ARB
Public Member Functions | List of all members
CLI Class Reference
Inheritance diagram for CLI:
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Collaboration diagram for CLI:
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Public Member Functions

 CLI (int argc, const char **argv)
 
bool help_wanted () const
 
void show_help_if_useful () const
 
GB_ERROR get_error () const
 
const charget_database () const
 
const charget_treename () const
 
const charget_aliname () const
 
const charget_database_savename () const
 
const charget_SAI_name () const
 
bool shall_import_tree () const
 
const charget_treeimport_filename () const
 
bool shall_delete_tree () const
 
 CLI (int argc, const char **argv)
 
void show_help () const
 
bool help_wanted () const
 
GB_ERROR get_error () const
 
const charget_database () const
 
const charget_tree () const
 
const charget_newick_file () const
 
const charget_leaf_aci () const
 
TREE_node_quoting get_quoting_mode () const
 
bool shall_add_branch_length () const
 
bool shall_add_bootstraps () const
 
bool shall_add_group_names () const
 
bool shall_replace_problem_chars () const
 
bool shall_be_pretty () const
 
 CLI (int argc, const char **argv)
 
bool help_wanted () const
 
void show_help_if_useful () const
 
GB_ERROR get_error () const
 
const charget_database () const
 
const charget_fasta () const
 
const charget_aliname () const
 
const charget_head_aci () const
 
const charget_seq_aci () const
 
const charget_basechars () const
 
bool shall_accept_missing_data () const
 
int get_min_bases_count () const
 
bool has_filters () const
 
GB_ERROR add_filters_to (FilteredExport &exporter) const
 

Detailed Description

Definition at line 17 of file arb_calc_pvp.cxx.

Constructor & Destructor Documentation

CLI::CLI ( int  argc,
const char **  argv 
)
inline

Definition at line 107 of file arb_calc_pvp.cxx.

References NULp.

CLI::CLI ( int  argc,
const char **  argv 
)
inline

Definition at line 89 of file arb_export_newick.cxx.

CLI::CLI ( int  argc,
const char **  argv 
)
inline

Definition at line 152 of file arb_export_seq_filtered.cxx.

Member Function Documentation

bool CLI::help_wanted ( ) const
inline

Definition at line 120 of file arb_calc_pvp.cxx.

Referenced by main().

void CLI::show_help_if_useful ( ) const
inline

Definition at line 121 of file arb_calc_pvp.cxx.

References show_help().

Referenced by main().

GB_ERROR CLI::get_error ( ) const
inline

Definition at line 122 of file arb_calc_pvp.cxx.

References error().

Referenced by main().

const char* CLI::get_database ( ) const
inline

Definition at line 124 of file arb_calc_pvp.cxx.

Referenced by calc_pvp(), export_newick(), and export_seq_data().

const char* CLI::get_treename ( ) const
inline

Definition at line 125 of file arb_calc_pvp.cxx.

Referenced by calc_pvp().

const char* CLI::get_aliname ( ) const
inline

Definition at line 126 of file arb_calc_pvp.cxx.

Referenced by calc_pvp(), and export_seq_data().

const char* CLI::get_database_savename ( ) const
inline

Definition at line 128 of file arb_calc_pvp.cxx.

Referenced by calc_pvp().

const char* CLI::get_SAI_name ( ) const
inline

Definition at line 129 of file arb_calc_pvp.cxx.

Referenced by calc_pvp().

bool CLI::shall_import_tree ( ) const
inline

Definition at line 131 of file arb_calc_pvp.cxx.

Referenced by calc_pvp().

const char* CLI::get_treeimport_filename ( ) const
inline

Definition at line 132 of file arb_calc_pvp.cxx.

References arb_assert.

Referenced by calc_pvp().

bool CLI::shall_delete_tree ( ) const
inline

Definition at line 134 of file arb_calc_pvp.cxx.

Referenced by calc_pvp().

void CLI::show_help ( ) const
inline

Definition at line 114 of file arb_export_newick.cxx.

References fputs().

bool CLI::help_wanted ( ) const
inline

Definition at line 144 of file arb_export_newick.cxx.

GB_ERROR CLI::get_error ( ) const
inline

Definition at line 145 of file arb_export_newick.cxx.

References error().

const char* CLI::get_database ( ) const
inline

Definition at line 147 of file arb_export_newick.cxx.

const char* CLI::get_tree ( ) const
inline

Definition at line 148 of file arb_export_newick.cxx.

Referenced by export_newick().

const char* CLI::get_newick_file ( ) const
inline

Definition at line 149 of file arb_export_newick.cxx.

Referenced by export_newick().

const char* CLI::get_leaf_aci ( ) const
inline

Definition at line 150 of file arb_export_newick.cxx.

Referenced by export_newick().

TREE_node_quoting CLI::get_quoting_mode ( ) const
inline

Definition at line 151 of file arb_export_newick.cxx.

Referenced by export_newick().

bool CLI::shall_add_branch_length ( ) const
inline

Definition at line 153 of file arb_export_newick.cxx.

Referenced by export_newick().

bool CLI::shall_add_bootstraps ( ) const
inline

Definition at line 154 of file arb_export_newick.cxx.

Referenced by export_newick().

bool CLI::shall_add_group_names ( ) const
inline

Definition at line 155 of file arb_export_newick.cxx.

Referenced by export_newick().

bool CLI::shall_replace_problem_chars ( ) const
inline

Definition at line 156 of file arb_export_newick.cxx.

Referenced by export_newick().

bool CLI::shall_be_pretty ( ) const
inline

Definition at line 157 of file arb_export_newick.cxx.

Referenced by export_newick().

bool CLI::help_wanted ( ) const
inline

Definition at line 175 of file arb_export_seq_filtered.cxx.

void CLI::show_help_if_useful ( ) const
inline

Definition at line 176 of file arb_export_seq_filtered.cxx.

References show_help().

GB_ERROR CLI::get_error ( ) const
inline

Definition at line 177 of file arb_export_seq_filtered.cxx.

References error().

const char* CLI::get_database ( ) const
inline

Definition at line 179 of file arb_export_seq_filtered.cxx.

const char* CLI::get_fasta ( ) const
inline

Definition at line 180 of file arb_export_seq_filtered.cxx.

Referenced by export_seq_data().

const char* CLI::get_aliname ( ) const
inline

Definition at line 181 of file arb_export_seq_filtered.cxx.

const char* CLI::get_head_aci ( ) const
inline

Definition at line 182 of file arb_export_seq_filtered.cxx.

Referenced by export_seq_data().

const char* CLI::get_seq_aci ( ) const
inline

Definition at line 183 of file arb_export_seq_filtered.cxx.

Referenced by export_seq_data().

const char* CLI::get_basechars ( ) const
inline

Definition at line 184 of file arb_export_seq_filtered.cxx.

Referenced by export_seq_data().

bool CLI::shall_accept_missing_data ( ) const
inline

Definition at line 186 of file arb_export_seq_filtered.cxx.

Referenced by export_seq_data().

int CLI::get_min_bases_count ( ) const
inline

Definition at line 188 of file arb_export_seq_filtered.cxx.

Referenced by export_seq_data().

bool CLI::has_filters ( ) const
inline

Definition at line 190 of file arb_export_seq_filtered.cxx.

Referenced by export_seq_data().

GB_ERROR CLI::add_filters_to ( FilteredExport exporter) const
inline

Definition at line 191 of file arb_export_seq_filtered.cxx.

References FilteredExport::add_SAI_filter(), arb_assert, and NULp.

Referenced by export_seq_data().


The documentation for this class was generated from the following files: