Table of Contents - genevalidator-2.1.5 Documentation
Classes and Modules
- Array
- GeneValidator
- GeneValidator::AliasDuplicationError
- GeneValidator::AlignmentValidation
- GeneValidator::AlignmentValidationOutput
- GeneValidator::BLASTDBError
- GeneValidator::BlastRFValidationOutput
- GeneValidator::BlastReadingFrameValidation
- GeneValidator::BlastUtils
- GeneValidator::ClasspathError
- GeneValidator::Cluster
- GeneValidator::DuplicationValidation
- GeneValidator::DuplicationValidationOutput
- GeneValidator::ExtraArrayMethods
- GeneValidator::FetchRawSequences
- GeneValidator::FileNotFoundException
- GeneValidator::GVArgValidation
- GeneValidator::GVArgValidation::Blast
- GeneValidator::GeneMergeValidation
- GeneValidator::GeneMergeValidationOutput
- GeneValidator::HierarchicalClusterization
- GeneValidator::Hsp
- GeneValidator::InconsistentTabularFormat
- GeneValidator::JsonToGVResults
- GeneValidator::LengthClusterValidation
- GeneValidator::LengthClusterValidationOutput
- GeneValidator::LengthRankValidation
- GeneValidator::LengthRankValidationOutput
- GeneValidator::MakerQIValidation
- GeneValidator::MakerQIValidationOutput
- GeneValidator::NoInternetError
- GeneValidator::NoMafftInstallationError
- GeneValidator::NoPIdentError
- GeneValidator::NoValidationError
- GeneValidator::NotEnoughEvidence
- GeneValidator::NotEnoughHitsError
- GeneValidator::ORFValidationOutput
- GeneValidator::OpenReadingFrameValidation
- GeneValidator::OtherError
- GeneValidator::Output
- GeneValidator::OutputFiles
- GeneValidator::PairCluster
- GeneValidator::Query
- GeneValidator::QueryError
- GeneValidator::RawSequences
- GeneValidator::ReadingFrameError
- GeneValidator::ReportClassError
- GeneValidator::SequenceTypeError
- GeneValidator::TabularParser
- GeneValidator::Validate
- GeneValidator::ValidationClassError
- GeneValidator::ValidationReport
- GeneValidator::ValidationTest
- GeneValidator::Validations
- Pool
Methods
- ::add_to_path — GeneValidator::GVArgValidation
- ::assert_BLAST_output_files — GeneValidator::GVArgValidation
- ::assert_blast_compatible — GeneValidator::GVArgValidation::Blast
- ::assert_blast_installation — GeneValidator::GVArgValidation::Blast
- ::assert_blast_installed — GeneValidator::GVArgValidation::Blast
- ::assert_dir_present — GeneValidator::GVArgValidation
- ::assert_file_present — GeneValidator::GVArgValidation
- ::assert_input_file_probably_fasta — GeneValidator::GVArgValidation
- ::assert_input_sequence — GeneValidator::GVArgValidation
- ::assert_local_blast_database_exists — GeneValidator::GVArgValidation::Blast
- ::assert_mafft_installation — GeneValidator::GVArgValidation
- ::assert_output_dir_does_not_exist — GeneValidator
- ::assert_tabular_options_exists — GeneValidator::GVArgValidation
- ::assert_validations_arg — GeneValidator::GVArgValidation
- ::batch_raw_seq_cmd — GeneValidator::FetchRawSequences
- ::blast_cmd — GeneValidator::BlastUtils
- ::calculate_no_quries_with_no_evidence — GeneValidator::Output
- ::calculate_run_time — GeneValidator::Output
- ::check_num_threads — GeneValidator::GVArgValidation
- ::command? — GeneValidator::GVArgValidation
- ::copy_blast_xml_files — GeneValidator
- ::copy_prev_json_output — GeneValidator
- ::copy_raw_seq_files — GeneValidator
- ::count_internet_errors — GeneValidator::Output
- ::count_mafft_errors — GeneValidator::Output
- ::cp_html_files — GeneValidator
- ::create_row_json_plot_files — GeneValidator::JsonToGVResults
- ::errors_overview — GeneValidator::Output
- ::export_bin_dirs — GeneValidator::GVArgValidation
- ::extract_from_index — GeneValidator::FetchRawSequences
- ::extract_from_local_db — GeneValidator::FetchRawSequences
- ::extract_from_remote_db — GeneValidator::FetchRawSequences
- ::extract_input_fasta_sequence — GeneValidator
- ::failed_raw_sequences — GeneValidator::FetchRawSequences
- ::general_overview — GeneValidator::Output
- ::generate_evaluation_text — GeneValidator::Output
- ::generate_overview — GeneValidator::Output
- ::guess_sequence_type — GeneValidator::BlastUtils
- ::guess_sequence_type_from_input_file — GeneValidator::BlastUtils
- ::index_raw_seq_file — GeneValidator::RawSequences
- ::index_the_input — GeneValidator
- ::init — GeneValidator::RawSequences
- ::init — GeneValidator::JsonToGVResults
- ::init — GeneValidator
- ::iterate_tabular — GeneValidator::RawSequences
- ::iterate_xml — GeneValidator::RawSequences
- ::load_json_file — GeneValidator::JsonToGVResults
- ::map_errors — GeneValidator::Output
- ::new — GeneValidator::PairCluster
- ::new — GeneValidator::Cluster
- ::new — GeneValidator::HierarchicalClusterization
- ::new — GeneValidator::Hsp
- ::new — GeneValidator::Output
- ::new — GeneValidator::OutputFiles
- ::new — Pool
- ::new — GeneValidator::Query
- ::new — GeneValidator::TabularParser
- ::new — GeneValidator::Validations
- ::new — GeneValidator::Validate
- ::new — GeneValidator::AlignmentValidationOutput
- ::new — GeneValidator::AlignmentValidation
- ::new — GeneValidator::BlastRFValidationOutput
- ::new — GeneValidator::BlastReadingFrameValidation
- ::new — GeneValidator::DuplicationValidationOutput
- ::new — GeneValidator::DuplicationValidation
- ::new — GeneValidator::GeneMergeValidationOutput
- ::new — GeneValidator::GeneMergeValidation
- ::new — GeneValidator::LengthClusterValidationOutput
- ::new — GeneValidator::LengthClusterValidation
- ::new — GeneValidator::LengthRankValidationOutput
- ::new — GeneValidator::LengthRankValidation
- ::new — GeneValidator::MakerQIValidationOutput
- ::new — GeneValidator::MakerQIValidation
- ::new — GeneValidator::ORFValidationOutput
- ::new — GeneValidator::OpenReadingFrameValidation
- ::new — GeneValidator::ValidationReport
- ::new — GeneValidator::ValidationTest
- ::overview_hash — GeneValidator::Output
- ::parse_blast_output_file — GeneValidator
- ::parse_next — GeneValidator::BlastUtils
- ::parse_prev_json — GeneValidator
- ::print_blast_info_text — GeneValidator::BlastUtils
- ::print_console_footer — GeneValidator::Output
- ::print_console_header — GeneValidator::JsonToGVResults
- ::print_directories_locations — GeneValidator
- ::print_output_console — GeneValidator::JsonToGVResults
- ::print_prev_json_to_console — GeneValidator
- ::produce_output — GeneValidator
- ::resume_from_previous_run — GeneValidator
- ::run — GeneValidator::RawSequences
- ::run — GeneValidator::FetchRawSequences
- ::run — GeneValidator::JsonToGVResults
- ::run — GeneValidator
- ::run_blast_on_input_file — GeneValidator::BlastUtils
- ::setup_config — GeneValidator
- ::setup_dirnames — GeneValidator
- ::setup_output_dir — GeneValidator
- ::single_raw_seq_cmd — GeneValidator::FetchRawSequences
- ::time_overview — GeneValidator::Output
- ::type_of_sequences — GeneValidator::BlastUtils
- ::validate — GeneValidator::GVArgValidation::Blast
- ::validate_args — GeneValidator::GVArgValidation
- ::write_a_raw_seq_file — GeneValidator::RawSequences
- ::write_an_index_file — GeneValidator::RawSequences
- #add — GeneValidator::PairCluster
- #add — GeneValidator::Cluster
- #add_basic_validation_info — GeneValidator::Output
- #add_explanation_data — GeneValidator::Output
- #all_html_filenames — GeneValidator::OutputFiles
- #all_quartiles — GeneValidator::ExtraArrayMethods
- #analayse_tabular_file — GeneValidator::TabularParser
- #array_to_ranges — GeneValidator::AlignmentValidation
- #assert_seq_type — GeneValidator::Hsp
- #check_hit_coverage — GeneValidator::Validate
- #check_if_maker_input? — GeneValidator::Validations
- #check_multiple_coverage — GeneValidator::DuplicationValidation
- #check_validations — GeneValidator::Validate
- #check_validations_output — GeneValidator::Validate
- #clusterization_by_length — GeneValidator::LengthClusterValidation
- #color — GeneValidator::DuplicationValidationOutput
- #color — GeneValidator::GeneMergeValidationOutput
- #color — GeneValidator::ValidationReport
- #compute_run_score — GeneValidator::Validate
- #conclude — GeneValidator::AlignmentValidationOutput
- #conclude — GeneValidator::BlastRFValidationOutput
- #conclude — GeneValidator::DuplicationValidationOutput
- #conclude — GeneValidator::GeneMergeValidationOutput
- #conclude — GeneValidator::LengthClusterValidationOutput
- #conclude — GeneValidator::LengthRankValidationOutput
- #conclude — GeneValidator::MakerQIValidationOutput
- #conclude — GeneValidator::ORFValidationOutput
- #consensus_validation — GeneValidator::AlignmentValidation
- #create_graphs_hash — GeneValidator::Output
- #create_overview_json_file — GeneValidator::OutputFiles
- #create_validation_hash — GeneValidator::Output
- #create_validation_tests — GeneValidator::Validate
- #csv_header — GeneValidator::OutputFiles
- #density — GeneValidator::PairCluster
- #density — GeneValidator::Cluster
- #deviation — GeneValidator::Cluster
- #distance — GeneValidator::PairCluster
- #distance — GeneValidator::Cluster
- #explain — GeneValidator::BlastRFValidationOutput
- #explain — GeneValidator::DuplicationValidationOutput
- #explain — GeneValidator::GeneMergeValidationOutput
- #explain — GeneValidator::LengthClusterValidationOutput
- #explain — GeneValidator::LengthRankValidationOutput
- #explain — GeneValidator::MakerQIValidationOutput
- #extra_sequence_validation — GeneValidator::AlignmentValidation
- #find_local_alignment — GeneValidator::DuplicationValidation
- #gap_validation — GeneValidator::AlignmentValidation
- #generate_json — GeneValidator::Output
- #generate_run_output — GeneValidator::Validate
- #generate_summary_data — GeneValidator::OutputFiles
- #get_consensus — GeneValidator::AlignmentValidation
- #get_info_on_query_sequence — GeneValidator::Validations
- #get_limits — GeneValidator::Cluster
- #get_orfs — GeneValidator::OpenReadingFrameValidation
- #get_sm_pssm — GeneValidator::AlignmentValidation
- #hierarchical_clusterization — GeneValidator::HierarchicalClusterization
- #hierarchical_clusterization_2d — GeneValidator::HierarchicalClusterization
- #in_range? — GeneValidator::DuplicationValidation
- #init_nucleotide_only_validations — GeneValidator::Validate
- #init_tabular_attribute — GeneValidator::Hsp
- #init_tabular_attribute — GeneValidator::Query
- #init_xml_attributes — GeneValidator::Hsp
- #initialise_classes — GeneValidator::TabularParser
- #inside_cluster — GeneValidator::Cluster
- #isalpha — GeneValidator::AlignmentValidation
- #length_validation_scores — GeneValidator::Validate
- #mean — GeneValidator::PairCluster
- #mean — GeneValidator::Cluster
- #mean — Array
- #mean — GeneValidator::ExtraArrayMethods
- #median — GeneValidator::ExtraArrayMethods
- #median_split — GeneValidator::ExtraArrayMethods
- #mode — GeneValidator::ExtraArrayMethods
- #most_dense_cluster — GeneValidator::HierarchicalClusterization
- #move_to_next_query — GeneValidator::TabularParser
- #multiple_align_mafft — GeneValidator::AlignmentValidation
- #next — GeneValidator::TabularParser
- #overview_html_hash — GeneValidator::OutputFiles
- #parse_next — GeneValidator::TabularParser
- #parse_next_iteration — GeneValidator::Validations
- #plot_2d_start_from — GeneValidator::GeneMergeValidation
- #plot_alignment — GeneValidator::AlignmentValidation
- #plot_histo_clusters — GeneValidator::LengthClusterValidation
- #plot_matched_regions — GeneValidator::GeneMergeValidation
- #plot_orfs — GeneValidator::OpenReadingFrameValidation
- #prettify_evalue — GeneValidator::DuplicationValidationOutput
- #print — GeneValidator::PairCluster
- #print — GeneValidator::Cluster
- #print — GeneValidator::AlignmentValidationOutput
- #print — GeneValidator::BlastRFValidationOutput
- #print — GeneValidator::DuplicationValidationOutput
- #print — GeneValidator::GeneMergeValidationOutput
- #print — GeneValidator::LengthClusterValidationOutput
- #print — GeneValidator::LengthRankValidationOutput
- #print — GeneValidator::MakerQIValidationOutput
- #print — GeneValidator::ORFValidationOutput
- #print — GeneValidator::ValidationReport
- #print_best_fasta — GeneValidator::OutputFiles
- #print_console_header — GeneValidator::Output
- #print_output_console — GeneValidator::Output
- #remove_identical_hits — GeneValidator::Validate
- #remove_isolated_residues — GeneValidator::AlignmentValidation
- #run — GeneValidator::AlignmentValidation
- #run — GeneValidator::BlastReadingFrameValidation
- #run — GeneValidator::DuplicationValidation
- #run — GeneValidator::GeneMergeValidation
- #run — GeneValidator::LengthClusterValidation
- #run — GeneValidator::LengthRankValidation
- #run — GeneValidator::MakerQIValidation
- #run — GeneValidator::OpenReadingFrameValidation
- #run — GeneValidator::ValidationTest
- #run_validations — GeneValidator::Validations
- #sample_variance — GeneValidator::ExtraArrayMethods
- #schedule — Pool
- #shutdown — Pool
- #slope — GeneValidator::GeneMergeValidation
- #slope_statsample — GeneValidator::GeneMergeValidation
- #standard_deviation — GeneValidator::Cluster
- #standard_deviation — GeneValidator::ExtraArrayMethods
- #sum — GeneValidator::ExtraArrayMethods
- #to_s — GeneValidator::SequenceTypeError
- #to_s — GeneValidator::ValidationClassError
- #to_s — GeneValidator::ReportClassError
- #to_s — GeneValidator::NoValidationError
- #to_s — GeneValidator::AliasDuplicationError
- #turn_off_automated_sorting — GeneValidator::OutputFiles
- #unimodality_test — GeneValidator::GeneMergeValidation
- #validate — GeneValidator::Validate
- #validation — GeneValidator::AlignmentValidationOutput
- #validation — GeneValidator::BlastRFValidationOutput
- #validation — GeneValidator::DuplicationValidationOutput
- #validation — GeneValidator::GeneMergeValidationOutput
- #validation — GeneValidator::LengthClusterValidationOutput
- #validation — GeneValidator::LengthRankValidationOutput
- #validation — GeneValidator::MakerQIValidationOutput
- #validation — GeneValidator::ORFValidationOutput
- #validation — GeneValidator::ValidationReport
- #wilcox_test — GeneValidator::DuplicationValidation
- #write_csv — GeneValidator::OutputFiles
- #write_html — GeneValidator::OutputFiles
- #write_json — GeneValidator::OutputFiles
- #write_summary — GeneValidator::OutputFiles
- #wss — GeneValidator::PairCluster
- #wss — GeneValidator::Cluster