arb_progress Class Reference

#include <arb_progress.h>

Inheritance diagram for arb_progress:

Collaboration diagram for arb_progress:

Public Member Functions
	arb_progress (const char *title, PINT overall_count)
	arb_progress (const char *title)
	arb_progress (PINT overall_count)
	arb_progress ()
	arb_progress (char *title)
	arb_progress (unsigned long overall_count)
	arb_progress (const char *title, unsigned long overall_count)
	arb_progress (WeightedProgressMarker, const char *title, double phase1_fraction)
	arb_progress (WeightedProgressMarker, double phase1_fraction)
void	allow_title_reuse ()
void	subtitle (const char *stitle)
GB_ERROR	error_if_aborted ()
GB_ERROR	inc_and_error_if_aborted ()
void	inc_and_check_user_abort (GB_ERROR &error)
void	inc_and_check_user_abort (ARB_ERROR &error)
bool	aborted ()
void	auto_subtitles (const char *prefix)
void	inc ()
const arb_progress &	operator++ ()
void	inc_by (PINT count)
void	inc_to (PINT x)
void	inc_to_avoid_overflow (PINT x)
void	sub_progress_skipped ()
void	done ()
void	dump () const
void	force_update ()

Static Public Member Functions
static void	show_comment (const char *comment)

Detailed Description

Definition at line 227 of file arb_progress.h.

Constructor & Destructor Documentation

arb_progress::arb_progress ( const char *  title, PINT  overall_count  )

inline

Definition at line 263 of file arb_progress.h.

arb_progress::arb_progress ( const char *  title )

inlineexplicit

Definition at line 275 of file arb_progress.h.

arb_progress::arb_progress ( PINT  overall_count )

inlineexplicit

Definition at line 283 of file arb_progress.h.

References NULp.

arb_progress::arb_progress ( )

inline

Definition at line 292 of file arb_progress.h.

References NULp.

arb_progress::arb_progress ( char *  title )

inlineexplicit

Definition at line 313 of file arb_progress.h.

arb_progress::arb_progress ( unsigned long  overall_count )

inlineexplicit

Definition at line 314 of file arb_progress.h.

References arb_assert, and NULp.

arb_progress::arb_progress ( const char *  title, unsigned long  overall_count  )

inline

Definition at line 315 of file arb_progress.h.

References arb_assert.

arb_progress::arb_progress ( WeightedProgressMarker  , const char *  title, double  phase1_fraction  )

inline

Definition at line 316 of file arb_progress.h.

arb_progress::arb_progress ( WeightedProgressMarker  , double  phase1_fraction  )

inline

Definition at line 317 of file arb_progress.h.

References NULp.

Member Function Documentation

void arb_progress::allow_title_reuse ( )

inline

Definition at line 319 of file arb_progress.h.

References ArbProgress::nestable::allow_title_reuse().

Referenced by FastAligner_start(), GBT_commit_rename_session(), and NT_database_optimization().

void arb_progress::subtitle ( const char *  stitle )

inline

Definition at line 321 of file arb_progress.h.

References ArbProgress::LEVEL_SUBTITLE, and ArbProgress::nestable::set_text().

Referenced by ST_ML::calc_st_ml(), calculate_clusters(), canvas_to_printer(), create_consense_tree_cb(), di_autodetect_callback(), RootSynchronizer::find_best_root_candidate(), RootSynchronizer::find_good_roots_for_trees(), GDE_startaction_cb(), ArbImporter::import_data(), ArbParsimony::kernighan_optimize_tree(), PrimerDesign::matchSequenceAgainstPrimerTrees(), mixtree_and_calclengths(), MP_aborted(), TreeNode::multifurcate_whole_tree(), nt_add(), NT_alltree_remove_leafs(), NTREE_move_tree_info(), ArbParsimony::optimize_tree(), pars_start_cb(), pd_export_pt_server(), pd_kill_pt_server(), probe_design_event(), probe_match_event(), probe_match_with_specificity_event(), PVP_calculate(), recursiveNNI(), rootsync_subsetTrees_vs_selected(), showDeconstructingSubtitle(), and sq_calc_seq_quality_cb().

GB_ERROR arb_progress::error_if_aborted ( )

inline

Definition at line 323 of file arb_progress.h.

References aborted(), and NULp.

Referenced by compress_sequence_tree(), DeconstructedTree::deconstruct_weighted(), di_calculate_tree_cb(), gb_read_bin_rek_V2(), ConsensusTreeBuilder::get(), ConsensusTree::get_consensus_tree(), inc_and_error_if_aborted(), and probe_match_with_specificity_event().

GB_ERROR arb_progress::inc_and_error_if_aborted ( )

inline

Definition at line 327 of file arb_progress.h.

References error_if_aborted(), and inc().

Referenced by inc_and_check_user_abort(), and GroupSearch::perform_search().

void arb_progress::inc_and_check_user_abort ( GB_ERROR &  error )

inline

Definition at line 332 of file arb_progress.h.

References inc_and_error_if_aborted().

Referenced by ALI_realign_marked(), ALI_translate_marked(), awtc_nn_search_all_listed(), AWTC_pars_names(), DI_MATRIX::calculate(), PH_filter::calculate_column_homology(), compress_sequence_tree(), concatenateAlignments(), create_new_species(), RootSynchronizer::deconstruct_all_trees(), export_sequence_data::detectVerticalGaps(), di_calculate_matrix(), di_mark_by_distance(), export_format_single(), export_to_DB(), DI_MATRIX::extract_from_tree(), RootSynchronizer::find_best_root_candidate(), gb_create_dictionaries(), GBT_commit_rename_session(), ArbImporter::import_data(), InsertDatainGDE(), DI_MATRIX::load(), di_protdist::makedists(), mark_action(), mergeSimilarSpecies(), mg_check_field_cb(), MG_merge_tagged_field_cb(), mg_transfer_listed_species(), modify_fields_of_queried_cb(), NT_alltree_remove_leafs(), NT_convert_gene_locations(), NT_count_different_chars(), NT_database_optimization(), NT_del_mark_move_REF(), NT_fix_gene_data(), NT_format_all_alignments(), pd_kill_pt_server(), perform_query_cb(), probe_match_with_specificity_event(), PVP_calculate(), rootsync_subsetTrees_vs_selected(), species_rename_join(), split_alignment(), SQ_pass1_no_tree(), SQ_pass2_no_tree(), st_ml_check_sequence_quality(), st_remove_entries(), trackAlignmentChanges(), transfer_field_of_listed_cb(), and ScopedTransporter::transferAllIn().

void arb_progress::inc_and_check_user_abort ( ARB_ERROR &  error )

inline

Definition at line 333 of file arb_progress.h.

References inc_and_error_if_aborted().

bool arb_progress::aborted ( )

inline

Definition at line 335 of file arb_progress.h.

References ArbProgress::nestable::aborted().

Referenced by Clusterer::buildInferableClusterStartingWith(), DI_MATRIX::calculate(), create_consense_tree_cb(), di_calculate_matrix(), error_if_aborted(), ProbeValuation::evolution(), DI_MATRIX::extract_from_tree(), EDB_root_bact::fill_species(), Clusterer::find_and_deliverTo(), SpecSetRegistry::find_best_matches_info(), RootSynchronizer::find_best_matching_PART_in(), RootSynchronizer::find_good_roots_for_trees(), find_species_candidates(), Clusterer::findBestClusterBasedOnWords(), g_b_create_master(), gb_read_bin_rek_V2(), ConsensusTree::get_consensus_tree(), InsertData::inc(), AP_tree_edge::mixTree(), MP_aborted(), multiroot_sync_subsetTrees(), neighbourjoining(), ArbParsimony::optimize_tree(), probe_match_with_specificity_enum_callback(), and recursiveNNI().

void arb_progress::auto_subtitles ( const char *  prefix )

inline

Definition at line 344 of file arb_progress.h.

References ArbProgress::nestable::auto_subtitles().

Referenced by ALI_realign_marked(), awtc_nn_search_all_listed(), CON_insertSequences(), di_calculate_tree_cb(), export_format_single(), mergeSimilarSpecies(), and split_alignment().

static void arb_progress::show_comment ( const char *  comment )

inlinestatic

Definition at line 349 of file arb_progress.h.

References ArbProgress::nestable::show_comment().

Referenced by NameServerConnection::connect(), ArbImporter::next_file(), ArbImporter::read_data(), and PrimerDesign::run().

void arb_progress::inc ( )

inline

Definition at line 358 of file arb_progress.h.

References ArbProgress::nestable::inc().

Referenced by Generation::calcFitness(), ED4_manager::create_consensus(), di_calculate_tree_cb(), do_mark_command_for_one_species(), ED4_get_marked_from_menu(), PrimerDesign::evaluatePrimerPairs(), ProbeValuation::evolution(), EDB_root_bact::fill_species(), find_SAI_candidates(), find_species_candidates(), ArbImporter::import_data(), InsertData::inc(), inc_and_error_if_aborted(), PrimerDesign::matchSequenceAgainstPrimerTrees(), operator++(), probe_match_with_specificity_enum_callback(), PT_init_input_data(), PT_prepare_data(), SpecSetRegistry::search_best_match(), SQ_pass1_on_tree(), and SQ_pass2_on_tree().

const arb_progress& arb_progress::operator++ ( )

inline

Definition at line 359 of file arb_progress.h.

References inc().

void arb_progress::inc_by ( PINT  count )

inline

Definition at line 361 of file arb_progress.h.

References arb_assert, and ArbProgress::nestable::inc_by().

Referenced by Clusterer::buildInferableClusterStartingWith(), ConsensusTree::get_consensus_tree(), insert_species_into_tree(), neighbourjoining(), and GroupSearch::perform_search().

void arb_progress::inc_to ( PINT  x )

inline

Definition at line 362 of file arb_progress.h.

References ArbProgress::nestable::inc_to().

Referenced by Clusterer::find_and_deliverTo(), and gb_read_bin_rek_V2().

void arb_progress::inc_to_avoid_overflow ( PINT  x )

inline

Definition at line 363 of file arb_progress.h.

References ArbProgress::nestable::inc_to_avoid_overflow().

void arb_progress::sub_progress_skipped ( )

inline

Definition at line 365 of file arb_progress.h.

References ArbProgress::nestable::child_terminated().

Referenced by AWTC_pars_names().

void arb_progress::done ( )

inline

Definition at line 367 of file arb_progress.h.

References ArbProgress::nestable::done().

Referenced by ALI_realign_marked(), AWTC_pars_names(), Clusterer::buildInferableClusterStartingWith(), compress_sequence_tree(), CON_insertSequences(), concatenateAlignments(), create_consense_tree_cb(), ED4_root::create_hierarchy(), RootSynchronizer::deconstruct_all_trees(), di_calculate_tree_cb(), di_mark_by_distance(), enter_stage_1_build_tree(), ProbeValuation::evolution(), export_to_DB(), DI_MATRIX::extract_from_tree(), Clusterer::find_and_deliverTo(), RootSynchronizer::find_best_root_candidate(), find_species_candidates(), GB_login(), ProbeCandidates::generate_for_sequence(), ConsensusTreeBuilder::get(), PrimerDesign::matchSequenceAgainstPrimerTrees(), MG_merge_tagged_field_cb(), modify_fields_of_queried_cb(), neighbourjoining(), NT_format_all_alignments(), NTREE_move_tree_info(), pd_kill_pt_server(), perform_query_cb(), probe_match_with_specificity_event(), PT_init_input_data(), PT_prepare_data(), sq_calc_seq_quality_cb(), ScopedTransporter::transferAllIn(), FilteredExport::write_fasta(), AliEditor::~AliEditor(), and EntryRemover::~EntryRemover().

void arb_progress::dump

(

)

const

void arb_progress::force_update ( )

inline

Definition at line 371 of file arb_progress.h.

References ArbProgress::nestable::force_update().

Referenced by di_calculate_tree_cb().

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

• CORE/arb_progress.h