Identifier Index

[ A B C D E F G H I J K L M N O P Q R S T U V W X Y Z _ ]

A

add_atom() (in PDB)	add_valid_external_entity_relation_participant_attribute_type() (in BianaDBaccess)	addUserEntitiesToGroup() (in UserEntitySet)
add_atom() (in PDBResidue)	add_valid_external_entity_relation_participant_attribute_type() (in BianaDatabase)	addUserEntityId() (in UserEntitySet)
add_attribute() (in ExternalEntity)	add_valid_external_entity_relation_type() (in BianaDBaccess)	addUserEntityRelation() (in UserEntitySet)
add_autoincrement_columns() (in DB)	add_valid_external_entity_relation_type() (in BianaDatabase)	addValue() (in XMLNode)
add_database() (in UnificationProtocol)	add_valid_external_entity_relation_type() (in ExternalDatabase)	addXRefAttributesToExternalEntityObject() (in Psi_MiFormattedDBParser)
add_element() (in SQLSelectStatement)	add_valid_external_entity_type() (in BianaDBaccess)	administration (in biana.biana_commands')
add_element() (in Ontology)	add_valid_external_entity_type() (in BianaDatabase)	allowed_formats (in FormattedFileProcessor)
add_external_entity_relation() (in UserEntityRelation)	add_valid_external_entity_type() (in ExternalDatabase)	aminoacid_codes_3to1 (in ProteinSequence)
add_field() (in TableDB)	add_valid_identifier_reference_type() (in BianaDatabase)	append_html_table_values() (in biana.BianaObjects.output_utilities)
add_hssp_info_to_pdb() (in BianaDBaccess)	add_valid_identifier_reference_types() (in BianaDBaccess)	append_sequence() (in SequenceAlignment)
add_indice() (in TableDB)	addChild() (in XMLNode)	append_sequence_fragments() (in SequenceAlignment)
add_match() (in CDHITCluster)	addEntry() (in Psi_MiXMLParser)	ascii_to_float() (in biana.utilities.int_ascii)
add_participant() (in ExternalEntityRelation)	addExperiment() (in Psi_MiEntry)	ascii_to_float_list() (in biana.utilities.int_ascii)
add_participant_attribute() (in ExternalEntityRelation)	addExternalEntity() (in UserEntity)	ascii_to_int() (in biana.utilities.int_ascii)
add_participant_attributes_to_relation() (in BiopaxPhysicalEntityParticipant)	addInteraction() (in Psi_MiEntry)	ascii_to_int_list() (in biana.utilities.int_ascii)
add_participants_to_eEr() (in BiopaxPathwayStep)	addInteractor() (in Psi_MiEntry)	ascii_to_unsigned_float() (in biana.utilities.int_ascii)
add_residue() (in PDB)	addNameAttributesToExternalEntityObject() (in Psi_MiFormattedDBParser)	ascii_to_unsigned_float_list() (in biana.utilities.int_ascii)
add_sequence_to_position() (in SequenceAlignment)	addParticipant() (in Psi_MiInteraction)	ascii_to_unsigned_int() (in biana.utilities.int_ascii)
add_table() (in Database)	addRestriction() (in UserEntitySet)	ascii_to_unsigned_int_list() (in biana.utilities.int_ascii)
add_to_log() (in BianaParser)	addResult() (in BianaReport)	ATTRIBUTE_IDENTIFIER_TO_OBJECT (in biana.BianaObjects.ExternalEntityAttribute')
add_unification_atom_elements() (in UnificationProtocol)	addResultToReport() (in BianaSessionManager)	autoincrement (in biana.utilities.autoincrement')
add_valid_external_entity_attribute_type() (in BianaDBaccess)	addTagToSelectedUE() (in UserEntitySet)	autoincrement' (in biana.utilities)
add_valid_external_entity_attribute_type() (in BianaDatabase)	addTagToSelectedUER() (in UserEntitySet)	available_sessions (in biana.biana_commands')
add_valid_external_entity_attribute_type() (in ExternalDatabase)	addText() (in BianaReport)
add_valid_external_entity_relation_attribute_type() (in ExternalDatabase)	addTextToReport() (in BianaSessionManager)

B

biana	biopax_objects_dict (in BiopaxLevel2Handler)	BiopaxPathwayStep (in biana.BianaParser.biopaxLevel2Parser)
biana_commands' (in biana)	BiopaxBiochemicalReaction (in biana.BianaParser.biopaxLevel2Parser)	BiopaxPhysicalEntity (in biana.BianaParser.biopaxLevel2Parser)
biana_globals (in biana)	BiopaxBioSource (in biana.BianaParser.biopaxLevel2Parser)	BiopaxPhysicalEntityParticipant (in biana.BianaParser.biopaxLevel2Parser)
biana_path (in biana.BianaParser.database2biana)	BiopaxCatalysis (in biana.BianaParser.biopaxLevel2Parser)	BiopaxPhysicalInteraction (in biana.BianaParser.biopaxLevel2Parser)
BIANA_SOURCE_CODE_VERSION (in biana.BianaDB.BianaDBaccess')	BiopaxComplex (in biana.BianaParser.biopaxLevel2Parser)	BiopaxProtein (in biana.BianaParser.biopaxLevel2Parser)
BianaDatabase (in biana.BianaDB.BianaDatabaseDefinition)	BiopaxComplexAssembly (in biana.BianaParser.biopaxLevel2Parser)	BiopaxRNA (in biana.BianaParser.biopaxLevel2Parser)
BianaDatabaseDefinition (in biana.BianaDB)	BiopaxControl (in biana.BianaParser.biopaxLevel2Parser)	BiopaxSmallMolecule (in biana.BianaParser.biopaxLevel2Parser)
BianaDB (in biana)	BiopaxConversion (in biana.BianaParser.biopaxLevel2Parser)	BiopaxTransport (in biana.BianaParser.biopaxLevel2Parser)
BianaDB_globals (in biana.BianaDB)	BiopaxDataSource (in biana.BianaParser.biopaxLevel2Parser)	BiopaxXREF (in biana.BianaParser.biopaxLevel2Parser)
BianaDBaccess (in biana.BianaDB.BianaDBaccess')	BiopaxDNA (in biana.BianaParser.biopaxLevel2Parser)	BL2SEQ_EXEC (in biana.biana_globals)
BianaDBaccess' (in biana.BianaDB)	BiopaxEntity (in biana.BianaParser.biopaxLevel2Parser)	blast_cd_hit_clusters() (in biana.BianaObjects.sequenceUtilities)
BianaObjects (in biana)	BiopaxInteraction (in biana.BianaParser.biopaxLevel2Parser)	blast_sequence() (in biana.BianaObjects.sequenceUtilities)
BianaParser (in biana)	BiopaxLevel2Handler (in BiopaxLevel2Parser)	BLASTALL_EXEC (in biana.biana_globals)
bianaParser (in biana.BianaParser)	biopaxLevel2Parser (in biana.BianaParser)	BlastallParserIterator (in biana.BianaObjects.sequenceUtilities)
BianaParser (in biana.BianaParser.bianaParser)	BiopaxLevel2Parser (in biana.BianaParser.biopaxLevel2Parser)	BlastResult (in biana.BianaObjects)
BianaReport (in biana.BianaObjects)	BiopaxLevel2XMLParser (in BiopaxLevel2Parser)	BlastResult (in biana.BianaObjects.BlastResult)
BianaReport (in biana.BianaObjects.BianaReport)	BiopaxModulation (in biana.BianaParser.biopaxLevel2Parser)	Buffer (in biana.BianaDB.ConnectorDB)
BianaSessionManager (in biana.BianaObjects)	BiopaxOpenControlledVocabulary (in biana.BianaParser.biopaxLevel2Parser)	BufferElement (in biana.BianaDB.ConnectorDB)
BianaSessionManager (in biana.BianaObjects.BianaSessionManager)	BiopaxPathway (in biana.BianaParser.biopaxLevel2Parser)

C

CD_HIT_PATH (in biana.biana_globals)	close() (in BianaSessionManager)	create_biana_database() (in administration)
CDHIT (in biana.BianaObjects)	close() (in BianaParser)	create_database() (in BianaDBaccess)
CDHITCluster (in biana.BianaObjects.CDHIT)	close() (in OutBianaInterface)	create_graph() (in biana.GraphUtilities.GraphUtilities)
CDHITMatch (in biana.BianaObjects.CDHIT)	close() (in biana.biana_commands')	create_graph_with_same_type() (in biana.GraphUtilities.GraphUtilities)
characters() (in BiopaxLevel2Handler)	closeReport() (in BianaReport)	create_mysql_query() (in TableDB)
characters() (in Psi_MiHandler)	closeReport() (in BianaSessionManager)	create_network() (in BianaSessionManager)
check_consistency_with_given_source_version() (in DB)	CLUSTALW_EXEC (in biana.biana_globals)	create_new_session() (in biana.biana_commands')
check_database() (in DB)	cluster_user_entities() (in BianaSessionManager)	create_new_user_entities() (in BianaDBaccess)
check_database() (in administration)	cogParser (in biana.BianaParser)	create_new_user_entity_set() (in BianaSessionManager)
check_time() (in STRINGParser)	CogParser (in biana.BianaParser.cogParser)	create_randomized_user_entity_set() (in BianaSessionManager)
checkOrInsertDBNamePrefix() (in Psi_MiFormattedDBParser)	concatenate_alignments() (in SequenceAlignment)	create_specific_database_tables() (in BianaDatabase)
clean_empty_sequences() (in SequenceAlignment)	concatenate_by_crossID() (in SequenceAlignment)	create_unification_protocol() (in administration)
clear_selected_user_entity_sets() (in BianaSessionManager)	connect_to_socket() (in OutBianaInterface)	credits (in biana)
clear_user_entity_relation_selection() (in UserEntitySet)	ConnectorDB (in biana.BianaDB)	CROSSABLE_ATTRIBUTES (in biana.biana_globals)
clear_user_entity_selection() (in UserEntitySet)	containsExternalEntity() (in UserEntity)	current_dir (in biana.BianaParser.database2biana)
close() (in BianaDBaccess)	controlled_relations (in BiopaxEntity)	current_file (in biana.BianaParser.database2biana)
close() (in DB)	copyright (in biana)	current_path_index (in biana.BianaParser.database2biana)

D

database (in biana.BianaDB)	DBUSER (in biana.biana_globals)	description (in KeggLigandParser)
Database (in biana.BianaDB.database)	DEBUG_BUFFER_INSERT_SINGLE (in biana.BianaDB.ConnectorDB)	description (in NcbiGenPeptParserGenpeptParser)
database (in BiopaxEntity)	DEBUG_PRINT_INSERT_QUERY (in biana.BianaDB.ConnectorDB)	description (in NrParser)
database2biana (in biana.BianaParser)	debug_web (in biana.BianaDB.BianaDBaccess')	description (in PFAMParser)
DATABASE_HOST (in biana.BianaDB.BianaDB_globals)	decideAliasTypeSpecificConversions() (in Psi_MiFormattedDBParser)	description (in Psi_MiFormattedDBParser)
DATABASE_NAME (in biana.BianaDB.BianaDB_globals)	decideDBReferenceSpecificConversions() (in Psi_MiFormattedDBParser)	description (in PSIMIOBOParser)
DATABASE_PASSWORD (in biana.BianaDB.BianaDB_globals)	decideInteractorTypeSpecificConversions() (in Psi_MiFormattedDBParser)	description (in SCOPParser)
DATABASE_PORT (in biana.BianaDB.BianaDB_globals)	decideRoleSpecificConversions() (in Psi_MiFormattedDBParser)	description (in STRINGParser)
DATABASE_SOCKET (in biana.BianaDB.BianaDB_globals)	decideSequenceTypeSpecificConversions() (in Psi_MiFormattedDBParser)	description (in TaxonomyParser)
DATABASE_USER (in biana.BianaDB.BianaDB_globals)	delete_biana_database() (in administration)	description (in UniprotParser)
datatype_operations (in BiopaxEntity)	delete_unification_protocol() (in administration)	detectIdentifierType() (in BianaSessionManager)
datatype_operations (in BiopaxLevel2Handler)	deliver_error_message() (in BianaSessionManager)	DICT_METHOD_CONVERSION_GRID_TO_PSI_MI (in biana.BianaParser.psi_Mi25Parser)
datatype_to_biana_type (in BiopaxEntity)	describe_user_entity_set() (in BianaSessionManager)	dictDBNameToPrefix (in Psi_MiFormattedDBParser)
datatype_to_biana_type (in STRINGParser)	description (in GenericParser)	dictionary (in DNASequence)
DB (in biana.BianaDB.ConnectorDB)	description (in MyDataParser)	dictionary (in ProteinSequence)
dbaccess (in BiopaxEntity)	description (in BiopaxLevel2Parser)	dictionary (in RNASequence)
DBHOST (in biana.biana_globals)	description (in CogParser)	DNASequence (in biana.BianaObjects.Sequence)
DBNAME (in biana.biana_globals)	description (in GOOBOParser)	drop_unification_protocol() (in BianaDBaccess)
DBPASS (in biana.biana_globals)	description (in HGNCParser)	DSSP_EXEC (in biana.biana_globals)
DBPORT (in biana.biana_globals)	description (in IPIParser)	duplicate_user_entity_set() (in BianaSessionManager)
DBReference (in biana.BianaParser.psi_MiXMLParser)	description (in KeggGeneParser)
DBSOCKET (in biana.biana_globals)	description (in KeggKOParser)

E

empty_temporal_table_sql_query() (in TableDB)	external_entity_definition (in UniprotParser)	external_entity_relations (in PSIMIOBOParser)
endDocument() (in BiopaxLevel2Handler)	EXTERNAL_ENTITY_DESCRIPTIVE_ATTRIBUTE_TYPES (in biana.biana_globals)	external_entity_relations (in SCOPParser)
endElement() (in BiopaxLevel2Handler)	EXTERNAL_ENTITY_DESCRIPTIVE_SEARCHABLE_ATTRIBUTE_TYPES (in biana.biana_globals)	external_entity_relations (in STRINGParser)
endElement() (in Psi_MiHandler)	EXTERNAL_ENTITY_GENERAL_ATTRIBUTES (in biana.biana_globals)	external_entity_relations (in TaxonomyParser)
Enum (in biana.BianaObjects.BianaSessionManager)	EXTERNAL_ENTITY_IDENTIFIER_ATTRIBUTES (in biana.biana_globals)	external_entity_relations (in UniprotParser)
expand_user_entity_set() (in BianaSessionManager)	EXTERNAL_ENTITY_NUMERIC_ATTRIBUTE_TYPES (in biana.biana_globals)	EXTERNAL_ENTITY_SPECIAL_ATTRIBUTE_TYPES (in biana.biana_globals)
external_entity_definition (in GenericParser)	external_entity_relation_id_col (in BianaDatabase)	EXTERNAL_ENTITY_TYPES (in biana.biana_globals)
external_entity_definition (in MyDataParser)	EXTERNAL_ENTITY_RELATION_PARTICIPANT_ATTRIBUTE_TYPES (in biana.biana_globals)	EXTERNAL_ENTITY_VERSIONABLE_IDENTIFIER_ATTRIBUTE_TYPES (in biana.biana_globals)
external_entity_definition (in BiopaxLevel2Parser)	external_entity_relation_participant_id_col (in BianaDatabase)	ExternalDatabase (in biana.BianaObjects.ExternalDatabase')
external_entity_definition (in CogParser)	EXTERNAL_ENTITY_RELATION_TYPES (in biana.biana_globals)	ExternalDatabase' (in biana.BianaObjects)
external_entity_definition (in GOOBOParser)	external_entity_relations (in GenericParser)	externalDatabaseID_col (in BianaDatabase)
external_entity_definition (in HGNCParser)	external_entity_relations (in MyDataParser)	externalDatabaseID_col_type (in BianaDatabase)
external_entity_definition (in IPIParser)	external_entity_relations (in BiopaxLevel2Parser)	ExternalEntity (in biana.BianaObjects.ExternalEntity')
external_entity_definition (in KeggGeneParser)	external_entity_relations (in CogParser)	ExternalEntity' (in biana.BianaObjects)
external_entity_definition (in KeggKOParser)	external_entity_relations (in GOOBOParser)	ExternalEntityAttribute (in biana.BianaObjects.ExternalEntityAttribute')
external_entity_definition (in KeggLigandParser)	external_entity_relations (in HGNCParser)	ExternalEntityAttribute' (in biana.BianaObjects)
external_entity_definition (in NcbiGenPeptParserGenpeptParser)	external_entity_relations (in IPIParser)	externalEntityID_col (in BianaDatabase)
external_entity_definition (in NrParser)	external_entity_relations (in KeggGeneParser)	externalEntityID_col_type (in BianaDatabase)
external_entity_definition (in PFAMParser)	external_entity_relations (in KeggKOParser)	ExternalEntityRelation (in biana.BianaObjects.ExternalEntityRelation')
external_entity_definition (in Psi_MiFormattedDBParser)	external_entity_relations (in KeggLigandParser)	ExternalEntityRelation' (in biana.BianaObjects)
external_entity_definition (in PSIMIOBOParser)	external_entity_relations (in NcbiGenPeptParserGenpeptParser)	ExternalEntityRelationAttribute (in biana.BianaObjects.ExternalEntityRelationAttribute')
external_entity_definition (in SCOPParser)	external_entity_relations (in NrParser)	ExternalEntityRelationAttribute' (in biana.BianaObjects)
external_entity_definition (in STRINGParser)	external_entity_relations (in PFAMParser)	ExternalEntityRelationParticipantAttribute (in biana.BianaObjects.ExternalEntityRelationParticipantAttribute')
external_entity_definition (in TaxonomyParser)	external_entity_relations (in Psi_MiFormattedDBParser)	ExternalEntityRelationParticipantAttribute' (in biana.BianaObjects)

F

G

gaps_re (in BlastallParserIterator)	get_hssp_accessibility() (in PDBResidue)	get_subalignment() (in SequenceAlignment)
GenericParser (in biana.BianaParser)	get_hssp_conservation() (in PDBResidue)	get_subalignment_for_sequence_without_gaps() (in SequenceAlignment)
GenericParser (in biana.BianaParser.GenericParser)	get_hssp_entropy() (in PDBResidue)	get_summary_str_list() (in UnificationProtocol)
get() (in Enum)	get_hssp_norm_entropy() (in PDBResidue)	get_table_name() (in TableDB)
get_accessibility() (in PDB)	get_hssp_variability() (in PDBResidue)	get_tables() (in BianaDatabase)
get_aligned_sequence() (in SequenceAlignment)	get_html_table() (in biana.BianaObjects.output_utilities)	get_tables() (in Database)
get_alignment() (in BianaDBaccess)	get_html_table_foot() (in biana.BianaObjects.output_utilities)	get_tabulated_table() (in biana.BianaObjects.output_utilities)
get_alignment() (in SequenceAlignment)	get_html_table_header() (in biana.BianaObjects.output_utilities)	get_taxonomies_from_species_name() (in BianaDBaccess)
get_alignment_length() (in SequenceAlignment)	get_id() (in ExternalDatabase)	get_taxonomy_names_taxID_dict() (in BianaDBaccess)
get_all_external_entity_ids() (in Ontology)	get_id() (in ExternalEntity)	get_temp_table() (in TableDB)
get_all_linked_attributes() (in Ontology)	get_id() (in UnificationProtocol)	get_temp_table_name() (in TableDB)
get_all_paths_from() (in biana.GraphUtilities.GraphUtilities)	get_id_type() (in biana.utilities.utilities)	get_type() (in ExternalEntity)
get_all_tables() (in Database)	get_in_pdb_format() (in PDB)	get_type() (in PDBAtom)
get_all_user_entity_relation_tags() (in UserEntitySet)	get_intersection_of_user_entity_set_list() (in BianaSessionManager)	get_type() (in Sequence)
get_all_user_entity_tags() (in UserEntitySet)	get_leafs() (in Ontology)	get_unconnected_nodes() (in UserEntitySet)
get_aminoacid_code_3to1() (in ProteinSequence)	get_length() (in Sequence)	get_unification_atom_elements() (in UnificationProtocol)
get_analyze_query() (in TableDB)	get_letter() (in Enum)	get_unification_protocol_atoms() (in BianaDBaccess)
get_atoms() (in PDBResidue)	get_level() (in UserEntitySet)	get_unification_protocol_atoms() (in administration)
get_attribute() (in ExternalEntity)	get_linked_attr_and_description_tuples() (in Ontology)	get_union_of_user_entity_set_list() (in BianaSessionManager)
get_attribute_data_type() (in BianaDatabase)	get_list_external_entities_IDs_by_attribute() (in BianaDBaccess)	get_user_entities_for_tag() (in UserEntitySet)
get_attributes_dict() (in ExternalEntity)	get_list_user_entities_IDs_by_attribute() (in BianaDBaccess)	get_user_entity() (in BianaSessionManager)
get_available_external_entity_attributes() (in administration)	get_log_string() (in BianaParser)	get_user_entity_attributes() (in BianaDBaccess)
get_available_external_entity_relation_types() (in administration)	get_matches() (in CDHITCluster)	get_user_entity_id_and_type_tuple_list() (in BianaDBaccess)
get_available_external_entity_types() (in administration)	get_mean_distance() (in PDBResidue)	get_user_entity_ids() (in UserEntitySet)
get_available_ontology_names() (in BianaDBaccess)	get_min_distance() (in PDBResidue)	get_user_entity_ids_by_linker_degree_cutoff() (in UserEntitySet)
get_available_parsers() (in administration)	get_mysql_query() (in FieldDB)	get_user_entity_relations() (in BianaDBaccess)
get_available_parsers_info() (in biana.BianaParser.database2biana)	get_name() (in ExternalDatabase)	get_user_entity_relations_by_sharing_attributes() (in BianaDBaccess)
get_available_unification_protocols_list() (in BianaDBaccess)	get_name() (in PDB)	get_user_entity_set() (in BianaSessionManager)
get_biana_data_type() (in BiopaxLevel2Handler)	get_name() (in PDBAtom)	get_user_entity_set_attribute_network() (in BianaSessionManager)
get_buffer() (in Buffer)	get_new_user_entity_set_from_user_entities() (in BianaSessionManager)	get_user_entity_tags() (in UserEntitySet)
get_buffer_element() (in Buffer)	get_next_autoincrement() (in DB)	get_user_entity_type() (in BianaDBaccess)
get_ca_distance() (in PDBResidue)	get_node_degree() (in UserEntitySet)	get_user_friendly_name() (in FieldDB)
get_cb_distance() (in PDBResidue)	get_norm_entropy() (in PDB)	get_valid_external_entity_attribute_type() (in ExternalDatabase)
get_cd_hit_clusters() (in biana.BianaObjects.sequenceUtilities)	get_not_optimized_query() (in FieldDB)	get_valid_external_entity_relation_attribute_type() (in ExternalDatabase)
get_chain() (in PDBFragment)	get_num() (in PDBAtom)	get_valid_external_entity_relation_type() (in ExternalDatabase)
get_chain_names() (in PDB)	get_num_atoms() (in PDB)	get_valid_external_entity_relation_types() (in BianaDBaccess)
get_chain_num_atoms() (in PDB)	get_num_atoms() (in PDBResidue)	get_valid_external_entity_relation_types() (in BianaDatabase)
get_clean_sequence() (in biana.utilities.utilities)	get_num_residues() (in PDB)	get_valid_external_entity_type() (in ExternalDatabase)
get_clustalw_alignment() (in biana.BianaObjects.sequenceUtilities)	get_number_atoms() (in PDBResidue)	get_valid_external_entity_types() (in BianaDBaccess)
get_connected_components() (in biana.GraphUtilities.GraphUtilities)	get_number_of_distinct_edges() (in biana.GraphUtilities.GraphUtilities)	get_valid_external_entity_types() (in BianaDatabase)
get_conservation() (in PDB)	get_number_of_sequences() (in SequenceAlignment)	get_valid_external_entity_types() (in ExternalEntity)
get_contacting_pairs_indices() (in PDB)	get_ontology() (in BianaDBaccess)	get_valid_relation_types() (in ExternalEntityRelation)
get_coordinates() (in PDBAtom)	get_ontology() (in BianaSessionManager)	get_variability() (in PDB)
get_data_type() (in FieldDB)	get_optimize_queries() (in TableDB)	get_version() (in ExternalDatabase)
get_database_ids() (in UnificationProtocol)	get_optimized_data_type() (in FieldDB)	get_x() (in PDBAtom)
get_default_eE_attribute() (in ExternalDatabase)	get_optimized_field_name() (in FieldDB)	get_xml() (in Ontology)
get_default_external_entity_ids() (in BianaDBaccess)	get_optimized_space() (in FieldDB)	get_y() (in PDBAtom)
get_defined_node_attributes() (in BianaSessionManager)	get_optimized_table() (in FieldDB)	get_z() (in PDBAtom)
get_defined_node_attributes_helper() (in BianaSessionManager)	get_parents_ids() (in Ontology)	getAllPathsFrom() (in UserEntitySet)
get_descendants() (in Ontology)	get_parsed_file() (in ExternalDatabase)	getChild() (in XMLNode)
get_description() (in ExternalDatabase)	get_parsing_date() (in ExternalDatabase)	getChilds() (in XMLNode)
get_description() (in UnificationProtocol)	get_parsing_time() (in ExternalDatabase)	getColumns() (in BufferElement)
get_distance() (in PDBAtom)	get_part_parents_ids() (in Ontology)	getEntries() (in Psi_MiXMLParser)
get_distances() (in PDB)	get_participant_attribute() (in ExternalEntityRelation)	getExperiments() (in Psi_MiEntry)
get_drop_query() (in TableDB)	get_participant_attributes() (in ExternalEntityRelation)	getIndexOfFirstOccurenceOfDigit() (in Psi_MiFormattedDBParser)
get_drop_sql_query() (in Database)	get_participant_external_entity_ids_list() (in ExternalEntityRelation)	getInteractions() (in Psi_MiEntry)
get_dssp() (in PDB)	get_path_network() (in biana.GraphUtilities.GraphUtilities)	getInteractors() (in Psi_MiEntry)
get_dssp() (in PDBResidue)	get_pdb_summary() (in PDB)	getIntersectionWithGivenUserEntitySet() (in UserEntitySet)
get_dssp_accessibility() (in PDB)	get_promiscuity() (in ExternalDatabase)	getNetwork() (in UserEntitySet)
get_dssp_as_horiz() (in PDB)	get_proteinIP() (in ProteinSequence)	getNodeLevel() (in UserEntitySet)
get_dssp_ss() (in PDB)	get_proteinMW() (in ProteinSequence)	getNodeLevelDict() (in UserEntitySet)
get_end_residue() (in PDBFragment)	get_query_coverage() (in BlastResult)	getNumberEdges() (in UserEntitySet)
get_entropy() (in PDB)	get_rel_dssp_accessibility() (in PDB)	getPathLengthNetwork() (in UserEntitySet)
get_equivalent_user_entities_from_list() (in BianaDBaccess)	get_relation_type() (in ExternalEntityRelation)	getRelationIds() (in UserEntitySet)
get_expanded_entity_relations() (in BianaDBaccess)	get_relations_hierarchy() (in BianaDBaccess)	getRelations() (in UserEntitySet)
get_external_attribute_list() (in UnificationAtomElement)	get_representant() (in CDHITCluster)	getRelationsBetweenGivenUserEntities() (in UserEntitySet)
get_external_database() (in BianaDBaccess)	get_residue_num() (in PDBResidue)	getRelationSelectionSize() (in UserEntitySet)
get_external_database_list() (in BianaDBaccess)	get_residue_type() (in PDBResidue)	getRelationsOfSelectedUserEntities() (in UserEntitySet)
get_external_entities_dict() (in BianaDBaccess)	get_residues() (in PDB)	getRestrictions() (in UserEntitySet)
get_external_entities_dict_by_attribute() (in BianaDBaccess)	get_sbjct_coverage() (in BlastResult)	getSelectedUserEntities() (in UserEntitySet)
get_external_entity_relation_ids() (in UserEntitySet)	get_selected_user_entity_set_ids() (in BianaSessionManager)	getSelectedUserEntityRelations() (in UserEntitySet)
get_external_entity_relation_ids_set() (in UserEntityRelation)	get_sequence() (in PDB)	getSelectionSize() (in UserEntitySet)
get_external_entity_relation_participants() (in UserEntitySet)	get_sequence() (in Sequence)	getShortestPathBetween() (in UserEntitySet)
get_external_entity_relation_tags() (in UserEntitySet)	get_sequence_fragments() (in SequenceAlignment)	getSize() (in BufferElement)
get_external_entity_relations_for_tag() (in UserEntitySet)	get_sequence_fragments_by_id() (in SequenceAlignment)	getSize() (in UserEntity)
get_externalDatabaseID_A() (in UnificationAtomElement)	get_sequence_fragments_by_pos() (in SequenceAlignment)	getSize() (in UserEntitySet)
get_externalDatabaseID_B() (in UnificationAtomElement)	get_sequence_fragments_in_ascii() (in SequenceAlignment)	getTable() (in BufferElement)
get_externalDatabaseIDs() (in UnificationAtomElement)	get_sequence_from_sequenceID() (in BianaDBaccess)	GetTableNames() (in DB)
get_externalEntitiesIds_set() (in UserEntity)	get_sequence_MD5() (in Sequence)	getTagLinkageDegree() (in UserEntitySet)
get_field() (in TableDB)	get_sequence_taxonomies() (in BianaDBaccess)	getUnionWithGivenUserEntitySet() (in UserEntitySet)
get_field() (in ExternalEntityAttribute)	get_sequenceID() (in Sequence)	getUserEntityGroups() (in UserEntitySet)
get_field_conditions_A() (in UnificationAtomElement)	get_shortest_path_between() (in biana.GraphUtilities.GraphUtilities)	getUserEntitySecondaryTagLinkageDegree() (in UserEntitySet)
get_field_conditions_B() (in UnificationAtomElement)	get_source_database() (in ExternalEntity)	getUserEntityTagConnectedMetrics() (in UserEntitySet)
get_field_cross_references() (in UnificationAtomElement)	get_species_ordered_alignment() (in SequenceAlignment)	getUserEntityTagLinkageDegree() (in UserEntitySet)
get_field_name() (in FieldDB)	get_sql_query() (in BianaDatabase)	getValue() (in XMLNode)
get_fields() (in TableDB)	get_sql_query() (in Database)	getValues() (in BufferElement)
get_foreign_key_mysql_query() (in FieldDB)	get_SQLSearchStatement() (in TableDB)	gooboParser (in biana.BianaParser)
get_fragmented_sequence() (in Sequence)	get_SQLSelectStatement() (in TableDB)	GOOBOParser (in biana.BianaParser.gooboParser)
get_group_user_entities() (in UserEntitySet)	get_start_residue() (in PDBFragment)	GraphUtilities (in biana)
get_groups_ids() (in UserEntitySet)	get_sub_user_entity_set() (in BianaSessionManager)	GraphUtilities (in biana.GraphUtilities)

H

has_element() (in Ontology)	has_indice() (in TableDB)	hasTag() (in UserEntitySet)
has_external_entity_type() (in ExternalDatabase)	has_optimized_fields() (in TableDB)	help (in biana)
has_field() (in TableDB)	has_tag() (in UserEntitySet)	hgncParser (in biana.BianaParser)
has_group() (in UserEntitySet)	has_user_entity() (in UserEntitySet)	HGNCParser (in biana.BianaParser.hgncParser)

I

identities_re (in BlastallParserIterator)	insert_pdb_object() (in BianaDBaccess)	is_valid_external_entity_relation_type() (in BianaDatabase)
ignorableWhitespace() (in Psi_MiHandler)	insert_values() (in BufferElement)	is_valid_external_entity_type() (in BianaDatabase)
imports (in biana.BianaParser.database2biana)	insertKeyIntoHistogramDictionary() (in biana.BianaParser.psi_Mi25Parser)	is_valid_identifier_reference_type() (in BianaDatabase)
includes() (in PDBFragment)	int_ascii (in biana.utilities)	isFullTextSearchable() (in ExternalEntityAttribute)
initialize_input_file_descriptor() (in BianaParser)	int_list_to_ascii() (in biana.utilities.int_ascii)	isIdentifierType() (in ExternalEntityAttribute)
initReport() (in BianaSessionManager)	int_to_ascii() (in biana.utilities.int_ascii)	isNetworkCreated() (in UserEntitySet)
insert2buffer() (in Buffer)	intervals_query_re (in BlastallParserIterator)	isNumericAttribute() (in ExternalEntityAttribute)
insert_alignment() (in BianaDBaccess)	inverse_user_entity_relations_selection() (in UserEntitySet)	isOptimizedForRunning() (in BianaDBaccess)
insert_cd_hit_clusters_to_biana_database() (in BianaDBaccess)	ipiParser (in biana.BianaParser)	isSpecialAttribute() (in ExternalEntityAttribute)
insert_db_content() (in DB)	IPIParser (in biana.BianaParser.ipiParser)	isValidAttribute() (in ExternalEntityAttribute)
insert_new_attribute_description() (in BianaDBaccess)	is_comparable() (in UnificationAtomElement)	isValidType() (in ExternalEntity)
insert_new_external_database() (in BianaDBaccess)	is_compressed() (in FieldDB)	isValidType() (in ExternalEntityRelation)
insert_new_external_entity() (in BianaDBaccess)	is_valid_external_entity_attribute_type() (in BianaDatabase)	isValidType() (in ExternalEntityRelationParticipantAttribute)
insert_ontology() (in BianaDBaccess)	is_valid_external_entity_relation_participant_attribute_type() (in BianaDatabase)	isVersionableIdentifier() (in ExternalEntityAttribute)

K

keggGeneParser (in biana.BianaParser)	keggKOParser (in biana.BianaParser)	keggligandParser (in biana.BianaParser)
KeggGeneParser (in biana.BianaParser.keggGeneParser)	KeggKOParser (in biana.BianaParser.keggKOParser)	KeggLigandParser (in biana.BianaParser.keggligandParser)

L

M

mandatory_columns (in GenericParser)	MAX_NUMBER_OF_TRIAL (in biana.GraphUtilities.GraphUtilities)	MyDataParser (in biana.BianaParser)
mandatory_relation_columns (in GenericParser)	merge() (in SQLSelectStatement)	MyDataParser (in biana.BianaParser.MyDataParser)
MAX_NAME_LENGTH (in biana.BianaParser.psi_Mi25Parser)	module1 (in biana.BianaDB.setup)

N

N_MAX_ENTRY_AT_ONCE (in STRINGParser)	name (in KeggLigandParser)	ncbiGenPeptParser (in biana.BianaParser)
name (in GenericParser)	name (in NcbiGenPeptParserGenpeptParser)	NcbiGenPeptParserGenpeptParser (in biana.BianaParser.ncbiGenPeptParser)
name (in MyDataParser)	name (in NrParser)	NEWget_user_entity_relations() (in BianaDBaccess)
name (in BiopaxLevel2Parser)	name (in PFAMParser)	next() (in BlastallParserIterator)
name (in CogParser)	name (in Psi_MiFormattedDBParser)	next() (in autoincrement)
name (in GOOBOParser)	name (in PSIMIOBOParser)	not_allowed_import_files (in biana.BianaParser.database2biana)
name (in HGNCParser)	name (in SCOPParser)	nrParser (in biana.BianaParser)
name (in IPIParser)	name (in STRINGParser)	NrParser (in biana.BianaParser.nrParser)
name (in KeggGeneParser)	name (in TaxonomyParser)
name (in KeggKOParser)	name (in UniprotParser)

O

OLDget_user_entity_relations() (in BianaDBaccess)	OutBianaInterface' (in biana)	output_user_entity_details() (in BianaSessionManager)
Ontology (in biana.BianaObjects.Ontology')	outmethod (in OutBianaInterface)	output_user_entity_details_with_only_defaults() (in BianaSessionManager)
Ontology' (in biana.BianaObjects)	output_external_entity_details() (in BianaSessionManager)	output_user_entity_set_details() (in BianaSessionManager)
optimize_database() (in Database)	output_external_entity_relation_details() (in BianaSessionManager)	output_user_entity_set_group() (in BianaSessionManager)
optimize_database_for() (in BianaDBaccess)	output_external_entity_relation_participant_details() (in BianaSessionManager)	output_user_entity_set_network() (in BianaSessionManager)
OPTIMIZE_SPACE (in biana.BianaDB.database)	output_ontology() (in BianaSessionManager)	output_user_entity_set_network_in_sif_format() (in BianaSessionManager)
out_format (in OutBianaInterface)	output_sequence() (in FastaWriter)	output_user_entity_set_sequences_in_fasta() (in BianaSessionManager)
OutBianaInterface (in biana.OutBianaInterface')	output_sequences() (in BianaDBaccess)	output_utilities (in biana.BianaObjects)

P

parse_alignment_line() (in BlastallParserIterator)	PDBAtom (in biana.BianaObjects.PDB')	PSI_MI_TAG_INTERACTOR_REFERENCE (in Psi_MiParticipant)
parse_bl2seq_output() (in biana.BianaObjects.sequenceUtilities)	PDBFragment (in biana.BianaObjects.PDB')	PSI_MI_TAG_LABEL (in Psi_MiNames)
parse_blastall_output() (in biana.BianaObjects.sequenceUtilities)	PDBResidue (in biana.BianaObjects.PDB')	PSI_MI_TAG_NAME (in Psi_MiNames)
parse_database() (in GenericParser)	pfamParser (in biana.BianaParser)	PSI_MI_TAG_NAMES (in Psi_MiNames)
parse_database() (in MyDataParser)	PFAMParser (in biana.BianaParser.pfamParser)	PSI_MI_TAG_NEGATIVE (in Psi_MiInteraction)
parse_database() (in BianaParser)	ping() (in biana.biana_commands')	PSI_MI_TAG_ORGANISM (in Psi_MiInteractor)
parse_database() (in BiopaxLevel2Parser)	positives_re (in BlastallParserIterator)	PSI_MI_TAG_ORGANISM_ATTRIBUTE_TAX_ID (in Psi_MiInteractor)
parse_database() (in CogParser)	print_alignment() (in SequenceAlignment)	PSI_MI_TAG_PARTICIPANT (in Psi_MiParticipant)
parse_database() (in GOOBOParser)	print_help() (in BianaParser)	PSI_MI_TAG_PARTICIPANT_ATTRIBUTE_ID (in Psi_MiParticipant)
parse_database() (in HGNCParser)	print_tree() (in Ontology)	PSI_MI_TAG_PARTICIPANT_IDENTIFICATION_METHOD (in Psi_MiExperiment)
parse_database() (in IPIParser)	process() (in FormattedFileProcessor)	PSI_MI_TAG_PARTICIPANT_LIST (in Psi_MiInteraction)
parse_database() (in KeggGeneParser)	process() (in TsvReader)	PSI_MI_TAG_REF_ATTRIBUTE_DB (in Psi_MiXRef)
parse_database() (in KeggKOParser)	processingInstruction() (in Psi_MiHandler)	PSI_MI_TAG_REF_ATTRIBUTE_ID (in Psi_MiXRef)
parse_database() (in KeggLigandParser)	PROMISCUOUS_EXTERNAL_ENTITY_TYPES_DICT (in ExternalEntity)	PSI_MI_TAG_REF_ATTRIBUTE_SECONDARY (in Psi_MiXRef)
parse_database() (in NcbiGenPeptParserGenpeptParser)	PROMISCUOUS_EXTERNAL_ENTITY_TYPES_DICT (in biana.biana_globals)	PSI_MI_TAG_REF_ATTRIBUTE_TYPE (in Psi_MiXRef)
parse_database() (in NrParser)	ProteinSequence (in biana.BianaObjects.Sequence)	PSI_MI_TAG_REF_PRIMARY (in Psi_MiXRef)
parse_database() (in PFAMParser)	psi_Mi25Parser (in biana.BianaParser)	PSI_MI_TAG_REF_SECONDARY (in Psi_MiXRef)
parse_database() (in Psi_MiFormattedDBParser)	PSI_MI_TAG_ALIAS (in Psi_MiNames)	PSI_MI_TAG_SEQUENCE (in Psi_MiInteractor)
parse_database() (in PSIMIOBOParser)	PSI_MI_TAG_ALIAS_ATTRIBUTE_TYPE (in Psi_MiNames)	PSI_MI_TAG_TYPE (in Psi_MiInteraction)
parse_database() (in SCOPParser)	PSI_MI_TAG_BIB_REF (in Psi_MiExperiment)	PSI_MI_TAG_TYPE (in Psi_MiInteractor)
parse_database() (in STRINGParser)	PSI_MI_TAG_BIOLOGICAL_ROLE (in Psi_MiParticipant)	PSI_MI_TAG_XREF (in Psi_MiXRef)
parse_database() (in TaxonomyParser)	PSI_MI_TAG_ENTRY (in Psi_MiEntry)	Psi_MiEntry (in biana.BianaParser.psi_MiXMLParser)
parse_database() (in UniprotParser)	PSI_MI_TAG_EXPERIMENT_ATTRIBUTE_ID (in Psi_MiExperiment)	Psi_MiExperiment (in biana.BianaParser.psi_MiXMLParser)
parse_fasta_file() (in NcbiGenPeptParserGenpeptParser)	PSI_MI_TAG_EXPERIMENT_DESCRIPTION (in Psi_MiExperiment)	Psi_MiFormattedDBParser (in biana.BianaParser.psi_Mi25Parser)
parse_file() (in IPIParser)	PSI_MI_TAG_EXPERIMENT_LIST (in Psi_MiEntry)	Psi_MiHandler (in biana.BianaParser.psi_MiXMLParser)
parse_genpept_entry() (in NcbiGenPeptParserGenpeptParser)	PSI_MI_TAG_EXPERIMENT_LIST (in Psi_MiInteraction)	Psi_MiInteraction (in biana.BianaParser.psi_MiXMLParser)
parse_nr_record() (in NrParser)	PSI_MI_TAG_EXPERIMENT_REFERENCE (in Psi_MiInteraction)	Psi_MiInteractor (in biana.BianaParser.psi_MiXMLParser)
parse_pfam_file() (in PFAMParser)	PSI_MI_TAG_EXPERIMENTAL_ROLE (in Psi_MiParticipant)	Psi_MiNames (in biana.BianaParser.psi_MiXMLParser)
parse_pfam_seq_record() (in PFAMParser)	PSI_MI_TAG_EXPERIMENTAL_ROLE_LIST (in Psi_MiParticipant)	Psi_MiParticipant (in biana.BianaParser.psi_MiXMLParser)
parse_string_field_value() (in biana.utilities.utilities)	PSI_MI_TAG_INTERACTION (in Psi_MiInteraction)	psi_MiXMLParser (in biana.BianaParser)
parseArguments() (in BianaParser)	PSI_MI_TAG_INTERACTION_ATTRIBUTE_ID (in Psi_MiInteraction)	Psi_MiXMLParser (in biana.BianaParser.psi_MiXMLParser)
parseFile() (in BiopaxLevel2XMLParser)	PSI_MI_TAG_INTERACTION_DETECTION_METHOD (in Psi_MiExperiment)	Psi_MiXRef (in biana.BianaParser.psi_MiXMLParser)
parseFile() (in Psi_MiXMLParser)	PSI_MI_TAG_INTERACTION_LIST (in Psi_MiEntry)	psimioboParser (in biana.BianaParser)
parserObjects (in biana.BianaParser.database2biana)	PSI_MI_TAG_INTERACTOR (in Psi_MiInteractor)	PSIMIOBOParser (in biana.BianaParser.psimioboParser)
PDB (in biana.BianaObjects.PDB')	PSI_MI_TAG_INTERACTOR_ATTRIBUTE_ID (in Psi_MiInteractor)
PDB' (in biana.BianaObjects)	PSI_MI_TAG_INTERACTOR_LIST (in Psi_MiEntry)

Q

query_re (in BlastallParserIterator)

R

randomize_graph() (in biana.GraphUtilities.GraphUtilities)	relationHasTag() (in UserEntitySet)	remove_user_entity_set() (in BianaSessionManager)
randomize_user_entity_set_network() (in BianaSessionManager)	remove_edge() (in UserEntitySet)	reset() (in BlastResult)
read() (in FormattedFileProcessor)	remove_external_entity_relation() (in UserEntitySet)	reset_biana_database() (in administration)
read_alignment() (in SequenceAlignment)	remove_node() (in UserEntitySet)	reset_columns() (in SQLSelectStatement)
read_identifier_list_from_file() (in BianaSessionManager)	remove_selected_relations() (in BianaSessionManager)	resources (in BiopaxEntity)
read_pdb_file() (in PDB)	remove_selected_relations() (in UserEntitySet)	restart_bufferElement() (in BufferElement)
read_sequences_file() (in Sequence)	remove_selected_user_entities() (in BianaSessionManager)	return_dic_gi_vs_tax() (in biana.utilities.utilities)
reconnect() (in BianaDBaccess)	REMOVE_SEQUENCE_DUPLICATES_PROCEDURE (in biana.BianaDB.BianaDatabaseDefinition)	return_non_commented_non_empty_lines() (in biana.utilities.utilities)
reconnect() (in BianaSessionManager)	remove_session() (in biana.biana_commands')	RNASequence (in biana.BianaObjects.Sequence)
refresh_database_information() (in BianaDBaccess)	remove_tables() (in Database)	run() (in biana.BianaParser.database2biana)
relation_has_tag() (in UserEntitySet)	remove_unconnected_nodes() (in UserEntitySet)

S

safe_traceback() (in PDB)	Sequence (in biana.BianaObjects)	set_parsing_time() (in ExternalDatabase)
save_session() (in biana.biana_commands')	Sequence (in biana.BianaObjects.Sequence)	set_primary_key() (in TableDB)
sbjct_intervals_re (in BlastallParserIterator)	sequence2md5() (in biana.utilities.utilities)	set_representant() (in CDHITCluster)
sbjct_re (in BlastallParserIterator)	SequenceAlignment (in biana.BianaObjects.SequenceAlignment')	set_resolution() (in PDB)
scopParser (in biana.BianaParser)	SequenceAlignment' (in biana.BianaObjects)	set_sequenceID() (in Sequence)
SCOPParser (in biana.BianaParser.scopParser)	sequenceUtilities (in biana.BianaObjects)	set_table_name() (in TableDB)
score_option2_re (in BlastallParserIterator)	set_alignment_length() (in SequenceAlignment)	set_taxIDlist() (in SequenceAlignment)
score_re (in BlastallParserIterator)	set_attributes() (in BiopaxBioSource)	setGroupsHierarchy() (in UserEntitySet)
select_all_user_entities() (in BianaSessionManager)	set_attributes() (in BiopaxBiochemicalReaction)	setIsNetworkCreated() (in UserEntitySet)
select_all_user_entity_relations() (in BianaSessionManager)	set_attributes() (in BiopaxCatalysis)	setNetwork() (in UserEntitySet)
select_db_content() (in DB)	set_attributes() (in BiopaxComplex)	setRestriction() (in UserEntitySet)
select_user_entities() (in UserEntitySet)	set_attributes() (in BiopaxControl)	setup (in biana.BianaDB)
select_user_entities_from_user_entity_set() (in BianaSessionManager)	set_attributes() (in BiopaxEntity)	site_packages_path (in biana.BianaParser.database2biana)
select_user_entities_using_attributes() (in BianaSessionManager)	set_attributes() (in BiopaxInteraction)	skippedEntity() (in Psi_MiHandler)
select_user_entity_relations_between_two_subsets() (in UserEntitySet)	set_attributes() (in BiopaxOpenControlledVocabulary)	SQLSelectStatement (in biana.BianaDB.database)
select_user_entity_relations_from_user_entity_set() (in BianaSessionManager)	set_attributes() (in BiopaxPathway)	start() (in BianaParser)
select_user_entity_relations_using_attributes() (in BianaSessionManager)	set_attributes() (in BiopaxPathwayStep)	startDocument() (in BiopaxLevel2Handler)
select_user_entity_set() (in BianaSessionManager)	set_attributes() (in BiopaxPhysicalEntityParticipant)	startDocument() (in Psi_MiHandler)
selectUserEntitiesByTag() (in UserEntitySet)	set_attributes() (in BiopaxXREF)	startElement() (in BiopaxLevel2Handler)
selectUserEntityRelations() (in UserEntitySet)	set_evalue() (in BlastResult)	startElement() (in Psi_MiHandler)
selectUserEntityRelationsByTag() (in UserEntitySet)	set_foreign_key() (in FieldDB)	stringParser (in biana.BianaParser)
self_blast_fasta_file() (in biana.BianaObjects.sequenceUtilities)	set_id() (in ExternalDatabase)	STRINGParser (in biana.BianaParser.stringParser)
send_data() (in OutBianaInterface)	set_id() (in ExternalEntity)	substitution_list (in BianaSessionManager)
send_end_process_message() (in OutBianaInterface)	set_lock_frequency() (in DB)	swissprot_re (in STRINGParser)
send_error_notification() (in OutBianaInterface)	set_lock_tables() (in DB)	symbol_per_line (in FastaWriter)
send_info_message() (in OutBianaInterface)	set_number_of_sequences() (in SequenceAlignment)
send_process_message() (in OutBianaInterface)	set_outmethod() (in OutBianaInterface)

T

TAB_EXT_ATT (in biana.BianaDB.BianaDB_globals)	taxonomyParser (in biana.BianaParser)	toBiana() (in BiopaxPathwayStep)
TAB_EXT_ENT (in biana.BianaDB.BianaDB_globals)	TaxonomyParser (in biana.BianaParser.taxonomyParser)	toBiana() (in BiopaxTransport)
TAB_EXT_ENT_REL (in biana.BianaDB.BianaDB_globals)	TCOFFEE_EXEC (in biana.biana_globals)	transform_expanded_attribute_restrictions() (in BianaDBaccess)
TAB_EXT_ENT_REL_PAR (in biana.BianaDB.BianaDB_globals)	temp_acc (in biana.BianaObjects.PDB')	translation_dict (in DNASequence)
TAB_TEM (in biana.BianaDB.BianaDB_globals)	TEMPORAL_PATH (in biana.biana_globals)	translation_dict (in ProteinSequence)
TAB_UNI (in biana.BianaDB.BianaDB_globals)	testfast_getUserEntityTagConnectedMetrics() (in UserEntitySet)	translation_dict (in RNASequence)
TableDB (in biana.BianaDB.database)	toBiana() (in BiopaxComplexAssembly)	TsvReader (in biana.utilities)
tag_selected_user_entities() (in BianaSessionManager)	toBiana() (in BiopaxEntity)	TsvReader (in biana.utilities.TsvReader)
tag_selected_user_entity_relations() (in BianaSessionManager)	toBiana() (in BiopaxLevel2Handler)

U

UnificationAtomElement (in biana.BianaObjects.UnificationProtocol')	unsigned_float_to_ascii() (in biana.utilities.int_ascii)	UserEntityRelation (in biana.BianaObjects.UserEntityRelation')
UnificationProtocol (in biana.BianaObjects.UnificationProtocol')	unsigned_int_list_to_ascii() (in biana.utilities.int_ascii)	UserEntityRelation' (in biana.BianaObjects)
UnificationProtocol' (in biana.BianaObjects)	unsigned_int_to_ascii() (in biana.utilities.int_ascii)	UserEntitySet (in biana.BianaObjects)
uniprotParser (in biana.BianaParser)	update_external_database_external_entity_attributes() (in BianaDBaccess)	UserEntitySet (in biana.BianaObjects.UserEntitySet)
UniprotParser (in biana.BianaParser.uniprotParser)	UserEntity (in biana.BianaObjects.UserEntity')	utilities (in biana)
unselect_user_entities_from_user_entity_set() (in BianaSessionManager)	UserEntity' (in biana.BianaObjects)	utilities (in biana.utilities)
unselect_user_entity_relations_from_user_entity_set() (in BianaSessionManager)	UserEntityExpandedRelation (in biana.BianaObjects.UserEntityExpandedRelation')
unsigned_float_list_to_ascii() (in biana.utilities.int_ascii)	UserEntityExpandedRelation' (in biana.BianaObjects)

V

VALID_IDENTIFIER_REFERENCE_TYPES (in biana.biana_globals)	verbose_detailed (in biana.utilities.utilities)	verbose_very_detailed (in biana.utilities.utilities)
verbose (in biana.utilities.utilities)	verbose_matrix (in biana.utilities.utilities)
verbose_blast_report (in biana.utilities.utilities)	verbose_string_utilities (in biana.utilities.utilities)

W

window_size (in DNASequence)	window_size (in RNASequence)
window_size (in ProteinSequence)	write() (in BlastResult)

X

x (in BiopaxEntity)	XMLNode (in biana.BianaParser)
x (in biana.BianaParser.database2biana)	XMLNode (in biana.BianaParser.XMLNode)

_

__del__() (in BiopaxLevel2XMLParser)	__init__() (in autoincrement)	_get_last_external_entity_id() (in BianaDBaccess)
__del__() (in DBReference)	__iter__() (in BlastallParserIterator)	_get_last_external_entity_relation_participant_id() (in BianaDBaccess)
__del__() (in Psi_MiEntry)	__repr__() (in BlastResult)	_get_last_key_id() (in BianaDBaccess)
__del__() (in Psi_MiExperiment)	__repr__() (in ExternalEntityAttribute)	_get_last_sequenceNucleotide_id() (in BianaDBaccess)
__del__() (in Psi_MiInteraction)	__repr__() (in PDBFragment)	_get_last_sequenceProtein_id() (in BianaDBaccess)
__del__() (in Psi_MiInteractor)	__repr__() (in UserEntitySet)	_get_last_stable_autoincrement() (in DB)
__del__() (in Psi_MiNames)	__setstate__() (in BianaDBaccess)	_get_last_stable_external_entity_id() (in BianaDBaccess)
__del__() (in Psi_MiParticipant)	__setstate__() (in DB)	_get_last_stable_external_entity_relation_participant_id() (in BianaDBaccess)
__del__() (in Psi_MiXMLParser)	__setstate__() (in BianaSessionManager)	_get_last_stable_key_id() (in BianaDBaccess)
__del__() (in Psi_MiXRef)	__str__() (in BianaDBaccess)	_get_last_stable_sequenceNucleotide_id() (in BianaDBaccess)
__eq__() (in ExternalEntity)	__str__() (in DB)	_get_last_stable_sequenceProtein_id() (in BianaDBaccess)
__eq__() (in ExternalEntityAttribute)	__str__() (in TableDB)	_get_link() (in BiopaxLevel2Handler)
__getnewargs__() (in BianaDBaccess)	__str__() (in BianaSessionManager)	_get_linked_attribute_ontology_name() (in BianaDBaccess)
__getnewargs__() (in DB)	__str__() (in BlastResult)	_get_list_eE_for_uE() (in BianaDBaccess)
__getstate__() (in BianaDBaccess)	__str__() (in ExternalDatabase)	_get_list_external_entities_for_user_entities() (in BianaDBaccess)
__getstate__() (in DB)	__str__() (in ExternalEntity)	_get_list_external_entities_IDs_by_attribute_SQLstat() (in BianaDBaccess)
__getstate__() (in BianaSessionManager)	__str__() (in ExternalEntityAttribute)	_get_list_user_entities_for_external_entities() (in BianaDBaccess)
__init__() (in BianaDBaccess)	__str__() (in PDBFragment)	_get_list_user_entities_IDs_by_attribute_transfer_query() (in BianaDBaccess)
__init__() (in BianaDatabase)	__str__() (in Sequence)	_get_max_packet() (in DB)
__init__() (in Buffer)	__str__() (in UnificationAtomElement)	_get_max_value() (in DB)
__init__() (in BufferElement)	__str__() (in UserEntity)	_get_multiple_insert_query() (in DB)
__init__() (in DB)	__str__() (in UserEntityExpandedRelation)	_get_nested_insert_sql_query() (in DB)
__init__() (in Database)	__str__() (in UserEntitySet)	_get_nested_queries_for_getting_equivalent_uE_by_sharing_attributes() (in BianaDBaccess)
__init__() (in FieldDB)	__str__() (in BiopaxLevel2XMLParser)	_get_new_external_entity_id() (in BianaDBaccess)
__init__() (in SQLSelectStatement)	__str__() (in DBReference)	_get_new_external_entity_relation_participant_id() (in BianaDBaccess)
__init__() (in TableDB)	__str__() (in Psi_MiEntry)	_get_new_key_id() (in BianaDBaccess)
__init__() (in BianaReport)	__str__() (in Psi_MiExperiment)	_get_new_sequenceNucleotide_id() (in BianaDBaccess)
__init__() (in BianaSessionManager)	__str__() (in Psi_MiInteraction)	_get_new_sequenceProtein_id() (in BianaDBaccess)
__init__() (in Enum)	__str__() (in Psi_MiInteractor)	_get_next() (in Enum)
__init__() (in BlastResult)	__str__() (in Psi_MiNames)	_get_next_uEs_id() (in BianaSessionManager)
__init__() (in CDHITCluster)	__str__() (in Psi_MiParticipant)	_get_protein_analyzer() (in ProteinSequence)
__init__() (in CDHITMatch)	__str__() (in Psi_MiXMLParser)	_get_select_sql_query() (in DB)
__init__() (in ExternalDatabase)	__str__() (in Psi_MiXRef)	_get_sequence_fragments() (in SequenceAlignment)
__init__() (in ExternalEntity)	_add_key_attribute() (in BianaDBaccess)	_get_sequence_fragments_from_ascii() (in SequenceAlignment)
__init__() (in ExternalEntityAttribute)	_add_transfer_attribute() (in BianaDBaccess)	_get_similar_sequences() (in BianaDBaccess)
__init__() (in ExternalEntityRelation)	_apply_negative_restrictions_to_query() (in BianaDBaccess)	_get_single_source_shortest_path() (in UserEntitySet)
__init__() (in ExternalEntityRelationParticipantAttribute)	_apply_relation_restrictions_to_query() (in BianaDBaccess)	_get_sorted_chains() (in PDB)
__init__() (in Ontology)	_apply_restrictions_to_query() (in BianaDBaccess)	_get_sorted_residues() (in PDB)
__init__() (in PDB)	_calculate_similarities() (in biana.BianaObjects.sequenceUtilities)	_get_source_code_version_in_db() (in DB)
__init__() (in PDBAtom)	_check_database_integrity() (in BianaDBaccess)	_get_table_names() (in BianaDBaccess)
__init__() (in PDBFragment)	_check_lock_frequency() (in DB)	_get_table_names() (in DB)
__init__() (in PDBResidue)	_check_locked_table() (in DB)	_get_union_queries() (in DB)
__init__() (in DNASequence)	_close_file_descriptor() (in STRINGParser)	_get_update_sql_query() (in DB)
__init__() (in ProteinSequence)	_convert_attribute_list_to_attribute_dictionary() (in BianaSessionManager)	_get_user_entity_relation_id() (in UserEntitySet)
__init__() (in RNASequence)	_convert_sequence_to_fasta() (in FastaWriter)	_get_user_entity_set_xml() (in BianaSessionManager)
__init__() (in Sequence)	_convertListSourceDBVersionToSourceDBIdList() (in BianaDBaccess)	_get_user_entity_table_name() (in BianaDBaccess)
__init__() (in SequenceAlignment)	_create_initial_tables() (in BianaDatabase)	_get_valid_source_databases_by_id() (in BianaDBaccess)
__init__() (in UnificationAtomElement)	_create_new_unification_protocol_tables() (in BianaDBaccess)	_get_valid_source_dbs() (in BianaDBaccess)
__init__() (in UnificationProtocol)	_disable_indices() (in DB)	_get_xml() (in BianaSessionManager)
__init__() (in UserEntity)	_empty_buffer() (in DB)	_get_xml() (in UserEntitySet)
__init__() (in UserEntityExpandedRelation)	_empty_sequences_table() (in BianaDBaccess)	_get_xml_foot() (in BianaSessionManager)
__init__() (in UserEntityRelation)	_enable_indices() (in DB)	_get_xml_foot() (in UserEntitySet)
__init__() (in UserEntitySet)	_entrez_funct() (in BiopaxEntity)	_get_xml_header() (in BianaSessionManager)
__init__() (in BlastallParserIterator)	_entrez_funct() (in BiopaxLevel2Handler)	_get_xml_header() (in UserEntitySet)
__init__() (in GenericParser)	_fetch_given_list_protein_information_from_database() (in STRINGParser)	_getAttribute() (in Psi_MiHandler)
__init__() (in MyDataParser)	_fetch_given_protein_information_from_database() (in STRINGParser)	_getRelationHash() (in UserEntitySet)
__init__() (in XMLNode)	_get_aligned_sequence() (in SequenceAlignment)	_has_optimized_fields() (in TableDB)
__init__() (in BianaParser)	_get_attribute_restrictions_query() (in BianaDBaccess)	_identity() (in BiopaxEntity)
__init__() (in BiopaxBioSource)	_get_attribute_value_list_for_transfer_attributes() (in BianaDBaccess)	_identity() (in BiopaxLevel2Handler)
__init__() (in BiopaxBiochemicalReaction)	_get_biana_object() (in BiopaxBioSource)	_indent() (in BianaParser)
__init__() (in BiopaxCatalysis)	_get_biana_object() (in BiopaxBiochemicalReaction)	_initialize_restrictions_dict() (in UserEntitySet)
__init__() (in BiopaxComplex)	_get_biana_object() (in BiopaxComplex)	_insert_blast_results_file() (in BianaDBaccess)
__init__() (in BiopaxControl)	_get_biana_object() (in BiopaxControl)	_insert_external_entity_attribute() (in BianaDBaccess)
__init__() (in BiopaxEntity)	_get_biana_object() (in BiopaxConversion)	_insert_external_entity_relation_participant_attribute() (in BianaDBaccess)
__init__() (in BiopaxInteraction)	_get_biana_object() (in BiopaxDNA)	_insert_new_string_protein_object_into_database() (in STRINGParser)
__init__() (in BiopaxLevel2Handler)	_get_biana_object() (in BiopaxEntity)	_insert_protein_information_from_alias_file_to_database() (in STRINGParser)
__init__() (in BiopaxLevel2XMLParser)	_get_biana_object() (in BiopaxInteraction)	_insert_protein_sequence_cd_hit_cluster() (in BianaDBaccess)
__init__() (in BiopaxLevel2Parser)	_get_biana_object() (in BiopaxOpenControlledVocabulary)	_insert_sequence() (in BianaDBaccess)
__init__() (in BiopaxOpenControlledVocabulary)	_get_biana_object() (in BiopaxPathway)	_insert_sequence_file() (in BianaDBaccess)
__init__() (in BiopaxPathway)	_get_biana_object() (in BiopaxPathwayStep)	_is_key_attribute() (in BianaDBaccess)
__init__() (in BiopaxPathwayStep)	_get_biana_object() (in BiopaxPhysicalEntity)	_is_ontology_linked_attribute() (in BianaDBaccess)
__init__() (in BiopaxPhysicalEntityParticipant)	_get_biana_object() (in BiopaxPhysicalEntityParticipant)	_is_transferred_attribute() (in BianaDBaccess)
__init__() (in BiopaxProtein)	_get_biana_object() (in BiopaxPhysicalInteraction)	_load_available_unification_protocols() (in BianaDBaccess)
__init__() (in BiopaxXREF)	_get_biana_object() (in BiopaxProtein)	_load_biana_database_information() (in BianaDBaccess)
__init__() (in CogParser)	_get_biana_object() (in BiopaxRNA)	_load_biana_types_and_attributes() (in BianaDBaccess)
__init__() (in GOOBOParser)	_get_biana_object() (in BiopaxSmallMolecule)	_load_database_tables() (in BianaDatabase)
__init__() (in HGNCParser)	_get_biana_object() (in BiopaxXREF)	_load_sequences() (in BianaDBaccess)
__init__() (in IPIParser)	_get_buffer_key() (in DB)	_lock_all_tables() (in DB)
__init__() (in KeggGeneParser)	_get_buffer_multiple_queries() (in DB)	_lock_tables() (in DB)
__init__() (in KeggKOParser)	_get_C_align() (in SequenceAlignment)	_not_recognized (in BiopaxEntity)
__init__() (in KeggLigandParser)	_get_cond_str() (in DB)	_parse_dssp_results() (in PDB)
__init__() (in NcbiGenPeptParserGenpeptParser)	_get_cross_ref() (in BiopaxLevel2Handler)	_printObjectStack() (in Psi_MiHandler)
__init__() (in NrParser)	_get_current_autoincrement() (in DB)	_reactome_funct() (in BiopaxEntity)
__init__() (in PFAMParser)	_get_data_file_names() (in STRINGParser)	_readGivenNumberOfSequencesToDictionary() (in STRINGParser)
__init__() (in Psi_MiFormattedDBParser)	_get_db_versions_list() (in BianaDBaccess)	_readNextSequenceInformationFromSequenceFile() (in STRINGParser)
__init__() (in DBReference)	_get_delete_sql_query() (in DB)	_recursive_tree_print() (in Ontology)
__init__() (in Psi_MiEntry)	_get_digested_code() (in DNASequence)	_recursive_tree_xml() (in Ontology)
__init__() (in Psi_MiExperiment)	_get_digested_code() (in ProteinSequence)	_remove_protein_information_from_database() (in STRINGParser)
__init__() (in Psi_MiHandler)	_get_digested_code() (in RNASequence)	_rollback() (in BianaDBaccess)
__init__() (in Psi_MiInteraction)	_get_drop_sql_query() (in DB)	_send_complete_user_entity_set_info() (in BianaSessionManager)
__init__() (in Psi_MiInteractor)	_get_dssp_results() (in PDB)	_set_external_entities_dict() (in Ontology)
__init__() (in Psi_MiNames)	_get_equivalent_external_entities() (in BianaDBaccess)	_set_source_code_version_in_db() (in DB)
__init__() (in Psi_MiParticipant)	_get_equivalent_user_entities_by_sharing_attributes() (in BianaDBaccess)	_splitsize() (in BianaParser)
__init__() (in Psi_MiXMLParser)	_get_expand_ontology_attribute_table_query() (in BianaDBaccess)	_transform_attribute_value_data_type_to_biana_database_attribute_data_type() (in BianaDBaccess)
__init__() (in Psi_MiXRef)	_get_externalDatabaseID_int() (in BianaDBaccess)	_traverse_tree_for_leafs() (in Ontology)
__init__() (in PSIMIOBOParser)	_get_file_descriptor() (in STRINGParser)	_unify_promiscuous_external_entities() (in BianaDBaccess)
__init__() (in SCOPParser)	_get_fragmented_sequence() (in DNASequence)	_unlock_tables() (in DB)
__init__() (in STRINGParser)	_get_fragmented_sequence() (in ProteinSequence)	_update_bianaDB_autoincrement_fields() (in BianaDBaccess)
__init__() (in TaxonomyParser)	_get_fragmented_sequence() (in RNASequence)	_update_bianaDB_version() (in BianaDBaccess)
__init__() (in UniprotParser)	_get_fragmented_sequence() (in Sequence)	_update_relations_hierarchy() (in BianaDBaccess)
__init__() (in FastaWriter)	_get_groups_xml() (in UserEntitySet)	_update_selected_external_ids_dict() (in UserEntitySet)
__init__() (in FormattedFileProcessor)	_get_insert_sql_query() (in DB)	_uses_buffer() (in DB)
__init__() (in TsvReader)	_get_key_attribute_table_name() (in BianaDBaccess)