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NCBI C++ ToolKit: src/gui/packages/pkg_alignment/blast_search_params.cpp Source File

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, m_FilterLowComplex(

)

, m_QueryGeneticCode(1)

, m_MaskLowercase(

)

, m_MaskRepeats(

)

thresh,

word,

ev,

low_c,

query_gen_code,

db_gen_code

, m_FilterLowComplex(low_c)

, m_QueryGeneticCode(query_gen_code)

, m_DbGeneticCode(db_gen_code)

, m_MaskLowercase(

)

, m_MaskRepeats(

)

it->second->m_NucInput;

it->second->m_UseDustFilter;

it->second->m_NucDB;

it->second->m_NeedsThreshold;

it->second->m_NeedsQueryGenCode;

it->second->m_NeedsDbGenCode;

.GetId();

+

);

(

.GetId() == code_id) {

.GetName();

+

list<CRef<CGenetic_code> >& codes = code_table.

();

name = (*it)->GetName();

labels.push_back(name);

(

= 0;

<

;

++) {

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}

libs.

(iter->first);

(iter != sc_RepeatMap.end()) {

vector<string> databases;

name =

+

;

vector<string> databases;

databases.insert(databases.end(),

databases.insert(databases.end(),

name =

+

;

(obj.HasField(name)) {

(

->m_NucInput == nuc_input) {

labels.push_back(

->m_Label);

it->second->m_Label;

(it->second->m_Label ==

) {

string::const_iterator end,

string::const_iterator& tok_begin,

string::const_iterator& tok_end)

s_WhiteSpace(

);

( ; tok_begin != end; ++tok_begin) {

(s_WhiteSpace.find_first_of(*tok_begin) == string::npos) {

(tok_begin != tok_end &&

(*tok_begin ==

|| *tok_begin ==

)) {

quot_balance = *tok_begin;

(++tok_begin, ++tok_end; tok_end != end; ++tok_end) {

(*tok_end == quot_balance) {

( ; tok_end != end; ++tok_end) {

(s_WhiteSpace.find_first_of(*tok_end) != string::npos) {

vector<string>& arg_vec,

( !opts )

;

arg_vec.push_back(

+

);

unique_ptr<CArgDescriptions> arg_descs( blast_args->SetCommandLine() );

unique_ptr<CArgs> args( arg_descs->CreateArgs( arg_vec.size(), arg_vec ) );

blast_args->SetOptionsHandle( opts );

opts = blast_args->SetOptions( *args );

( !opts )

;

unique_ptr<CArgDescriptions> arg_descs( blast_args->SetCommandLine() );

unique_ptr<CArgs> args( arg_descs->CreateArgs( argv.size(), argv ) );

blast_args->SetOptionsHandle( opts );

opts = blast_args->SetOptions( *args );

opts->SetOptions().Validate();

( !repeat_lib.empty() && repeat_lib !=

){

( !repeat_db.empty() ){

arg_vec.push_back( repeat_db );

& wm_dir =

();

( !wm_dir.empty() ){

(

<<

);

(

<<

);

s_whitespace(

);

( arg_params, s_whitespace, arg_vec );

vector<string>::iterator argit;

argit = find( arg_vec.begin(), arg_vec.end(),

+

);

(argit == arg_vec.end()) {

vector<string> argv;

argv.insert( argv.end(), arg_vec.begin(), arg_vec.end() );

unique_ptr<CArgDescriptions> arg_descs( blast_args->SetCommandLine() );

unique_ptr<CArgs> args( arg_descs->CreateArgs( argv.size(), argv ) );

args.release();

& cmd_line, blast::CBlastOptions& opts

string::const_iterator begin = cmd_line.begin();

string::const_iterator end = cmd_line.end();

string::const_iterator tok_begin = begin;

string::const_iterator tok_end = end;

arg(tok_begin, tok_end);

( arg[0] !=

|| arg.size() != 2 ){

(

);

(tok_begin, tok_end);

* err_postfix =

;

err_postfix =

;

err_postfix =

;

err_postfix =

;

err_postfix =

;

err_postfix =

;

opts.SetMatrixName(

.c_str());

err_postfix =

;

err_postfix =

;

err_postfix =

;

err =

+ arg;

err =

+ arg +

;

<< prog_params.

<<

Declares the CBlastNucleotideOptionsHandle class.

Declares class to encapsulate all BLAST options.

Declares the CBlastProteinOptionsHandle class.

static CBLASTParams::SProgParams s_DefaultParams(blast::EProgram prg)

static const char * kGeneticCodeTag

static const char * kLocalDBLoader

static const char * kMaskLowercaseTag

static const char * kNucMRUDBsTag

static const char * kSubjectType

static const char * kAdvParamsTag

static const char * kNucDBTag

static const CBLASTParams::SProgInfo sc_ProgPairs[]

static const char * kWordSizeTag

static void s_NextToken(string::const_iterator &begin, string::const_iterator end, string::const_iterator &tok_begin, string::const_iterator &tok_end)

static const char * keValueTag

SStaticPair< const char *, const char * > TRepeatName

static const char * kThresholdTag

static const char * kDbGeneticCodeTag

DEFINE_STATIC_ARRAY_MAP(TRepeatMap, sc_RepeatMap, sc_RepeatLibs)

CStaticPairArrayMap< const char *, const char *, PNocase_CStr > TRepeatMap

static const char * kFilterLowComplexTag

static const char * kBLASTParamsTag

static TRepeatName sc_RepeatLibs[]

static const char * kLocalProtDB

static const char * kJobTitleTag

static const char * kMaskRepeatsTag

static const char * kProtDBTag

static const char * kProtMRUDBsTag

static const char * kEntrezQueryTag

static const char * kLocalNucDB

static const char * kProtProgTag

static const char * kNucProgTag

EProgram

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

@ eBlastNotSet

Not yet set.

@ eTblastx

Translated nucl-Translated nucl.

@ eBlastn

Nucl-Nucl (traditional blastn)

@ eBlastp

Protein-Protein.

@ eTblastn

Protein-Translated nucl.

@ eMegablast

Nucl-Nucl (traditional megablast)

@ eDiscMegablast

Nucl-Nucl using discontiguous megablast.

@ eBlastx

Translated nucl-Protein.

Main argument class for BLASTN application.

Main argument class for BLASTP application.

Main argument class for BLASTX application.

Declares the CBlastxOptionsHandle class.

CBLASTParams - save user-specified parameters and preferences.

@ eLocal

To be used for running BLAST locally.

@ eRemote

To be used when running BLAST remotely.

Handles command line arguments for blastn binary.

Handles command line arguments for blastp binary.

Handles command line arguments for blastx binary.

static const CGenetic_code_table & GetCodeTable(void)

const TItems & GetItems() const

void SetItems(const TItems &items)

class CStaticArrayMap<> is an array adaptor that provides an STLish interface to statically-defined a...

TBase::const_iterator const_iterator

static unsigned int GetCpuCount(void)

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

Handles command line arguments for Tblastn binary.

Handles command line arguments for blastx binary.

bool HasField(const string &str, const string &delim=".", NStr::ECase use_case=NStr::eCase) const

Verify that a named field exists.

CUser_object & AddField(const string &label, const string &value, EParseField parse=eParse_String)

add a data field to the user object that holds a given value

const CUser_field & GetField(const string &str, const string &delim=".", NStr::ECase use_case=NStr::eCase) const

Access a named field in this user object.

container_type::const_iterator const_iterator

container_type::iterator iterator

const_iterator end() const

iterator_bool insert(const value_type &val)

container_type::value_type value_type

const_iterator find(const key_type &key) const

iterator_bool insert(const value_type &val)

const string kDfltArgApplyFiltering

Default argument to specify filtering.

const string kArgDbGeneticCode

Database genetic code.

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 kArgDustFiltering

Argument to specify DUST filtering on query sequence(s)

const string kTask

Task to perform.

const string kArgEvalue

Argument for expectation value cutoff.

const string kArgWindowMaskerTaxId

Argument to specify a taxid for Window Masker.

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 kArgQueryGeneticCode

Query genetic code.

const string kArgWordScoreThreshold

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

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

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

string EProgramToTaskName(EProgram p)

Convert a EProgram enumeration value to a task name (as those used in the BLAST command line binaries...

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define NON_CONST_ITERATE(Type, Var, Cont)

Non constant version of ITERATE macro.

#define ERR_POST(message)

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

#define LOG_POST(message)

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

void Error(CExceptionArgs_Base &args)

#define NCBI_THROW(exception_class, err_code, message)

Generic macro to throw an exception, given the exception class, error code and message string.

void Warning(CExceptionArgs_Base &args)

void Info(CExceptionArgs_Base &args)

TMRUDatabases & GetCurrMRUDatabases()

returns MRU databases for the current program

CRef< blast::CBlastOptionsHandle > ToBlastOptions(bool local=false) const

static bool NeedsThreshold(blast::EProgram program)

static void GetGeneticCodeLabels(vector< string > &labels)

TMRUDatabases m_NucMRUDatabases

TConstScopedObjects m_SubjSeqLocs

Params applying only to BLAST Sequences.

TConstScopedObjects & GetSeqLocs()

const string & GetWmDir() const

TConstScopedObjects & GetSubjSeqLocs()

void x_ArgsToBlastOptions(const string &cmd_line, blast::CBlastOptions &opts) const

TMRUDatabases m_ProtMRUDatabases

static string GetRepeatLib(const string &repeat_db)

CRef< blast::CBlastOptionsHandle > ToArgVecBlastOptions(vector< string > &arg_vec, bool local=true) const

TProgramParamsMap m_ProgToParams

Common parameters.

void FromUserObject(const objects::CUser_object &user_obj)

TConstScopedObjects m_SeqLocs

static string GetGeneticCodeLabel(int code_id)

static void x_FromUserObject(const objects::CUser_object &user_obj, blast::EProgram prg, SProgParams &params)

reads SProgParams fields from CUser_object

static blast::EProgram GetProgramByLabel(const string &str)

static objects::CUser_object * x_ToUserObject(blast::EProgram prg, const SProgParams &params)

converts SProgParams into CUser_object

static bool UseDustFilter(blast::EProgram program)

CArgs * ToArgs(vector< string > &argv) const

static string GetRepeatDb(const string &repeat_lib)

static TProgramAttrMap sm_ProgramToAttr

static bool IsNucDatabase(blast::EProgram program)

static bool NeedsQueryGeneticCode(blast::EProgram program)

blast::EProgram & GetProgram(bool nuc)

returns the selected programs for the given input type

static TRepeatLibs GetAllRepeatLibs()

blast::EProgram m_NucProgram

SProgParams & GetCurrParams()

returns params for the current program

int m_WM_TaxId

winmask tax id

bool m_MaskLowercase

mask Lowercase features

static int GetGeneticCodeByLabel(const string &label)

vector< string > & ToArgVec(vector< string > &arg_vec) const

blast::EProgram & GetCurrProgram()

returns the current program for the currently selected input type

blast::EProgram m_ProtProgram

TMRUDatabases & GetMRUDatabases(bool nuc_db)

void PrintParams(const string &log_title) const

LOG_POST params for forensic purposes.

string & GetCurrDatabase()

returns the current database for the current program

ESubjectType m_SubjectType

bool m_MaskRepeats

mask Repeat features

static void GetProgramLabels(bool nuc_input, vector< string > &labels)

static bool NeedsDbGeneticCode(blast::EProgram program)

bool IsSubjNucInput() const

string m_EntrezQuery

Params applying only to BLAST Search.

string & GetDatabase(bool nuc_db)

returns the database of the specified type

string & GetEntrezQuery()

objects::CUser_object * ToUserObject() const

string & GetAdvancedParams()

static string GetProgramLabel(blast::EProgram program)

vector< SConstScopedObject > TConstScopedObjects

void Reset(void)

Reset reference object.

TObjectType * Release(void)

Release a reference to the object and return a pointer to the object.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

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

Convert string to double.

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

Convert int to string.

static bool EqualNocase(const CTempString s1, SIZE_TYPE pos, SIZE_TYPE n, const char *s2)

Case-insensitive equality of a substring with another string.

static const char label[]

const TStr & GetStr(void) const

Get the variant data.

const TData & GetData(void) const

Get the Data member data.

TBool GetBool(void) const

Get the variant data.

TInt GetInt(void) const

Get the variant data.

const TObject & GetObject(void) const

Get the variant data.

TReal GetReal(void) const

Get the variant data.

void SetType(TType &value)

Assign a value to Type data member.

list< CRef< CGenetic_code > > Tdata

const Tdata & Get(void) const

Get the member data.

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

describes static attributes of a BLAST program

describes parameters for a BLAST program

Template structure SStaticPair is simlified replacement of STL pair<> Main reason of introducing this...

Main argument class for TBLASTN application.

Declares the CTBlastnOptionsHandle class.

Main argument class for TBLASTX application.

Declares the CTBlastxOptionsHandle class.

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