Module: BELParser

Defined in:

lib/bel_parser/resource/file_resource.rb,
lib/bel_parser/quoting.rb,
lib/bel_parser/version.rb,
lib/bel_parser/language.rb,
lib/bel_parser/resource.rb,
lib/bel_parser/resources.rb,
lib/bel_parser/ast_filter.rb,
lib/bel_parser/completion.rb,
lib/bel_parser/ast_generator.rb,
lib/bel_parser/script/filter.rb,
lib/bel_parser/script/parser.rb,
lib/bel_parser/parsers/tracer.rb,
lib/bel_parser/resource/value.rb,
lib/bel_parser/language/syntax.rb,
lib/bel_parser/resource/reader.rb,
lib/bel_parser/script/keywords.rb,
lib/bel_parser/parsers/ast/node.rb,
lib/bel_parser/resource/concept.rb,
lib/bel_parser/resource/dataset.rb,
lib/bel_parser/script/state/set.rb,
lib/bel_parser/script/validator.rb,
lib/bel_parser/expression/filter.rb,
lib/bel_parser/expression/parser.rb,
lib/bel_parser/language/function.rb,
lib/bel_parser/mixin/levenshtein.rb,
lib/bel_parser/script/first_node.rb,
lib/bel_parser/language/semantics.rb,
lib/bel_parser/language/signature.rb,
lib/bel_parser/mixin/line_mapping.rb,
lib/bel_parser/parsers/serializer.rb,
lib/bel_parser/resource/lru_cache.rb,
lib/bel_parser/script/state/unset.rb,
lib/bel_parser/language/amino_acid.rb,
lib/bel_parser/language/version1_0.rb,
lib/bel_parser/language/version2_0.rb,
lib/bel_parser/parsers/common/list.rb,
lib/bel_parser/resource/lru_reader.rb,
lib/bel_parser/expression/validator.rb,
lib/bel_parser/parsers/mixin/buffer.rb,
lib/bel_parser/expression/model/term.rb,
lib/bel_parser/language/relationship.rb,
lib/bel_parser/language/syntax_error.rb,
lib/bel_parser/parsers/common/string.rb,
lib/bel_parser/resource/eager_reader.rb,
lib/bel_parser/script/nanopub_mapper.rb,
lib/bel_parser/script/state_function.rb,
lib/bel_parser/language/semantics_ast.rb,
lib/bel_parser/language/specification.rb,
lib/bel_parser/language/syntax_result.rb,
lib/bel_parser/parsers/bel_script/set.rb,
lib/bel_parser/resource/sparql_reader.rb,
lib/bel_parser/language/syntax_warning.rb,
lib/bel_parser/parsers/common/function.rb,
lib/bel_parser/parsers/expression/term.rb,
lib/bel_parser/resource/concept_scheme.rb,
lib/bel_parser/script/state_aggregator.rb,
lib/bel_parser/language/semantics_match.rb,
lib/bel_parser/language/syntax_function.rb,
lib/bel_parser/parsers/bel_script/unset.rb,
lib/bel_parser/resource/jena_tdb_reader.rb,
lib/bel_parser/script/state/bel_version.rb,
lib/bel_parser/language/semantics_result.rb,
lib/bel_parser/parsers/common/blank_line.rb,
lib/bel_parser/parsers/common/identifier.rb,
lib/bel_parser/script/apply_resource_uri.rb,
lib/bel_parser/expression/model/namespace.rb,
lib/bel_parser/expression/model/parameter.rb,
lib/bel_parser/expression/model/statement.rb,
lib/bel_parser/language/semantics_warning.rb,
lib/bel_parser/parsers/expression/comment.rb,
lib/bel_parser/expression/model/annotation.rb,
lib/bel_parser/language/base_specification.rb,
lib/bel_parser/language/semantics_function.rb,
lib/bel_parser/parsers/common/comment_line.rb,
lib/bel_parser/language/term_transformation.rb,
lib/bel_parser/parsers/expression/parameter.rb,
lib/bel_parser/resource/eager_sparql_reader.rb,
lib/bel_parser/resource/file_resource_value.rb,
lib/bel_parser/resource/resource_url_reader.rb,
lib/bel_parser/language/expression_validator.rb,
lib/bel_parser/script/state/document_property.rb,
lib/bel_parser/language/semantics_ast_warnings.rb,
lib/bel_parser/language/semantics_type_warning.rb,
lib/bel_parser/parsers/bel_script/set_document.rb,
lib/bel_parser/parsers/common/multi_identifier.rb,
lib/bel_parser/parsers/expression/relationship.rb,
lib/bel_parser/language/apply_default_namespace.rb,
lib/bel_parser/language/syntax/invalid_function.rb,
lib/bel_parser/parsers/expression/observed_term.rb,
lib/bel_parser/language/apply_namespace_encoding.rb,
lib/bel_parser/script/state/namespace_definition.rb,
lib/bel_parser/language/semantics/non_object_list.rb,
lib/bel_parser/language/version1_0/functions/list.rb,
lib/bel_parser/language/version2_0/functions/list.rb,
lib/bel_parser/script/state/annotation_definition.rb,
lib/bel_parser/script/syntax/undefined_annotation.rb,
lib/bel_parser/language/syntax/undefined_namespace.rb,
lib/bel_parser/parsers/bel_script/define_namespace.rb,
lib/bel_parser/parsers/expression/nested_statement.rb,
lib/bel_parser/parsers/expression/simple_statement.rb,
lib/bel_parser/script/syntax/expression_validation.rb,
lib/bel_parser/script/syntax/invalid_regex_pattern.rb,
lib/bel_parser/language/semantics/signature_mapping.rb,
lib/bel_parser/language/syntax/invalid_relationship.rb,
lib/bel_parser/language/version1_0/functions/fusion.rb,
lib/bel_parser/language/version1_0/return_types/any.rb,
lib/bel_parser/language/version2_0/functions/fusion.rb,
lib/bel_parser/language/version2_0/return_types/any.rb,
lib/bel_parser/parsers/bel_script/define_annotation.rb,
lib/bel_parser/script/syntax/unresolvable_namespace.rb,
lib/bel_parser/language/version1_0/return_types/list.rb,
lib/bel_parser/language/version2_0/functions/variant.rb,
lib/bel_parser/language/version2_0/return_types/list.rb,
lib/bel_parser/script/syntax/unsupported_bel_version.rb,
lib/bel_parser/language/covalent_protein_modification.rb,
lib/bel_parser/language/version1_0/functions/products.rb,
lib/bel_parser/language/version1_0/functions/reaction.rb,
lib/bel_parser/language/version1_0/relationships/is_a.rb,
lib/bel_parser/language/version2_0/functions/activity.rb,
lib/bel_parser/language/version2_0/functions/fragment.rb,
lib/bel_parser/language/version2_0/functions/location.rb,
lib/bel_parser/language/version2_0/functions/products.rb,
lib/bel_parser/language/version2_0/functions/reaction.rb,
lib/bel_parser/language/version2_0/relationships/is_a.rb,
lib/bel_parser/language/semantics/function_deprecation.rb,
lib/bel_parser/language/version1_0/functions/abundance.rb,
lib/bel_parser/language/version1_0/functions/pathology.rb,
lib/bel_parser/language/version1_0/functions/reactants.rb,
lib/bel_parser/language/version1_0/return_types/fusion.rb,
lib/bel_parser/language/version1_0/value_encodings/any.rb,
lib/bel_parser/language/version2_0/functions/abundance.rb,
lib/bel_parser/language/version2_0/functions/pathology.rb,
lib/bel_parser/language/version2_0/functions/reactants.rb,
lib/bel_parser/language/version2_0/return_types/fusion.rb,
lib/bel_parser/language/version2_0/value_encodings/any.rb,
lib/bel_parser/language/semantics/list_function_subject.rb,
lib/bel_parser/language/version1_0/functions/truncation.rb,
lib/bel_parser/language/version2_0/return_types/variant.rb,
lib/bel_parser/script/syntax/undefined_annotation_value.rb,
lib/bel_parser/language/syntax/undefined_namespace_value.rb,
lib/bel_parser/language/version1_0/functions/degradation.rb,
lib/bel_parser/language/version1_0/relationships/acts_in.rb,
lib/bel_parser/language/version1_0/return_types/products.rb,
lib/bel_parser/language/version2_0/functions/degradation.rb,
lib/bel_parser/language/version2_0/functions/to_location.rb,
lib/bel_parser/language/version2_0/relationships/acts_in.rb,
lib/bel_parser/language/version2_0/return_types/activity.rb,
lib/bel_parser/language/version2_0/return_types/fragment.rb,
lib/bel_parser/language/version2_0/return_types/location.rb,
lib/bel_parser/language/version2_0/return_types/products.rb,
lib/bel_parser/parsers/expression/statement_autocomplete.rb,
lib/bel_parser/language/semantics/deeply_nested_statement.rb,
lib/bel_parser/language/semantics/multiple_subject_object.rb,
lib/bel_parser/language/version1_0/functions/substitution.rb,
lib/bel_parser/language/version1_0/relationships/includes.rb,
lib/bel_parser/language/version1_0/return_types/abundance.rb,
lib/bel_parser/language/version1_0/return_types/pathology.rb,
lib/bel_parser/language/version1_0/return_types/reactants.rb,
lib/bel_parser/language/version2_0/relationships/includes.rb,
lib/bel_parser/language/version2_0/return_types/abundance.rb,
lib/bel_parser/language/version2_0/return_types/pathology.rb,
lib/bel_parser/language/version2_0/return_types/reactants.rb,
lib/bel_parser/language/semantics/relationship_deprecation.rb,
lib/bel_parser/language/version1_0/functions/rna_abundance.rb,
lib/bel_parser/language/version1_0/functions/translocation.rb,
lib/bel_parser/language/version1_0/relationships/analogous.rb,
lib/bel_parser/language/version1_0/relationships/decreases.rb,
lib/bel_parser/language/version1_0/relationships/increases.rb,
lib/bel_parser/language/version1_0/return_types/truncation.rb,
lib/bel_parser/language/version2_0/functions/from_location.rb,
lib/bel_parser/language/version2_0/functions/rna_abundance.rb,
lib/bel_parser/language/version2_0/functions/translocation.rb,
lib/bel_parser/language/version2_0/relationships/analogous.rb,
lib/bel_parser/language/version2_0/relationships/decreases.rb,
lib/bel_parser/language/version2_0/relationships/increases.rb,
lib/bel_parser/language/version2_0/relationships/regulates.rb,
lib/bel_parser/language/version2_0/upgrades/transformation.rb,
lib/bel_parser/language/semantics/relationship_not_listable.rb,
lib/bel_parser/language/version1_0/functions/cell_secretion.rb,
lib/bel_parser/language/version1_0/functions/gene_abundance.rb,
lib/bel_parser/language/version1_0/relationships/has_member.rb,
lib/bel_parser/language/version2_0/functions/cell_secretion.rb,
lib/bel_parser/language/version2_0/functions/gene_abundance.rb,
lib/bel_parser/language/version2_0/relationships/has_member.rb,
lib/bel_parser/language/version2_0/return_types/to_location.rb,
lib/bel_parser/language/version2_0/value_encodings/activity.rb,
lib/bel_parser/language/version2_0/value_encodings/location.rb,
lib/bel_parser/language/version1_0/functions/kinase_activity.rb,
lib/bel_parser/language/version1_0/relationships/association.rb,
lib/bel_parser/language/version1_0/relationships/has_members.rb,
lib/bel_parser/language/version1_0/relationships/has_product.rb,
lib/bel_parser/language/version1_0/relationships/has_variant.rb,
lib/bel_parser/language/version1_0/relationships/orthologous.rb,
lib/bel_parser/language/version1_0/relationships/reactant_in.rb,
lib/bel_parser/language/version1_0/return_types/substitution.rb,
lib/bel_parser/language/version1_0/value_encodings/abundance.rb,
lib/bel_parser/language/version1_0/value_encodings/pathology.rb,
lib/bel_parser/language/version2_0/relationships/association.rb,
lib/bel_parser/language/version2_0/relationships/has_members.rb,
lib/bel_parser/language/version2_0/relationships/has_product.rb,
lib/bel_parser/language/version2_0/relationships/has_variant.rb,
lib/bel_parser/language/version2_0/relationships/orthologous.rb,
lib/bel_parser/language/version2_0/relationships/reactant_in.rb,
lib/bel_parser/language/version2_0/value_encodings/abundance.rb,
lib/bel_parser/language/version2_0/value_encodings/pathology.rb,
lib/bel_parser/language/semantics/non_causal_nested_statement.rb,
lib/bel_parser/language/version1_0/relationships/translocates.rb,
lib/bel_parser/language/version1_0/return_types/rna_abundance.rb,
lib/bel_parser/language/version2_0/relationships/translocates.rb,
lib/bel_parser/language/version2_0/return_types/from_location.rb,
lib/bel_parser/language/version2_0/return_types/rna_abundance.rb,
lib/bel_parser/language/version1_0/functions/complex_abundance.rb,
lib/bel_parser/language/version1_0/functions/protein_abundance.rb,
lib/bel_parser/language/version1_0/relationships/biomarker_for.rb,
lib/bel_parser/language/version1_0/relationships/has_component.rb,
lib/bel_parser/language/version1_0/relationships/translated_to.rb,
lib/bel_parser/language/version1_0/return_types/gene_abundance.rb,
lib/bel_parser/language/version2_0/functions/complex_abundance.rb,
lib/bel_parser/language/version2_0/functions/protein_abundance.rb,
lib/bel_parser/language/version2_0/relationships/biomarker_for.rb,
lib/bel_parser/language/version2_0/relationships/has_component.rb,
lib/bel_parser/language/version2_0/relationships/translated_to.rb,
lib/bel_parser/language/version2_0/return_types/gene_abundance.rb,
lib/bel_parser/language/version1_0/functions/biological_process.rb,
lib/bel_parser/language/version1_0/functions/catalytic_activity.rb,
lib/bel_parser/language/version1_0/functions/chaperone_activity.rb,
lib/bel_parser/language/version1_0/functions/gtp_bound_activity.rb,
lib/bel_parser/language/version1_0/functions/molecular_activity.rb,
lib/bel_parser/language/version1_0/functions/peptidase_activity.rb,
lib/bel_parser/language/version1_0/functions/transport_activity.rb,
lib/bel_parser/language/version1_0/relationships/has_components.rb,
lib/bel_parser/language/version1_0/relationships/sub_process_of.rb,
lib/bel_parser/language/version1_0/relationships/transcribed_to.rb,
lib/bel_parser/language/version1_0/return_types/kinase_activity.rb,
lib/bel_parser/language/version2_0/functions/biological_process.rb,
lib/bel_parser/language/version2_0/functions/molecular_activity.rb,
lib/bel_parser/language/version2_0/relationships/has_components.rb,
lib/bel_parser/language/version2_0/relationships/sub_process_of.rb,
lib/bel_parser/language/version2_0/relationships/transcribed_to.rb,
lib/bel_parser/language/version1_0/functions/composite_abundance.rb,
lib/bel_parser/language/version1_0/functions/micro_rna_abundance.rb,
lib/bel_parser/language/version1_0/value_encodings/rna_abundance.rb,
lib/bel_parser/language/version2_0/functions/composite_abundance.rb,
lib/bel_parser/language/version2_0/functions/micro_rna_abundance.rb,
lib/bel_parser/language/version2_0/value_encodings/rna_abundance.rb,
lib/bel_parser/language/semantics/nested_statement_without_object.rb,
lib/bel_parser/language/version1_0/functions/phosphatase_activity.rb,
lib/bel_parser/language/version1_0/functions/protein_modification.rb,
lib/bel_parser/language/version1_0/relationships/causes_no_change.rb,
lib/bel_parser/language/version1_0/relationships/has_modification.rb,
lib/bel_parser/language/version1_0/return_types/complex_abundance.rb,
lib/bel_parser/language/version1_0/return_types/protein_abundance.rb,
lib/bel_parser/language/version1_0/upgrades/fusion_transformation.rb,
lib/bel_parser/language/version1_0/value_encodings/gene_abundance.rb,
lib/bel_parser/language/version2_0/functions/protein_modification.rb,
lib/bel_parser/language/version2_0/relationships/causes_no_change.rb,
lib/bel_parser/language/version2_0/relationships/has_modification.rb,
lib/bel_parser/language/version2_0/return_types/complex_abundance.rb,
lib/bel_parser/language/version2_0/return_types/protein_abundance.rb,
lib/bel_parser/language/version2_0/value_encodings/gene_abundance.rb,
lib/bel_parser/language/version1_0/functions/ribosylation_activity.rb,
lib/bel_parser/language/version1_0/return_types/biological_process.rb,
lib/bel_parser/language/version1_0/return_types/catalytic_activity.rb,
lib/bel_parser/language/version1_0/return_types/chaperone_activity.rb,
lib/bel_parser/language/version1_0/return_types/gtp_bound_activity.rb,
lib/bel_parser/language/version1_0/return_types/molecular_activity.rb,
lib/bel_parser/language/version1_0/return_types/peptidase_activity.rb,
lib/bel_parser/language/version1_0/return_types/transport_activity.rb,
lib/bel_parser/language/version2_0/return_types/biological_process.rb,
lib/bel_parser/language/version2_0/return_types/molecular_activity.rb,
lib/bel_parser/language/version1_0/relationships/directly_decreases.rb,
lib/bel_parser/language/version1_0/relationships/directly_increases.rb,
lib/bel_parser/language/version1_0/return_types/micro_rna_abundance.rb,
lib/bel_parser/language/version1_0/upgrades/activity_transformation.rb,
lib/bel_parser/language/version2_0/relationships/directly_decreases.rb,
lib/bel_parser/language/version2_0/relationships/directly_increases.rb,
lib/bel_parser/language/version2_0/return_types/micro_rna_abundance.rb,
lib/bel_parser/language/version1_0/functions/cell_surface_expression.rb,
lib/bel_parser/language/version1_0/return_types/phosphatase_activity.rb,
lib/bel_parser/language/version1_0/return_types/protein_modification.rb,
lib/bel_parser/language/version1_0/upgrades/variation_transformation.rb,
lib/bel_parser/language/version1_0/value_encodings/complex_abundance.rb,
lib/bel_parser/language/version1_0/value_encodings/protein_abundance.rb,
lib/bel_parser/language/version2_0/functions/cell_surface_expression.rb,
lib/bel_parser/language/version2_0/return_types/protein_modification.rb,
lib/bel_parser/language/version2_0/value_encodings/complex_abundance.rb,
lib/bel_parser/language/version2_0/value_encodings/protein_abundance.rb,
lib/bel_parser/language/version1_0/functions/transcriptional_activity.rb,
lib/bel_parser/language/version1_0/relationships/negative_correlation.rb,
lib/bel_parser/language/version1_0/relationships/positive_correlation.rb,
lib/bel_parser/language/version1_0/return_types/ribosylation_activity.rb,
lib/bel_parser/language/version1_0/value_encodings/biological_process.rb,
lib/bel_parser/language/version2_0/relationships/negative_correlation.rb,
lib/bel_parser/language/version2_0/relationships/positive_correlation.rb,
lib/bel_parser/language/version2_0/value_encodings/biological_process.rb,
lib/bel_parser/language/version1_0/relationships/rate_limiting_step_of.rb,
lib/bel_parser/language/version1_0/value_encodings/micro_rna_abundance.rb,
lib/bel_parser/language/version2_0/relationships/rate_limiting_step_of.rb,
lib/bel_parser/language/version2_0/value_encodings/micro_rna_abundance.rb,
lib/bel_parser/language/version2_0/value_encodings/protein_modification.rb,
lib/bel_parser/language/version1_0/return_types/transcriptional_activity.rb,
lib/bel_parser/language/version1_0/upgrades/translocation_transformation.rb,
lib/bel_parser/language/version1_0/relationships/prognostic_biomarker_for.rb,
lib/bel_parser/language/version2_0/relationships/prognostic_biomarker_for.rb,
lib/bel_parser/language/version1_0/upgrades/protein_modification_transformation.rb

Overview

FileResourceValue is a Value obtained from a Annotation or Namespace file.

Defined Under Namespace

Modules: Completion, Expression, Language, Levenshtein, LineMapping, Parsers, Quoting, Resource, Resources, Script, Version Classes: ASTFilter, ASTGenerator