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#* GeneValidator::Pair
#+ GeneValidator::Pair
#- GeneValidator::Pair
#/ GeneValidator::Pair
#== GeneValidator::Pair
#accession_no GeneValidator::Query
#add GeneValidator::PairCluster
#add GeneValidator::Cluster
#align_len GeneValidator::Hsp
#all_quartiles GeneValidator::ExtraArrayMethods
#analayse_tabular_file GeneValidator::TabularParser
#approach GeneValidator::ValidationReport
#array_to_ranges GeneValidator::AlignmentValidation
assert_blast_installation GeneValidator::GVArgValidation::Blast
assert_local_blast_database_exists GeneValidator::GVArgValidation::Blast
#assert_seq_type GeneValidator::Hsp
#aux1 GeneValidator::Plot
#aux2 GeneValidator::Plot
#average GeneValidator::DuplicationValidationOutput
batch_raw_seq_cmd GeneValidator::FetchRawSequences
#bit_score GeneValidator::Hsp
calculate_no_quries_with_no_evidence GeneValidator::Output
calculate_run_time GeneValidator::Output
#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
#cli_name GeneValidator::ValidationTest
#clusterization_by_length GeneValidator::LengthClusterValidation
#clusters GeneValidator::HierarchicalClusterization
#clusters GeneValidator::LengthClusterValidation
#color GeneValidator::GeneMergeValidationOutput
#color GeneValidator::ValidationReport
#color GeneValidator::DuplicationValidationOutput
#column_names GeneValidator::TabularParser
command? GeneValidator::GVArgValidation
#compute_run_score GeneValidator::Validate
#conclude GeneValidator::AlignmentValidationOutput
#conclude GeneValidator::LengthRankValidationOutput
#conclude GeneValidator::DuplicationValidationOutput
#conclude GeneValidator::ORFValidationOutput
#conclude GeneValidator::BlastRFValidationOutput
#conclude GeneValidator::GeneMergeValidationOutput
#conclude GeneValidator::MakerQIValidationOutput
#conclude GeneValidator::LengthClusterValidationOutput
#conclusion GeneValidator::ValidationReport
config GeneValidator
#consensus GeneValidator::AlignmentValidationOutput
#consensus_validation GeneValidator::AlignmentValidation
count_internet_errors GeneValidator::Output
count_mafft_errors GeneValidator::Output
#coverage GeneValidator::ORFValidationOutput
#create_validation_tests GeneValidator::Validate
#data GeneValidator::Plot
#definition GeneValidator::Query
#density GeneValidator::PairCluster
#density GeneValidator::Cluster
#description GeneValidator::ValidationReport
#description GeneValidator::ValidationTest
#deviation GeneValidator::Cluster
dirs GeneValidator
#distance GeneValidator::PairCluster
#distance GeneValidator::Cluster
#eql? GeneValidator::Pair
#errors GeneValidator::ValidationReport
#expected GeneValidator::ValidationReport
#explain GeneValidator::GeneMergeValidationOutput
#explain GeneValidator::MakerQIValidationOutput
#explain GeneValidator::LengthRankValidationOutput
#explain GeneValidator::BlastRFValidationOutput
#explain GeneValidator::LengthClusterValidationOutput
#explain GeneValidator::DuplicationValidationOutput
#explanation GeneValidator::ValidationReport
#extra_seq GeneValidator::AlignmentValidationOutput
#extra_sequence_validation GeneValidator::AlignmentValidation
extract_from_index GeneValidator::FetchRawSequences
extract_from_local_db GeneValidator::FetchRawSequences
extract_from_remote_db GeneValidator::FetchRawSequences
extract_input_fasta_sequence GeneValidator
#extreme_hits GeneValidator::LengthRankValidationOutput
failed_raw_sequences GeneValidator::FetchRawSequences
#fails GeneValidator::Output
#find_local_alignment GeneValidator::DuplicationValidation
#footer GeneValidator::Plot
#frames GeneValidator::BlastRFValidationOutput
#gap_validation GeneValidator::AlignmentValidation
#gaps GeneValidator::Hsp
#gaps GeneValidator::AlignmentValidationOutput
generate_evaluation_text GeneValidator::Output
#generate_json GeneValidator::Output
generate_overview GeneValidator::Output
#generate_run_output GeneValidator::Validate
#get_consensus GeneValidator::AlignmentValidation
#get_info_on_query_sequence GeneValidator::Validations
#get_limits GeneValidator::Cluster
#get_orfs GeneValidator::OpenReadingFrameValidation
#get_sm_pssm GeneValidator::AlignmentValidation
guess_sequence_type GeneValidator::BlastUtils
guess_sequence_type_from_input_file GeneValidator::BlastUtils
#hash GeneValidator::Pair
#header GeneValidator::ValidationReport
#header GeneValidator::ValidationTest
#hierarchical_clusterization GeneValidator::HierarchicalClusterization
#hierarchical_clusterization_2d GeneValidator::HierarchicalClusterization
#hit_alignment GeneValidator::Hsp
#hit_from GeneValidator::Hsp
#hit_to GeneValidator::Hsp
#hits GeneValidator::ValidationTest
#hits GeneValidator::GeneMergeValidation
#hsp_evalue GeneValidator::Hsp
#hsp_list GeneValidator::Query
#hsp_score GeneValidator::Hsp
#identifier GeneValidator::Query
#identity GeneValidator::Hsp
#idx GeneValidator::Output
#in_range? GeneValidator::DuplicationValidation
#index_file_name GeneValidator::DuplicationValidation
#index_file_name GeneValidator::AlignmentValidation
index_raw_seq_file GeneValidator::RawSequences
init GeneValidator::RawSequences
init GeneValidator::JsonToGVResults
init GeneValidator
#init_nucleotide_only_validations GeneValidator::Validate
#init_tabular_attribute GeneValidator::Query
#init_tabular_attribute GeneValidator::Hsp
#init_xml_attributes GeneValidator::Hsp
#initialize GeneValidator::BlastReadingFrameValidation
#initialize GeneValidator::Validate
#initialize GeneValidator::Validations
#initialize GeneValidator::LengthRankValidationOutput
#initialize GeneValidator::OutputFiles
#initialize GeneValidator::LengthRankValidation
#initialize GeneValidator::ORFValidationOutput
#initialize GeneValidator::HierarchicalClusterization
#initialize GeneValidator::Output
#initialize GeneValidator::Query
#initialize GeneValidator::BlastRFValidationOutput
#initialize Pool
#initialize GeneValidator::Hsp
#initialize GeneValidator::MakerQIValidation
#initialize GeneValidator::AlignmentValidationOutput
#initialize GeneValidator::DuplicationValidation
#initialize GeneValidator::DuplicationValidationOutput
#initialize GeneValidator::ValidationTest
#initialize GeneValidator::Cluster
#initialize GeneValidator::OpenReadingFrameValidation
#initialize GeneValidator::ValidationReport
#initialize GeneValidator::LengthClusterValidationOutput
#initialize GeneValidator::LengthClusterValidation
#initialize GeneValidator::PairCluster
#initialize GeneValidator::GeneMergeValidation
#initialize GeneValidator::GeneMergeValidationOutput
#initialize GeneValidator::MakerQIValidationOutput
#initialize GeneValidator::AlignmentValidation
#initialize GeneValidator::TabularParser
#inside_cluster GeneValidator::Cluster
#isalpha GeneValidator::AlignmentValidation
#largest_hit GeneValidator::LengthRankValidationOutput
#length_protein GeneValidator::Query
#length_validation_scores GeneValidator::Validate
#lengths GeneValidator::Cluster
#limits GeneValidator::LengthClusterValidationOutput
#mainORFFrame GeneValidator::ORFValidationOutput
map_errors GeneValidator::Output
#match_query_from GeneValidator::Hsp
#match_query_to GeneValidator::Hsp
#max_density_cluster GeneValidator::LengthClusterValidation
#mean Array
#mean GeneValidator::ExtraArrayMethods
#mean GeneValidator::PairCluster
#mean GeneValidator::LengthRankValidationOutput
#mean GeneValidator::Cluster
#median GeneValidator::ExtraArrayMethods
#median GeneValidator::LengthRankValidationOutput
#median_split GeneValidator::ExtraArrayMethods
#message GeneValidator::ValidationReport
#middles GeneValidator::Hsp
#mode GeneValidator::ExtraArrayMethods
#most_dense_cluster GeneValidator::HierarchicalClusterization
#msg GeneValidator::BlastRFValidationOutput
#msg GeneValidator::LengthRankValidationOutput
#multiple_align_mafft GeneValidator::AlignmentValidation
#multiple_alignment GeneValidator::AlignmentValidation
mutex GeneValidator
mutex_array GeneValidator
#next GeneValidator::TabularParser
#no_of_hits GeneValidator::LengthRankValidationOutput
#nr_hits GeneValidator::Output
#nucleotide_rf GeneValidator::Query
#objects GeneValidator::PairCluster
opt GeneValidator
#orfs GeneValidator::ORFValidationOutput
#overall_score GeneValidator::Output
overview GeneValidator
overview_hash GeneValidator::Output
parse_blast_output_file GeneValidator
#parse_next GeneValidator::TabularParser
parse_next GeneValidator::BlastUtils
#parse_next_iteration GeneValidator::Validations
#percentage GeneValidator::LengthRankValidationOutput
#pidentity GeneValidator::Hsp
#plot_2d_start_from GeneValidator::GeneMergeValidation
#plot_alignment GeneValidator::AlignmentValidation
#plot_files GeneValidator::ValidationReport
#plot_histo_clusters GeneValidator::LengthClusterValidation
#plot_matched_regions GeneValidator::GeneMergeValidation
#plot_orfs GeneValidator::OpenReadingFrameValidation
#positive GeneValidator::Hsp
#prediction GeneValidator::ValidationTest
#prediction GeneValidator::GeneMergeValidation
#prediction_def GeneValidator::Output
#print GeneValidator::Cluster
#print GeneValidator::PairCluster
#print GeneValidator::Pair
#print GeneValidator::BlastRFValidationOutput
#print GeneValidator::LengthRankValidationOutput
#print GeneValidator::ORFValidationOutput
#print GeneValidator::DuplicationValidationOutput
#print GeneValidator::GeneMergeValidationOutput
#print GeneValidator::AlignmentValidationOutput
#print GeneValidator::MakerQIValidationOutput
#print GeneValidator::ValidationReport
#print GeneValidator::LengthClusterValidationOutput
#print_best_fasta GeneValidator::OutputFiles
print_console_footer GeneValidator::Output
print_console_header GeneValidator::JsonToGVResults
#print_output_console GeneValidator::Output
print_output_console GeneValidator::JsonToGVResults
produce_output GeneValidator
#protein_translation GeneValidator::Query
#pvalue GeneValidator::DuplicationValidationOutput
#query_alignment GeneValidator::Hsp
query_idx GeneValidator
#query_length GeneValidator::LengthRankValidationOutput
#query_length GeneValidator::LengthClusterValidationOutput
#query_reading_frame GeneValidator::Hsp
#raw_seq_file GeneValidator::DuplicationValidation
#raw_seq_file GeneValidator::AlignmentValidation
raw_seq_file_index GeneValidator
#raw_seq_file_load GeneValidator::DuplicationValidation
raw_seq_file_load GeneValidator
#raw_seq_file_load GeneValidator::AlignmentValidation
#raw_sequence GeneValidator::Query
#reading_frame GeneValidator::Query
#remove_identical_hits GeneValidator::Validate
#remove_isolated_residues GeneValidator::AlignmentValidation
#result GeneValidator::BlastRFValidationOutput
#result GeneValidator::LengthRankValidationOutput
#result GeneValidator::GeneMergeValidationOutput
#result GeneValidator::DuplicationValidationOutput
#result GeneValidator::AlignmentValidationOutput
#result GeneValidator::ORFValidationOutput
#result GeneValidator::ValidationReport
#result GeneValidator::LengthClusterValidationOutput
#rows GeneValidator::TabularParser
#run GeneValidator::ValidationTest
run GeneValidator::RawSequences
run GeneValidator::FetchRawSequences
#run GeneValidator::LengthClusterValidation
#run GeneValidator::LengthRankValidation
run GeneValidator
#run GeneValidator::DuplicationValidation
#run GeneValidator::AlignmentValidation
#run GeneValidator::MakerQIValidation
run GeneValidator::JsonToGVResults
#run GeneValidator::OpenReadingFrameValidation
#run GeneValidator::BlastReadingFrameValidation
#run GeneValidator::GeneMergeValidation
run_blast_on_input_file GeneValidator::BlastUtils
#run_time GeneValidator::ValidationTest
#run_time GeneValidator::ValidationReport
#run_validations GeneValidator::Validations
#sample_variance GeneValidator::ExtraArrayMethods
#schedule Pool
setup_dirnames GeneValidator
#short_header GeneValidator::ValidationTest
#short_header GeneValidator::ValidationReport
#shutdown Pool
single_raw_seq_cmd GeneValidator::FetchRawSequences
#slope GeneValidator::GeneMergeValidationOutput
#slope GeneValidator::GeneMergeValidation
#slope_statsample GeneValidator::GeneMergeValidation
#smallest_hit GeneValidator::LengthRankValidationOutput
#species GeneValidator::Query
#standard_deviation GeneValidator::Cluster
#standard_deviation GeneValidator::ExtraArrayMethods
#successes GeneValidator::Output
#sum GeneValidator::ExtraArrayMethods
#tab_results GeneValidator::TabularParser
#threshold GeneValidator::DuplicationValidationOutput
#threshold GeneValidator::AlignmentValidationOutput
#threshold GeneValidator::ORFValidationOutput
#threshold_down GeneValidator::GeneMergeValidationOutput
#threshold_up GeneValidator::GeneMergeValidationOutput
#title GeneValidator::Plot
#to_s GeneValidator::AliasDuplicationError
#to_s GeneValidator::NoValidationError
#to_s GeneValidator::ValidationClassError
#to_s GeneValidator::SequenceTypeError
#to_s GeneValidator::ReportClassError
#total_hsp GeneValidator::BlastRFValidationOutput
#type GeneValidator::Plot
#type GeneValidator::ValidationTest
#type GeneValidator::TabularParser
#type GeneValidator::Query
type_of_sequences GeneValidator::BlastUtils
#unimodality GeneValidator::GeneMergeValidationOutput
#unimodality_test GeneValidator::GeneMergeValidation
validate GeneValidator::GVArgValidation::Blast
#validate GeneValidator::Validate
validate_args GeneValidator::GVArgValidation
#validation GeneValidator::DuplicationValidationOutput
#validation GeneValidator::GeneMergeValidationOutput
#validation GeneValidator::AlignmentValidationOutput
#validation GeneValidator::ValidationReport
#validation GeneValidator::MakerQIValidationOutput
#validation GeneValidator::LengthRankValidationOutput
#validation GeneValidator::BlastRFValidationOutput
#validation GeneValidator::ORFValidationOutput
#validation GeneValidator::LengthClusterValidationOutput
#validation_report GeneValidator::ValidationTest
#validation_result GeneValidator::ValidationReport
#validations GeneValidator::Output
#values GeneValidator::HierarchicalClusterization
#wilcox_test GeneValidator::DuplicationValidation
#write_csv GeneValidator::OutputFiles
#write_html GeneValidator::OutputFiles
#write_json GeneValidator::OutputFiles
#write_summary GeneValidator::OutputFiles
#wss GeneValidator::Cluster
#wss GeneValidator::PairCluster
#x GeneValidator::Pair
#x GeneValidator::Pair1
#xtitle GeneValidator::Plot
#y GeneValidator::Pair
#y GeneValidator::Pair1
#ytitle GeneValidator::Plot