Index

_

__call__() (trifusion.process.base.CleanUp method) (trifusion.process.sequence.LookupDatabase method) _check_partitions() (trifusion.process.sequence.Alignment method) _create_table() (trifusion.process.sequence.Alignment method) (trifusion.process.sequence.AlignmentList method) _eval_missing_symbol() (trifusion.process.sequence.Alignment method) _filter_columns() (trifusion.process.sequence.Alignment method) _filter_terminals() (trifusion.process.sequence.Alignment method) _get_filename_list() (trifusion.process.sequence.AlignmentList method) _get_informative_sites() (trifusion.process.sequence.AlignmentList method) _get_interleave_data() (trifusion.process.sequence.Alignment method) _get_similarity (trifusion.process.sequence.AlignmentList attribute) _get_taxa_list() (trifusion.process.sequence.AlignmentList method) _mad_based_outlier() (trifusion.process.sequence.AlignmentList static method) _read_fasta() (trifusion.process.sequence.Alignment method) _read_interleave_nexus() (trifusion.process.sequence.Alignment method) _read_interleave_phylip() (trifusion.process.sequence.Alignment method) _read_loci() (trifusion.process.sequence.Alignment method) _read_nexus() (trifusion.process.sequence.Alignment method)

_read_phylip() (trifusion.process.sequence.Alignment method) _read_stockholm() (trifusion.process.sequence.Alignment method) _reset_pipes() (trifusion.process.sequence.Alignment static method) (trifusion.process.sequence.AlignmentList static method) _reset_summary_stats() (trifusion.process.sequence.AlignmentList method) _set_format() (trifusion.process.sequence.Alignment method) _set_pipes() (trifusion.process.sequence.Alignment static method) (trifusion.process.sequence.AlignmentList method) _table_exists() (trifusion.process.sequence.Alignment method) (trifusion.process.sequence.AlignmentList method) _test_range() (trifusion.process.sequence.Alignment static method) _update_pipes() (trifusion.process.sequence.Alignment static method) (trifusion.process.sequence.AlignmentList static method) _write_fasta() (trifusion.process.sequence.Alignment method) _write_gphocs() (trifusion.process.sequence.Alignment method) _write_ima2() (trifusion.process.sequence.Alignment method) _write_mcmctree() (trifusion.process.sequence.Alignment method) _write_nexus() (trifusion.process.sequence.Alignment method) _write_phylip() (trifusion.process.sequence.Alignment method) _write_stockholm() (trifusion.process.sequence.Alignment method)

A

AboutDialog (class in trifusion.data.resources.custom_widgets) action (trifusion.data.resources.custom_widgets.InputTextDialog attribute) active_file_inf (trifusion.app.TriFusionApp attribute) active_file_list (trifusion.app.TriFusionApp attribute) active_group (trifusion.app.TriFusionApp attribute) active_group_name (trifusion.app.TriFusionApp attribute) active_partitions (trifusion.app.TriFusionApp attribute) active_proteome_files (trifusion.app.TriFusionApp attribute) active_taxa_list (trifusion.app.TriFusionApp attribute) active_tx_inf (trifusion.app.TriFusionApp attribute) add_alignment_files() (trifusion.process.sequence.AlignmentList method) add_alignments() (trifusion.process.sequence.AlignmentList method) add_bookmark_bt() (trifusion.app.TriFusionApp method) add_dataset_bt() (trifusion.app.TriFusionApp method) add_group() (trifusion.ortho.OrthomclToolbox.MultiGroups method) (trifusion.ortho.OrthomclToolbox.MultiGroupsLight method) add_multigroups() (trifusion.ortho.OrthomclToolbox.MultiGroups method) (trifusion.ortho.OrthomclToolbox.MultiGroupsLight method) add_partition() (trifusion.process.data.Partitions method) add_project_bt() (trifusion.app.TriFusionApp method) add_widget() (trifusion.data.resources.custom_widgets.ShowcaseScreen method) AdditionalProcessContents (class in trifusion.data.resources.custom_widgets)

adjust_fasta() (in module trifusion.orthomcl_pipeline) AFS (class in trifusion.data.resources.custom_widgets) AlignedTextInput (class in trifusion.data.resources.custom_widgets) Alignment (class in trifusion.process.sequence) alignment_list (trifusion.app.TriFusionApp attribute) AlignmentException AlignmentList (class in trifusion.process.sequence) alignments (trifusion.process.sequence.AlignmentList attribute) alignments_range (trifusion.process.data.Partitions attribute) AlignmentUnequalLength allele_frequency_spectrum() (trifusion.process.sequence.AlignmentList method) allele_frequency_spectrum_gene() (trifusion.process.sequence.AlignmentList method) allvsall_usearch() (in module trifusion.orthomcl_pipeline) aln_names() (trifusion.process.sequence.AlignmentList method) apply_filter() (trifusion.ortho.OrthomclToolbox.Cluster method) ArgumentError arrow_block (trifusion.app.TriFusionApp attribute) AutoCompTextInput (class in trifusion.data.resources.custom_widgets) autofinder() (trifusion.process.base.Base method) available_screens (trifusion.app.TriFusionApp attribute) average_seqsize() (trifusion.process.sequence.AlignmentList method) average_seqsize_per_species() (trifusion.process.sequence.AlignmentList method) avg_func (trifusion.data.resources.custom_widgets.StatsToggleWgt attribute)

B

BackButton (class in trifusion.data.resources.custom_widgets) background_export_groups() (in module trifusion.data.resources.background_tasks) background_process() (in module trifusion.data.resources.background_tasks) bad_alignments (trifusion.process.sequence.AlignmentList attribute) bar_genecopy_distribution() (trifusion.ortho.OrthomclToolbox.Group method) (trifusion.ortho.OrthomclToolbox.GroupLight method) bar_genecopy_per_species() (trifusion.ortho.OrthomclToolbox.GroupLight method) bar_orthologs() (trifusion.ortho.OrthomclToolbox.MultiGroups method) (trifusion.ortho.OrthomclToolbox.MultiGroupsLight method) bar_plot() (in module trifusion.base.plotter) bar_species_coverage() (trifusion.ortho.OrthomclToolbox.Group method) (trifusion.ortho.OrthomclToolbox.GroupLight method) bar_species_distribution() (trifusion.ortho.OrthomclToolbox.Group method) (trifusion.ortho.OrthomclToolbox.GroupLight method)

Base (class in trifusion.process.base) basic_group_statistics() (trifusion.ortho.OrthomclToolbox.Group method) (trifusion.ortho.OrthomclToolbox.GroupLight method) basic_multigroup_statistics() (trifusion.ortho.OrthomclToolbox.MultiGroups method) blast_parser() (in module trifusion.orthomcl_pipeline) bm_file (trifusion.app.TriFusionApp attribute) bookmark_init() (trifusion.app.TriFusionApp method) bookmark_load() (trifusion.app.TriFusionApp method) bookmarks (trifusion.app.TriFusionApp attribute) bookmarks_bt (trifusion.app.TriFusionApp attribute) box_plot() (in module trifusion.base.plotter) BtList (class in trifusion.data.resources.custom_widgets) build() (trifusion.app.TriFusionApp method) BWCheck (class in trifusion.data.resources.custom_widgets)

C

calls (trifusion.ortho.OrthomclToolbox.MultiGroupsLight attribute) cancel (trifusion.data.resources.custom_widgets.BtList attribute) (trifusion.data.resources.custom_widgets.CheckDialog attribute) (trifusion.data.resources.custom_widgets.CheckProject attribute) (trifusion.data.resources.custom_widgets.CloseBox attribute) (trifusion.data.resources.custom_widgets.CodonFilterDialog attribute) (trifusion.data.resources.custom_widgets.DataSetTriageDialog attribute) (trifusion.data.resources.custom_widgets.DialogMCLFix attribute) (trifusion.data.resources.custom_widgets.DialogUSEARCHFix attribute) (trifusion.data.resources.custom_widgets.ExecutionDialog attribute) (trifusion.data.resources.custom_widgets.ExportGraphics attribute) (trifusion.data.resources.custom_widgets.ExportGroupDialog attribute) (trifusion.data.resources.custom_widgets.FastaExtra attribute) (trifusion.data.resources.custom_widgets.FileOverwriteDialog attribute) (trifusion.data.resources.custom_widgets.FilePopup attribute) (trifusion.data.resources.custom_widgets.FilterDialog attribute) (trifusion.data.resources.custom_widgets.FilterGraphicReport attribute) (trifusion.data.resources.custom_widgets.FormatDialog attribute) (trifusion.data.resources.custom_widgets.IMa2Extra attribute) (trifusion.data.resources.custom_widgets.InflationDialog attribute) (trifusion.data.resources.custom_widgets.InfoPopup attribute) (trifusion.data.resources.custom_widgets.InputList attribute) (trifusion.data.resources.custom_widgets.InputTextDialog attribute) (trifusion.data.resources.custom_widgets.InputType attribute) (trifusion.data.resources.custom_widgets.LoadDialog attribute) (trifusion.data.resources.custom_widgets.LoadMultipleDialog attribute) (trifusion.data.resources.custom_widgets.MySQLDialog attribute) (trifusion.data.resources.custom_widgets.NexusExtra attribute) (trifusion.data.resources.custom_widgets.OrthoReportDialog attribute) (trifusion.data.resources.custom_widgets.OrtoExecutionDialog attribute) (trifusion.data.resources.custom_widgets.OrtoFilterDialog attribute) (trifusion.data.resources.custom_widgets.OrtoSetFiltersDialog attribute) (trifusion.data.resources.custom_widgets.PartitionActiveDialog attribute) (trifusion.data.resources.custom_widgets.PhylipExtra attribute) (trifusion.data.resources.custom_widgets.PlotTriageDialog attribute) (trifusion.data.resources.custom_widgets.ProteinFilterDialog attribute) (trifusion.data.resources.custom_widgets.ProteomePopup attribute) (trifusion.data.resources.custom_widgets.RevConcDialog attribute) (trifusion.data.resources.custom_widgets.SaveDialog attribute) (trifusion.data.resources.custom_widgets.SelectGeneDialog attribute) (trifusion.data.resources.custom_widgets.SplitPartitions attribute) (trifusion.data.resources.custom_widgets.TaxaFilterDialog attribute) (trifusion.data.resources.custom_widgets.TaxaGroupDialog attribute) (trifusion.data.resources.custom_widgets.TextDialog attribute) (trifusion.data.resources.custom_widgets.VariationFilterDialog attribute) (trifusion.data.resources.custom_widgets.WarningDialog attribute) (trifusion.data.resources.custom_widgets.ZorroDialog attribute) cds_db (trifusion.app.TriFusionApp attribute) change_name() (trifusion.process.data.Partitions method) change_taxa_name() (trifusion.app.TriFusionApp method) change_taxon_name() (trifusion.process.sequence.Alignment method) (trifusion.process.sequence.AlignmentList method) characters_proportion() (trifusion.process.sequence.AlignmentList method) characters_proportion_per_species() (trifusion.process.sequence.AlignmentList method) check_action() (trifusion.app.TriFusionApp method) check_data() (in module trifusion.process.sequence) check_file() (trifusion.app.TriFusionApp method)

check_filters() (trifusion.app.TriFusionApp static method) check_infile_list() (in module trifusion.base.sanity) check_partition_split() (trifusion.app.TriFusionApp static method) check_partitions_file() (trifusion.app.TriFusionApp method) check_unique_field() (in module trifusion.orthomcl_pipeline) check_variation_filters() (trifusion.app.TriFusionApp static method) CheckDialog (class in trifusion.data.resources.custom_widgets) CheckProject (class in trifusion.data.resources.custom_widgets) CleanUp (class in trifusion.process.base) clear_alignments() (trifusion.process.sequence.AlignmentList method) clear_groups() (trifusion.ortho.OrthomclToolbox.MultiGroupsLight method) clear_orto_input() (trifusion.app.TriFusionApp method) clear_process_input() (trifusion.app.TriFusionApp method) CloseBox (class in trifusion.data.resources.custom_widgets) CloseFloat (class in trifusion.data.resources.custom_widgets) Cluster (class in trifusion.ortho.OrthomclToolbox) code_gaps() (trifusion.process.sequence.Alignment method) (trifusion.process.sequence.AlignmentList method) codon_filter_settings (trifusion.app.TriFusionApp attribute) CodonFilterDialog (class in trifusion.data.resources.custom_widgets) collapse() (trifusion.process.sequence.Alignment method) (trifusion.process.sequence.AlignmentList method) commonTempTables() (in module trifusion.ortho.orthomclPairs) con (trifusion.process.sequence.AlignmentList attribute) concatenate() (trifusion.process.sequence.AlignmentList method) consensus() (trifusion.process.sequence.Alignment method) (trifusion.process.sequence.AlignmentList method) control (trifusion.data.resources.custom_widgets.FileChooserM attribute) conversion_suffix (trifusion.app.TriFusionApp attribute) convert_group() (in module trifusion.ortho.protein2dna) convert_protein_file() (in module trifusion.ortho.protein2dna) coorthologs() (in module trifusion.ortho.orthomclPairs) count_files (trifusion.app.TriFusionApp attribute) count_partitions (trifusion.app.TriFusionApp attribute) counter (trifusion.process.data.Partitions attribute) create_db() (in module trifusion.ortho.protein2dna) create_folder() (trifusion.app.TriFusionApp method) create_partfile (trifusion.app.TriFusionApp attribute) create_query() (in module trifusion.ortho.protein2dna) create_query_from_dict() (in module trifusion.ortho.protein2dna) create_ref_label() (trifusion.data.resources.custom_widgets.LinkedLabel static method) createCoOrthologTable() (in module trifusion.ortho.orthomclInstallSchema) createInParalogTable() (in module trifusion.ortho.orthomclInstallSchema) createInterTaxonMatchView() (in module trifusion.ortho.orthomclInstallSchema) createOrthologTable() (in module trifusion.ortho.orthomclInstallSchema) createSimilarSequencesTable() (in module trifusion.ortho.orthomclInstallSchema) CrunchData (class in trifusion.data.resources.custom_widgets) cumulative_missing_genes() (trifusion.process.sequence.AlignmentList method) CumulativeMissingOrto (class in trifusion.data.resources.custom_widgets) cur (in module trifusion.ortho.orthomclBlastParser) (trifusion.process.sequence.AlignmentList attribute) cur_dir (trifusion.app.TriFusionApp attribute) current_lgd (trifusion.app.TriFusionApp attribute) current_plot (trifusion.app.TriFusionApp attribute) current_plt_idx (trifusion.app.TriFusionApp attribute) current_screen (trifusion.app.TriFusionApp attribute) current_table (trifusion.app.TriFusionApp attribute) CustomPopup (class in trifusion.data.resources.custom_widgets)

D

dataset_file (trifusion.app.TriFusionApp attribute) DataSetTriageDialog (class in trifusion.data.resources.custom_widgets) DEFAULT_PADDING (trifusion.data.resources.custom_widgets.AlignedTextInput attribute) DescriptionBox (class in trifusion.data.resources.custom_widgets) dialog_about() (trifusion.app.TriFusionApp method) dialog_codonfilter() (trifusion.app.TriFusionApp method) dialog_create_group_from_file() (trifusion.app.TriFusionApp method) dialog_dataset_creator() (trifusion.app.TriFusionApp method) dialog_exclude_orto_taxa() (trifusion.app.TriFusionApp method) dialog_execution() (trifusion.app.TriFusionApp method) dialog_export_graphic() (trifusion.app.TriFusionApp method) dialog_export_groups() (trifusion.app.TriFusionApp method) dialog_export_groups_filechooser() (trifusion.app.TriFusionApp method) dialog_fasta_extra() (trifusion.app.TriFusionApp method) dialog_filechooser() (trifusion.app.TriFusionApp method) dialog_fileoverwrite() (trifusion.app.TriFusionApp method) dialog_filter() (trifusion.app.TriFusionApp method) dialog_filter_report() (trifusion.app.TriFusionApp method) dialog_floatcheck() (trifusion.app.TriFusionApp method) dialog_format() (trifusion.app.TriFusionApp method) dialog_general_info() (trifusion.app.TriFusionApp method) dialog_ima2_extra() (trifusion.app.TriFusionApp method) dialog_import_groups() (trifusion.app.TriFusionApp method) dialog_import_partitions() (trifusion.app.TriFusionApp method) dialog_inflation() (trifusion.app.TriFusionApp method) dialog_load_partfile() (trifusion.app.TriFusionApp method) dialog_mcl_fix() (trifusion.app.TriFusionApp method) dialog_nexus_extra() (trifusion.app.TriFusionApp method) dialog_ortho_filter() (trifusion.app.TriFusionApp method) dialog_orto_execution() (trifusion.app.TriFusionApp method) dialog_orto_setfilter() (trifusion.app.TriFusionApp method) dialog_partition_files() (trifusion.app.TriFusionApp method) dialog_partitions() (trifusion.app.TriFusionApp method) dialog_partitions_split() (trifusion.app.TriFusionApp method)

dialog_phylip_extra() (trifusion.app.TriFusionApp method) dialog_plot_check_filters() (trifusion.app.TriFusionApp method) dialog_protein_filter() (trifusion.app.TriFusionApp method) dialog_remove_from_file() (trifusion.app.TriFusionApp method) dialog_reverse_concatenation() (trifusion.app.TriFusionApp method) dialog_reverse_inlist() (trifusion.app.TriFusionApp method) dialog_search_report() (trifusion.app.TriFusionApp method) dialog_select_from_file() (trifusion.app.TriFusionApp method) dialog_select_gene() (trifusion.app.TriFusionApp method) dialog_select_taxa_group() (trifusion.app.TriFusionApp method) dialog_set_exclude_orto_taxa() (trifusion.app.TriFusionApp method) dialog_taxafilter() (trifusion.app.TriFusionApp method) dialog_taxagroup() (trifusion.app.TriFusionApp method) dialog_text() (trifusion.app.TriFusionApp method) dialog_usearch_fix() (trifusion.app.TriFusionApp method) dialog_variationfilter() (trifusion.app.TriFusionApp method) dialog_warning() (trifusion.app.TriFusionApp method) dialog_zorro() (trifusion.app.TriFusionApp method) DialogMCLFix (class in trifusion.data.resources.custom_widgets) DialogUSEARCHFix (class in trifusion.data.resources.custom_widgets) disengage_groups() (trifusion.app.TriFusionApp method) dismiss_all_popups() (trifusion.app.TriFusionApp method) dismiss_close_float() (trifusion.app.TriFusionApp method) dismiss_exit() (trifusion.app.TriFusionApp method) dismiss_plot_wgt() (trifusion.app.TriFusionApp method) dismiss_popup() (trifusion.app.TriFusionApp method) dismiss_stats_toggle() (trifusion.app.TriFusionApp method) dismiss_subpopup() (trifusion.app.TriFusionApp method) drag_c (trifusion.app.TriFusionApp attribute) drag_files (trifusion.app.TriFusionApp attribute) dump_pairs() (in module trifusion.orthomcl_pipeline) duplicate_alignments (trifusion.process.sequence.AlignmentList attribute) duplicate_taxa() (trifusion.process.base.Base static method) DuplicateTaxa

E

e (trifusion.process.sequence.Alignment attribute) EmptyAlignment EmptyData entry_released() (trifusion.data.resources.custom_widgets.FileChooserM method) entry_touched() (trifusion.data.resources.custom_widgets.FileChooserL method) (trifusion.data.resources.custom_widgets.FileChooserM method) exclude_taxa() (trifusion.ortho.OrthomclToolbox.Group method) (trifusion.ortho.OrthomclToolbox.GroupLight method) execute() (in module trifusion.ortho.orthomclDumpPairsFiles) (in module trifusion.ortho.orthomclInstallSchema) (in module trifusion.ortho.orthomclLoadBlast) (in module trifusion.ortho.orthomclPairs)

ExecutionDialog (class in trifusion.data.resources.custom_widgets) export_filtered_group() (trifusion.ortho.OrthomclToolbox.Group method) (trifusion.ortho.OrthomclToolbox.GroupLight method) export_filtered_groups() (in module trifusion.orthomcl_pipeline) export_graphic() (trifusion.app.TriFusionApp method) export_mode (trifusion.app.TriFusionApp attribute) export_names() (trifusion.app.TriFusionApp method) export_table() (trifusion.app.TriFusionApp method) ExportGraphics (class in trifusion.data.resources.custom_widgets) ExportGroupDialog (class in trifusion.data.resources.custom_widgets) ExtLabel (class in trifusion.data.resources.custom_widgets) ExtSpinner (class in trifusion.data.resources.custom_widgets)

F

fancy_bt (trifusion.app.TriFusionApp attribute) fancy_dropped (trifusion.app.TriFusionApp attribute) FancyButton (class in trifusion.data.resources.custom_widgets) FancyDropDown (class in trifusion.data.resources.custom_widgets) FancyMarker (class in trifusion.data.resources.custom_widgets) FancyMarkerPersist (class in trifusion.data.resources.custom_widgets) FastaExtra (class in trifusion.data.resources.custom_widgets) file_apply_all (trifusion.app.TriFusionApp attribute) file_groups (trifusion.app.TriFusionApp attribute) file_list (trifusion.app.TriFusionApp attribute) file_overwrite (trifusion.app.TriFusionApp attribute) FileChooserL (class in trifusion.data.resources.custom_widgets) FileChooserM (class in trifusion.data.resources.custom_widgets) filename_map (trifusion.app.TriFusionApp attribute) FileOverwriteDialog (class in trifusion.data.resources.custom_widgets) FilePopup (class in trifusion.data.resources.custom_widgets) filter_by_taxa() (trifusion.process.sequence.AlignmentList method)

filter_codon_positions() (trifusion.process.sequence.Alignment method) (trifusion.process.sequence.AlignmentList method) filter_fasta() (in module trifusion.orthomcl_pipeline) filter_informative_sites() (trifusion.process.sequence.Alignment method) (trifusion.process.sequence.AlignmentList method) filter_min_taxa() (trifusion.process.sequence.AlignmentList method) filter_missing_data() (trifusion.process.sequence.Alignment method) (trifusion.process.sequence.AlignmentList method) filter_segregating_sites() (trifusion.process.sequence.Alignment method) (trifusion.process.sequence.AlignmentList method) FilterDialog (class in trifusion.data.resources.custom_widgets) filtered_alignments (trifusion.process.sequence.AlignmentList attribute) FilterGraphicReport (class in trifusion.data.resources.custom_widgets) FixButton (class in trifusion.data.resources.custom_widgets) format_evalue() (in module trifusion.ortho.orthomclBlastParser) format_list() (trifusion.process.sequence.AlignmentList method) FormatDialog (class in trifusion.data.resources.custom_widgets) fullscreen (trifusion.data.resources.custom_widgets.ShowcaseScreen attribute)

G

gap_symbol (trifusion.process.sequence.AlignmentList attribute) GaugePlot (class in trifusion.data.resources.custom_widgets) gen_wgt() (in module trifusion.TriSeq) gene_master_table (trifusion.app.TriFusionApp attribute) gene_occupancy() (trifusion.process.sequence.AlignmentList method) gene_table_selection (trifusion.app.TriFusionApp attribute) GeneOccupancy (class in trifusion.data.resources.custom_widgets) generate_cfg_template() (in module trifusion.TriStats) GeneTable (class in trifusion.data.resources.custom_widgets) get_active_group() (in module trifusion.data.resources.background_tasks) get_active_group_light() (trifusion.app.TriFusionApp method) get_active_sets() (trifusion.app.TriFusionApp method) get_args() (in module trifusion.TriSeq) get_file_information() (trifusion.app.TriFusionApp method) get_filters() (trifusion.ortho.OrthomclToolbox.Group method) get_gene_table_stats() (trifusion.process.sequence.AlignmentList method) get_genes() (in module trifusion.ortho.orthomclBlastParser) get_gnames() (trifusion.ortho.OrthomclToolbox.MultiGroups method) get_group() (trifusion.ortho.OrthomclToolbox.MultiGroups method) (trifusion.ortho.OrthomclToolbox.MultiGroupsLight method) get_loci_taxa() (trifusion.process.base.Base static method) get_model_name() (trifusion.process.data.Partitions method) get_multigroup_statistics() (trifusion.ortho.OrthomclToolbox.MultiGroupsLight method)

get_orto_data() (in module trifusion.data.resources.background_tasks) get_pairs() (in module trifusion.ortho.protein2dna) get_partition_names() (trifusion.process.data.Partitions method) get_popup_info() (trifusion.app.TriFusionApp method) get_proteome_information() (trifusion.app.TriFusionApp static method) get_sequence() (trifusion.process.sequence.Alignment method) get_start_end() (in module trifusion.ortho.orthomclBlastParser) get_stats_data() (in module trifusion.data.resources.background_tasks) get_stats_summary() (in module trifusion.data.resources.background_tasks) get_summary_stats() (trifusion.process.sequence.AlignmentList method) get_tables() (trifusion.process.sequence.AlignmentList method) get_taxa_information() (trifusion.app.TriFusionApp method) get_taxon_and_length() (in module trifusion.ortho.orthomclBlastParser) get_taxon_information() (trifusion.app.TriFusionApp method) go_carousel() (trifusion.app.TriFusionApp method) go_previous_screen() (trifusion.app.TriFusionApp method) go_screen() (trifusion.app.TriFusionApp method) Group (class in trifusion.ortho.OrthomclToolbox) group_overlap() (trifusion.ortho.OrthomclToolbox.MultiGroups method) group_prefix (trifusion.app.TriFusionApp attribute) GroupLight (class in trifusion.ortho.OrthomclToolbox) groups() (trifusion.ortho.OrthomclToolbox.GroupLight method) guess_code() (trifusion.process.base.Base static method) gui_exec() (in module trifusion.TriFusion)

H

halign (trifusion.data.resources.custom_widgets.AlignedTextInput attribute) HandledException hap_prefix (trifusion.app.TriFusionApp attribute) histogram_plot() (in module trifusion.base.plotter)

histogram_smooth() (in module trifusion.base.plotter) home_path (trifusion.app.TriFusionApp attribute) HseparatorFooter (class in trifusion.data.resources.custom_widgets) HtmlTemplate (class in trifusion.base.html_creator)

I

IconFloat (class in trifusion.data.resources.custom_widgets) ima2_options (trifusion.app.TriFusionApp attribute) IMa2Extra (class in trifusion.data.resources.custom_widgets) index (trifusion.app.TriFusionApp attribute) IndividualFilterWgt (class in trifusion.data.resources.custom_widgets) InflationDialog (class in trifusion.data.resources.custom_widgets) InfoPopup (class in trifusion.data.resources.custom_widgets) inparalogs() (in module trifusion.ortho.orthomclPairs) input_format (trifusion.process.sequence.Alignment attribute) InputError InputList (class in trifusion.data.resources.custom_widgets) InputTextDialog (class in trifusion.data.resources.custom_widgets) InputType (class in trifusion.data.resources.custom_widgets) InputTypeError insert_text() (trifusion.data.resources.custom_widgets.AutoCompTextInput method) (trifusion.data.resources.custom_widgets.StringInput method)

install_schema() (in module trifusion.orthomcl_pipeline) interleave_data (trifusion.process.sequence.Alignment attribute) interpolation_plot() (in module trifusion.base.plotter) InvalidPartitionFile InvalidSequenceType is_control_pressed (trifusion.app.TriFusionApp attribute) is_shift_pressed (trifusion.app.TriFusionApp attribute) is_single() (trifusion.process.data.Partitions method) iter_alignment() (trifusion.process.sequence.Alignment method) iter_alignment_files() (trifusion.process.sequence.AlignmentList method) iter_columns() (trifusion.process.sequence.Alignment method) iter_columns_uniq() (trifusion.process.sequence.Alignment method) iter_files() (trifusion.process.data.Partitions method) iter_gnames() (trifusion.ortho.OrthomclToolbox.MultiGroups method) iter_sequences() (trifusion.process.sequence.Alignment method) iter_species_frequency() (trifusion.ortho.OrthomclToolbox.GroupLight method)

K

keyboard_listen() (trifusion.data.resources.custom_widgets.FileChooserM method)

KillByUser

L

last_sp_bt (trifusion.app.TriFusionApp attribute) ld_hat (trifusion.app.TriFusionApp attribute) length_polymorphism_correlation() (trifusion.process.sequence.AlignmentList method) LinkedLabel (class in trifusion.data.resources.custom_widgets) load_files() (trifusion.app.TriFusionApp method) load_files_dragndrop() (trifusion.app.TriFusionApp method) load_files_startup() (trifusion.app.TriFusionApp method) load_files_subproc() (trifusion.app.TriFusionApp method) load_group_files() (in module trifusion.data.resources.background_tasks) load_groups() (trifusion.app.TriFusionApp method) load_plot() (trifusion.app.TriFusionApp static method) load_proc() (in module trifusion.data.resources.background_tasks) load_proteomes() (trifusion.app.TriFusionApp method) load_screen() (trifusion.app.TriFusionApp method)

LoadCounter (class in trifusion.data.resources.custom_widgets) LoadDialog (class in trifusion.data.resources.custom_widgets) loaded_screens (trifusion.app.TriFusionApp attribute) LoadMoreBt (class in trifusion.data.resources.custom_widgets) LoadMultipleDialog (class in trifusion.data.resources.custom_widgets) LoadProgressDialog (class in trifusion.data.resources.custom_widgets) LoadSpinner (class in trifusion.data.resources.custom_widgets) lock_side_panel (trifusion.app.TriFusionApp attribute) lock_stats (trifusion.app.TriFusionApp attribute) locus_length (trifusion.process.sequence.Alignment attribute) log() (in module trifusion.ortho.orthomclPairs) log_file (trifusion.app.TriFusionApp attribute) LookupDatabase (class in trifusion.process.sequence) LVCorrelation (class in trifusion.data.resources.custom_widgets)

M

main() (in module trifusion.app) (in module trifusion.TriSeq) (in module trifusion.TriStats) (in module trifusion.orthomcl_pipeline) main_checks() (in module trifusion.TriStats) main_nodes (trifusion.app.TriFusionApp attribute) main_operations (trifusion.app.TriFusionApp attribute) MAX_FILE_BUTTON (trifusion.app.TriFusionApp attribute) MAX_PARTITION_BUTTON (trifusion.app.TriFusionApp attribute) MAX_TABLE_N (trifusion.app.TriFusionApp attribute) mcl() (in module trifusion.orthomcl_pipeline) mcl_file (trifusion.app.TriFusionApp attribute) mcl_groups() (in module trifusion.orthomcl_pipeline) mcl_inflation (trifusion.app.TriFusionApp attribute) mcl_to_groups() (in module trifusion.ortho.orthomclMclToGroups) merge_partitions() (trifusion.process.data.Partitions method) merged_files (trifusion.process.data.Partitions attribute) merger() (in module trifusion.process.base) mfilters() (in module trifusion.base.sanity) missing_data_distribution() (trifusion.process.sequence.AlignmentList method) missing_data_per_species() (trifusion.process.sequence.AlignmentList method)

missing_filter_settings (trifusion.app.TriFusionApp attribute) missing_genes_average() (trifusion.process.sequence.AlignmentList method) missing_genes_per_species() (trifusion.process.sequence.AlignmentList method) MissingData (class in trifusion.data.resources.custom_widgets) MissingOrto (class in trifusion.data.resources.custom_widgets) ModalView (class in trifusion.data.resources.custom_widgets) models (trifusion.process.data.Partitions attribute) ModelSpinner (class in trifusion.data.resources.custom_widgets) more_stats_table_bts() (trifusion.app.TriFusionApp method) MoreTableBt (class in trifusion.data.resources.custom_widgets) mouse_over_bts (trifusion.app.TriFusionApp attribute) mouse_over_ready (trifusion.app.TriFusionApp attribute) mouse_position (trifusion.app.TriFusionApp attribute) mouse_zoom() (trifusion.app.TriFusionApp method) MouseOverLabel (class in trifusion.data.resources.custom_widgets) multi_bar_plot() (in module trifusion.base.plotter) MultiGroups (class in trifusion.ortho.OrthomclToolbox) MultiGroupsLight (class in trifusion.ortho.OrthomclToolbox) MultipleSequenceTypes multiselect (trifusion.data.resources.custom_widgets.TreeViewM attribute) MySlider (class in trifusion.data.resources.custom_widgets) MySQLDialog (class in trifusion.data.resources.custom_widgets)

N

name (trifusion.process.sequence.Alignment attribute) NexusExtra (class in trifusion.data.resources.custom_widgets) NoDataLabel (class in trifusion.data.resources.custom_widgets) non_alignments (trifusion.process.sequence.AlignmentList attribute)

non_overlapping_match() (in module trifusion.ortho.orthomclBlastParser) normalizeOrthologsSub() (in module trifusion.ortho.orthomclPairs) NoUniqueField NucAAProportions (class in trifusion.data.resources.custom_widgets)

O

old_mouse_over (trifusion.app.TriFusionApp attribute) on_dir_entry() (trifusion.data.resources.custom_widgets.FileChooserL method) (trifusion.data.resources.custom_widgets.FileChooserM method) on_double_click() (trifusion.data.resources.custom_widgets.FileChooserL method) (trifusion.data.resources.custom_widgets.FileChooserM method) on_release() (trifusion.data.resources.custom_widgets.MySlider method) on_size() (trifusion.data.resources.custom_widgets.AlignedTextInput method) on_text() (trifusion.data.resources.custom_widgets.AlignedTextInput method) on_touch_down() (trifusion.data.resources.custom_widgets.FancyDropDown method) (trifusion.data.resources.custom_widgets.SimpleModal method) (trifusion.data.resources.custom_widgets.TFButton method) on_touch_up() (trifusion.data.resources.custom_widgets.FancyDropDown method) (trifusion.data.resources.custom_widgets.MySlider method) (trifusion.data.resources.custom_widgets.SimpleModal method) (trifusion.data.resources.custom_widgets.TFButton method) open_entry() (trifusion.data.resources.custom_widgets.FileChooserL method) (trifusion.data.resources.custom_widgets.FileChooserM method) open_project() (trifusion.app.TriFusionApp method) operation_queue_init() (trifusion.app.TriFusionApp method) operation_tv (trifusion.app.TriFusionApp attribute) OptsGrid (class in trifusion.data.resources.custom_widgets) original_file_inf (trifusion.app.TriFusionApp attribute) original_tx_inf (trifusion.app.TriFusionApp attribute) ortho_dir (trifusion.app.TriFusionApp attribute) ortho_group_files (trifusion.app.TriFusionApp attribute) ortho_groups (trifusion.app.TriFusionApp attribute) ortho_search_options (trifusion.app.TriFusionApp attribute) OrthoGraphicReport (class in trifusion.data.resources.custom_widgets) OrthoGroupException ortholog_num (trifusion.data.resources.custom_widgets.GaugePlot attribute) ortholog_prefix (trifusion.app.TriFusionApp attribute) ortholog_txt (trifusion.data.resources.custom_widgets.DescriptionBox attribute) orthologs() (in module trifusion.ortho.orthomclPairs) orthologTaxonSub() (in module trifusion.ortho.orthomclPairs) orthology_card() (trifusion.app.TriFusionApp method) orthology_clear_options() (trifusion.app.TriFusionApp method) orthology_search_exec() (trifusion.app.TriFusionApp method) OrthologySearchGrid (class in trifusion.data.resources.custom_widgets)

orthomcl_blast_parser() (in module trifusion.ortho.orthomclBlastParser) orthomcl_filter_fasta() (in module trifusion.ortho.orthomclFilterFasta) OrthoReportDialog (class in trifusion.data.resources.custom_widgets) orto_change_state() (trifusion.app.TriFusionApp method) orto_check_state() (trifusion.app.TriFusionApp method) orto_compare_groups() (trifusion.app.TriFusionApp method) orto_execution() (in module trifusion.data.resources.background_tasks) orto_export_dir (trifusion.app.TriFusionApp attribute) orto_export_groups() (trifusion.app.TriFusionApp method) orto_generate_report() (trifusion.app.TriFusionApp method) orto_max_gene (trifusion.app.TriFusionApp attribute) orto_min_sp (trifusion.app.TriFusionApp attribute) orto_plt_method (trifusion.app.TriFusionApp attribute) orto_report_dialog() (trifusion.app.TriFusionApp method) orto_search_height (trifusion.app.TriFusionApp attribute) orto_show_plot() (trifusion.app.TriFusionApp method) orto_update_filters() (in module trifusion.data.resources.background_tasks) orto_write_plot() (trifusion.app.TriFusionApp method) OrtoExecutionDialog (class in trifusion.data.resources.custom_widgets) OrtoFilterDialog (class in trifusion.data.resources.custom_widgets) OrtoPlotToolbar (class in trifusion.data.resources.custom_widgets) OrtoProgressDialog (class in trifusion.data.resources.custom_widgets) OrtoSetFiltersDialog (class in trifusion.data.resources.custom_widgets) outlier_densisty_dist() (in module trifusion.base.plotter) outlier_missing_data() (trifusion.process.sequence.AlignmentList method) outlier_missing_data_sp() (trifusion.process.sequence.AlignmentList method) outlier_segregating() (trifusion.process.sequence.AlignmentList method) outlier_segregating_sp() (trifusion.process.sequence.AlignmentList method) outlier_sequence_size() (trifusion.process.sequence.AlignmentList method) outlier_sequence_size_sp() (trifusion.process.sequence.AlignmentList method) OutlierFooter (class in trifusion.data.resources.custom_widgets) OutlierMissing (class in trifusion.data.resources.custom_widgets) OutlierSegregating (class in trifusion.data.resources.custom_widgets) OutlierSize (class in trifusion.data.resources.custom_widgets) output_dir (trifusion.app.TriFusionApp attribute) output_file (trifusion.app.TriFusionApp attribute) output_formats (trifusion.app.TriFusionApp attribute) OutputFormatError

P

pair_search() (in module trifusion.ortho.protein2dna) pairs() (in module trifusion.orthomcl_pipeline) paralog_per_species_statistic() (trifusion.ortho.OrthomclToolbox.Group method) parse_nexus_model() (trifusion.process.data.Partitions method) parse_string() (trifusion.ortho.OrthomclToolbox.Cluster method) partition_length (trifusion.process.data.Partitions attribute) PartitionActiveDialog (class in trifusion.data.resources.custom_widgets) PartitionException Partitions (class in trifusion.process.data) partitions (trifusion.process.data.Partitions attribute) (trifusion.process.sequence.Alignment attribute) partitions_alignments (trifusion.process.data.Partitions attribute) partitions_change_name() (trifusion.app.TriFusionApp method) partitions_file (trifusion.app.TriFusionApp attribute) partitions_import_scheme() (trifusion.app.TriFusionApp method) partitions_index (trifusion.process.data.Partitions attribute) partitions_merge() (trifusion.app.TriFusionApp method) partitions_merge_dialog() (trifusion.app.TriFusionApp method) partitions_split() (trifusion.app.TriFusionApp method) PartitionsDialog (class in trifusion.data.resources.custom_widgets) path (trifusion.process.sequence.Alignment attribute) path_list (trifusion.process.sequence.AlignmentList attribute) PathLabel (class in trifusion.data.resources.custom_widgets) PathText (class in trifusion.data.resources.custom_widgets) phylip_truncate_name (trifusion.app.TriFusionApp attribute) PhylipExtra (class in trifusion.data.resources.custom_widgets) plot_backups (trifusion.app.TriFusionApp attribute) plot_screens (trifusion.app.TriFusionApp attribute) PlotChangeFilters (class in trifusion.data.resources.custom_widgets) PlotTriageDialog (class in trifusion.data.resources.custom_widgets) plt_patch (trifusion.app.TriFusionApp attribute) populate_input_files() (trifusion.app.TriFusionApp method) populate_partitions() (trifusion.app.TriFusionApp method) populate_species() (trifusion.app.TriFusionApp method) populate_stats_footer() (trifusion.app.TriFusionApp method) popup_info() (trifusion.app.TriFusionApp method) PopupMod (class in trifusion.data.resources.custom_widgets)

post_aln_checks() (in module trifusion.base.sanity) prep_fasta() (in module trifusion.orthomcl_pipeline) prev_tb (trifusion.app.TriFusionApp attribute) prev_touch (trifusion.data.resources.custom_widgets.FileChooserM attribute) previous_mouse_over (trifusion.app.TriFusionApp attribute) previous_screen (trifusion.app.TriFusionApp attribute) previous_sets (trifusion.app.TriFusionApp attribute) previous_stats_toggle (trifusion.app.TriFusionApp attribute) print_col() (in module trifusion.process.base) print_previous_subject() (in module trifusion.ortho.orthomclBlastParser) printCoOrthologsFile() (in module trifusion.ortho.orthomclDumpPairsFiles) printInparalogsFile() (in module trifusion.ortho.orthomclDumpPairsFiles) printMclAbcFile() (in module trifusion.ortho.orthomclDumpPairsFiles) printOrthologsFile() (in module trifusion.ortho.orthomclDumpPairsFiles) process_clear_options() (trifusion.app.TriFusionApp method) process_exec() (trifusion.app.TriFusionApp method) process_execution() (in module trifusion.data.resources.background_tasks) process_grid_wgt (trifusion.app.TriFusionApp attribute) process_height (trifusion.app.TriFusionApp attribute) process_options (trifusion.app.TriFusionApp attribute) ProcessExecutionProgress (class in trifusion.data.resources.custom_widgets) ProcessGeneral (class in trifusion.data.resources.custom_widgets) ProgressBox (class in trifusion.data.resources.custom_widgets) ProgressFinished (class in trifusion.data.resources.custom_widgets) ProgressWaiting (class in trifusion.data.resources.custom_widgets) ProjectOrtoBt (class in trifusion.data.resources.custom_widgets) ProjectProcBt (class in trifusion.data.resources.custom_widgets) projects_file (trifusion.app.TriFusionApp attribute) projects_init() (trifusion.app.TriFusionApp method) proportion (trifusion.data.resources.custom_widgets.GaugePlot attribute) PropSwitcher (class in trifusion.data.resources.custom_widgets) prot_txt (trifusion.data.resources.custom_widgets.DescriptionBox attribute) protein_db (trifusion.app.TriFusionApp attribute) protein_max_stop (trifusion.app.TriFusionApp attribute) protein_min_len (trifusion.app.TriFusionApp attribute) ProteinFilterDialog (class in trifusion.data.resources.custom_widgets) proteome_files (trifusion.app.TriFusionApp attribute) ProteomePopup (class in trifusion.data.resources.custom_widgets)

R

read_alignment() (trifusion.process.sequence.Alignment method) read_basic_csv() (trifusion.process.base.Base static method) read_from_dict() (trifusion.process.data.Partitions method) read_from_file() (trifusion.process.data.Partitions method) read_from_nexus_string() (trifusion.process.data.Partitions method) redraw() (trifusion.data.resources.custom_widgets.AlignedTextInput method) release_shift() (trifusion.data.resources.custom_widgets.FileChooserM method) removable_media (trifusion.app.TriFusionApp attribute) remove_alignment() (trifusion.process.sequence.Alignment method) remove_all() (trifusion.app.TriFusionApp method) remove_all_groups() (trifusion.app.TriFusionApp method) remove_bookmark_bt() (trifusion.app.TriFusionApp method) remove_bt() (trifusion.app.TriFusionApp method) remove_bt_from_selection() (trifusion.app.TriFusionApp method) remove_fancy_dropdown() (trifusion.app.TriFusionApp method) remove_file() (trifusion.process.sequence.AlignmentList method) remove_group() (trifusion.ortho.OrthomclToolbox.MultiGroups method) (trifusion.ortho.OrthomclToolbox.MultiGroupsLight method) remove_groups() (trifusion.app.TriFusionApp method) remove_partition() (trifusion.process.data.Partitions method) remove_partition_box() (trifusion.app.TriFusionApp method)

remove_project() (trifusion.app.TriFusionApp method) remove_tables() (trifusion.process.sequence.AlignmentList method) remove_taxa() (trifusion.ortho.OrthomclToolbox.Cluster method) (trifusion.process.sequence.Alignment method) (trifusion.process.sequence.AlignmentList method) remove_taxa_bt() (trifusion.app.TriFusionApp static method) remove_taxa_group() (trifusion.app.TriFusionApp method) remove_tmp() (in module trifusion.data.resources.background_tasks) RemoveFloat (class in trifusion.data.resources.custom_widgets) repopulate_partitions() (trifusion.app.TriFusionApp method) reset() (trifusion.process.data.Partitions method) restriction_range (trifusion.process.sequence.Alignment attribute) resume_database() (trifusion.process.sequence.AlignmentList method) retrieve_alignment() (trifusion.process.sequence.AlignmentList method) retrieve_sequences() (trifusion.ortho.OrthomclToolbox.Group method) (trifusion.ortho.OrthomclToolbox.GroupLight method) rev_infile (trifusion.app.TriFusionApp attribute) RevConcDialog (class in trifusion.data.resources.custom_widgets) reverse_concatenate() (trifusion.process.sequence.Alignment method) (trifusion.process.sequence.AlignmentList method) rm_illegal() (trifusion.process.base.Base static method) run_in_background() (trifusion.app.TriFusionApp method)

S

save (trifusion.data.resources.custom_widgets.SaveDialog attribute) save_bookmark() (trifusion.app.TriFusionApp method) save_codonfilter() (trifusion.app.TriFusionApp method) save_dataset_group() (trifusion.app.TriFusionApp method) save_file() (trifusion.app.TriFusionApp method) save_format() (trifusion.app.TriFusionApp method) save_gapfilter() (trifusion.app.TriFusionApp method) save_ima2_opts() (trifusion.app.TriFusionApp method) save_inflation() (trifusion.app.TriFusionApp method) save_main_operation() (trifusion.app.TriFusionApp method) save_model() (trifusion.app.TriFusionApp method) save_operation_queue() (trifusion.app.TriFusionApp method) save_ortho_filters() (trifusion.app.TriFusionApp method) save_project() (trifusion.app.TriFusionApp method) save_protein_filters() (trifusion.app.TriFusionApp method) save_reverseconc_partfile() (trifusion.app.TriFusionApp method) save_reverseconc_settings() (trifusion.app.TriFusionApp method) save_taxafilter() (trifusion.app.TriFusionApp method) save_text() (trifusion.app.TriFusionApp method) save_variationfilter() (trifusion.app.TriFusionApp method) save_zorro_settings() (trifusion.app.TriFusionApp method) SaveDialog (class in trifusion.data.resources.custom_widgets) scatter_plot() (in module trifusion.base.plotter) screen (trifusion.app.TriFusionApp attribute) screen_names (trifusion.app.TriFusionApp attribute) search_add_gene_table_line() (trifusion.app.TriFusionApp method) search_sort_gene_table() (trifusion.app.TriFusionApp method) search_statistics_clear() (trifusion.app.TriFusionApp method) search_statistics_gene_table() (trifusion.app.TriFusionApp method) secondary_operations (trifusion.app.TriFusionApp attribute) secondary_options (trifusion.app.TriFusionApp attribute) SegregatingSites (class in trifusion.data.resources.custom_widgets) select_bt() (trifusion.app.TriFusionApp method) select_bt_from_file() (trifusion.app.TriFusionApp method) select_by_taxa() (trifusion.process.sequence.AlignmentList method) select_node() (trifusion.data.resources.custom_widgets.TreeViewM method) select_taxa_group() (trifusion.app.TriFusionApp method) SelectGeneDialog (class in trifusion.data.resources.custom_widgets) sequence_code (trifusion.process.sequence.AlignmentList attribute) sequence_segregation() (trifusion.process.sequence.AlignmentList method) sequence_segregation_gene() (trifusion.process.sequence.AlignmentList method) sequence_segregation_per_species() (trifusion.process.sequence.AlignmentList method) sequence_similarity() (trifusion.process.sequence.AlignmentList method) sequence_similarity_gene() (trifusion.process.sequence.AlignmentList method) sequence_similarity_per_species() (trifusion.process.sequence.AlignmentList method) sequence_types (trifusion.app.TriFusionApp attribute) SequenceSimilarity (class in trifusion.data.resources.custom_widgets) set_codon_model() (trifusion.app.TriFusionApp method) set_database_connections() (trifusion.process.sequence.AlignmentList method) set_length() (trifusion.process.data.Partitions method) set_model() (trifusion.process.data.Partitions method) set_partition_from_alignment() (trifusion.process.sequence.AlignmentList method) set_partitions() (trifusion.process.sequence.Alignment method) set_props() (in module trifusion.base.plotter) setup_database() (in module trifusion.process.sequence) setup_intable() (in module trifusion.process.sequence) shelve_alignments (trifusion.process.sequence.AlignmentList attribute) shelve_taxa() (trifusion.process.sequence.Alignment method) shelved_taxa (trifusion.process.sequence.Alignment attribute) (trifusion.process.sequence.AlignmentList attribute)

shift (trifusion.data.resources.custom_widgets.FileChooserM attribute) ShortenButton (class in trifusion.data.resources.custom_widgets) ShortenToggleButton (class in trifusion.data.resources.custom_widgets) show_back_bt() (trifusion.app.TriFusionApp method) show_plot_toolbar() (trifusion.app.TriFusionApp method) show_popup() (trifusion.app.TriFusionApp method) show_side_panel (trifusion.app.TriFusionApp attribute) show_stats_toggle() (trifusion.app.TriFusionApp method) ShowcaseScreen (class in trifusion.data.resources.custom_widgets) SideLabel (class in trifusion.data.resources.custom_widgets) sidepanel_add_bts() (trifusion.app.TriFusionApp method) sidepanel_animation() (trifusion.app.TriFusionApp static method) sidepanel_clear_search() (trifusion.app.TriFusionApp method) sidepanel_create_bts() (trifusion.app.TriFusionApp method) sidepanel_create_part_bts() (trifusion.app.TriFusionApp method) sidepanel_invert_selection() (trifusion.app.TriFusionApp method) sidepanel_load_more_filebts() (trifusion.app.TriFusionApp method) sidepanel_moreopts_dialog() (trifusion.app.TriFusionApp method) sidepanel_on_touch() (trifusion.app.TriFusionApp method) sidepanel_remove_moreopts() (trifusion.app.TriFusionApp method) sidepanel_search_bts() (trifusion.app.TriFusionApp method) SidepanelToggle (class in trifusion.data.resources.custom_widgets) SimpleModal (class in trifusion.data.resources.custom_widgets) SingleAlignment SizeDistribution (class in trifusion.data.resources.custom_widgets) sliding_window() (in module trifusion.base.plotter) sname (trifusion.process.sequence.Alignment attribute) sp_file_bts (trifusion.app.TriFusionApp attribute) sp_func (trifusion.data.resources.custom_widgets.StatsToggleWgt attribute) sp_moreopts (trifusion.app.TriFusionApp attribute) SP_MoreOpts_Dialog (class in trifusion.data.resources.custom_widgets) sp_partition_bts (trifusion.app.TriFusionApp attribute) sp_taxa_bts (trifusion.app.TriFusionApp attribute) split_partition() (trifusion.process.data.Partitions method) SplitPartitions (class in trifusion.data.resources.custom_widgets) sql_path (trifusion.process.sequence.AlignmentList attribute) sqldb (trifusion.app.TriFusionApp attribute) stacked_bar_plot() (in module trifusion.base.plotter) statistics_populate_groups() (trifusion.app.TriFusionApp method) statistics_show_summary() (trifusion.app.TriFusionApp method) stats_clear_search() (trifusion.app.TriFusionApp method) stats_handle_outliers() (trifusion.app.TriFusionApp method) stats_load_more_genes() (trifusion.app.TriFusionApp method) stats_plt_method (trifusion.app.TriFusionApp attribute) stats_search_genes() (trifusion.app.TriFusionApp method) stats_select_plot() (trifusion.app.TriFusionApp method) stats_sethline() (trifusion.app.TriFusionApp method) stats_show_plot() (trifusion.app.TriFusionApp method) stats_summary (trifusion.app.TriFusionApp attribute) stats_table (trifusion.app.TriFusionApp attribute) stats_write_plot() (trifusion.app.TriFusionApp method) StatsBox (class in trifusion.data.resources.custom_widgets) StatsLoading (class in trifusion.data.resources.custom_widgets) StatsMoreBt (class in trifusion.data.resources.custom_widgets) StatsPlotToolbar (class in trifusion.data.resources.custom_widgets) StatsSummary (class in trifusion.data.resources.custom_widgets) StatsToggleWgt (class in trifusion.data.resources.custom_widgets) StringInput (class in trifusion.data.resources.custom_widgets) summary_gene_table (trifusion.process.sequence.AlignmentList attribute) summary_stats (trifusion.process.sequence.AlignmentList attribute) switch_path_wgt() (trifusion.app.TriFusionApp method)

T

table_name (trifusion.process.sequence.Alignment attribute) TableCell (class in trifusion.data.resources.custom_widgets) TableLine (class in trifusion.data.resources.custom_widgets) tables (trifusion.process.sequence.Alignment attribute) taxa_distribution() (trifusion.process.sequence.AlignmentList method) taxa_filter_settings (trifusion.app.TriFusionApp attribute) taxa_groups (trifusion.app.TriFusionApp attribute) taxa_idx (trifusion.process.sequence.Alignment attribute) taxa_list (trifusion.process.sequence.Alignment attribute) taxa_names (trifusion.process.sequence.AlignmentList attribute) taxa_txt (trifusion.data.resources.custom_widgets.DescriptionBox attribute) TaxaDistribution (class in trifusion.data.resources.custom_widgets) TaxaEdit (class in trifusion.data.resources.custom_widgets) TaxaFilterDialog (class in trifusion.data.resources.custom_widgets) taxagroup_move_taxa() (trifusion.app.TriFusionApp method) TaxaGroupDialog (class in trifusion.data.resources.custom_widgets) taxagroups_add_group() (trifusion.app.TriFusionApp method) taxagroups_display_group() (trifusion.app.TriFusionApp method) taxagroups_show_taxa() (trifusion.app.TriFusionApp method) TaxaPopup (class in trifusion.data.resources.custom_widgets) temp_dir (trifusion.app.TriFusionApp attribute) terminate_background (trifusion.app.TriFusionApp attribute) terminate_group_export (trifusion.app.TriFusionApp attribute) terminate_load_files (trifusion.app.TriFusionApp attribute) terminate_orto_search (trifusion.app.TriFusionApp attribute) terminate_process_exec (trifusion.app.TriFusionApp attribute) terminate_stats (trifusion.app.TriFusionApp attribute) text_input (trifusion.data.resources.custom_widgets.SaveDialog attribute) TextDialog (class in trifusion.data.resources.custom_widgets) texture_update() (trifusion.data.resources.custom_widgets.LinkedLabel method) TFButton (class in trifusion.data.resources.custom_widgets) TFButtonOff (class in trifusion.data.resources.custom_widgets) TFTextInput (class in trifusion.data.resources.custom_widgets) TGToggleButton (class in trifusion.data.resources.custom_widgets) toggle_fancy_dropdown() (trifusion.app.TriFusionApp method) toggle_groups() (trifusion.app.TriFusionApp static method) toggle_multi_selection() (trifusion.app.TriFusionApp method) toggle_orto_soptions() (trifusion.app.TriFusionApp method) toggle_process_options() (trifusion.app.TriFusionApp method) toggle_selection() (trifusion.app.TriFusionApp method) toggle_sidepanel() (trifusion.app.TriFusionApp method) toggle_stats_options() (trifusion.app.TriFusionApp method)

toggle_stats_panel() (trifusion.app.TriFusionApp method) touch (trifusion.app.TriFusionApp attribute) translate() (in module trifusion.ortho.protein2dna) TreeViewM (class in trifusion.data.resources.custom_widgets) triangular_heat() (in module trifusion.base.plotter) trifusion (module) trifusion.app (module) trifusion.base (module) trifusion.base.html_creator (module) trifusion.base.plotter (module) trifusion.base.sanity (module) trifusion.data (module) trifusion.data.resources (module) trifusion.data.resources.background_tasks (module) trifusion.data.resources.custom_widgets (module) trifusion.data.resources.info_data (module) trifusion.data.resources.stats (module) trifusion.ortho (module) trifusion.ortho.complement_orthologs (module) trifusion.ortho.error_handling (module) trifusion.ortho.orthomclBlastParser (module) trifusion.ortho.orthomclDumpPairsFiles (module) trifusion.ortho.orthomclFilterFasta (module) trifusion.ortho.orthomclInstallSchema (module) trifusion.ortho.orthomclLoadBlast (module) trifusion.ortho.orthomclMclToGroups (module) trifusion.ortho.orthomclPairs (module) trifusion.ortho.OrthomclToolbox (module) trifusion.ortho.protein2dna (module) trifusion.orthomcl_pipeline (module) trifusion.process (module) trifusion.process.base (module) trifusion.process.data (module) trifusion.process.error_handling (module) trifusion.process.sequence (module) trifusion.TriFusion (module) trifusion.TriSeq (module) trifusion.TriStats (module) TriFusionApp (class in trifusion.app) trigger_taxa_update (trifusion.app.TriFusionApp attribute) triseq_arg_check() (in module trifusion.base.sanity) txt (trifusion.data.resources.custom_widgets.GaugePlot attribute)

U

update_active_alignment() (trifusion.process.sequence.AlignmentList method) update_active_alignments() (trifusion.process.sequence.AlignmentList method) update_active_fileset() (in module trifusion.data.resources.background_tasks) update_active_taxaset() (in module trifusion.data.resources.background_tasks) update_file_label() (trifusion.app.TriFusionApp method) update_filtered_group() (trifusion.ortho.OrthomclToolbox.Group method) update_filters() (trifusion.ortho.OrthomclToolbox.Group method) (trifusion.ortho.OrthomclToolbox.GroupLight method) (trifusion.ortho.OrthomclToolbox.MultiGroups method) (trifusion.ortho.OrthomclToolbox.MultiGroupsLight method) update_main_operations() (trifusion.app.TriFusionApp method) update_partition_label() (trifusion.app.TriFusionApp method) update_partitions() (trifusion.app.TriFusionApp method)

update_process_switch() (trifusion.app.TriFusionApp method) update_rect() (trifusion.data.resources.custom_widgets.CustomPopup method) update_sp_label() (trifusion.app.TriFusionApp method) update_tabs() (trifusion.app.TriFusionApp method) update_taxa() (trifusion.app.TriFusionApp method) update_taxa_names() (trifusion.process.sequence.AlignmentList method) use_app_partitions (trifusion.app.TriFusionApp attribute) use_nexus_models (trifusion.app.TriFusionApp attribute) use_nexus_partitions (trifusion.app.TriFusionApp attribute) usearch_db (trifusion.app.TriFusionApp attribute) usearch_evalue (trifusion.app.TriFusionApp attribute) usearch_file (trifusion.app.TriFusionApp attribute) usearch_output (trifusion.app.TriFusionApp attribute)

V

valign (trifusion.data.resources.custom_widgets.AlignedTextInput attribute)

variation_filter (trifusion.app.TriFusionApp attribute) VariationFilterDialog (class in trifusion.data.resources.custom_widgets)

W

WarningDialog (class in trifusion.data.resources.custom_widgets) WarningFloat (class in trifusion.data.resources.custom_widgets) write_file() (trifusion.base.html_creator.HtmlTemplate method) write_loci_correspondence() (trifusion.process.sequence.Alignment static method)

write_taxa_to_file() (trifusion.process.sequence.AlignmentList method) write_to_file() (trifusion.process.data.Partitions method) (trifusion.process.data.Zorro method) (trifusion.process.sequence.Alignment method) (trifusion.process.sequence.AlignmentList method)

Z

Zorro (class in trifusion.process.data) zorro_dir (trifusion.app.TriFusionApp attribute)

zorro_suffix (trifusion.app.TriFusionApp attribute) ZorroDialog (class in trifusion.data.resources.custom_widgets)