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CBLASTParams Class Reference

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CBLASTParams - save user-specified parameters and preferences. More...

#include <gui/packages/pkg_alignment/blast_search_params.hpp>

+ Collaboration diagram for CBLASTParams:

Classes

struct  SProgInfo
 describes static attributes of a BLAST program More...
 
struct  SProgParams
 describes parameters for a BLAST program More...
 

Public Types

enum  ESubjectType { eSequences , eNCBIDB , eLocalDB }
 
typedef CMRUList< stringTMRUDatabases
 
typedef CMRUList< stringTMRUQueries
 
typedef set< string, PNocaseTRepeatLibs
 

Public Member Functions

 CBLASTParams ()
 
boolIsNucInput ()
 
bool IsNucInput () const
 
TConstScopedObjectsGetSeqLocs ()
 
const TConstScopedObjectsGetSeqLocs () const
 
blast::EProgramGetCurrProgram ()
 returns the current program for the currently selected input type More...
 
const blast::EProgram GetCurrProgram () const
 
blast::EProgramGetProgram (bool nuc)
 returns the selected programs for the given input type More...
 
const blast::EProgram GetProgram (bool nuc) const
 
stringGetCurrDatabase ()
 returns the current database for the current program More...
 
const stringGetCurrDatabase () const
 
stringGetDatabase (bool nuc_db)
 returns the database of the specified type More...
 
const stringGetDatabase (bool nuc_db) const
 
TMRUDatabasesGetCurrMRUDatabases ()
 returns MRU databases for the current program More...
 
TMRUDatabasesGetMRUDatabases (bool nuc_db)
 
stringGetEntrezQuery ()
 
string GetEntrezQuery () const
 
bool IsSubjNucInput () const
 
TConstScopedObjectsGetSubjSeqLocs ()
 
const TConstScopedObjectsGetSubjSeqLocs () const
 
SProgParamsGetCurrParams ()
 returns params for the current program More...
 
const SProgParamsGetCurrParams () const
 
void ResetCurrParams ()
 
stringGetAdvancedParams ()
 
string GetAdvancedParams () const
 
stringGetJobTitle ()
 
string GetJobTitle () const
 
bool IsStandaloneRequested () const
 
void StandaloneRequested (bool req)
 
bool IsCompartmentsRequested () const
 
void FindCompartments (bool req)
 
void SetWM_Dir (const string &wm_dir_path)
 
const stringGetWmDir () const
 
vector< string > & ToArgVec (vector< string > &arg_vec) const
 
CArgsToArgs (vector< string > &argv) const
 
CRef< blast::CBlastOptionsHandle > ToBlastOptions (bool local=false) const
 
CRef< blast::CBlastOptionsHandle > ToArgVecBlastOptions (vector< string > &arg_vec, bool local=true) const
 
objects::CUser_object * ToUserObject () const
 
void FromUserObject (const objects::CUser_object &user_obj)
 
void PrintParams (const string &log_title) const
 LOG_POST params for forensic purposes. More...
 
string GetLocalNucDB () const
 
void SetLocalNucDB (const string &value)
 
string GetLocalProtDB () const
 
void SetLocalProtDB (const string &value)
 
ESubjectType GetSubjectType () const
 
void SetSubjectType (ESubjectType subjectType)
 
bool GetLocalDBLoader () const
 
void SetLocalDBLoader (bool value)
 

Static Public Member Functions

static TRepeatLibs GetAllRepeatLibs ()
 
static string GetRepeatLib (const string &repeat_db)
 
static string GetRepeatDb (const string &repeat_lib)
 
static void GetProgramLabels (bool nuc_input, vector< string > &labels)
 
static string GetProgramLabel (blast::EProgram program)
 
static blast::EProgram GetProgramByLabel (const string &str)
 
static bool IsNucInput (blast::EProgram program)
 
static bool IsNucDatabase (blast::EProgram program)
 
static bool UseDustFilter (blast::EProgram program)
 
static bool NeedsThreshold (blast::EProgram program)
 
static bool NeedsDbGeneticCode (blast::EProgram program)
 
static bool NeedsQueryGeneticCode (blast::EProgram program)
 
static int GetGeneticCodeByLabel (const string &label)
 
static string GetGeneticCodeLabel (int code_id)
 
static void GetGeneticCodeLabels (vector< string > &labels)
 

Protected Types

typedef map< blast::EProgram, const SProgInfo * > TProgramAttrMap
 
typedef map< blast::EProgram, SProgParamsTProgramParamsMap
 

Protected Member Functions

void x_AddProgramParams (blast::EProgram program, int thresh, int word, int ev)
 
void x_ArgsToBlastOptions (const string &cmd_line, blast::CBlastOptions &opts) const
 

Static Protected Member Functions

static objects::CUser_object * x_ToUserObject (blast::EProgram prg, const SProgParams &params)
 converts SProgParams into CUser_object More...
 
static void x_FromUserObject (const objects::CUser_object &user_obj, blast::EProgram prg, SProgParams &params)
 reads SProgParams fields from CUser_object More...
 

Protected Attributes

bool m_NucInput
 
TConstScopedObjects m_SeqLocs
 
blast::EProgram m_NucProgram
 
blast::EProgram m_ProtProgram
 
string m_NucDatabase
 
string m_ProtDatabase
 
TMRUDatabases m_NucMRUDatabases
 
TMRUDatabases m_ProtMRUDatabases
 
string m_EntrezQuery
 Params applying only to BLAST Search. More...
 
TMRUQueries m_MRUQueries
 
TConstScopedObjects m_SubjSeqLocs
 Params applying only to BLAST Sequences. More...
 
TProgramParamsMap m_ProgToParams
 Common parameters. More...
 
string m_AdvancedParams
 
string m_JobTitle
 
bool mf_FindComparts
 
bool mf_Standalone
 
string m_WM_Dir
 path to WM statistics databases More...
 
string m_LocalNucDB
 
string m_LocalProtDB
 
ESubjectType m_SubjectType
 
bool m_LocalDBLoader
 

Static Protected Attributes

static TProgramAttrMap sm_ProgramToAttr
 

Detailed Description

CBLASTParams - save user-specified parameters and preferences.

Definition at line 60 of file blast_search_params.hpp.


The documentation for this class was generated from the following files:
Modified on Sat Jun 22 10:40:59 2024 by modify_doxy.py rev. 669887