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NCBI C++ ToolKit: include/gui/packages/pkg_alignment/blast_search_params.hpp Source File

1 #ifndef PKG_ALIGNMENT___BLAST_SEARCH_PARAMS__HPP 2 #define PKG_ALIGNMENT___BLAST_SEARCH_PARAMS__HPP 100  SProgParams

(

int

thresh,

int

word,

double

ev,

bool

low_c,

int

query_gen_code,

int

db_gen_code);

107  bool

IsNucInput()

const

;

121  string

& GetCurrDatabase();

122  const string

& GetCurrDatabase()

const

;

125  string

& GetDatabase(

bool

nuc_db);

126  const string

& GetDatabase(

bool

nuc_db)

const

;

133  string

& GetEntrezQuery();

134  string

GetEntrezQuery()

const

;

136  bool

IsSubjNucInput()

const

;

145  void

ResetCurrParams();

148  string

& GetAdvancedParams();

149  string

GetAdvancedParams()

const

;

153  static string

GetRepeatLib(

const string

& repeat_db);

154  static string

GetRepeatDb(

const string

& repeat_lib);

156  string

& GetJobTitle();

157  string

GetJobTitle()

const

;

165  void SetWM_Dir

(

const string

& wm_dir_path) { m_WM_Dir = wm_dir_path; }

166  const string

&

GetWmDir

()

const

{

return

m_WM_Dir; }

168

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

const

;

169  CArgs

* ToArgs( vector<string>& argv )

const

;

173

objects::CUser_object* ToUserObject()

const

;

174  void

FromUserObject(

const

objects::CUser_object& user_obj);

176  static void

GetProgramLabels(

bool

nuc_input, vector<string>& labels);

190  static int

GetGeneticCodeByLabel(

const string

&

label

);

191  static string

GetGeneticCodeLabel(

int

code_id);

192  static void

GetGeneticCodeLabels(vector<string>& labels);

196  void

PrintParams(

const string

& log_title)

const

;

213  void

x_ArgsToBlastOptions(

const string

& cmd_line, blast::CBlastOptions& opts)

const

;

217  static void

x_FromUserObject(

const

objects::CUser_object& user_obj,

Declares class to encapsulate all BLAST options.

Declares the CBlastOptionsHandle and CBlastOptionsFactory classes.

Definitions of special type used in BLAST.

EProgram

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

CBLASTParams - save user-specified parameters and preferences.

static const char * str(char *buf, int n)

bool GetLocalDBLoader() const

string m_WM_Dir

path to WM statistics databases

void StandaloneRequested(bool req)

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

TMRUDatabases m_NucMRUDatabases

TConstScopedObjects m_SubjSeqLocs

Params applying only to BLAST Sequences.

set< string, PNocase > TRepeatLibs

void SetLocalNucDB(const string &value)

const string & GetWmDir() const

void FindCompartments(bool req)

TMRUDatabases m_ProtMRUDatabases

void x_AddProgramParams(blast::EProgram program, int thresh, int word, int ev)

TProgramParamsMap m_ProgToParams

Common parameters.

string GetLocalNucDB() const

TConstScopedObjects m_SeqLocs

void SetLocalProtDB(const string &value)

void SetSubjectType(ESubjectType subjectType)

static TProgramAttrMap sm_ProgramToAttr

blast::EProgram m_NucProgram

int m_WM_TaxId

winmask tax id

bool IsCompartmentsRequested() const

bool m_MaskLowercase

mask Lowercase features

void SetLocalDBLoader(bool value)

blast::EProgram m_Program

CMRUList< string > TMRUQueries

blast::EProgram m_ProtProgram

string GetLocalProtDB() const

ESubjectType m_SubjectType

bool m_MaskRepeats

mask Repeat features

CMRUList< string > TMRUDatabases

string m_EntrezQuery

Params applying only to BLAST Search.

ESubjectType GetSubjectType() const

void SetWM_Dir(const string &wm_dir_path)

map< blast::EProgram, SProgParams > TProgramParamsMap

bool IsStandaloneRequested() const

vector< SConstScopedObject > TConstScopedObjects

#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.

static const char label[]

const GenericPointer< typename T::ValueType > T2 value

Portable reference counted smart and weak pointers using CWeakRef, CRef, CObject and CObjectEx.

The NCBI C++/STL use hints.

describes static attributes of a BLAST program

describes parameters for a BLAST program

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