Everything
All Classes
biana.BianaDB.BianaDBaccess'.BianaDBaccess
biana.BianaDB.BianaDatabaseDefinition.BianaDatabase
biana.BianaDB.ConnectorDB.Buffer
biana.BianaDB.ConnectorDB.BufferElement
biana.BianaDB.ConnectorDB.DB
biana.BianaDB.database.Database
biana.BianaDB.database.FieldDB
biana.BianaDB.database.SQLSelectStatement
biana.BianaDB.database.TableDB
biana.BianaObjects.BianaReport.BianaReport
biana.BianaObjects.BianaSessionManager.BianaSessionManager
biana.BianaObjects.BianaSessionManager.Enum
biana.BianaObjects.BlastResult.BlastResult
biana.BianaObjects.CDHIT.CDHITCluster
biana.BianaObjects.CDHIT.CDHITMatch
biana.BianaObjects.ExternalDatabase'.ExternalDatabase
biana.BianaObjects.ExternalEntity'.ExternalEntity
biana.BianaObjects.ExternalEntityAttribute'.ExternalEntityAttribute
biana.BianaObjects.ExternalEntityRelation'.ExternalEntityRelation
biana.BianaObjects.ExternalEntityRelationAttribute'.ExternalEntityRelationAttribute
biana.BianaObjects.ExternalEntityRelationParticipantAttribute'.ExternalEntityRelationParticipantAttribute
biana.BianaObjects.Ontology'.Ontology
biana.BianaObjects.PDB'.PDB
biana.BianaObjects.PDB'.PDBAtom
biana.BianaObjects.PDB'.PDBFragment
biana.BianaObjects.PDB'.PDBResidue
biana.BianaObjects.Sequence.DNASequence
biana.BianaObjects.Sequence.ProteinSequence
biana.BianaObjects.Sequence.RNASequence
biana.BianaObjects.Sequence.Sequence
biana.BianaObjects.SequenceAlignment'.SequenceAlignment
biana.BianaObjects.UnificationProtocol'.UnificationAtomElement
biana.BianaObjects.UnificationProtocol'.UnificationProtocol
biana.BianaObjects.UserEntity'.UserEntity
biana.BianaObjects.UserEntityExpandedRelation'.UserEntityExpandedRelation
biana.BianaObjects.UserEntityRelation'.UserEntityRelation
biana.BianaObjects.UserEntitySet.UserEntitySet
biana.BianaObjects.sequenceUtilities.BlastallParserIterator
biana.BianaParser.GenericParser.GenericParser
biana.BianaParser.MyDataParser.MyDataParser
biana.BianaParser.XMLNode.XMLNode
biana.BianaParser.bianaParser.BianaParser
biana.BianaParser.biopaxLevel2Parser.BiopaxBioSource
biana.BianaParser.biopaxLevel2Parser.BiopaxBiochemicalReaction
biana.BianaParser.biopaxLevel2Parser.BiopaxCatalysis
biana.BianaParser.biopaxLevel2Parser.BiopaxComplex
biana.BianaParser.biopaxLevel2Parser.BiopaxComplexAssembly
biana.BianaParser.biopaxLevel2Parser.BiopaxControl
biana.BianaParser.biopaxLevel2Parser.BiopaxConversion
biana.BianaParser.biopaxLevel2Parser.BiopaxDNA
biana.BianaParser.biopaxLevel2Parser.BiopaxDataSource
biana.BianaParser.biopaxLevel2Parser.BiopaxEntity
biana.BianaParser.biopaxLevel2Parser.BiopaxInteraction
biana.BianaParser.biopaxLevel2Parser.BiopaxLevel2Parser
biana.BianaParser.biopaxLevel2Parser.BiopaxLevel2Parser.BiopaxLevel2Handler
biana.BianaParser.biopaxLevel2Parser.BiopaxLevel2Parser.BiopaxLevel2XMLParser
biana.BianaParser.biopaxLevel2Parser.BiopaxModulation
biana.BianaParser.biopaxLevel2Parser.BiopaxOpenControlledVocabulary
biana.BianaParser.biopaxLevel2Parser.BiopaxPathway
biana.BianaParser.biopaxLevel2Parser.BiopaxPathwayStep
biana.BianaParser.biopaxLevel2Parser.BiopaxPhysicalEntity
biana.BianaParser.biopaxLevel2Parser.BiopaxPhysicalEntityParticipant
biana.BianaParser.biopaxLevel2Parser.BiopaxPhysicalInteraction
biana.BianaParser.biopaxLevel2Parser.BiopaxProtein
biana.BianaParser.biopaxLevel2Parser.BiopaxRNA
biana.BianaParser.biopaxLevel2Parser.BiopaxSmallMolecule
biana.BianaParser.biopaxLevel2Parser.BiopaxTransport
biana.BianaParser.biopaxLevel2Parser.BiopaxXREF
biana.BianaParser.cogParser.CogParser
biana.BianaParser.gooboParser.GOOBOParser
biana.BianaParser.hgncParser.HGNCParser
biana.BianaParser.ipiParser.IPIParser
biana.BianaParser.keggGeneParser.KeggGeneParser
biana.BianaParser.keggKOParser.KeggKOParser
biana.BianaParser.keggligandParser.KeggLigandParser
biana.BianaParser.ncbiGenPeptParser.NcbiGenPeptParserGenpeptParser
biana.BianaParser.nrParser.NrParser
biana.BianaParser.pfamParser.PFAMParser
biana.BianaParser.psi_Mi25Parser.Psi_MiFormattedDBParser
biana.BianaParser.psi_MiXMLParser.DBReference
biana.BianaParser.psi_MiXMLParser.Psi_MiEntry
biana.BianaParser.psi_MiXMLParser.Psi_MiExperiment
biana.BianaParser.psi_MiXMLParser.Psi_MiHandler
biana.BianaParser.psi_MiXMLParser.Psi_MiInteraction
biana.BianaParser.psi_MiXMLParser.Psi_MiInteractor
biana.BianaParser.psi_MiXMLParser.Psi_MiNames
biana.BianaParser.psi_MiXMLParser.Psi_MiParticipant
biana.BianaParser.psi_MiXMLParser.Psi_MiXMLParser
biana.BianaParser.psi_MiXMLParser.Psi_MiXRef
biana.BianaParser.psimioboParser.PSIMIOBOParser
biana.BianaParser.scopParser.SCOPParser
biana.BianaParser.stringParser.STRINGParser
biana.BianaParser.taxonomyParser.TaxonomyParser
biana.BianaParser.uniprotParser.UniprotParser
biana.OutBianaInterface'.OutBianaInterface
biana.biana_commands'.administration
biana.utilities.FastaWriter.FastaWriter
biana.utilities.FormattedFileProcessor.FormattedFileProcessor
biana.utilities.TsvReader.TsvReader
biana.utilities.autoincrement'.autoincrement
All Functions
biana.BianaObjects.output_utilities.append_html_table_values
biana.BianaObjects.output_utilities.get_html_table
biana.BianaObjects.output_utilities.get_html_table_foot
biana.BianaObjects.output_utilities.get_html_table_header
biana.BianaObjects.output_utilities.get_tabulated_table
biana.BianaObjects.sequenceUtilities.blast_cd_hit_clusters
biana.BianaObjects.sequenceUtilities.blast_sequence
biana.BianaObjects.sequenceUtilities.get_cd_hit_clusters
biana.BianaObjects.sequenceUtilities.get_clustalw_alignment
biana.BianaObjects.sequenceUtilities.parse_bl2seq_output
biana.BianaObjects.sequenceUtilities.parse_blastall_output
biana.BianaObjects.sequenceUtilities.self_blast_fasta_file
biana.BianaParser.database2biana.get_available_parsers_info
biana.BianaParser.database2biana.run
biana.BianaParser.psi_Mi25Parser.insertKeyIntoHistogramDictionary
biana.GraphUtilities.GraphUtilities.create_graph
biana.GraphUtilities.GraphUtilities.create_graph_with_same_type
biana.GraphUtilities.GraphUtilities.get_all_paths_from
biana.GraphUtilities.GraphUtilities.get_connected_components
biana.GraphUtilities.GraphUtilities.get_number_of_distinct_edges
biana.GraphUtilities.GraphUtilities.get_path_network
biana.GraphUtilities.GraphUtilities.get_shortest_path_between
biana.GraphUtilities.GraphUtilities.randomize_graph
biana.biana_commands'.close
biana.biana_commands'.create_new_session
biana.biana_commands'.load_session
biana.biana_commands'.ping
biana.biana_commands'.remove_session
biana.biana_commands'.save_session
biana.utilities.int_ascii.ascii_to_float
biana.utilities.int_ascii.ascii_to_float_list
biana.utilities.int_ascii.ascii_to_int
biana.utilities.int_ascii.ascii_to_int_list
biana.utilities.int_ascii.ascii_to_unsigned_float
biana.utilities.int_ascii.ascii_to_unsigned_float_list
biana.utilities.int_ascii.ascii_to_unsigned_int
biana.utilities.int_ascii.ascii_to_unsigned_int_list
biana.utilities.int_ascii.float_list_to_ascii
biana.utilities.int_ascii.float_to_ascii
biana.utilities.int_ascii.int_list_to_ascii
biana.utilities.int_ascii.int_to_ascii
biana.utilities.int_ascii.unsigned_float_list_to_ascii
biana.utilities.int_ascii.unsigned_float_to_ascii
biana.utilities.int_ascii.unsigned_int_list_to_ascii
biana.utilities.int_ascii.unsigned_int_to_ascii
biana.utilities.utilities.get_clean_sequence
biana.utilities.utilities.get_id_type
biana.utilities.utilities.parse_string_field_value
biana.utilities.utilities.return_dic_gi_vs_tax
biana.utilities.utilities.return_non_commented_non_empty_lines
biana.utilities.utilities.sequence2md5
All Variables
biana.BianaDB.BianaDB_globals.DATABASE_HOST
biana.BianaDB.BianaDB_globals.DATABASE_NAME
biana.BianaDB.BianaDB_globals.DATABASE_PASSWORD
biana.BianaDB.BianaDB_globals.DATABASE_PORT
biana.BianaDB.BianaDB_globals.DATABASE_SOCKET
biana.BianaDB.BianaDB_globals.DATABASE_USER
biana.BianaDB.BianaDB_globals.TAB_EXT_ATT
biana.BianaDB.BianaDB_globals.TAB_EXT_ENT
biana.BianaDB.BianaDB_globals.TAB_EXT_ENT_REL
biana.BianaDB.BianaDB_globals.TAB_EXT_ENT_REL_PAR
biana.BianaDB.BianaDB_globals.TAB_TEM
biana.BianaDB.BianaDB_globals.TAB_UNI
biana.BianaDB.BianaDBaccess'.BIANA_SOURCE_CODE_VERSION
biana.BianaDB.BianaDBaccess'.debug_web
biana.BianaDB.BianaDatabaseDefinition.REMOVE_SEQUENCE_DUPLICATES_PROCEDURE
biana.BianaDB.ConnectorDB.DEBUG_BUFFER_INSERT_SINGLE
biana.BianaDB.ConnectorDB.DEBUG_PRINT_INSERT_QUERY
biana.BianaDB.database.OPTIMIZE_SPACE
biana.BianaDB.setup.module1
biana.BianaObjects.ExternalEntityAttribute'.ATTRIBUTE_IDENTIFIER_TO_OBJECT
biana.BianaObjects.PDB'.temp_acc
biana.BianaParser.database2biana.biana_path
biana.BianaParser.database2biana.current_dir
biana.BianaParser.database2biana.current_file
biana.BianaParser.database2biana.current_path_index
biana.BianaParser.database2biana.imports
biana.BianaParser.database2biana.list_all_files
biana.BianaParser.database2biana.list_python_files
biana.BianaParser.database2biana.not_allowed_import_files
biana.BianaParser.database2biana.parserObjects
biana.BianaParser.database2biana.site_packages_path
biana.BianaParser.database2biana.x
biana.BianaParser.psi_Mi25Parser.DICT_METHOD_CONVERSION_GRID_TO_PSI_MI
biana.BianaParser.psi_Mi25Parser.MAX_NAME_LENGTH
biana.GraphUtilities.GraphUtilities.MAX_NUMBER_OF_TRIAL
biana.biana_commands'.available_sessions
biana.biana_globals.BL2SEQ_EXEC
biana.biana_globals.BLASTALL_EXEC
biana.biana_globals.CD_HIT_PATH
biana.biana_globals.CLUSTALW_EXEC
biana.biana_globals.CROSSABLE_ATTRIBUTES
biana.biana_globals.DBHOST
biana.biana_globals.DBNAME
biana.biana_globals.DBPASS
biana.biana_globals.DBPORT
biana.biana_globals.DBSOCKET
biana.biana_globals.DBUSER
biana.biana_globals.DSSP_EXEC
biana.biana_globals.EXTERNAL_ENTITY_DESCRIPTIVE_ATTRIBUTE_TYPES
biana.biana_globals.EXTERNAL_ENTITY_DESCRIPTIVE_SEARCHABLE_ATTRIBUTE_TYPES
biana.biana_globals.EXTERNAL_ENTITY_GENERAL_ATTRIBUTES
biana.biana_globals.EXTERNAL_ENTITY_IDENTIFIER_ATTRIBUTES
biana.biana_globals.EXTERNAL_ENTITY_NUMERIC_ATTRIBUTE_TYPES
biana.biana_globals.EXTERNAL_ENTITY_RELATION_PARTICIPANT_ATTRIBUTE_TYPES
biana.biana_globals.EXTERNAL_ENTITY_RELATION_TYPES
biana.biana_globals.EXTERNAL_ENTITY_SPECIAL_ATTRIBUTE_TYPES
biana.biana_globals.EXTERNAL_ENTITY_TYPES
biana.biana_globals.EXTERNAL_ENTITY_VERSIONABLE_IDENTIFIER_ATTRIBUTE_TYPES
biana.biana_globals.FORMATDB_EXEC
biana.biana_globals.PROMISCUOUS_EXTERNAL_ENTITY_TYPES_DICT
biana.biana_globals.TCOFFEE_EXEC
biana.biana_globals.TEMPORAL_PATH
biana.biana_globals.VALID_IDENTIFIER_REFERENCE_TYPES
biana.copyright
biana.credits
biana.help
biana.license
biana.utilities.utilities.verbose
biana.utilities.utilities.verbose_blast_report
biana.utilities.utilities.verbose_detailed
biana.utilities.utilities.verbose_matrix
biana.utilities.utilities.verbose_string_utilities
biana.utilities.utilities.verbose_very_detailed
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