_string[1]) ==

) {

,

arg_desc.

(

, ARG_GAPPED);

((cbs[0] !=

)&& (cbs[0] !=

) && (cbs[0] !=

)) {

);

gcs[] = {1,2,3,4,5,6,9,10,11,12,13,14,15,16,21,22,23,24,25,26,27,28,29,30,31,33};

genetic_codes(gcs, gcs+

(gcs)/

(*gcs));

(genetic_codes.

(

) != genetic_codes.

());

;

,

,

,

,

,

,

,

,

,

);

vector<string> msa_exclusions;

,

(vector<string>, exclusion, msa_exclusions) {

(vector<string>, exclusion, msa_exclusions) {

,

);

vector<string> ignore_pssm_master_exclusions;

ignore_pssm_master_exclusions.push_back(

);

(vector<string>, exclusion, msa_exclusions) {

,

msa_master_idx,

ignore_pssm_tmplt_seq)

pssm_engine.

();

kSaveAllPssms

(kSaveAsciiPssm) {

msa_master_idx = 0;

);

(

);

+=

;

,

(

.getline(

, 4096)) {

ltype = line.substr(0, 2);

name = line.substr(4);

(ltype ==

)

pattern = line.substr(4);

(!pattern.empty())

);

,

,

,

,

,

s = args[

].AsString();

list<string> tokens;

vector<double> coeffs;

(tokens.size() < 3) {

(

)

+

s +

);

it = tokens.begin();

(; it != tokens.end(); ++it) {

(

)

+

s +

);

(

)

+

s +

);

ref_type =

;

suffix[] =

;

df_num_align[3] = {3,3,3};

(

gene=0; gene<num_genes; ++gene) {

arg_db.push_back(suffix[gene]);

,

arg_na.push_back(suffix[gene]);

,

,

,

,

,

,

,

,

,

,

,

,

,

arg_desc.

(

,

,

);

,

,

,

arg_desc.

(

,

,

);

,

,

(

<< retval <<

<<

paths[2] =

;

paths[2] = paths[0];

(

=0;

<3;

++) {

(

=0;

<3;

++) {

+ df_db_name +

);

suffix[] =

;

(

gene=0; gene< num_genes; ++gene) {

arg_sub.push_back(suffix[gene]);

arg_db.push_back(suffix[gene]);

arg_na.push_back(suffix[gene]);

(args.

(arg_sub) && args[arg_sub]) {

& subj_input_stream = args[arg_sub].AsInputFile();

subj_range, parse_deflines,

use_lcase_masks, subjects);

blast::CObjMgr_QueryFactory(*subjects));

sub_seqs, opts_hndl));

gl_db_name.push_back(suffix[gene]);

db_name = (args.

(arg_db) && args[arg_db])

? args[arg_db].AsString() : gl_db_name;

(args.

(arg_db +

) && args[arg_db +

]) {

,

);

,

,

,

);

}

(

==

) {

}

(

==

) {

);

,

);

,

,

,

,

));

,

,

,

+

(!line.empty()) {

);

: m_RequestMoleculeType(request_mol_type),

m_IsRpsBlast(is_rpsblast),

m_IsIgBlast(is_igblast),

m_IsProtein(

),

m_IsMapper(is_mapper),

m_IsKBlast(is_kblast),

m_SupportsDatabaseMasking(

),

m_SupportIPGFiltering(

)

,

vector<string> database_args;

database_args.push_back(

);

,

,

,

,

,

,

,

,

,

,

,

vector<string> kBlastDBFilteringOptions = {

(

= 0;

< kBlastDBFilteringOptions.size();

++) {

(

j =

+1; j < kBlastDBFilteringOptions.size(); j++) {

kBlastDBFilteringOptions[j]);

(

& s: kBlastDBFilteringOptions) {

,

,

,

,

(vector<string>, dbarg, database_args) {

,

(vector<string>, dbarg, database_args) {

(!reader.

()) {

unique_ptr<ITaxonomy4Blast> tb;

( !isTargetOnly ) {

(

<<

);

(

: ids) {

( isTargetOnly ) {

tb->GetLeafNodeTaxids(taxid, desc);

(

: desc)

(isNegativeList) {

unique_ptr<CDecompressIStream> decompress_stream;

decompress_stream.reset(

subj_input_stream = decompress_stream.get();

subj_input_stream = &args[

].AsInputFile();

);

subj_range, parse_deflines,

);

kOutputFormatDescription =

(

);

kOutputFormatDescription +=

;

kOutputFormatDescription +=

;

kOutputFormatDescription +=

;

kOutputFormatDescription +=

;

kOutputFormatDescription +=

;

kOutputFormatDescription +=

+

kOutputFormatDescription =

(

) +

kOutputFormatDescription,

,

,

ignore1, ignore2;

=

;

(custom_fmt_spec.empty())

;

kFieldsWithSemicolSeparator =

;

kFramesField =

;

kAllTitlesField =

;

(customDelim ==

) {

vector <string> tokens;

(kFieldsWithSemicolSeparator,

, tokens);

(

= 0;

< tokens.size();

++) {

checkfield = tokens[

];

(customDelim ==

) {

checkfield = kFramesField;

(customDelim ==

) {

checkfield = kAllTitlesField;

(!checkfield.empty() &&

(custom_fmt_spec,checkfield) !=

) {

(

+ customDelim +

+ checkfield +

);

& custom_fmt_spec,

& custom_delim)

custom_fmt_spec.clear();

string::size_type pos;

( (pos = fmt_choice.find_first_of(

)) != string::npos) {

custom_fmt_spec.assign(fmt_choice, pos+1,

fmt_choice.size()-(pos+1));

fmt_choice.erase(pos);

(!custom_fmt_spec.empty()) {

vector <string> tokens;

(tokens.size() > 0) {

(

);

custom_fmt_spec =

(custom_fmt_spec,tokens[0],

);

os <<

<< fmt_choice <<

;

(val < 0 || val >=

(

)) {

(

);

std::out_of_range(

);

(

);

std::out_of_range(

);

fmt_type ==

) ) {

custom_fmt_spec.clear();

(custom_delim.empty()) {

custom_delim =

;

custom_delim =

;

);

);

);

(

<<

);

(

<<

);

(

<<

);

(hitlist_size < 5){

(

<<

);

kOutputFormatDescription =

(

);

kUnalignedOutputFormatDescription =

(

) +

kOutputFormatDescription,

allowed_formats = {

,

,

};

kUnalignedOutputFormatDescription,

allowed_unaligned_formats = {

,

,

};

\

);

,

(fmt_choice ==

) {

(fmt_choice ==

) {

(fmt_choice ==

) {

os <<

<< fmt_choice <<

;

(fmt_choice ==

) {

(fmt_choice ==

) {

(fmt_choice ==

) {

os <<

<< fmt_choice

<<

;

,

,

(

<< (

)

+

);

<<

<<

<<

);

arg_desc.

(

,

,

arg_desc.

(

,

,

);

arg_desc.

(

,

,

);

(args[

]) {

,

+

+

,

,

use_index =

;

force_index =

;

old_style_index =

;

( args[

].AsBoolean() ) force_index =

;

use_index =

;

args[

].AsString() !=

) {

old_style_index =

;

index_name = args[

].AsString();

);

opts.

(

, index_name, force_index, old_style_index );

,

,

,

,

(*arg)->ExtractAlgorithmOptions(args, opts);

(*arg)->ExtractAlgorithmOptions(args, opts);

(*arg)->ExtractAlgorithmOptions(args, opts);

retval->SetCurrentGroup(

);

retval->SetCurrentGroup(

);

retval->SetCurrentGroup(

);

retval->SetCurrentGroup(

);

retval->SetCurrentGroup(

);

retval->SetCurrentGroup(

);

retval->SetCurrentGroup(

);

retval->SetCurrentGroup(

);

retval->SetCurrentGroup(

);

retval->SetCurrentGroup(

);

retval->SetCurrentGroup(

);

retval->SetCurrentGroup(

);

(*arg)->SetArgumentDescriptions(*retval);

retval.release();

can_override.

(

);

can_override.

(

);

vector< CRef<CArgValue> > TArgs;

TArgs arguments = args.

();

& arg_name = (*a)->GetName();

& arg_value = (*a)->AsString();

(has_defaults.

(arg_name) != has_defaults.

()) {

(has_defaults[arg_name] == arg_value) {

(arg_name ==

&& arg_value ==

) {

);

(can_override.

(arg_name) == can_override.

()) {

);

(*arg)->ExtractAlgorithmOptions(args, opts);

User-defined methods of the data storage class.

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

static void s_ValidateCustomDelim(const string &customFmtSpec, const string &customDelim)

static void s_GetTaxIDList(const string &in, bool isFile, bool isNegativeList, CRef< CSearchDatabase > &sdb, bool isTargetOnly)

static bool s_IsDefaultWordThreshold(EProgram program, double threshold)

static void s_SetCompositionBasedStats(CBlastOptions &opt, const string &comp_stat_string, bool smith_waterman_value, bool *ungapped)

Auxiliary function to set the composition based statistics and smith waterman options.

const char * kTemplType_Coding

Value to specify coding template type.

const char * kTemplType_Optimal

Value to specify optimal template type.

const char * kTemplType_CodingAndOptimal

Value to specify coding+optimal template type.

CArgDescriptions * SetUpCommandLineArguments(TBlastCmdLineArgs &args)

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

static string s_RegisterOMDataLoader(CRef< CSeqDB > db_handle)

Interface for converting blast-related command line arguments into blast options.

vector< CRef< IBlastCmdLineArgs > > TBlastCmdLineArgs

Type definition of a container of IBlastCmdLineArgs.

Contains C++ wrapper classes to structures in algo/blast/core as well as some auxiliary functions to ...

Declares the BLAST exception class.

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

TSeqRange ParseSequenceRange(const string &range_str, const char *error_prefix=NULL)

Parse and extract a sequence range from argument provided to this function.

CRef< objects::CScope > ReadSequencesToBlast(CNcbiIstream &in, bool read_proteins, const TSeqRange &range, bool parse_deflines, bool use_lcase_masking, CRef< CBlastQueryVector > &sequences, bool gaps_to_Ns=false)

Read sequence input for BLAST.

Routines for creating nucleotide BLAST lookup tables.

EDiscWordType

General types of discontiguous word templates.

#define PSI_INCLUSION_ETHRESH

Defaults for PSI-BLAST and DELTA-BLAST options.

#define BLAST_HITLIST_SIZE

Number of database sequences to save hits for.

#define BLAST_WORD_THRESHOLD_BLASTX

default threshold (blastx)

Int2 BLAST_GetSuggestedThreshold(EBlastProgramType program_number, const char *matrixName, double *threshold)

Get thresholds for word-finding suggested by Stephen Altschul.

@ eDynProgScoreOnly

standard affine gapping

Int2 BLAST_GetSuggestedWindowSize(EBlastProgramType program_number, const char *matrixName, Int4 *window_size)

Get window sizes for two hit algorithm suggested by Stephen Altschul.

#define BLAST_GAP_TRIGGER_NUCL

default bit score that will trigger a gapped extension for blastn

#define MAX_DB_WORD_COUNT_MAPPER

Default max frequency for a database word.

#define BLAST_EXPECT_VALUE

Default parameters for saving hits.

#define DELTA_INCLUSION_ETHRESH

Inclusion threshold for DELTA-BLAST.

#define BLAST_WORD_THRESHOLD_BLASTP

neighboring word score thresholds; a threshold of zero means that only query and subject words that m...

#define BLAST_GAP_TRIGGER_PROT

default bit score that will trigger gapped extension

#define PSI_PSEUDO_COUNT_CONST

Pseudo-count constant for PSI-BLAST.

@ eDynProgTbck

standard affine gapping

Int2 PSIBlastOptionsNew(PSIBlastOptions **psi_options)

Initialize default options for PSI BLAST.

#define BLAST_GENETIC_CODE

Default genetic code for query and/or database.

#define BLAST_WORD_THRESHOLD_TBLASTN

default neighboring threshold (tblastn/rpstblastn)

@ eCompressedAaLookupTable

compressed alphabet (blastp) lookup table

Boolean Blast_SubjectIsNucleotide(EBlastProgramType p)

Returns true if the subject is nucleotide.

Boolean Blast_QueryIsNucleotide(EBlastProgramType p)

Returns true if the query is nucleotide.

Boolean Blast_QueryIsProtein(EBlastProgramType p)

Returns true if the query is protein.

Boolean Blast_ProgramIsRpsBlast(EBlastProgramType p)

Returns true if program is RPS-BLAST (i.e.

EBlastProgramType

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

PSIDiagnosticsRequest * PSIDiagnosticsRequestNewEx(Boolean save_ascii_pssm)

Allocates a PSIDiagnosticsRequest structure, setting fields to their default values for their use in ...

Int2 BLAST_GetProteinGapExistenceExtendParams(const char *matrixName, Int4 *gap_existence, Int4 *gap_extension)

Extract the recommended gap existence and extension values.

EProgram

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

@ eTblastx

Translated nucl-Translated nucl.

@ eBlastn

Nucl-Nucl (traditional blastn)

@ eRPSBlast

protein-pssm (reverse-position-specific BLAST)

@ eBlastp

Protein-Protein.

@ eTblastn

Protein-Translated nucl.

@ eDeltaBlast

Delta Blast.

@ ePSITblastn

PSI Tblastn.

@ eRPSTblastn

nucleotide-pssm (RPS blast with translated query)

@ eBlastx

Translated nucl-Protein.

Auxiliary class to validate the genetic code input.

virtual string GetUsage(void) const

Overloaded method from CArgAllow.

virtual bool Verify(const string &value) const

Overloaded method from CArgAllow.

Class to constrain the length of the file name passed to a given CArgDescriptions key.

Class to constrain the values of an argument to those in between the values specified in the construc...

Class to constrain the values of an argument to those greater than or equal to the value specified in...

Class to constrain the values of an argument to those less than or equal to the value specified in th...

Auxiliary class to store the name of an output file, which is reset every time its GetStream method i...

CRef< CRemoteArgs > m_RemoteArgs

remote vs. local execution options

CRef< CBlastOptionsHandle > SetOptionsForSavedStrategy(const CArgs &args)

Combine the command line arguments into a CBlastOptions object recovered from saved search strategy.

string GetTask() const

Get the task for this object.

virtual CNcbiIstream & GetInputStream()

Get the input stream.

CRef< CBlastOptionsHandle > m_OptsHandle

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

CRef< CQueryOptionsArgs > m_QueryOptsArgs

query options object

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< CBlastOptionsHandle > SetOptions(const CArgs &args)

Extract the command line arguments into a CBlastOptionsHandle object.

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< CBlastOptionsHandle > x_CreateOptionsHandleWithTask(CBlastOptions::EAPILocality locality, const string &task)

Creates the BLAST options handle based on the task argument.

CBlastAppArgs()

Default constructor.

CRef< CMTArgs > m_MTArgs

multi-threaded options

CArgDescriptions * SetCommandLine()

Set the command line arguments.

CRef< CFormattingArgs > m_FormattingArgs

formatting options

void x_IssueWarningsForIgnoredOptions(const CArgs &args)

Issue warnings when recovering from a search strategy (command line applications only)

bool m_IsUngapped

Is this application being run ungapped.

TBlastCmdLineArgs m_Args

Set of command line argument objects.

CNcbiOstream * GetExportSearchStrategyStream(const CArgs &args)

Get the output stream for the search strategy.

void SetTask(const string &task)

Set the task for this object.

virtual CNcbiOstream & GetOutputStream()

Get the output stream.

CRef< CStdCmdLineArgs > m_StdCmdLineArgs

standard command line arguments class

Argument class to collect database/subject arguments.

CBlastDatabaseArgs(bool request_mol_type=false, bool is_rpsblast=false, bool is_igblast=false, bool is_mapper=false, bool is_kblast=false)

Constructor.

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

Interface method,.

static bool HasBeenSet(const CArgs &args)

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

CRef< objects::CScope > m_Scope

CScope object in which all subject sequences read are kept.

virtual void SetArgumentDescriptions(CArgDescriptions &arg_desc)

Interface method,.

bool m_IsMapper

true for short read mapper

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.

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.

bool m_IsRpsBlast

true if the search is RPS-BLAST

CRef< CSearchDatabase > m_SearchDb

Description of the BLAST database.

bool m_SupportIPGFiltering

true if IPG filtering is supported

bool m_IsKBlast

true for Kblastp

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)

Encapsulates ALL the BLAST algorithm's options.

EAPILocality

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

@ eLocal

To be used for running BLAST locally.

@ eRemote

To be used when running BLAST remotely.

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

bool m_Is2and3Supported

Are options 2 and 3 supported.

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

Interface method,.

string m_ZeroOptDescr

Non standard description for option zero.

string m_DefaultOpt

Default option.

virtual void SetArgumentDescriptions(CArgDescriptions &arg_desc)

Interface method,.

bool m_DebugOutput

Should debugging (verbose) output be printed.

bool m_RmtDebugOutput

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

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

Interface method,.

virtual void SetArgumentDescriptions(CArgDescriptions &arg_desc)

Interface method,.

virtual void SetArgumentDescriptions(CArgDescriptions &arg_desc)

Interface method,.

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

Interface method,.

CRef< CSearchDatabase > m_DomainDb

Conserved Domain Database.

bool m_ShowDomainHits

Is printing CDD hits requested.

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

Interface method,.

virtual void SetArgumentDescriptions(CArgDescriptions &arg_desc)

Interface method,.

virtual void SetArgumentDescriptions(CArgDescriptions &arg_desc)

Interface method,.

bool m_QueryIsProtein

true if the query is protein

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

Interface method,.

void x_TokenizeFilteringArgs(const string &filtering_args, vector< string > &output) const

Auxiliary method to tokenize the filtering string.

bool m_FilterByDefault

Should filtering be applied by default?

Class implements different ad-hoc unreliable file format identifications.

@ eBinaryASN

Binary ASN.1.

TSeqPos m_NumDescriptions

Number of 1-line descr. to show.

TSeqPos m_DfltNumDescriptions

Default value for num descriptions.

TSeqPos m_NumAlignments

Number of alignments to show.

virtual bool ArchiveFormatRequested(const CArgs &args) const

virtual void SetArgumentDescriptions(CArgDescriptions &arg_desc)

Interface method,.

EFormatFlags m_FormatFlags

virtual void ParseFormattingString(const CArgs &args, EOutputFormat &fmt_type, string &custom_fmt_spec, string &custom_delim) const

Parses the output format command line option value, returns the requested output format type and any ...

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

Interface method,.

EOutputFormat

Defines the output formats supported by our command line formatter.

@ eEndValue

Sentinel value for error checking.

@ ePairwise

Standard pairwise alignments.

@ 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

@ eFasta

unaligned reads in magicblast

@ eFlatQueryAnchoredNoIdentities

@ eTabularWithComments

Tabular output with comments.

bool m_IsIgBlast

IgBlast has a different default num_alignments.

string m_CustomOutputFormatSpec

The format specification for custom output, e.g.

EOutputFormat m_OutputFormat

Choice of formatting output.

TSeqPos m_DfltNumAlignments

Default value for num alignments.

bool m_ShowGis

Display NCBI GIs?

bool m_Html

Display HTML output?

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

Interface method,.

virtual void SetArgumentDescriptions(CArgDescriptions &arg_desc)

Interface method,.

bool m_QueryIsProtein

true if the query is protein

virtual void SetArgumentDescriptions(CArgDescriptions &arg_desc)

Interface method,.

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

Interface method,.

virtual void SetArgumentDescriptions(CArgDescriptions &arg_desc)

Interface method,.

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

Interface method,.

bool m_QueryIsProtein

true if the query is protein

bool m_IsRpsBlast

true if the search is RPS-BLAST

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

Interface method,.

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.

virtual void SetArgumentDescriptions(CArgDescriptions &arg_desc)

Interface method,.

bool m_SuppressSumStats

true if search is blastn or blastp

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

Interface method,.

virtual void SetArgumentDescriptions(CArgDescriptions &arg_desc)

Interface method,.

ETarget m_Target

Genetic code target.

@ eQuery

Query genetic code.

@ eDatabase

Database genetic code.

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

Interface method,.

virtual void SetArgumentDescriptions(CArgDescriptions &arg_desc)

Interface method,.

CRef< CIgBlastOptions > m_IgOptions

Igblast options to fill.

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

Interface method,.

bool m_IsProtein

Is this a protein search?

virtual void SetArgumentDescriptions(CArgDescriptions &arg_desc)

Interface method,.

CRef< objects::CScope > m_Scope

scope to get sequences

Defines user input exceptions.

double m_JDistance

Jaccard distance.

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

Interface method,.

int m_CandidateSeqs

Number of candidate sequences to try BLAST on.

virtual void SetArgumentDescriptions(CArgDescriptions &arg_desc)

Interface method,.

int m_MinHits

Minimum number of hits in LSH phase.

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

Interface method,.

virtual void SetArgumentDescriptions(CArgDescriptions &arg_desc)

Interface method,.

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

size_t m_NumThreads

Number of threads to spawn.

void x_ExtractAlgorithmOptions(const CArgs &args)

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

Default Constructor.

virtual void SetArgumentDescriptions(CArgDescriptions &arg_desc)

Interface method,.

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

Interface method,.

virtual void SetArgumentDescriptions(CArgDescriptions &arg_desc)

Interface method,.

EOutputFormat m_UnalignedOutputFormat

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

Interface method,.

bool m_OnlyStrandSpecific

virtual void SetArgumentDescriptions(CArgDescriptions &arg_desc)

Interface method,.

CNcbiIstream * m_MateInputStream

EInputFormat m_InputFormat

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

Interface method,.

vector< string > m_SraAccessions

unique_ptr< CDecompressIStream > m_DecompressIStream

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

Interface method,.

virtual void SetArgumentDescriptions(CArgDescriptions &arg_desc)

Interface method,.

virtual void SetArgumentDescriptions(CArgDescriptions &arg_desc)

Interface method,.

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

Interface method,.

Argument class to retrieve megablast database indexing options.

static bool HasBeenSet(const CArgs &args)

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

virtual void SetArgumentDescriptions(CArgDescriptions &arg_desc)

Interface method,.

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

Interface method,.

static CNcbiApplication * Instance(void)

Singleton method.

CNcbiOstrstreamToString class helps convert CNcbiOstrstream to a string Sample usage:

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

Interface method,.

virtual void SetArgumentDescriptions(CArgDescriptions &arg_desc)

Interface method,.

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

Interface method,.

virtual void SetArgumentDescriptions(CArgDescriptions &arg_desc)

Interface method,.

Wrapper class for PSIBlastOptions .

Wrapper class for PSIDiagnosticsRequest .

virtual void SetArgumentDescriptions(CArgDescriptions &arg_desc)

Interface method,.

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

Interface method,.

virtual void SetArgumentDescriptions(CArgDescriptions &arg_desc)

Interface method,.

string m_ProgDesc

Application's description.

string m_ProgName

Application's name.

CProgramDescriptionArgs(const string &program_name, const string &program_description)

Constructor.

virtual void SetArgumentDescriptions(CArgDescriptions &arg_desc)

Interface method,.

bool m_SaveLastPssm

Save PSSM after the last database search.

CRef< CAutoOutputFileReset > m_AsciiMatrixOutput

ASCII matrix output file.

bool m_IsDeltaBlast

Are the aruments set up for Delta Blast.

@ eProteinDb

Traditional, iterated PSI-BLAST.

@ eNucleotideDb

PSI-Tblastn, non-iterated.

CRef< CAutoOutputFileReset > m_CheckPointOutput

checkpoint output file

ETargetDatabase m_DbTarget

Molecule of the database.

CRef< objects::CPssmWithParameters > x_CreatePssmFromMsa(CNcbiIstream &input_stream, CBlastOptions &opt, bool save_ascii_pssm, unsigned int msa_master_idx, bool ignore_pssm_tmpl_seq)

Auxiliary function to create a PSSM from a multiple sequence alignment file.

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

Interface method,.

CRef< objects::CPssmWithParameters > m_Pssm

PSSM.

size_t m_NumIterations

number of iterations to perform

This class is a concrete strategy for IPssmInputData which converts the CLUSTALW-style output contain...

bool m_IsDeltaBlast

Are these arumnets for Delta Blast.

virtual void SetArgumentDescriptions(CArgDescriptions &arg_desc)

Interface method,.

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

Interface method,.

Computes a PSSM as specified in PSI-BLAST.

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

Interface method,.

bool m_UseLCaseMask

use lowercase masking in FASTA input

virtual void SetArgumentDescriptions(CArgDescriptions &arg_desc)

Interface method,.

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

virtual void SetArgumentDescriptions(CArgDescriptions &arg_desc)

Interface method,.

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

Interface method,.

bool m_IsRemote

Should the search be executed remotely?

virtual void SetArgumentDescriptions(CArgDescriptions &arg_desc)

Interface method,.

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

Interface method,.

Argument class to import/export the search strategy.

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

Interface method,.

CNcbiIstream * GetImportStream(const CArgs &args) const

Get the input stream for the search strategy.

CNcbiOstream * GetExportStream(const CArgs &args) const

Get the output stream for the search strategy.

virtual void SetArgumentDescriptions(CArgDescriptions &arg_desc)

Interface method,.

void AddTaxIds(const set< TTaxId > &tax_ids)

EStatType

Counts statistics formats.

static EStatType DiscoverStatType(string const &name)

Return the format of the counts statistics file.

Root class for all serialization exceptions.

bool m_GzipEnabled

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

virtual void SetArgumentDescriptions(CArgDescriptions &arg_desc)

Interface method,.

CNcbiIstream & GetInputStream() const

Get the input stream for a command line application.

unique_ptr< CDecompressIStream > m_DecompressIStream

CNcbiOstream & GetOutputStream() const

Get the output stream for a command line application.

CRef< CTmpFile > m_QueryTmpInputFile

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

unique_ptr< CCompressOStream > m_CompressOStream

CNcbiOstream * m_OutputStream

Application's output stream.

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

Interface method,.

CNcbiIstream * m_InputStream

Application's input stream.

bool m_SRAaccessionEnabled

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

void SetInputStream(CRef< CTmpFile > input_file)

Set the input stream if read from a saved search strategy.

CNcbiOstream * m_UnalignedOutputStream

Output stream to report unaligned sequences/reads.

unique_ptr< CCompressOStream > m_UnalignedCompressOStream

Simple implementation of ILineReader for i(o)streams.

static unsigned int GetCpuCount(void)

Return number of active CPUs/cores (never less than 1).

const set< string > m_SupportedTasks

Set of supported tasks by this command line argument.

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

Interface method,.

CTaskCmdLineArgs(const set< string > &supported_tasks, const string &default_task)

Constructor.

string m_DefaultTask

Default task for this command line argument.

virtual void SetArgumentDescriptions(CArgDescriptions &arg_desc)

Interface method,.

Clas to retrieve taxonomic information for filtering BLASTDBs.

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

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

Interface method,.

virtual void SetArgumentDescriptions(CArgDescriptions &arg_desc)

Interface method,.

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

Interface method,.

virtual void SetArgumentDescriptions(CArgDescriptions &arg_desc)

Interface method,.

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

const_iterator end() const

const_iterator find(const key_type &key) const

iterator_bool insert(const value_type &val)

const_iterator find(const key_type &key) const

const_iterator end() const

const string kArgMatrixName

Argument for scoring matrix.

const string kArgWindowMaskerDatabase

Argument to specify a path to a Window Masker database.

const string kArgGLChainType

Argument to specify the germline database chaintype name for igblast.

const string kArgAsciiPssmOutputFile

Argument to specify the file name for saving the ASCII representation of the PSSM.

const string kArgMaxDbWordCount

Argument to specify a maximum number of times a word can be repeated in a database.

const string kArgGLOrigin

Argument to specify the germline origin for igblast.

const string kDfltArgJDistance

Jaccard default value.

const string kArgPSIPseudocount

Argument to specify the pseudo-count value used when constructing PSSM.

const string kArgNoGreedyExtension

Argument to specify non-greedy dynamic programming extension.

const string kDfltArgApplyFiltering

Default argument to specify filtering.

const string kArgPSIOutputChkPntFile

Argument to specify a 'checkpoint' file to write the PSSM.

const string kArgSplice

Argument to specify whether to search for spliced alignments.

const string kArgMinRawGappedScore

Argument for minimum raw gapped score for preliminary gapped and traceback stages.

const string kArgGLNumAlign

Argument to specify the number of alignments for germline database.

const string kArgLookupStride

Argument to sepcify the stride when creating a lookup table.

const string kArgDbSize

Effective length of BLAST database.

const string kArgDbGeneticCode

Database genetic code.

const string kArgPSIInclusionEThreshold

Argument to specify the evalue inclusion threshold for considering aligned sequences for PSSM constru...

const string kArgRevFwd

Argument to specify reverse/forward strand specificity.

const string kArgPSIInputChkPntFile

Argument to specify a 'checkpoint' file to recover the PSSM from.

const string kArgScore

Argument to specify cutoff score for accepting a spliced alignment.

const string kArgMaxIntronLength

Argument to specify the maximum length of an intron when linking multiple distinct alignments (applic...

const string kArgTranslate

Arugment to specify if Igblast alignment should be translated to protein.

const bool kDfltArgParseDeflines

Default argument to specify whether sequences deflines should be parsed.

const string kArgDMBTemplateLength

Argument to specify the discontinuous megablast template length.

const string kArgOutput

Output file name.

const string kArgClonotypeFile

Argument to specify number of clonotype file.

const int kDfltArgCullingLimit

Default argument to specify the culling limit.

const string kArgPercentIdentity

Argument to specify the target percent identity.

const string kArgStrand

Argument to select the query strand(s) to search.

const string kDfltArgCompBasedStatsDelta

const string kArgDMBTemplateType

Argument to specify the discontinuous megablast template type.

const string kArgCandidateSeqs

Number of sequences to attempt BLAST on.

const string kArgOutputSearchStrategy

Argument to specify the file name to save the search strategy used for a BLAST search.

const string kArgDPenalty

Argument to specify mismatch penalty for D gene search.

const string kArgGapExtend

Argument to select the gap extending penalty.

const string kArgRemote

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

const string kArgQueryLocation

Argument to specify a location to restrict the query sequence(s)

const string kArgDbHardMask

const string kArgDbSoftMask

List of filtering algorithms to apply to subjects as soft masking.

const string kArgOnlyStrandSpecific

Argument to specify only strand specific results.

const int kDfltArgMaxIntronLength

Default value for maximum intron length.

const double kDfltArgBestHitOverhang

Default argument for the overhang parameter to the best hit algorithm.

const string kArgJPenalty

Argument to specify mismatch penalty for J gene search.

const string kArgFilteringDb

Argument to specify a filtering database (i.e.

const string kArgSegFiltering

Argument to specify SEG filtering on query sequence(s)

const string kArgDbType

BLAST database molecule type.

const string kArgTaxIdListFile

Argument to specify file with taxonomy ids for filtering.

const string kArgUnalignedOutput

Argument to output unaligned reads in a separate file.

const string kArgNoTaxIdExpansion

Argument to not to resolve TaxId to descendant.

const string kArgMinJLength

Argument to specify minimal required J gene length.

const string kArgPrintMdTag

Argument to specify printing SAN MD tag.

const string kArgGappedXDropoff

Argument to select the gapped X dropoff value.

const string kArgUseSWTraceback

Argument to specify that Smith-Waterman algorithm should be used to compute locally optimal alignment...

const string kArgIndexName

Megablast database index name.

const string kArgGapOpen

Argument to select the gap opening penalty.

const string kArgDustFiltering

Argument to specify DUST filtering on query sequence(s)

const string kArgSubjectBestHit

Argument to specify the culling limit.

const string kArgQueryMate

Mates for the query sequences if given in a separate file.

const string kArgFinalGappedXDropoff

Argument to select the final gapped X dropoff value.

const string kArgBestHitOverhang

Argument to specify the overhang parameter to the best hit algorithm.

const string kArgNegativeSeqidList

argument for gi list to exclude from a BLAST database search

const string kArgEntrezQuery

Entrez query.

const string kArgJDistance

KBLASTP arguments Specifies Jaccard distance (threshold)

const string kArgGLDatabase

Argument to specify the germline database name for igblast.

const string kArgGLFocusV

Arugment to specify if Igblast alignment should restrict to V seg.

const string kTask

Task to perform.

const string kArgSraAccessionBatch

Argument to specify a file with a list of SRA accessions.

const string kArgLineLength

Argument to specify line length for displaying alignments.

const string kArgMaxTargetSequences

Argument to specify the maximum number of target sequences to keep (a.k.a.

const string kArgFrameShiftPenalty

Argument to specify the frame shift penality.

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 kArgMinDMatch

Arugment to specify if Igblast min D gene match.

const string kDfltArgQuery

Default value for query sequence input.

const string kArgRpsDb

Argument to specify domain database name for DELTA-BLAST.

const string kArgQualityFilter

Argyment to specify whether quality filtering is to be done.

const string kArgNegativeGiList

argument for seqid list to exclude from a BLAST database search

const string kArgInputFormat

Argument to specify input format.

const string kArgLookupTableMaskingOnly

Argument to specify to mask query during lookup table creation.

const string kArgMismatch

Argument to select the nucleotide mismatch penalty.

const string kArgParseDeflines

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

const string kArgSaveAllPssms

Argument to specify whether to save PSSM after each psiblast iteration.

const string kDfltArgCandidateSeqs

const string kArgIgnoreMsaMaster

Argument to specify whether the template sequence (usually the query) should be ignored for the purpo...

const string kArgEvalue

Argument for expectation value cutoff.

const string kArgFwdRev

Argument to specify forward/reverse strand specificity.

const string kArgOldStyleIndex

Use old style megablast index.

const string kArgMaskLevel

const string kArgIgSeqType

Argument to specify IgBlast sequence type.

const string kArgGLDomainSystem

Argument to specify the Ig domain system.

const string kArgIpgList

IPG list file name to restrict BLAST database.

const string kArgMaxEditDist

Argument to specify a cutoff edit distance fot an alignment.

const string kArgEnableSraCache

Argument to enable SRA caching in local files.

const bool kDfltArgUseLCaseMasking

Default argument to specify whether lowercase masking should be used.

const string kArgCullingLimit

Argument to specify the culling limit.

const string kArgGapTrigger

Argument to specify number of bits to initiate gapping.

const string kArgEffSearchSpace

Argument to specify the effective length of the search space.

const string kArgSubjectLocation

Argument to specify a location to restrict the subject sequence(s)

const string kArgOffDiagonalRange

Argument to select the off-diagonal scan range in the 2-hit wordfinder algorithm.

const string kDfltArgStrand

Default value for strand selection.

const string kArgPaired

Argument to specify whether mapped reads are paired.

const string kArgQueryCovHspPerc

Argument to specify min query coverage percentage for each hsp.

const string kDfltArgSegFiltering

Default arguments to apply SEG filtering on query sequence(s)

const string kArgMTMode

Argument to specify mt mode (split by db or split by queries)

const string kArgPSINumIterations

Argument to select the number of iterations to perform in PSI-BLAST.

const string kArgQuery

Query sequence(s)

const string kArgNumClonotype

Argument to specify number of clonotype to show.

const string kArgMinVLength

Argument to specify minimal required V length.

const string kArgNegativeIpgList

argument for IPG list to exclude from a BLAST database search

const string kArgNoUnaligned

Argument to trun off printing of unaligned reads.

const string kArgComplexityAdj

const string kArgMSAInputFile

Argument to specify a multiple sequence alignment file to create a PSSM from.

const string kArgUnalignedFormat

Argument to specify format for reporting unaligned reads.

const string kArgNegativeTaxIdList

Argument to specify negative taxonomy ids filtering.

const string kDfltArgOldStyleIndex

Default value for use old style megablast index.

const string kArgVPenalty

Argument to specify mismatch penalty for V gene search.

const string kDfltArgDustFiltering

Default arguments to apply DUST filtering on query sequence(s)

const string kArgSeqIdList

seqid list file name to restrict BLAST database

const string kDfltArgLookupTableMaskingOnlyProt

Default argument mask a protein query during lookup table construction.

const unsigned int kDfltArgPSINumIterations

const string kArgRevOnly

Argument to specify reverse-only strand specificity.

const string kArgDb

BLAST database name.

const string kArgOutputGzip

Argument to specify that the output will be compressed with gzip.

const string kArgCustomInternalData

Argument to specify custom internal data file.

const string kArgWindowMaskerTaxId

Argument to specify a taxid for Window Masker.

const string kArgCRegionNumAlign

Argument to specify the number of alignments for c gene db.

const string kArgWindowSize

Argument to select the window size in the 2-hit wordfinder algorithm.

const string kArgRefType

Reference type: genome or transcriptome.

const string kArgWordSize

Argument to select the wordfinder's word size.

const string kArgUseLCaseMasking

Argument to specify whether lowercase masking in the query sequence(s) should be interpreted as maski...

const string kArgNumThreads

Argument to determine the number of threads to use when running BLAST.

const string kDfltArgLookupTableMaskingOnlyNucl

Default argument mask a nucleotide query during lookup table construction.

const string kArgMatch

Argument to select the nucleotide match reward.

const string kDfltArgMaskLevel

const string kDfltArgNoFiltering

Default argument to specify no filtering.

const string kArgPHIPatternFile

Argument to specify a PHI-BLAST pattern file.

const string kArgTaxIdList

Argument to specify taxonomy ids for filtering.

const string kArgDetectOverlap

Arugment to to detect overlap at vdj junction.

const string kArgCRegionDatabase

Argument to specify the C region gene database.

const string kArgMaxHSPsPerSubject

Argument to specify the maximum number of HPSs to save per subject for each query.

const string kArgUngapped

Argument to specify whether the search should be ungapped only.

const string kArgQueryGeneticCode

Query genetic code.

const string kArgSraAccession

Argument to specify SRA accessions.

const string kArgShowDomainHits

Argument to specify whether show domain hits in DELTA-BLAST.

const string kArgGLSubject

Argument to specify the germline subject file for igblast.

const string kArgNoDiscordant

Argument to specify if non-concordant pairs should be displayed.

const double kDfltArgBestHitScoreEdge

Default argument for the score edge parameter to the best hit algorithm.

const string kArgDomainInclusionEThreshold

Argument to specify inclusion e-value threshold for conserved domains.

const string kArgSumStats

Argument to turn on sum statistics.

const string kArgUserTag

Argument to specify user tag for alignments (magicblast)

const string kArgNoReadIdTrim

Argument to specify not trimming of '.1' and '.2' at the end of read ids in SAM format for paired rea...

const string kArgInputSearchStrategy

Argument to specify the search strategy file to read and use for a BLAST search.

const string kArgMinHits

Specifies minimal number of LSH matches.

const string kArgBestHitScoreEdge

Argument to specify the score edge parameter to the best hit algorithm.

const string kArgNegativeTaxIdListFile

Argument to specify file with taxonomy ids for Negative filtering.

const string kArgExtendAlign3end

Arugment to specify if Igblast alignment should be extends at 3' end.

const string kDfltArgMinHits

LSH matches default value.

const int kDfltOffDiagonalRange

const string kArgSubject

Subject input file to search.

const string kDfltArgCompBasedStats

Default argument for composition based statistics.

const string kArgWordScoreThreshold

Argument to specify the minimum word score such that the word is added to the lookup table.

const string kArgMSAMasterIndex

Argument to specify the index (1-based) of the sequence in the multiple sequence alignment to use as ...

const string kDfltArgRpsDb

Default value for domain database name.

const string kArgSaveLastPssm

Argument to specify whether the PSSM after the last psiblast database search should be saved.

const string kArgDFrameDefinitionFile

Argument to specify d gene frame definition data file.

const string kArgExtendAlign5end

Arugment to specify if Igblast alignment should be extends at 5' end.

const string kArgUngappedXDropoff

Argument to select the ungapped X dropoff value.

const string kArgCompBasedStats

Argument to specify the composition based statistics mode to sue.

const string kArgFwdOnly

Argument to specify forward-only strand specificity.

const string kArgGiList

gi list file name to restrict BLAST database

const string kArgLimitLookup

Argument to specify filtering lookup tables words by frequency in the searched database.

void Print(const CCompactSAMApplication::AlignInfo &ai)

ECompoAdjustModes

An collection of constants that specify all permissible modes of composition adjustment.

@ eCompositionBasedStats

Composition-based statistics as in NAR 29:2994-3005, 2001.

@ eCompoForceFullMatrixAdjust

Composition-based score adjustment as in Bioinformatics 21:902-911, 2005, unconditionally.

@ eNoCompositionBasedStats

Don't use composition based statistics.

@ eCompositionMatrixAdjust

Composition-based score adjustment as in Bioinformatics 21:902-911, 2005, conditioned on sequence pro...

const char * kArgSortHSPs

const int kDfltArgOutputFormat

Default value for formatted output type.

const char * kArgNumDescriptions

Argument to specify the number of one-line descriptions to show in the traditional BLAST report.

string DescribeSAMOutputFormatSpecifiers()

Returns a string documenting the available format specifiers.

const char * kArgProduceHtml

Argument to specify whether to create output as HTML or not.

const size_t kDfltLineLength

const char * kArgShowGIs

Argument to specify whether the GIs should be shown in the deflines in the traditional BLAST report.

const char * kArgSortHits

string DescribeTabularOutputFormatSpecifiers(bool is_igblast=false)

Returns a string documenting the available format specifiers.

const char * kArgOutputFormat

Argument to select formatted output type.

const char * kArgNumAlignments

Argument to specify the number of alignments to show in the traditional BLAST report.

static SQLCHAR output[256]

static void des(const char *src, const char *out)

void SetEntrezQueryLimitation(const string &entrez_query)

Mutator for the entrez query.

void SetPHIPattern(const char *pattern, bool is_dna)

void SetInclusionThreshold(double u)

void SetCompositionBasedStats(ECompoAdjustModes mode)

CRef< objects::CPssmWithParameters > Run()

Runs the PSSM engine to compute the PSSM.

void SetLookupDbFilter(bool val)

void SetPseudoCount(int u)

void SetWindowSize(int w)

void SetNegativeGiList(CSeqDBGiList *gilist)

Mutator for the negative gi list.

void SetGapExtnAlgorithm(EBlastPrelimGapExt a)

void SetEvalueThreshold(double eval)

void SetWindowMaskerTaxId(int taxid)

Sets the tax id to select an appropriate windowmasker database Conversion algorithm from tax id to da...

void SetQueryCovHspPerc(double p)

void SetOutOfFrameMode(bool m=true)

void SetDomainInclusionThreshold(double th)

void SetDustFilteringLinker(int m)

CRef< CSeqDB > GetSeqDb() const

Obtain a reference to the database.

void SetSegFilteringHicut(double m)

void SetGapOpeningCost(int g)

void SetHitlistSize(int s)

void SetQueryGeneticCode(int gc)

CRef< CLocalDbAdapter > m_Db[5]

void SetEffectiveSearchSpace(Int8 eff)

void SetComplexityAdjMode(bool m=true)

void SetFrameShiftPenalty(int p)

void SetReadQualityFiltering(bool val=true)

Turn on/off next-generation read quality filtering with deafult parameters.

void SetRepeatFilteringDB(const char *db)

Sets the repeat filtering database to use.

void SetGapTracebackAlgorithm(EBlastTbackExt a)

void SetWindowMaskerDatabase(const char *db)

Sets the windowmasker database to use.

void SetIgnoreMsaMaster(bool val)

static CBlastOptionsHandle * Create(EProgram program, EAPILocality locality=CBlastOptions::eLocal)

Creates an options handle object configured with default options for the requested program,...

int GetHitlistSize() const

void SetWordThreshold(double w)

Sets WordThreshold.

CBlastOptions & SetOptions()

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

void SetGapExtensionCost(int e)

void SetSumStatisticsMode(bool m=true)

void SetUnifiedP(int u=0)

void SetUseIndex(bool use_index=true, const string &index_name="", bool force_index=false, bool old_style_index=false)

void SetDustFilteringWindow(int m)

void SetCutoffScoreCoeffs(const vector< double > &c)

int GetGapExtensionCost() const

void SetMismatchPenalty(int p)

void SetOffDiagonalRange(int r)

void SetGapXDropoffFinal(double x)

void SetMatrixName(const char *matrix)

EBlastProgramType GetProgramType() const

Returns the CORE BLAST notion of program type.

void SetBestHitOverhang(double overhang)

void SetSpliceAlignments(bool s)

void SetGapXDropoff(double x)

EProgram GetProgram() const

Accessors/Mutators for individual options.

void SetPercentIdentity(double p)

const CBlastOptions & GetOptions() const

Return the object which this object is a handle for.

void SetSegFilteringLocut(double m)

double GetWordThreshold() const

Returns WordThreshold.

bool Validate() const

Validate the options contained in this object.

void SetMBTemplateType(unsigned char type)

void SetGapTrigger(double g)

void SetDbGeneticCode(int gc)

void SetMBTemplateLength(unsigned char len)

void SetXDropoff(double x)

void SetMaskAtHash(bool val=true)

void SetBestHitScoreEdge(double score_edge)

void SetDustFilteringLevel(int m)

int GetGapOpeningCost() const

void SetDustFiltering(bool val=true)

void SetSegFiltering(bool val=true)

void SetSegFilteringWindow(int m)

void ThrowIfInvalidTask(const string &task)

Validates that the task provided is indeed a valid task, otherwise throws a CBlastException.

void SetCutoffScore(int s)

void SetFilteringAlgorithm(int filt_algorithm_id)

Temporary fix for backwards compatibility with other 6.0 SCs.

void SetSmithWatermanMode(bool m=true)

void SetMaxDbWordCount(Uint1 num)

Set maximum word count for lookup table word masking by database frequency.

void SetGappedMode(bool m=true)

Int8 GetEffectiveSearchSpace() const

string m_CustomInternalData

const char * GetMatrixName() const

void SetLongestIntronLength(int l)

for linking HSPs with uneven gaps

void SetMaxEditDistance(int e)

void SetLookupTableStride(Uint4 val)

void SetMaxHspsPerSubject(int m)

EMoleculeType

Molecule of the BLAST database.

void SetCullingLimit(int s)

void SetLookupTableType(ELookupTableType type)

static CBlastOptionsHandle * CreateTask(string task, EAPILocality locality=CBlastOptions::eLocal)

Creates an options handle object configured with default options for the requested task,...

bool GetGappedMode() const

Returns true if gapped BLAST is set, false otherwise.

void SetMatchReward(int r)

void SetGiList(CSeqDBGiList *gilist)

Mutator for the gi list.

@ eBlastDbIsNucleotide

nucleotide

@ eBlastDbIsProtein

protein

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.

SStrictId_Tax::TId TTaxId

Taxon id type.

@ eFollowLinks

Follow symbolic links.

void AddFlag(const string &name, const string &comment, CBoolEnum< EFlagValue > set_value=eFlagHasValueIfSet, TFlags flags=0)

Add description for flag argument.

void SetConstraint(const string &name, const CArgAllow *constraint, EConstraintNegate negate=eConstraint)

Set additional user defined constraint on argument value.

void SetDependency(const string &arg1, EDependency dep, const string &arg2)

Define a dependency.

bool Exist(const string &name) const

Check existence of argument description.

void AddKey(const string &name, const string &synopsis, const string &comment, EType type, TFlags flags=0)

Add description for mandatory key.

void SetUsageContext(const string &usage_name, const string &usage_description, bool usage_sort_args=false, SIZE_TYPE usage_width=78)

Set extra info to be used by PrintUsage().

void AddAlias(const string &alias, const string &arg_name)

Add argument alias.

void AddOptionalKey(const string &name, const string &synopsis, const string &comment, EType type, TFlags flags=0)

Add description for optional key without default value.

vector< CRef< CArgValue > > GetAll(void) const

Get all available arguments.

void SetCurrentGroup(const string &group)

Set current arguments group name.

void AddDefaultKey(const string &name, const string &synopsis, const string &comment, EType type, const string &default_value, TFlags flags=0, const string &env_var=kEmptyStr, const char *display_value=nullptr)

Add description for optional key with default value.

@ fOptionalSeparator

Allow to ignore separator between the argument's name and value.

@ eRequires

One argument requires another.

@ eExcludes

One argument excludes another.

@ eInt8

Convertible into an integer number (Int8 only)

@ eInputFile

Name of file (must exist and be readable)

@ eBoolean

{'true', 't', 'false', 'f'}, case-insensitive

@ eDouble

Convertible into a floating point number (double)

@ eString

An arbitrary string.

@ eOutputFile

Name of file (must be writable)

@ eInteger

Convertible into an integer number (int or Int8)

@ eGZipFile

.gz file (including concatenated files)

#define ERR_POST(message)

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

#define LOG_POST(message)

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

void Set(const string &name, const string &value)

Set an environment variable by name.

#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)

static string NormalizePath(const string &path, EFollowLinks follow_links=eIgnoreLinks)

Normalize a path.

virtual bool Exists(void) const

Check the entry existence.

bool IsDir(EFollowLinks follow=eFollowLinks) const

Check whether a directory entry is a directory.

bool IsFile(EFollowLinks follow=eFollowLinks) const

Check whether a directory entry is a file.

static string ConcatPath(const string &first, const string &second)

Concatenate two parts of the path for the current OS.

static string GetCwd(void)

Get the current working directory.

@ eIfExists_Throw

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

#define MSerial_AsnBinary

#define MSerial_AsnText

I/O stream manipulators –.

CTempString GetCurrentLine(void) const

bool AtEOF(void) const

Indicates (negatively) whether there is any more input.

static CRef< CObjectManager > GetInstance(void)

Return the existing object manager or create one.

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.

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

Get the parameter value.

bool Set(const string &section, const string &name, const string &value, TFlags flags=0, const string &comment=kEmptyStr)

Set the configuration parameter 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.

IO_PREFIX::ifstream CNcbiIfstream

Portable alias for ifstream.

static string DoubleToString(double value, int precision=-1, TNumToStringFlags flags=0)

Convert double 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 bool EndsWith(const CTempString str, const CTempString end, ECase use_case=eCase)

Check if a string ends with a specified suffix value.

static bool IsBlank(const CTempString str, SIZE_TYPE pos=0)

Check if a string is blank (has no text).

static double StringToDouble(const CTempStringEx str, TStringToNumFlags flags=0)

Convert string to double.

static const string BoolToString(bool value)

Convert bool to string.

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

Convert int to string.

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.

static string & Replace(const string &src, const string &search, const string &replace, string &dst, SIZE_TYPE start_pos=0, SIZE_TYPE max_replace=0, SIZE_TYPE *num_replace=0)

Replace occurrences of a substring within a string.

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

Check if a string starts with a specified prefix value.

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

Split a string into two pieces using the specified delimiters.

TErrCode GetErrCode(void) const

Get error code.

static enable_if< is_arithmetic< TNumeric >::value||is_convertible< TNumeric, Int8 >::value, string >::type NumericToString(TNumeric value, TNumToStringFlags flags=0, int base=10)

Convert numeric value to string.

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

Truncate whitespace in a string.

@ fAllowTrailingSpaces

Ignore trailing whitespace characters.

@ fAllowLeadingSpaces

Ignore leading whitespace characters in converted string.

@ fSplit_Tokenize

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

@ eConvert

Failure to convert string.

@ eNocase

Case insensitive compare.

#define DEF_CONN_REG_SECTION

#define REG_CONN_SERVICE_NAME

@ eNa_strand_both

in forward orientation

Implementation of a number of BlastHSPWriters to save hits from a BLAST search, and subsequently retu...

#define kBestHit_OverhangMax

Maximum value for overhang.

#define kBestHit_OverhangMin

Minimum value for overhang.

#define kBestHit_ScoreEdgeMin

Minimum value for score_edge.

#define kBestHit_ScoreEdgeMax

Maximum value for score_edge.

Lightweight interface for getting lines of data with minimal memory copying.

Defines a concrete strategy to obtain PSSM input data for PSI-BLAST from a multiple sequence alignmen...

const GenericPointer< typename T::ValueType > T2 value

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

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

C++ API for the PSI-BLAST PSSM engine.

Defines BLAST database access classes.

Defines exception class and several constants for SeqDB.

string SeqDB_ResolveDbPath(const string &filename)

Resolve a file path using SeqDB's path algorithms.

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

CRef< objects::CObjectManager > om

Boolean nsg_compatibility_mode

Compatibility option for the NCBI's structure group (note nsg_ prefix, stands for NCBI's structure gr...

static string kMaxValue("MaxValue")

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