Index _ | A | B | C | D | E | F | G | H | I | K | L | M | N | O | P | R | S | T | U | V | W _ __delitem__() (panorama.geneFamily.GeneFamily method) (panorama.region.GeneContext method) (panorama.region.Module method) (panorama.region.Region method) (panorama.region.Spot method) (panorama.systems.system.System method) __eq__() (panorama.geneFamily.GeneFamily method) (panorama.region.GeneContext method) (panorama.region.Module method) (panorama.region.Region method) (panorama.systems.system.System method) (panorama.systems.system.SystemUnit method) __getitem__() (panorama.geneFamily.Akin method) (panorama.geneFamily.GeneFamily method) (panorama.region.GeneContext method) (panorama.region.Module method) (panorama.region.Region method) (panorama.region.Spot method) (panorama.systems.system.ClusterSystems method) (panorama.systems.system.System method) (panorama.systems.system.SystemUnit method) __hash__() (panorama.geneFamily.GeneFamily method) (panorama.region.GeneContext method) (panorama.region.Module method) (panorama.region.Region method) (panorama.systems.system.System method) (panorama.systems.system.SystemUnit method) __init__() (panorama.geneFamily.Akin method) (panorama.geneFamily.GeneFamily method) (panorama.info.info.HTMLExporter method) (panorama.info.info.PangenomeInfoExtractor method) (panorama.pangenomes.Pangenome method) (panorama.pangenomes.Pangenomes method) (panorama.region.ConservedSpots method) (panorama.region.GeneContext method) (panorama.region.Module method) (panorama.region.Region method) (panorama.region.Spot method) (panorama.systems.models._BasicFeatures method) (panorama.systems.models._FuFamFeatures method) (panorama.systems.models._ModFuFeatures method) (panorama.systems.models.Family method) (panorama.systems.models.FuncUnit method) (panorama.systems.models.Model method) (panorama.systems.models.Models method) (panorama.systems.system.ClusterSystems method) (panorama.systems.system.System method) (panorama.systems.system.SystemUnit method) (panorama.systems.systems_association.AssociationVisualizationBuilder method) (panorama.systems.systems_partitions.SystemsPartitionVisualizer method) (panorama.systems.utils.VisualizationBuilder method) __iter__() (panorama.pangenomes.Pangenomes method) (panorama.systems.models.Models method) __len__() (panorama.geneFamily.GeneFamily method) (panorama.pangenomes.Pangenomes method) (panorama.region.GeneContext method) (panorama.region.Module method) (panorama.region.Region method) (panorama.region.Spot method) (panorama.systems.system.System method) (panorama.systems.system.SystemUnit method) __ne__() (panorama.geneFamily.GeneFamily method) __repr__() (panorama.geneFamily.GeneFamily method) (panorama.region.GeneContext method) (panorama.region.Module method) (panorama.region.Region method) (panorama.region.Spot method) (panorama.systems.models._BasicFeatures method) (panorama.systems.models.Family method) (panorama.systems.models.FuncUnit method) (panorama.systems.models.Model method) (panorama.systems.system.System method) (panorama.systems.system.SystemUnit method) __setitem__() (panorama.geneFamily.Akin method) (panorama.geneFamily.GeneFamily method) (panorama.region.GeneContext method) (panorama.region.Module method) (panorama.region.Region method) (panorama.region.Spot method) (panorama.systems.system.ClusterSystems method) (panorama.systems.system.System method) (panorama.systems.system.SystemUnit method) __str__() (panorama.region.GeneContext method) (panorama.region.Module method) (panorama.region.Spot method) (panorama.systems.models._BasicFeatures method) (panorama.systems.models.Family method) (panorama.systems.models.FuncUnit method) (panorama.systems.models.Model method) _add_families_to_functional_unit() (in module panorama.utility.translate.padloc_translator) _akin (panorama.geneFamily.GeneFamily attribute) _asso_modules() (panorama.systems.system.SystemUnit method) _BasicFeatures (class in panorama.systems.models) _calculate_max_lengths_for_system() (in module panorama.format.write_binaries) _check() (panorama.systems.models._ModFuFeatures method) (panorama.systems.models.FuncUnit method) (panorama.systems.models.Model method) _child_names() (panorama.systems.models._ModFuFeatures method) (panorama.systems.models.FuncUnit method) (panorama.systems.models.Model method) _configure_bar_plot_style() (panorama.systems.systems_association.AssociationVisualizationBuilder static method) (panorama.systems.systems_partitions.SystemsPartitionVisualizer static method) (panorama.systems.utils.VisualizationBuilder static method) _configure_minimal_plot() (panorama.systems.systems_association.AssociationVisualizationBuilder static method) (panorama.systems.systems_partitions.SystemsPartitionVisualizer static method) (panorama.systems.utils.VisualizationBuilder static method) _configure_plot_style() (panorama.systems.systems_association.AssociationVisualizationBuilder method) (panorama.systems.systems_partitions.SystemsPartitionVisualizer method) (panorama.systems.utils.VisualizationBuilder method) _create_boolean_filters() (panorama.info.info.HTMLExporter static method) _create_column_visibility_control() (panorama.info.info.HTMLExporter method) _create_download_button() (panorama.info.info.HTMLExporter method) _create_filter_button() (panorama.info.info.HTMLExporter method) _create_gene_family() (panorama.pangenomes.Pangenome method) _create_main_figure() (panorama.systems.systems_association.AssociationVisualizationBuilder method) (panorama.systems.systems_partitions.SystemsPartitionVisualizer method) (panorama.systems.utils.VisualizationBuilder method) _create_metric_plot() (panorama.systems.systems_association.AssociationVisualizationBuilder method) _create_range_sliders() (panorama.info.info.HTMLExporter method) _custom_agg() (in module panorama.systems.systems_projection) _duplicate() (panorama.systems.models._ModFuFeatures method) (panorama.systems.models.FuncUnit method) (panorama.systems.models.Model method) _execute_alignment() (in module panorama.alignment.align) _execute_cluster() (in module panorama.alignment.cluster) _execute_clustering_command() (in module panorama.alignment.cluster) _execute_linclust() (in module panorama.alignment.cluster) _extract_content() (panorama.info.info.PangenomeInfoExtractor static method) _extract_metadata() (panorama.info.info.PangenomeInfoExtractor static method) _extract_parameters() (panorama.info.info.PangenomeInfoExtractor static method) _extract_status() (panorama.info.info.PangenomeInfoExtractor static method) _families (panorama.geneFamily.Akin attribute) _FuFamFeatures (class in panorama.systems.models) _get_content() (panorama.region.Spot method) _get_element_frequency() (in module panorama.systems.systems_association) _get_help_string() (panorama.utils.RawTextArgumentDefaultsHelpFormatter method) _get_model_families() (panorama.systems.system.SystemUnit method) _get_ordered_set() (panorama.region.Spot method) _get_region_frequency() (in module panorama.systems.systems_association) _getattr_from_ppanggolin() (panorama.geneFamily.GeneFamily method) _hmm (panorama.geneFamily.GeneFamily attribute) _layout_content_components() (panorama.info.info.HTMLExporter static method) _load_js_file() (panorama.info.info.HTMLExporter method) _make_spot_getter() (panorama.systems.system.SystemUnit method) _mk_child_getter() (panorama.systems.models._ModFuFeatures method) (panorama.systems.models.FuncUnit method) (panorama.systems.models.Model method) _mk_contig_getter() (panorama.pangenomes.Pangenome method) _mk_fam2unit() (panorama.systems.system.System method) _mk_gene_getter() (panorama.pangenomes.Pangenome method) _mk_uniq_content() (panorama.region.Spot method) _mk_uniq_ordered_set_obj() (panorama.region.Spot method) _ModFuFeatures (class in panorama.systems.models) _prepare_mmseqs2_options() (in module panorama.alignment.cluster) _rename_content_columns() (panorama.info.info.HTMLExporter static method) _reorder_content_columns() (panorama.info.info.HTMLExporter static method) _save_figure() (panorama.systems.systems_association.AssociationVisualizationBuilder method) (panorama.systems.systems_partitions.SystemsPartitionVisualizer method) (panorama.systems.utils.VisualizationBuilder method) _save_html() (panorama.info.info.HTMLExporter method) _setup_slider_callbacks() (panorama.info.info.HTMLExporter method) _systems_getter (panorama.geneFamily.GeneFamily attribute) (panorama.systems.system.ClusterSystems attribute) _units_getter (panorama.geneFamily.GeneFamily attribute) _unpack_content_dict() (panorama.info.info.HTMLExporter static method) _validate_alignment_parameters() (in module panorama.alignment.align) _validate_clustering_parameters() (in module panorama.alignment.cluster) _validate_directory_access() (in module panorama.alignment.align) (in module panorama.alignment.cluster) _validate_js_files() (panorama.info.info.HTMLExporter method) _validate_seq_files() (in module panorama.alignment.utils) A accessory (panorama.systems.models._ModFuFeatures attribute) (panorama.systems.models.FuncUnit attribute) (panorama.systems.models.Model attribute) add() (panorama.geneFamily.Akin method) (panorama.geneFamily.GeneFamily method) (panorama.pangenomes.Pangenomes method) (panorama.region.ConservedSpots method) (panorama.region.Module method) (panorama.region.Region method) (panorama.region.Spot method) (panorama.systems.models._ModFuFeatures method) (panorama.systems.models.FuncUnit method) (panorama.systems.models.Model method) (panorama.systems.system.ClusterSystems method) add_argument() (panorama.utils.RawTextArgumentDefaultsHelpFormatter method) add_arguments() (panorama.utils.RawTextArgumentDefaultsHelpFormatter method) add_canonical() (panorama.systems.system.System method) add_cluster() (panorama.pangenomes.Pangenomes method) add_cluster_systems() (panorama.pangenomes.Pangenomes method) add_common_arguments() (in module panorama.utils) add_conserved_spots() (panorama.pangenomes.Pangenomes method) add_edge() (panorama.pangenomes.Pangenome method) add_family() (panorama.region.GeneContext method) (panorama.systems.system.SystemUnit method) add_file() (panorama.pangenomes.Pangenome method) add_gene_family() (panorama.pangenomes.Pangenome method) add_metadata() (panorama.geneFamily.GeneFamily method) (panorama.region.Module method) (panorama.region.Region method) (panorama.region.Spot method) (panorama.systems.system.System method) (panorama.systems.system.SystemUnit method) add_model() (panorama.systems.models.Models method) add_module() (panorama.pangenomes.Pangenome method) (panorama.systems.system.SystemUnit method) add_note() (panorama.alignment.align.AlignmentError method) (panorama.alignment.align.AlignmentValidationError method) (panorama.alignment.cluster.ClusteringError method) (panorama.alignment.cluster.ClusteringValidationError method) (panorama.alignment.utils.MMSeqsError method) (panorama.alignment.utils.PangenomeProcessingError method) (panorama.compare.systems.SystemsComparisonError method) (panorama.utility.translate.translate.HMMProcessingError method) (panorama.utility.translate.translate.ModelTranslationError method) add_organism() (panorama.pangenomes.Pangenome method) add_region() (panorama.pangenomes.Pangenome method) (panorama.systems.system.SystemUnit method) add_sequence() (panorama.geneFamily.GeneFamily method) add_spot() (panorama.geneFamily.GeneFamily method) (panorama.pangenomes.Pangenome method) (panorama.systems.system.SystemUnit method) add_system() (panorama.pangenomes.Pangenome method) add_system_metadata_to_graph() (in module panorama.compare.systems) add_systems_info() (in module panorama.compare.spots) add_text() (panorama.utils.RawTextArgumentDefaultsHelpFormatter method) add_unit() (panorama.region.Module method) (panorama.systems.system.System method) add_usage() (panorama.utils.RawTextArgumentDefaultsHelpFormatter method) Akin (class in panorama.geneFamily) akin (panorama.geneFamily.GeneFamily property) ALIGN_COLUMNS (panorama.alignment.align.AlignmentConfig attribute) align_db() (in module panorama.alignment.align) ALIGN_FORMAT (panorama.alignment.align.AlignmentConfig attribute) align_pangenomes() (in module panorama.alignment.align) align_pangenomes_pair() (in module panorama.alignment.align) AlignmentConfig (class in panorama.alignment.align) AlignmentError (class in panorama.alignment.align) AlignmentValidationError (class in panorama.alignment.align) all_against_all_align() (in module panorama.alignment.align) ALL_AGAINST_ALL_OUTPUT (panorama.alignment.align.AlignmentConfig attribute) annot_pangenomes() (in module panorama.annotate.annotate) annot_pangenomes_with_hmm() (in module panorama.annotate.annotate) annot_with_hmm() (in module panorama.annotate.hmm_search) annot_with_hmmscan() (in module panorama.annotate.hmm_search) annot_with_hmmsearch() (in module panorama.annotate.hmm_search) annotation_sources() (panorama.systems.system.System method) (panorama.systems.system.SystemUnit method) args (panorama.alignment.align.AlignmentError attribute) (panorama.alignment.align.AlignmentValidationError attribute) (panorama.alignment.cluster.ClusteringError attribute) (panorama.alignment.cluster.ClusteringValidationError attribute) (panorama.alignment.utils.MMSeqsError attribute) (panorama.alignment.utils.PangenomeProcessingError attribute) (panorama.compare.systems.SystemsComparisonError attribute) (panorama.utility.translate.translate.HMMProcessingError attribute) (panorama.utility.translate.translate.ModelTranslationError attribute) assign_hit() (in module panorama.annotate.hmm_search) association (panorama.systems.systems_association.AssociationVisualizationBuilder attribute) AssociationVisualizationBuilder (class in panorama.systems.systems_association) B BELOW_HEIGHT (panorama.systems.systems_association.AssociationVisualizationBuilder attribute) (panorama.systems.systems_partitions.SystemsPartitionVisualizer attribute) (panorama.systems.utils.VisualizationBuilder attribute) borders() (panorama.region.Spot method) C calculate_system_table_sizes() (in module panorama.format.write_binaries) canonical (panorama.systems.models.Model attribute) (panorama.systems.system.System attribute) canonical_models() (panorama.systems.system.System method) canonical_sizes (panorama.format.write_binaries.SystemTableSizes attribute) canonical_unit_sizes (panorama.format.write_binaries.SystemTableSizes attribute) CENTER_WIDTH (panorama.systems.systems_association.AssociationVisualizationBuilder attribute) (panorama.systems.systems_partitions.SystemsPartitionVisualizer attribute) (panorama.systems.utils.VisualizationBuilder attribute) check_align_parameters() (in module panorama.alignment.align) check_annotate_args() (in module panorama.annotate.annotate) check_cluster_parameters() (in module panorama.alignment.cluster) check_compare_spots_args() (in module panorama.compare.spots) check_compare_systems_args() (in module panorama.compare.systems) check_context_comparison() (in module panorama.compare.context) check_detection_args() (in module panorama.systems.detection) check_dict() (in module panorama.systems.models) check_flat_parameters() (in module panorama.format.write_flat) check_for_families() (in module panorama.systems.utils) check_for_forbidden_unit() (in module panorama.systems.detection) check_for_needed_units() (in module panorama.systems.detection) check_func_unit() (panorama.systems.models.FuncUnit method) check_info_args() (in module panorama.info.info) check_input_files() (in module panorama.workflow.pansystems) check_instance_of_system() (in module panorama.systems.system) check_instance_of_system_unit() (in module panorama.systems.system) check_key() (in module panorama.systems.models) check_log() (in module panorama.utils) check_model() (panorama.systems.models.Model method) check_models() (in module panorama.utility.utility) check_needed_families() (in module panorama.systems.utils) check_pangenome_align() (in module panorama.alignment.align) check_pangenome_annotation() (in module panorama.annotate.annotate) check_pangenome_cluster() (in module panorama.alignment.cluster) check_pangenome_cs() (in module panorama.compare.spots) check_pangenome_detection() (in module panorama.systems.detection) check_pangenome_info() (in module panorama.format.read_binaries) check_pangenome_pansystems() (in module panorama.workflow.pansystems) check_pangenome_write_flat() (in module panorama.format.write_flat) check_pangenome_write_flat_annotations() (in module panorama.format.write_flat) check_pangenome_write_flat_hmm() (in module panorama.format.write_flat) check_pangenome_write_systems() (in module panorama.systems.write_systems) check_pansystems_parameters() (in module panorama.workflow.pansystems) check_parameters() (in module panorama.systems.models) (in module panorama.utility.utility) check_tsv_sanity() (in module panorama.utils) check_write_systems_args() (in module panorama.systems.write_systems) child_type (panorama.systems.models._ModFuFeatures property) (panorama.systems.models.FuncUnit property) (panorama.systems.models.Model property) CHOICES (panorama.alignment.cluster.ClusteringMethod attribute) clean_context_objects() (in module panorama.compare.context) CLUSTER (panorama.alignment.cluster.ClusteringMethod attribute) CLUSTER_COLUMN_NAMES (panorama.alignment.cluster.ClusteringConfig attribute) cluster_gene_families() (in module panorama.alignment.cluster) cluster_id (panorama.systems.system.System attribute) cluster_launcher() (in module panorama.alignment.cluster) cluster_on_gfrr() (in module panorama.compare.utils) cluster_systems (panorama.pangenomes.Pangenomes property) CLUSTERING_OUTPUT (panorama.alignment.cluster.ClusteringConfig attribute) ClusteringConfig (class in panorama.alignment.cluster) ClusteringError (class in panorama.alignment.cluster) ClusteringMethod (class in panorama.alignment.cluster) ClusteringValidationError (class in panorama.alignment.cluster) ClusterSystems (class in panorama.systems.system) cmd_line() (in module panorama.main) color_bar (panorama.systems.systems_association.AssociationVisualizationBuilder property) (panorama.systems.systems_partitions.SystemsPartitionVisualizer property) (panorama.systems.utils.VisualizationBuilder property) common_launch() (in module panorama.compare.utils) compare_gene_contexts_graph_mp() (in module panorama.compare.context) compare_gene_contexts_on_cluster_families() (in module panorama.compare.context) compare_pair_of_context_graphs() (in module panorama.compare.context) compare_pair_of_contexts() (in module panorama.compare.context) compare_spots() (in module panorama.compare.spots) compare_systems() (in module panorama.compare.systems) compute_CCC() (in module panorama.compare.context) compute_family_bitarrays() (panorama.pangenomes.Pangenome method) compute_gene_components() (in module panorama.systems.systems_projection) compute_genes_graph() (in module panorama.systems.systems_projection) compute_gfrr() (in module panorama.compare.utils) compute_gfrr_edges() (in module panorama.compare.spots) (in module panorama.compare.systems) compute_mod_bitarrays() (panorama.pangenomes.Pangenome method) compute_org_bitarrays() (panorama.pangenomes.Pangenome method) conciliate_partition() (in module panorama.systems.utils) conserved (panorama.region.Spot property) conserved_spots (panorama.pangenomes.Pangenomes property) ConservedSpots (class in panorama.region) contains_gene_id() (panorama.geneFamily.GeneFamily method) context_comparison() (in module panorama.compare.context) contig (panorama.region.Region property) contig_lengths_unavailable() (panorama.pangenomes.Pangenome method) contigs (panorama.pangenomes.Pangenome property) coordinates (panorama.region.Region property) count_uniq_content() (panorama.region.Spot method) count_uniq_ordered_set() (panorama.region.Spot method) create_bar_plots() (panorama.systems.systems_association.AssociationVisualizationBuilder method) (panorama.systems.systems_partitions.SystemsPartitionVisualizer method) create_color_bar() (panorama.systems.systems_association.AssociationVisualizationBuilder method) (panorama.systems.systems_partitions.SystemsPartitionVisualizer method) create_color_palette() (panorama.systems.systems_association.AssociationVisualizationBuilder static method) create_coverage_dataframe() (in module panorama.systems.systems_association) create_coverage_plot() (panorama.systems.systems_association.AssociationVisualizationBuilder method) create_frequency_plot() (panorama.systems.systems_association.AssociationVisualizationBuilder method) create_hmm_list_file() (in module panorama.utility.genInput) create_left_bar() (panorama.systems.systems_partitions.SystemsPartitionVisualizer method) create_left_bar_plot() (panorama.systems.systems_association.AssociationVisualizationBuilder method) (panorama.systems.systems_partitions.SystemsPartitionVisualizer method) (panorama.systems.utils.VisualizationBuilder method) create_macsyfinder_hmm_list() (in module panorama.utility.translate.macsymodel_translator) create_main_figure() (panorama.systems.systems_association.AssociationVisualizationBuilder method) (panorama.systems.systems_partitions.SystemsPartitionVisualizer method) (panorama.systems.utils.VisualizationBuilder method) create_metanodes() (in module panorama.compare.context) create_models_list() (in module panorama.utility.utility) create_pangenome_spots_graph() (in module panorama.compare.spots) create_pangenome_system_associations() (in module panorama.systems.systems_association) create_pangenome_system_graph() (in module panorama.compare.spots) (in module panorama.compare.systems) create_pangenome_systems_heatmaps() (in module panorama.compare.systems) create_spots_graph() (in module panorama.compare.spots) create_system_description() (in module panorama.format.write_binaries) create_system_tables() (in module panorama.format.write_binaries) create_system_unit_description() (in module panorama.format.write_binaries) create_systems_graph() (in module panorama.compare.spots) (in module panorama.compare.systems) create_top_bar_plot() (panorama.systems.systems_association.AssociationVisualizationBuilder method) (panorama.systems.systems_partitions.SystemsPartitionVisualizer method) (panorama.systems.utils.VisualizationBuilder method) create_tsv() (in module panorama.alignment.cluster) createdb() (in module panorama.alignment.utils) custom_agg() (in module panorama.systems.systems_projection) custom_agg_unique() (in module panorama.systems.systems_projection) D DEFAULT_COV_MODE (panorama.alignment.align.AlignmentConfig attribute) (panorama.alignment.cluster.ClusteringConfig attribute) DEFAULT_COVERAGE (panorama.alignment.align.AlignmentConfig attribute) (panorama.alignment.cluster.ClusteringConfig attribute) DEFAULT_DB_TYPE (panorama.alignment.utils.MMSeqsConfig attribute) DEFAULT_EVAL (panorama.alignment.cluster.ClusteringConfig attribute) DEFAULT_FORMAT (panorama.systems.systems_association.AssociationVisualizationBuilder attribute) (panorama.systems.systems_partitions.SystemsPartitionVisualizer attribute) (panorama.systems.utils.VisualizationBuilder attribute) DEFAULT_IDENTITY (panorama.alignment.align.AlignmentConfig attribute) (panorama.alignment.cluster.ClusteringConfig attribute) DEFAULT_MMSEQS2_OPTIONS (panorama.alignment.cluster.ClusteringConfig attribute) DEFAULT_THREADS (panorama.alignment.align.AlignmentConfig attribute) (panorama.alignment.cluster.ClusteringConfig attribute) del_metadata_by_attribute() (panorama.geneFamily.GeneFamily method) (panorama.region.Module method) (panorama.region.Region method) (panorama.region.Spot method) (panorama.systems.system.System method) (panorama.systems.system.SystemUnit method) del_metadata_by_source() (panorama.geneFamily.GeneFamily method) (panorama.region.Module method) (panorama.region.Region method) (panorama.region.Spot method) (panorama.systems.system.System method) (panorama.systems.system.SystemUnit method) dict_families_context() (in module panorama.systems.utils) difference() (panorama.systems.system.SystemUnit method) digit_family_sequences() (in module panorama.annotate.hmm_search) digit_gene_sequences() (in module panorama.annotate.hmm_search) duplicate (panorama.systems.models._FuFamFeatures attribute) (panorama.systems.models.Family attribute) (panorama.systems.models.FuncUnit attribute) duplicate_fam() (panorama.systems.models.FuncUnit method) duplicate_fu() (panorama.systems.models.Model method) duplication_ratio() (panorama.geneFamily.GeneFamily method) E edges (panorama.geneFamily.GeneFamily property) (panorama.pangenomes.Pangenome property) eliminate_empty() (in module panorama.systems.systems_projection) eliminate_systems() (in module panorama.systems.systems_projection) end_section() (panorama.utils.RawTextArgumentDefaultsHelpFormatter method) erase_pangenome() (in module panorama.format.write_binaries) exact_core_families() (panorama.pangenomes.Pangenome method) exchangeable (panorama.systems.models._FuFamFeatures attribute) (panorama.systems.models.Family attribute) (panorama.systems.models.FuncUnit attribute) export_content() (panorama.info.info.HTMLExporter method) export_info() (in module panorama.info.info) export_status() (panorama.info.info.HTMLExporter method) extract_info() (panorama.info.info.PangenomeInfoExtractor method) extract_numeric_for_sorting() (in module panorama.systems.systems_projection) F families (panorama.region.GeneContext property) (panorama.region.Module property) (panorama.region.Region property) (panorama.region.Spot property) (panorama.systems.models.FuncUnit property) (panorama.systems.models.Model property) (panorama.systems.models.Models property) (panorama.systems.system.System property) (panorama.systems.system.SystemUnit property) families_names() (panorama.systems.models.FuncUnit method) families_to_model() (panorama.systems.models.Models method) Family (class in panorama.systems.models) FAMILY_FILTER_ALL (panorama.alignment.utils.MMSeqsConfig attribute) filter_global_context() (in module panorama.systems.utils) filter_local_context() (in module panorama.systems.utils) filter_local_context_old() (in module panorama.systems.utils) find_cluster_canonical() (in module panorama.utility.translate.macsymodel_translator) find_type_subtype_canonical() (in module panorama.utility.translate.macsymodel_translator) forbidden (panorama.systems.models._ModFuFeatures attribute) (panorama.systems.models.FuncUnit attribute) (panorama.systems.models.Model attribute) format_help() (panorama.utils.RawTextArgumentDefaultsHelpFormatter method) formatted_metadata_dict() (panorama.geneFamily.GeneFamily method) (panorama.region.Module method) (panorama.region.Region method) (panorama.region.Spot method) (panorama.systems.system.System method) (panorama.systems.system.SystemUnit method) formatted_metadata_dict_to_string() (panorama.geneFamily.GeneFamily method) (panorama.region.Module method) (panorama.region.Region method) (panorama.region.Spot method) (panorama.systems.system.System method) (panorama.systems.system.SystemUnit method) func_unit (panorama.systems.models.Family property) func_units (panorama.systems.models.Model property) (panorama.systems.models.Models property) func_units_names() (panorama.systems.models.Model method) func_units_to_model() (panorama.systems.models.Models method) functional_unit (panorama.systems.system.SystemUnit property) FuncUnit (class in panorama.systems.models) G gene_families (panorama.pangenomes.Pangenome property) (panorama.region.Module property) GeneContext (class in panorama.region) GeneFamily (class in panorama.geneFamily) generate_heatmap() (in module panorama.compare.systems) generate_unique_accession() (in module panorama.utility.genInput) genes (panorama.geneFamily.GeneFamily property) (panorama.pangenomes.Pangenome property) (panorama.region.Region property) get() (panorama.geneFamily.Akin method) (panorama.geneFamily.GeneFamily method) (panorama.pangenomes.Pangenomes method) (panorama.region.ConservedSpots method) (panorama.region.Module method) (panorama.region.Region method) (panorama.region.Spot method) (panorama.systems.models._ModFuFeatures method) (panorama.systems.models.FuncUnit method) (panorama.systems.models.Model method) (panorama.systems.system.ClusterSystems method) get_association_dataframes() (in module panorama.systems.systems_association) get_bordering_genes() (panorama.region.Region method) get_cluster_systems() (panorama.pangenomes.Pangenomes method) get_connected_components() (in module panorama.compare.context) get_conserved_genomics_contexts() (in module panorama.compare.context) get_conserved_spots() (panorama.pangenomes.Pangenomes method) get_contexts_from_result() (in module panorama.compare.context) get_contig() (panorama.pangenomes.Pangenome method) get_edge() (panorama.geneFamily.GeneFamily method) get_elem_by_metadata() (panorama.pangenomes.Pangenome method) get_elem_by_source() (panorama.pangenomes.Pangenome method) get_fam_index() (panorama.pangenomes.Pangenome method) get_family() (panorama.pangenomes.Pangenomes method) get_functional_unit_gene_families() (in module panorama.systems.detection) get_gene() (panorama.pangenomes.Pangenome method) get_gene_contexts_from_results_mp() (in module panorama.compare.context) get_gene_family() (panorama.pangenomes.Pangenome method) get_genes_per_org() (panorama.geneFamily.GeneFamily method) get_gfs_matrix_combination() (in module panorama.systems.utils) get_k_best_hit() (in module panorama.annotate.annotate) get_metadata() (panorama.geneFamily.GeneFamily method) (panorama.region.Module method) (panorama.region.Region method) (panorama.region.Spot method) (panorama.systems.system.System method) (panorama.systems.system.SystemUnit method) get_metadata_by_attribute() (panorama.geneFamily.GeneFamily method) (panorama.region.Module method) (panorama.region.Region method) (panorama.region.Spot method) (panorama.systems.system.System method) (panorama.systems.system.SystemUnit method) get_metadata_by_source() (panorama.geneFamily.GeneFamily method) (panorama.region.Module method) (panorama.region.Region method) (panorama.region.Spot method) (panorama.systems.system.System method) (panorama.systems.system.SystemUnit method) get_metadata_df() (in module panorama.annotate.hmm_search) get_metadata_to_families() (in module panorama.systems.utils) get_metainfo() (panorama.systems.system.System method) (panorama.systems.system.SystemUnit method) get_model() (panorama.systems.models.Models method) get_models_path() (in module panorama.utility.translate.macsymodel_translator) get_module() (panorama.pangenomes.Pangenome method) (panorama.systems.system.System method) (panorama.systems.system.SystemUnit method) get_msa() (in module panorama.annotate.hmm_search) get_multigenics() (panorama.pangenomes.Pangenome method) get_multigraph_edges() (in module panorama.compare.context) get_ordered_genes() (panorama.region.Region method) get_org_df() (in module panorama.systems.systems_projection) get_org_df_one_unit_per_fam() (in module panorama.systems.systems_projection) get_org_dict() (panorama.geneFamily.GeneFamily method) get_org_index() (panorama.pangenomes.Pangenome method) get_organism() (panorama.pangenomes.Pangenome method) get_pangenomes_to_systems_data() (in module panorama.compare.systems) get_partition() (in module panorama.systems.systems_projection) get_region() (panorama.pangenomes.Pangenome method) (panorama.systems.system.System method) (panorama.systems.system.SystemUnit method) get_shortest_path_edges_cc_strategy() (in module panorama.compare.context) get_single_copy_persistent_families() (panorama.pangenomes.Pangenome method) get_spot() (panorama.pangenomes.Pangenome method) (panorama.systems.system.System method) (panorama.systems.system.SystemUnit method) get_status() (in module panorama.format.read_binaries) get_subcombinations() (in module panorama.systems.detection) get_system() (panorama.pangenomes.Pangenome method) get_system_by_source() (panorama.pangenomes.Pangenome method) get_system_unit_combinations() (in module panorama.systems.detection) get_uniq_content() (panorama.region.Spot method) get_uniq_ordered_set() (panorama.region.Spot method) get_uniq_to_rgp() (panorama.region.Spot method) get_unit() (panorama.region.Module method) (panorama.systems.system.System method) glyph (panorama.systems.systems_association.AssociationVisualizationBuilder property) (panorama.systems.systems_partitions.SystemsPartitionVisualizer property) (panorama.systems.utils.VisualizationBuilder property) glyph_renderer (panorama.systems.systems_association.AssociationVisualizationBuilder property) (panorama.systems.systems_partitions.SystemsPartitionVisualizer property) (panorama.systems.utils.VisualizationBuilder property) graph (panorama.region.GeneContext property) graph_systems_link_with_conserved_spots() (in module panorama.compare.spots) H has_metadata() (panorama.geneFamily.GeneFamily method) (panorama.pangenomes.Pangenome method) (panorama.region.Module method) (panorama.region.Region method) (panorama.region.Spot method) (panorama.systems.system.System method) (panorama.systems.system.SystemUnit method) has_module (panorama.geneFamily.GeneFamily property) has_short_path() (in module panorama.systems.systems_projection) has_source() (panorama.geneFamily.GeneFamily method) (panorama.region.Module method) (panorama.region.Region method) (panorama.region.Spot method) (panorama.systems.system.System method) (panorama.systems.system.SystemUnit method) hash_content() (panorama.systems.system.SystemUnit method) HMM (panorama.geneFamily.GeneFamily property) HMMProcessingError (class in panorama.utility.translate.translate) HTMLExporter (class in panorama.info.info) I ID (panorama.geneFamily.Akin attribute) (panorama.systems.system.ClusterSystems attribute) (panorama.systems.system.System attribute) (panorama.systems.system.SystemUnit attribute) id_counter (panorama.region.Region attribute) identify_rgp_last_and_first_genes() (panorama.region.Region method) init_lock() (in module panorama.utils) inter_pangenome_align() (in module panorama.alignment.align) INTER_PANGENOMES_OUTPUT (panorama.alignment.align.AlignmentConfig attribute) intersection() (panorama.systems.system.System method) (panorama.systems.system.SystemUnit method) is_contig_border (panorama.region.Region property) is_empty() (in module panorama.utils) is_multigenic() (panorama.geneFamily.GeneFamily method) is_multigenic_in_org() (panorama.geneFamily.GeneFamily method) is_single_copy() (panorama.geneFamily.GeneFamily method) is_subset() (panorama.systems.system.System method) (panorama.systems.system.SystemUnit method) is_superset() (panorama.systems.system.System method) (panorama.systems.system.SystemUnit method) is_true_value() (in module panorama.utils) is_whole_contig (panorama.region.Region property) items() (panorama.pangenomes.Pangenomes method) K keep_best_hit() (in module panorama.annotate.annotate) L launch() (in module panorama.alignment.align) (in module panorama.alignment.cluster) (in module panorama.annotate.annotate) (in module panorama.compare.context) (in module panorama.compare.spots) (in module panorama.compare.systems) (in module panorama.format.write_flat) (in module panorama.info.info) (in module panorama.systems.detection) (in module panorama.systems.write_systems) (in module panorama.utility.utility) (in module panorama.workflow.pansystems) launch_compare_pair_of_context_graphs() (in module panorama.compare.context) launch_context_comparison() (in module panorama.compare.context) launch_pangenomes_alignment() (in module panorama.alignment.align) launch_ppanggolin_context() (in module panorama.compare.context) launch_translate() (in module panorama.utility.translate.translate) left_bar (panorama.systems.systems_association.AssociationVisualizationBuilder property) (panorama.systems.systems_partitions.SystemsPartitionVisualizer property) (panorama.systems.utils.VisualizationBuilder property) LEFT_WIDTH (panorama.systems.systems_association.AssociationVisualizationBuilder attribute) (panorama.systems.systems_partitions.SystemsPartitionVisualizer attribute) (panorama.systems.utils.VisualizationBuilder attribute) length (panorama.region.Region property) LINCLUST (panorama.alignment.cluster.ClusteringMethod attribute) linclust_launcher() (in module panorama.alignment.cluster) load_pangenome() (in module panorama.format.read_binaries) load_pangenomes() (in module panorama.format.read_binaries) M main() (in module panorama.main) main_plot (panorama.systems.systems_association.AssociationVisualizationBuilder property) (panorama.systems.systems_partitions.SystemsPartitionVisualizer property) (panorama.systems.utils.VisualizationBuilder property) make_gene_context_from_context_graph() (in module panorama.compare.context) make_gene_context_from_context_table() (in module panorama.compare.context) mandatory (panorama.systems.models._ModFuFeatures attribute) (panorama.systems.models.FuncUnit attribute) (panorama.systems.models.Model attribute) mapper (panorama.systems.systems_partitions.SystemsPartitionVisualizer attribute) max_fam_id (panorama.pangenomes.Pangenome property) max_metadata_by_source() (panorama.geneFamily.GeneFamily method) (panorama.region.Module method) (panorama.region.Region method) (panorama.region.Spot method) (panorama.systems.system.System method) (panorama.systems.system.SystemUnit method) merge() (panorama.systems.system.System method) (panorama.systems.system.SystemUnit method) merge_aln_res() (in module panorama.alignment.align) metadata (panorama.geneFamily.GeneFamily property) (panorama.region.Module property) (panorama.region.Region property) (panorama.region.Spot property) (panorama.systems.system.System property) (panorama.systems.system.SystemUnit property) metadata() (panorama.pangenomes.Pangenome method) metadata_sources() (panorama.pangenomes.Pangenome method) MIDDLE_HEIGHT (panorama.systems.systems_association.AssociationVisualizationBuilder attribute) (panorama.systems.systems_partitions.SystemsPartitionVisualizer attribute) (panorama.systems.utils.VisualizationBuilder attribute) min_mandatory (panorama.systems.models._ModFuFeatures attribute) (panorama.systems.models.FuncUnit attribute) (panorama.systems.models.Model attribute) min_total (panorama.systems.models._ModFuFeatures attribute) (panorama.systems.models.FuncUnit attribute) (panorama.systems.models.Model attribute) mk_bitarray() (panorama.geneFamily.GeneFamily method) (panorama.region.Module method) mk_families_to_pangenome() (panorama.pangenomes.Pangenomes method) mkdir() (in module panorama.utils) MMSeqsConfig (class in panorama.alignment.utils) MMSeqsError (class in panorama.alignment.utils) Model (class in panorama.systems.models) model (panorama.systems.models.Family property) (panorama.systems.models.FuncUnit property) (panorama.systems.system.System attribute) (panorama.systems.system.SystemUnit property) model_families (panorama.systems.system.System property) (panorama.systems.system.SystemUnit property) model_organisms (panorama.systems.system.System property) (panorama.systems.system.SystemUnit property) Models (class in panorama.systems.models) ModelTranslationError (class in panorama.utility.translate.translate) module panorama.alignment.align panorama.alignment.cluster panorama.alignment.utils panorama.annotate.annotate panorama.annotate.hmm_search panorama.compare.context panorama.compare.spots panorama.compare.systems panorama.compare.utils panorama.format.read_binaries panorama.format.write_binaries panorama.format.write_flat panorama.format.write_proksee panorama.geneFamily panorama.info.info panorama.main panorama.pangenomes panorama.region panorama.systems.detection panorama.systems.models panorama.systems.system panorama.systems.systems_association panorama.systems.systems_partitions panorama.systems.systems_projection panorama.systems.utils panorama.systems.write_systems panorama.utility.genInput panorama.utility.translate.macsymodel_translator panorama.utility.translate.padloc_translator panorama.utility.translate.translate panorama.utility.utility panorama.utils panorama.workflow.pansystems Module (class in panorama.region) module (panorama.geneFamily.GeneFamily property) modules (panorama.pangenomes.Pangenome property) (panorama.region.Region property) (panorama.systems.system.System property) (panorama.systems.system.SystemUnit property) multi_model (panorama.systems.models._FuFamFeatures attribute) (panorama.systems.models.Family attribute) (panorama.systems.models.FuncUnit attribute) multi_system (panorama.systems.models._FuFamFeatures attribute) (panorama.systems.models.Family attribute) (panorama.systems.models.FuncUnit attribute) N name (panorama.geneFamily.GeneFamily attribute) (panorama.systems.models._BasicFeatures attribute) (panorama.systems.models.Family attribute) (panorama.systems.models.FuncUnit attribute) (panorama.systems.models.Model attribute) (panorama.systems.system.System property) (panorama.systems.system.SystemUnit property) named_partition (panorama.geneFamily.GeneFamily property) nb_model_families (panorama.systems.system.SystemUnit property) nb_organisms (panorama.systems.system.SystemUnit property) neighbors (panorama.geneFamily.GeneFamily property) neutral (panorama.systems.models._ModFuFeatures attribute) (panorama.systems.models.FuncUnit attribute) (panorama.systems.models.Model attribute) number_of_cluster_systems (panorama.pangenomes.Pangenomes property) number_of_conserved_spots (panorama.pangenomes.Pangenomes property) number_of_contigs (panorama.pangenomes.Pangenome property) number_of_edges (panorama.geneFamily.GeneFamily property) (panorama.pangenomes.Pangenome property) number_of_families (panorama.region.Region property) (panorama.region.Spot property) (panorama.systems.system.System property) number_of_gene_families (panorama.pangenomes.Pangenome property) number_of_genes (panorama.geneFamily.GeneFamily property) (panorama.pangenomes.Pangenome property) number_of_metadata (panorama.geneFamily.GeneFamily property) (panorama.region.Module property) (panorama.region.Region property) (panorama.region.Spot property) (panorama.systems.system.System property) (panorama.systems.system.SystemUnit property) number_of_model_gene_families (panorama.systems.system.System property) number_of_modules (panorama.pangenomes.Pangenome property) number_of_neighbors (panorama.geneFamily.GeneFamily property) number_of_organisms (panorama.geneFamily.GeneFamily property) (panorama.pangenomes.Pangenome property) (panorama.region.Module property) (panorama.region.Spot property) number_of_rgp (panorama.pangenomes.Pangenome property) number_of_rnas (panorama.pangenomes.Pangenome property) number_of_spots (panorama.geneFamily.GeneFamily property) (panorama.pangenomes.Pangenome property) number_of_systems() (panorama.pangenomes.Pangenome method) O optimized_profile (panorama.geneFamily.GeneFamily attribute) organism (panorama.region.Region property) organisms (panorama.geneFamily.GeneFamily property) (panorama.pangenomes.Pangenome property) (panorama.region.Module property) (panorama.region.Spot property) (panorama.systems.system.System property) (panorama.systems.system.SystemUnit property) OUTPUT_FORMATS (panorama.systems.systems_association.AssociationVisualizationBuilder attribute) (panorama.systems.systems_partitions.SystemsPartitionVisualizer attribute) (panorama.systems.utils.VisualizationBuilder attribute) overlaps_contig_edge (panorama.region.Region property) P palette() (in module panorama.format.write_proksee) Pangenome (class in panorama.pangenomes) pangenome (panorama.systems.system.System attribute) PangenomeInfoExtractor (class in panorama.info.info) PangenomeProcessingError (class in panorama.alignment.utils) Pangenomes (class in panorama.pangenomes) pangenomes() (panorama.region.ConservedSpots method) (panorama.systems.system.ClusterSystems method) panorama.alignment.align module panorama.alignment.cluster module panorama.alignment.utils module panorama.annotate.annotate module panorama.annotate.hmm_search module panorama.compare.context module panorama.compare.spots module panorama.compare.systems module panorama.compare.utils module panorama.format.read_binaries module panorama.format.write_binaries module panorama.format.write_flat module panorama.format.write_proksee module panorama.geneFamily module panorama.info.info module panorama.main module panorama.pangenomes module panorama.region module panorama.systems.detection module panorama.systems.models module panorama.systems.system module panorama.systems.systems_association module panorama.systems.systems_partitions module panorama.systems.systems_projection module panorama.systems.utils module panorama.systems.write_systems module panorama.utility.genInput module panorama.utility.translate.macsymodel_translator module panorama.utility.translate.padloc_translator module panorama.utility.translate.translate module panorama.utility.utility module panorama.utils module panorama.workflow.pansystems module pansystems() (in module panorama.workflow.pansystems) parse_context_results() (in module panorama.compare.context) parse_hmm_info() (in module panorama.utility.genInput) parse_macsyfinder_hmm() (in module panorama.utility.translate.macsymodel_translator) parse_meta_padloc() (in module panorama.utility.translate.padloc_translator) parser_align() (in module panorama.alignment.align) parser_annot() (in module panorama.annotate.annotate) parser_annot_hmm() (in module panorama.annotate.annotate) parser_cluster() (in module panorama.alignment.cluster) parser_comparison() (in module panorama.compare.utils) parser_comparison_context() (in module panorama.compare.context) parser_comparison_spots() (in module panorama.compare.spots) parser_comparison_systems() (in module panorama.compare.systems) parser_detection() (in module panorama.systems.detection) parser_info() (in module panorama.info.info) parser_mmseqs2_align() (in module panorama.alignment.align) parser_mmseqs2_cluster() (in module panorama.alignment.cluster) parser_pansystems() (in module panorama.workflow.pansystems) parser_utils() (in module panorama.utility.utility) parser_write() (in module panorama.format.write_flat) (in module panorama.systems.write_systems) partition (panorama.geneFamily.GeneFamily property) partition2color (panorama.systems.systems_partitions.SystemsPartitionVisualizer attribute) partitions (panorama.systems.systems_partitions.SystemsPartitionVisualizer attribute) pass_graph_attribute_to_multigraph() (in module panorama.compare.context) plot() (panorama.systems.systems_association.AssociationVisualizationBuilder method) (panorama.systems.systems_partitions.SystemsPartitionVisualizer method) (panorama.systems.utils.VisualizationBuilder method) PNG_EXPORT_HEIGHT (panorama.systems.systems_association.AssociationVisualizationBuilder attribute) (panorama.systems.systems_partitions.SystemsPartitionVisualizer attribute) (panorama.systems.utils.VisualizationBuilder attribute) PNG_EXPORT_WIDTH (panorama.systems.systems_association.AssociationVisualizationBuilder attribute) (panorama.systems.systems_partitions.SystemsPartitionVisualizer attribute) (panorama.systems.utils.VisualizationBuilder attribute) pop_specific_action_grp() (in module panorama.utils) preprocess_association_data() (in module panorama.systems.systems_association) preprocess_data() (in module panorama.systems.systems_partitions) preprocess_partition_data() (in module panorama.systems.systems_partitions) presence (panorama.systems.models._FuFamFeatures attribute) (panorama.systems.models.Family attribute) (panorama.systems.models.FuncUnit attribute) process_attributes() (in module panorama.utility.translate.macsymodel_translator) process_exchangeable() (in module panorama.utility.translate.macsymodel_translator) process_hmm_accession() (in module panorama.utility.genInput) process_hmm_name() (in module panorama.utility.genInput) process_system() (in module panorama.systems.systems_association) profile (panorama.geneFamily.GeneFamily attribute) profile_gf() (in module panorama.annotate.hmm_search) profile_gfs() (in module panorama.annotate.hmm_search) project_pangenome_systems() (in module panorama.systems.systems_projection) project_unit_on_organisms() (in module panorama.systems.systems_projection) PROTEIN_FAMILIES_FILENAME (panorama.alignment.utils.MMSeqsConfig attribute) R RawTextArgumentDefaultsHelpFormatter (class in panorama.utils) read() (panorama.systems.models.Family method) (panorama.systems.models.FuncUnit method) (panorama.systems.models.Model method) (panorama.systems.models.Models method) read_clustering() (panorama.pangenomes.Pangenomes method) read_data() (in module panorama.format.write_proksee) read_families_metadata() (in module panorama.annotate.annotate) read_families_metadata_mp() (in module panorama.annotate.annotate) read_gene_families() (in module panorama.format.read_binaries) read_gene_families_info() (in module panorama.format.read_binaries) read_hmm() (in module panorama.utility.genInput) read_hmms() (in module panorama.annotate.hmm_search) read_metadata() (in module panorama.utility.genInput) read_model() (panorama.systems.models.Model static method) read_modules() (in module panorama.format.read_binaries) read_pangenome() (in module panorama.format.read_binaries) read_parameters() (panorama.systems.models._BasicFeatures method) (panorama.systems.models.Family method) (panorama.systems.models.FuncUnit method) (panorama.systems.models.Model method) read_settings() (in module panorama.format.write_proksee) read_spots() (in module panorama.format.read_binaries) read_systems() (in module panorama.format.read_binaries) read_systems_by_source() (in module panorama.format.read_binaries) read_xml() (in module panorama.utility.translate.translate) read_yaml() (in module panorama.utility.translate.translate) recast() (panorama.geneFamily.GeneFamily static method) reference (panorama.geneFamily.Akin attribute) Region (class in panorama.region) regions (panorama.pangenomes.Pangenome property) (panorama.region.Spot property) (panorama.systems.system.System property) (panorama.systems.system.SystemUnit property) remove() (panorama.geneFamily.GeneFamily method) (panorama.region.Module method) (panorama.region.Region method) (panorama.region.Spot method) remove_redundant_annotation() (in module panorama.annotate.annotate) representative (panorama.geneFamily.GeneFamily property) resolve_path() (in module panorama.utils) RIGHT_WIDTH (panorama.systems.systems_association.AssociationVisualizationBuilder attribute) (panorama.systems.systems_partitions.SystemsPartitionVisualizer attribute) (panorama.systems.utils.VisualizationBuilder attribute) RNAs (panorama.pangenomes.Pangenome property) S same_strand (panorama.systems.models._ModFuFeatures attribute) (panorama.systems.models.FuncUnit attribute) (panorama.systems.models.Model attribute) search_canonical_macsyfinder() (in module panorama.utility.translate.macsymodel_translator) search_canonical_padloc() (in module panorama.utility.translate.padloc_translator) search_for_system() (in module panorama.systems.detection) search_system() (in module panorama.systems.detection) search_system_units() (in module panorama.systems.detection) search_systems() (in module panorama.systems.detection) search_systems_in_pangenomes() (in module panorama.systems.detection) search_unit_in_cc() (in module panorama.systems.detection) search_unit_in_combination() (in module panorama.systems.detection) search_unit_in_context() (in module panorama.systems.detection) select_elem() (panorama.pangenomes.Pangenome method) set_edge() (panorama.geneFamily.GeneFamily method) set_module() (panorama.geneFamily.GeneFamily method) set_verbosity_level() (in module panorama.utils) size (panorama.systems.models.FuncUnit property) (panorama.systems.models.Model property) (panorama.systems.models.Models property) soft_core_families() (panorama.pangenomes.Pangenome method) source (panorama.systems.system.System attribute) (panorama.systems.system.SystemUnit attribute) sources (panorama.geneFamily.GeneFamily property) (panorama.region.Module property) (panorama.region.Region property) (panorama.region.Spot property) (panorama.systems.system.System property) (panorama.systems.system.SystemUnit property) Spot (class in panorama.region) spot (panorama.region.Region property) spot_2_families() (panorama.region.Spot method) spots (panorama.geneFamily.GeneFamily property) (panorama.pangenomes.Pangenome property) (panorama.region.ConservedSpots property) (panorama.systems.system.System property) (panorama.systems.system.SystemUnit property) start (panorama.region.Region property) start_section() (panorama.utils.RawTextArgumentDefaultsHelpFormatter method) starter (panorama.region.Region property) stop (panorama.region.Region property) stopper (panorama.region.Region property) string_coordinates() (panorama.region.Region method) subparser() (in module panorama.alignment.align) (in module panorama.alignment.cluster) (in module panorama.annotate.annotate) (in module panorama.compare.context) (in module panorama.compare.spots) (in module panorama.compare.systems) (in module panorama.format.write_flat) (in module panorama.info.info) (in module panorama.systems.detection) (in module panorama.systems.write_systems) (in module panorama.utility.utility) (in module panorama.workflow.pansystems) summarize() (panorama.region.GeneContext method) symmetric_difference() (panorama.systems.system.SystemUnit method) System (class in panorama.systems.system) system (panorama.systems.system.SystemUnit property) system_projection() (in module panorama.systems.systems_projection) system_sizes (panorama.format.write_binaries.SystemTableSizes attribute) system_to_canonical_rows (panorama.format.write_binaries.SystemTableSizes attribute) systems (panorama.pangenomes.Pangenome property) (panorama.region.Module property) (panorama.systems.system.ClusterSystems property) systems_partition() (in module panorama.systems.systems_partitions) systems_sources (panorama.pangenomes.Pangenome property) systems_sources_to_metadata_source() (panorama.pangenomes.Pangenome method) SystemsComparisonError (class in panorama.compare.systems) SystemsPartitionVisualizer (class in panorama.systems.systems_partitions) SystemTableSizes (class in panorama.format.write_binaries) SystemUnit (class in panorama.systems.system) T to_list() (panorama.pangenomes.Pangenomes method) to_set() (panorama.pangenomes.Pangenomes method) top_bar (panorama.systems.systems_association.AssociationVisualizationBuilder property) (panorama.systems.systems_partitions.SystemsPartitionVisualizer property) (panorama.systems.utils.VisualizationBuilder property) TOP_HEIGHT (panorama.systems.systems_association.AssociationVisualizationBuilder attribute) (panorama.systems.systems_partitions.SystemsPartitionVisualizer attribute) (panorama.systems.utils.VisualizationBuilder attribute) TOTAL_HEIGHT (panorama.systems.systems_association.AssociationVisualizationBuilder attribute) (panorama.systems.systems_partitions.SystemsPartitionVisualizer attribute) (panorama.systems.utils.VisualizationBuilder attribute) TOTAL_WIDTH (panorama.systems.systems_association.AssociationVisualizationBuilder attribute) (panorama.systems.systems_partitions.SystemsPartitionVisualizer attribute) (panorama.systems.utils.VisualizationBuilder attribute) transitivity (panorama.systems.models._BasicFeatures attribute) (panorama.systems.models.Family attribute) (panorama.systems.models.FuncUnit attribute) (panorama.systems.models.Model attribute) translate_functional_unit() (in module panorama.utility.translate.macsymodel_translator) translate_gene() (in module panorama.utility.translate.macsymodel_translator) translate_macsyfinder() (in module panorama.utility.translate.macsymodel_translator) translate_macsyfinder_model() (in module panorama.utility.translate.macsymodel_translator) translate_model_padloc() (in module panorama.utility.translate.padloc_translator) translate_padloc() (in module panorama.utility.translate.padloc_translator) U unit_projection() (in module panorama.systems.systems_projection) unit_sizes (panorama.format.write_binaries.SystemTableSizes attribute) units (panorama.region.Module property) (panorama.systems.system.System property) V value (panorama.systems.models.Models property) VisualizationBuilder (class in panorama.systems.utils) W window (panorama.systems.models._BasicFeatures attribute) (panorama.systems.models.Family attribute) (panorama.systems.models.FuncUnit attribute) (panorama.systems.models.Model attribute) with_traceback() (panorama.alignment.align.AlignmentError method) (panorama.alignment.align.AlignmentValidationError method) (panorama.alignment.cluster.ClusteringError method) (panorama.alignment.cluster.ClusteringValidationError method) (panorama.alignment.utils.MMSeqsError method) (panorama.alignment.utils.PangenomeProcessingError method) (panorama.compare.systems.SystemsComparisonError method) (panorama.utility.translate.translate.HMMProcessingError method) (panorama.utility.translate.translate.ModelTranslationError method) write_alignment() (in module panorama.alignment.align) write_annotations_to_pangenome() (in module panorama.annotate.annotate) write_annotations_to_pangenomes() (in module panorama.annotate.annotate) write_clustering() (in module panorama.alignment.cluster) write_conserved_spots() (in module panorama.compare.spots) write_conserved_systems() (in module panorama.compare.systems) write_context_summary() (in module panorama.compare.context) write_contig() (in module panorama.format.write_proksee) write_correlation_matrix_visualization() (in module panorama.systems.systems_association) write_flat_files() (in module panorama.format.write_flat) write_flat_systems_to_pangenome() (in module panorama.systems.write_systems) write_genes() (in module panorama.format.write_proksee) write_hmm() (in module panorama.format.write_flat) (in module panorama.utility.genInput) write_hmm_profile() (in module panorama.format.write_flat) write_legend_items() (in module panorama.format.write_proksee) write_model() (in module panorama.utility.translate.translate) write_modules() (in module panorama.format.write_proksee) write_pangenome() (in module panorama.format.write_binaries) write_pangenome_families_annotations() (in module panorama.format.write_flat) write_pangenome_status() (in module panorama.format.write_binaries) write_pangenomes_families_annotations() (in module panorama.format.write_flat) write_pangenomes_families_sequences() (in module panorama.alignment.utils) write_pangenomes_systems() (in module panorama.systems.write_systems) write_partition() (in module panorama.format.write_proksee) write_projection_systems() (in module panorama.systems.systems_projection) write_proksee() (in module panorama.format.write_proksee) write_proksee_organism() (in module panorama.format.write_proksee) write_protein_families_sequences() (in module panorama.alignment.utils) write_rgp() (in module panorama.format.write_proksee) write_spots() (in module panorama.format.write_proksee) write_system_data_to_tables() (in module panorama.format.write_binaries) write_systems() (in module panorama.format.write_proksee) write_systems_to_hdf5() (in module panorama.format.write_binaries) write_systems_to_pangenome() (in module panorama.systems.detection) write_systems_to_pangenomes() (in module panorama.systems.detection) write_top_hits() (in module panorama.annotate.hmm_search) write_tracks() (in module panorama.format.write_proksee)
