Index

A

agn_array_copy (C function) agn_attribute_filter_stream_new (C function) agn_attribute_filter_stream_unit_test (C function) agn_calc_splice_complexity (C function) agn_clique_pair_classify (C function) agn_clique_pair_compare (C function) agn_clique_pair_compare_direct (C function) agn_clique_pair_compare_reverse (C function) agn_clique_pair_comparison_aggregate (C function) agn_clique_pair_delete (C function) agn_clique_pair_get_pred_clique (C function) agn_clique_pair_get_refr_clique (C function) agn_clique_pair_get_stats (C function) agn_clique_pair_new (C function) agn_clique_pair_unit_test (C function) agn_comp_class_desc_aggregate (C function) agn_comp_class_desc_init (C function) agn_comp_class_summary_aggregate (C function) agn_comp_class_summary_init (C function) agn_comp_info_aggregate (C function) agn_comp_info_init (C function) agn_comp_stats_binary_aggregate (C function) agn_comp_stats_binary_init (C function) agn_comp_stats_binary_print (C function) agn_comp_stats_binary_resolve (C function) agn_comp_stats_binary_test (C function) agn_comp_stats_scaled_aggregate (C function) agn_comp_stats_scaled_init (C function) agn_comp_stats_scaled_print (C function) agn_comp_stats_scaled_resolve (C function) agn_comp_stats_scaled_test (C function) agn_compare_report_html_create_summary (C function) agn_compare_report_html_new (C function) agn_compare_report_html_reset_summary_title (C function) agn_compare_report_html_set_overview_func (C function) agn_compare_report_text_create_summary (C function) agn_compare_report_text_new (C function) agn_comparison_aggregate (C function) agn_comparison_data_aggregate (C function) agn_comparison_data_init (C function) agn_comparison_init (C function) agn_comparison_print (C function) agn_comparison_resolve (C function) agn_comparison_test (C function) agn_feature_index_copy_regions (C function) agn_feature_index_copy_regions_pairwise (C function) agn_feature_node_get_cds_range (C function) agn_feature_node_get_children (C function) agn_feature_node_get_label (C function) agn_feature_node_remove_tree (C function) agn_feature_overlap_check (C function) agn_filter_stream_new (C function) agn_filter_stream_unit_test (C function) agn_gaeval_stream_new (C function) agn_gaeval_visitor_new (C function) agn_gaeval_visitor_unit_test (C function) agn_gene_stream_new (C function) agn_gene_stream_set_source (C function) agn_gene_stream_unit_test (C function) agn_genome_node_compare (C function) agn_infer_cds_stream_new (C function) agn_infer_cds_visitor_new (C function) agn_infer_cds_visitor_set_source (C function) agn_infer_cds_visitor_unit_test (C function) agn_infer_exons_stream_new (C function) agn_infer_exons_visitor_new (C function) agn_infer_exons_visitor_set_source (C function) agn_infer_exons_visitor_unit_test (C function) agn_infer_parent_stream_new (C function) agn_infer_parent_stream_set_source (C function) agn_infer_parent_stream_unit_test (C function) agn_locus_add (C function) agn_locus_array_compare (C function) agn_locus_cds_length (C function) agn_locus_clone (C function) agn_locus_comparative_analysis (C function) agn_locus_comparison_aggregate (C function) agn_locus_data_aggregate (C function) agn_locus_delete (C function) agn_locus_exon_num (C function) agn_locus_filter_parse (C function) agn_locus_filter_stream_new (C function) agn_locus_filter_stream_unit_test (C function) agn_locus_filter_test (C function) agn_locus_gene_ids (C function) agn_locus_gene_num (C function) agn_locus_genes (C function) agn_locus_get (C function) agn_locus_get_unique_pred_cliques (C function) agn_locus_get_unique_refr_cliques (C function) agn_locus_inner_orientation (C function) agn_locus_map_stream_new (C function) agn_locus_map_visitor_new (C function) agn_locus_mrna_ids (C function) agn_locus_mrna_num (C function) agn_locus_mrnas (C function) agn_locus_new (C function) agn_locus_pairs_to_report (C function) agn_locus_png_track_selector (C function) agn_locus_print_png (C function) agn_locus_print_transcript_mapping (C function) agn_locus_refine_stream_new (C function) agn_locus_refine_stream_set_name_format (C function) agn_locus_refine_stream_set_source (C function) agn_locus_refine_stream_track_ilens (C function)

agn_locus_refine_stream_unit_test (C function) agn_locus_set_range (C function) agn_locus_splice_complexity (C function) agn_locus_stream_label_pairwise (C function) agn_locus_stream_new (C function) agn_locus_stream_set_endmode (C function) agn_locus_stream_set_name_format (C function) agn_locus_stream_set_source (C function) agn_locus_stream_skip_iiLoci (C function) agn_locus_stream_track_ilens (C function) agn_locus_stream_unit_test (C function) agn_locus_unit_test (C function) agn_mrna_3putr_length (C function) agn_mrna_5putr_length (C function) agn_mrna_cds_length (C function) agn_mrna_rep_stream_new (C function) agn_mrna_rep_visitor_new (C function) agn_mrna_rep_visitor_set_parent_type (C function) agn_mrna_rep_visitor_unit_test (C function) agn_multi_child_range (C function) agn_overlap_ilocus (C function) agn_print_version (C function) agn_pseudogene_fix_stream_new (C function) agn_pseudogene_fix_visitor_new (C function) agn_pseudogene_fix_visitor_unit_test (C function) agn_remove_children_stream_new (C function) agn_remove_children_visitor_new (C function) agn_remove_children_visitor_unit_test (C function) agn_sprintf_comma (C function) agn_str_array_union (C function) agn_string_compare (C function) agn_transcript_clique_add (C function) agn_transcript_clique_cds_length (C function) agn_transcript_clique_copy (C function) agn_transcript_clique_delete (C function) agn_transcript_clique_get_model_vector (C function) agn_transcript_clique_has_id_in_hash (C function) agn_transcript_clique_id (C function) agn_transcript_clique_ids (C function) agn_transcript_clique_new (C function) agn_transcript_clique_num_exons (C function) agn_transcript_clique_num_utrs (C function) agn_transcript_clique_put_ids_in_hash (C function) agn_transcript_clique_size (C function) agn_transcript_clique_to_array (C function) agn_transcript_clique_to_gff3 (C function) agn_transcript_clique_traverse (C function) agn_transcript_clique_unit_test (C function) agn_typecheck_cds (C function) agn_typecheck_count (C function) agn_typecheck_exon (C function) agn_typecheck_feature_combined_length (C function) agn_typecheck_gene (C function) agn_typecheck_intron (C function) agn_typecheck_mrna (C function) agn_typecheck_pseudogene (C function) agn_typecheck_select (C function) agn_typecheck_select_str (C function) agn_typecheck_start_codon (C function) agn_typecheck_stop_codon (C function) agn_typecheck_transcript (C function) agn_typecheck_utr (C function) agn_typecheck_utr3p (C function) agn_typecheck_utr5p (C function) agn_unit_test_delete (C function) agn_unit_test_new (C function) agn_unit_test_print (C function) agn_unit_test_result (C function) agn_unit_test_run (C function) agn_unit_test_success (C function) AgnCliquePair (C type) AgnCliqueVisitFunc (C type) AgnCompareReportHTML (C type) AgnCompareReportHTMLOverviewFunc (C type) AgnCompareReportText (C type) AgnComparison (C type) AgnComparisonData (C type) AgnComparisonSource (C type) AgnCompClassDesc (C type) AgnCompClassification (C type) AgnCompClassSummary (C type) AgnCompInfo (C type) AgnCompStatsBinary (C type) AgnCompStatsScaled (C type) AgnFilterStream (C type), [1] AgnGaevalParams (C type) AgnGaevalVisitor (C type) AgnGeneStream (C type) AgnInferCDSVisitor (C type) AgnInferExonsVisitor (C type) AgnInferParentStream (C type) AgnLocus (C type) AgnLocusFilter (C type) AgnLocusFilterOp (C type) AgnLocusFilterStream (C type) AgnLocusMapVisitor (C type) AgnLocusPngMetadata (C type) AgnLocusRefineStream (C type) AgnLocusStream (C type) AgnMrnaRepVisitor (C type) AgnPseudogeneFixVisitor (C type) AgnRemoveChildrenVisitor (C type) AgnSequenceRegion (C type) AgnTranscriptClique (C type) AgnUnitTest (C type)