Method List
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#* GeneValidator::Pair
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#+ GeneValidator::Pair
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#- GeneValidator::Pair
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#/ GeneValidator::Pair
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#== GeneValidator::Pair
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#accession_no GeneValidator::Query
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#add GeneValidator::Cluster
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#add GeneValidator::PairCluster
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#add_basic_validation_info GeneValidator::Output
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#add_explanation_data GeneValidator::Output
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#align_len GeneValidator::Hsp
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#analayse_tabular_file GeneValidator::TabularParser
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#approach GeneValidator::ValidationReport
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#array_to_ranges GeneValidator::AlignmentValidation
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assert_blast_installation GeneValidator::GVArgValidation::Blast
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assert_local_blast_database_exists GeneValidator::GVArgValidation::Blast
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#assert_seq_type GeneValidator::Hsp
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#aux1 GeneValidator::Plot
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#aux2 GeneValidator::Plot
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#average GeneValidator::DuplicationValidationOutput
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batch_raw_seq_cmd GeneValidator::FetchRawSequences
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#bit_score GeneValidator::Hsp
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calculate_no_quries_with_no_evidence GeneValidator::JsonToGVResults
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calculate_overall_score GeneValidator::JsonToGVResults
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#check_validations GeneValidator::Validate
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#check_validations_output GeneValidator::Validate
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#cli_name GeneValidator::ValidationTest
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#clusterization_by_length GeneValidator::LengthClusterValidation
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#clusters GeneValidator::HierarchicalClusterization
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#clusters GeneValidator::LengthClusterValidation
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#color GeneValidator::GeneMergeValidationOutput
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#color GeneValidator::DuplicationValidationOutput
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#color GeneValidator::ValidationReport
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#column_names GeneValidator::TabularParser
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command? GeneValidator::GVArgValidation
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#compute_scores GeneValidator::Validate
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#conclude GeneValidator::GeneMergeValidationOutput
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#conclude GeneValidator::DuplicationValidationOutput
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#conclude GeneValidator::LengthClusterValidationOutput
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#conclude GeneValidator::BlastRFValidationOutput
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#conclude GeneValidator::AlignmentValidationOutput
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#conclude GeneValidator::ORFValidationOutput
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#conclude GeneValidator::LengthRankValidationOutput
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#conclusion GeneValidator::ValidationReport
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config GeneValidator
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#consensus GeneValidator::AlignmentValidationOutput
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#consensus_validation GeneValidator::AlignmentValidation
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#coverage GeneValidator::ORFValidationOutput
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#create_graphs_hash GeneValidator::Output
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create_json_file GeneValidator::JsonToGVResults
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create_output_folder GeneValidator
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create_overview_json GeneValidator::Output
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#create_validation_hashes GeneValidator::Output
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#create_validation_tests GeneValidator::Validate
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#data GeneValidator::Plot
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#definition GeneValidator::Query
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#density GeneValidator::PairCluster
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#density GeneValidator::Cluster
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#description GeneValidator::ValidationTest
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#description GeneValidator::ValidationReport
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#deviation GeneValidator::Cluster
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#distance GeneValidator::PairCluster
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#distance GeneValidator::Cluster
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#eql? GeneValidator::Pair
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#errors GeneValidator::ValidationReport
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errors_overview GeneValidator::Output
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#expected GeneValidator::ValidationReport
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#explain GeneValidator::LengthClusterValidationOutput
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#explain GeneValidator::LengthRankValidationOutput
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#explain GeneValidator::GeneMergeValidationOutput
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#explain GeneValidator::BlastRFValidationOutput
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#explain GeneValidator::DuplicationValidationOutput
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#explanation GeneValidator::ValidationReport
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#extra_seq GeneValidator::AlignmentValidationOutput
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#extra_sequence_validation GeneValidator::AlignmentValidation
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extract_from_index GeneValidator::FetchRawSequences
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extract_from_local_db GeneValidator::FetchRawSequences
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extract_from_remote_db GeneValidator::FetchRawSequences
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#extreme_hits GeneValidator::LengthRankValidationOutput
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failed_raw_sequences GeneValidator::FetchRawSequences
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#fails GeneValidator::Output
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#footer GeneValidator::Plot
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#frames GeneValidator::BlastRFValidationOutput
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#gap_validation GeneValidator::AlignmentValidation
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#gaps GeneValidator::Hsp
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#gaps GeneValidator::AlignmentValidationOutput
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general_overview GeneValidator::Output
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generate_evaluation GeneValidator::JsonToGVResults
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#generate_html GeneValidator::Output
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generate_html_header GeneValidator::JsonToGVResults
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generate_html_query GeneValidator::JsonToGVResults
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#generate_json GeneValidator::Output
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#generate_run_output GeneValidator::Validate
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#generate_run_overview GeneValidator::Validate
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#get_consensus GeneValidator::AlignmentValidation
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#get_info_on_query_sequence GeneValidator::Validations
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#get_limits GeneValidator::Cluster
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#get_orfs GeneValidator::OpenReadingFrameValidation
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#get_sm_pssm GeneValidator::AlignmentValidation
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guess_sequence_type GeneValidator::BlastUtils
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guess_sequence_type_from_input_file GeneValidator::BlastUtils
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#hash GeneValidator::Pair
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#header GeneValidator::ValidationReport
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#header GeneValidator::ValidationTest
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#hierarchical_clusterization GeneValidator::HierarchicalClusterization
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#hierarchical_clusterization_2d GeneValidator::HierarchicalClusterization
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#hit_alignment GeneValidator::Hsp
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#hit_from GeneValidator::Hsp
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#hit_to GeneValidator::Hsp
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#hits GeneValidator::ValidationTest
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#hits GeneValidator::GeneMergeValidation
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#hsp_evalue GeneValidator::Hsp
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#hsp_list GeneValidator::Query
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#hsp_score GeneValidator::Hsp
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html_footer GeneValidator::JsonToGVResults
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#identifier GeneValidator::Query
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#identity GeneValidator::Hsp
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#idx GeneValidator::Output
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#in_range? GeneValidator::DuplicationValidation
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#index_file_name GeneValidator::AlignmentValidation
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#index_file_name GeneValidator::DuplicationValidation
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index_raw_seq_file GeneValidator::RawSequences
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index_the_input GeneValidator
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init GeneValidator::RawSequences
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init GeneValidator
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init GeneValidator::JsonToGVResults
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#init_tabular_attribute GeneValidator::Query
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#init_tabular_attribute GeneValidator::Hsp
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#initialize GeneValidator::Validate
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#initialize GeneValidator::Validations
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#initialize GeneValidator::LengthClusterValidationOutput
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#initialize GeneValidator::OpenReadingFrameValidation
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#initialize GeneValidator::LengthRankValidation
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#initialize GeneValidator::AlignmentValidationOutput
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#initialize GeneValidator::ValidationTest
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#initialize GeneValidator::ValidationReport
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#initialize GeneValidator::Output
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#initialize GeneValidator::DuplicationValidationOutput
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#initialize GeneValidator::Query
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#initialize GeneValidator::TabularParser
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#initialize Pool
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#initialize GeneValidator::Hsp
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#initialize GeneValidator::LengthClusterValidation
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#initialize GeneValidator::ORFValidationOutput
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#initialize GeneValidator::AlignmentValidation
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#initialize GeneValidator::BlastRFValidationOutput
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#initialize GeneValidator::BlastReadingFrameValidation
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#initialize GeneValidator::DuplicationValidation
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#initialize GeneValidator::GeneMergeValidation
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#initialize GeneValidator::Cluster
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#initialize GeneValidator::PairCluster
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#initialize GeneValidator::LengthRankValidationOutput
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#initialize GeneValidator::GeneMergeValidationOutput
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#initialize GeneValidator::HierarchicalClusterization
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#inside_cluster GeneValidator::Cluster
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#isalpha GeneValidator::AlignmentValidation
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#largest_hit GeneValidator::LengthRankValidationOutput
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#length_protein GeneValidator::Query
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#length_validation_scores GeneValidator::Validate
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#lengths GeneValidator::Cluster
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#limits GeneValidator::LengthClusterValidationOutput
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load_json_file GeneValidator::JsonToGVResults
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#mainORFFrame GeneValidator::ORFValidationOutput
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#match_query_from GeneValidator::Hsp
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#match_query_to GeneValidator::Hsp
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#max_density_cluster GeneValidator::LengthClusterValidation
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#mean GeneValidator::ExtraArrayMethods
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#mean GeneValidator::LengthRankValidationOutput
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#mean GeneValidator::PairCluster
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#mean GeneValidator::Cluster
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#median GeneValidator::ExtraArrayMethods
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#median GeneValidator::LengthRankValidationOutput
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#message GeneValidator::ValidationReport
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#middles GeneValidator::Hsp
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#mode GeneValidator::ExtraArrayMethods
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#most_dense_cluster GeneValidator::HierarchicalClusterization
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#msg GeneValidator::LengthRankValidationOutput
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#msg GeneValidator::BlastRFValidationOutput
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#multiple_align_mafft GeneValidator::AlignmentValidation
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#multiple_alignment GeneValidator::AlignmentValidation
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mutex GeneValidator
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mutex_array GeneValidator
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mutex_html GeneValidator
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mutex_json GeneValidator
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#next GeneValidator::TabularParser
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#no_of_hits GeneValidator::LengthRankValidationOutput
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#nr_hits GeneValidator::Output
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#nucleotide_rf GeneValidator::Query
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#objects GeneValidator::PairCluster
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opt GeneValidator
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#orfs GeneValidator::ORFValidationOutput
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output_filename GeneValidator::JsonToGVResults
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#output_filename GeneValidator::Output
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#overall_score GeneValidator::Output
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overview GeneValidator::Output
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overview GeneValidator
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parse_blast_output_file GeneValidator
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#parse_next GeneValidator::TabularParser
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parse_next GeneValidator::BlastUtils
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#parse_next_iteration GeneValidator::Validations
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#percentage GeneValidator::LengthRankValidationOutput
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#pidentity GeneValidator::Hsp
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#plot_2d_start_from GeneValidator::GeneMergeValidation
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#plot_alignment GeneValidator::AlignmentValidation
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#plot_files GeneValidator::ValidationReport
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#plot_histo_clusters GeneValidator::LengthClusterValidation
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#plot_matched_regions GeneValidator::GeneMergeValidation
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#plot_orfs GeneValidator::OpenReadingFrameValidation
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#positive GeneValidator::Hsp
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#prediction GeneValidator::GeneMergeValidation
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#prediction GeneValidator::ValidationTest
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#prediction_def GeneValidator::Output
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#print GeneValidator::LengthClusterValidationOutput
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#print GeneValidator::GeneMergeValidationOutput
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#print GeneValidator::Cluster
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#print GeneValidator::PairCluster
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#print GeneValidator::Pair
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#print GeneValidator::BlastRFValidationOutput
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#print GeneValidator::LengthRankValidationOutput
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#print GeneValidator::DuplicationValidationOutput
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#print GeneValidator::ORFValidationOutput
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#print GeneValidator::AlignmentValidationOutput
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#print GeneValidator::ValidationReport
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#print_console_header GeneValidator::Output
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print_footer GeneValidator::Output
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#print_output_console GeneValidator::Output
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print_summary_to_console GeneValidator::Output
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#protein_translation GeneValidator::Query
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#pvalue GeneValidator::DuplicationValidationOutput
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#query_alignment GeneValidator::Hsp
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query_idx GeneValidator
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#query_length GeneValidator::LengthClusterValidationOutput
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#query_length GeneValidator::LengthRankValidationOutput
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#query_reading_frame GeneValidator::Hsp
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#raw_seq_file GeneValidator::DuplicationValidation
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#raw_seq_file GeneValidator::AlignmentValidation
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raw_seq_file_index GeneValidator
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#raw_seq_file_load GeneValidator::DuplicationValidation
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raw_seq_file_load GeneValidator
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#raw_seq_file_load GeneValidator::AlignmentValidation
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#raw_sequence GeneValidator::Query
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#reading_frame GeneValidator::Query
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#remove_identical_hits GeneValidator::Validate
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#remove_isolated_residues GeneValidator::AlignmentValidation
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#result GeneValidator::BlastRFValidationOutput
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#result GeneValidator::LengthRankValidationOutput
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#result GeneValidator::DuplicationValidationOutput
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#result GeneValidator::GeneMergeValidationOutput
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#result GeneValidator::AlignmentValidationOutput
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#result GeneValidator::LengthClusterValidationOutput
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#result GeneValidator::ValidationReport
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#result GeneValidator::ORFValidationOutput
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#rows GeneValidator::TabularParser
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#run GeneValidator::ValidationTest
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#run GeneValidator::BlastReadingFrameValidation
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run GeneValidator::RawSequences
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#run GeneValidator::LengthClusterValidation
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#run GeneValidator::LengthRankValidation
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#run GeneValidator::DuplicationValidation
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run GeneValidator
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#run GeneValidator::GeneMergeValidation
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#run GeneValidator::AlignmentValidation
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#run GeneValidator::OpenReadingFrameValidation
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run GeneValidator::JsonToGVResults
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run GeneValidator::FetchRawSequences
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run_blast GeneValidator::BlastUtils
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run_blast_on_input_file GeneValidator::BlastUtils
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#run_time GeneValidator::ValidationTest
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#run_time GeneValidator::ValidationReport
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#run_validations GeneValidator::Validations
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#sample_variance GeneValidator::ExtraArrayMethods
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#schedule Pool
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set_overall_evaluation GeneValidator::Output
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#set_up_html GeneValidator::Output
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#short_header GeneValidator::ValidationTest
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#short_header GeneValidator::ValidationReport
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#shutdown Pool
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single_raw_seq_cmd GeneValidator::FetchRawSequences
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#slope GeneValidator::GeneMergeValidationOutput
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#slope GeneValidator::GeneMergeValidation
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#slope_statsample GeneValidator::GeneMergeValidation
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#smallest_hit GeneValidator::LengthRankValidationOutput
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#species GeneValidator::Query
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#standard_deviation GeneValidator::Cluster
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#standard_deviation GeneValidator::ExtraArrayMethods
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#successes GeneValidator::Output
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#sum GeneValidator::ExtraArrayMethods
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#tab_results GeneValidator::TabularParser
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#threshold GeneValidator::DuplicationValidationOutput
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#threshold GeneValidator::AlignmentValidationOutput
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#threshold GeneValidator::ORFValidationOutput
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#threshold_down GeneValidator::GeneMergeValidationOutput
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#threshold_up GeneValidator::GeneMergeValidationOutput
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time_overview GeneValidator::Output
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#title GeneValidator::Plot
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#to_s GeneValidator::NoValidationError
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#to_s GeneValidator::ValidationClassError
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#to_s GeneValidator::SequenceTypeError
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#to_s GeneValidator::ReportClassError
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#to_s GeneValidator::AliasDuplicationError
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#total_hsp GeneValidator::BlastRFValidationOutput
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turn_off_automated_sorting GeneValidator::JsonToGVResults
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turn_off_sorting GeneValidator::Output
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#type GeneValidator::Plot
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#type GeneValidator::ValidationTest
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#type GeneValidator::TabularParser
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#type GeneValidator::Query
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type_of_sequences GeneValidator::BlastUtils
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#unimodality GeneValidator::GeneMergeValidationOutput
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#unimodality_test GeneValidator::GeneMergeValidation
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validate GeneValidator::GVArgValidation::Blast
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#validate GeneValidator::Validate
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validate_args GeneValidator::GVArgValidation
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#validation GeneValidator::DuplicationValidationOutput
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#validation GeneValidator::GeneMergeValidationOutput
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#validation GeneValidator::AlignmentValidationOutput
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#validation GeneValidator::ValidationReport
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#validation GeneValidator::LengthRankValidationOutput
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#validation GeneValidator::BlastRFValidationOutput
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#validation GeneValidator::ORFValidationOutput
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#validation GeneValidator::LengthClusterValidationOutput
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#validation_report GeneValidator::ValidationTest
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#validation_result GeneValidator::ValidationReport
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#validations GeneValidator::Output
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#values GeneValidator::HierarchicalClusterization
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warn_if_remote_database GeneValidator::GVArgValidation::Blast
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#wilcox_test GeneValidator::DuplicationValidation
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write_html_footer GeneValidator::JsonToGVResults
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#write_html_header GeneValidator::Output
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write_json_file GeneValidator::Output
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#write_row_json GeneValidator::Output
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#wss GeneValidator::PairCluster
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#wss GeneValidator::Cluster
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#x GeneValidator::Pair
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#x GeneValidator::Pair1
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#xtitle GeneValidator::Plot
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#y GeneValidator::Pair
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#y GeneValidator::Pair1
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#ytitle GeneValidator::Plot