Home
Trees
Indices
Help
BIANA
[
hide private
]
[
frames
] |
no frames
]
[
Module Hierarchy
|
Class Hierarchy
]
Class Hierarchy
xml.sax.handler.ContentHandler
:
Interface for receiving logical document content events.
biana.BianaParser.biopaxLevel2Parser.BiopaxLevel2Parser.BiopaxLevel2Handler
:
Class to handle content in Biopax Level2 XML files
biana.BianaParser.psi_MiXMLParser.Psi_MiHandler
:
Class to handle content in PSI-MI XML files
biana.BianaParser.psi_MiXMLParser.DBReference
:
Class representing reference information to a database with db, id and type fields
biana.BianaParser.psi_MiXMLParser.Psi_MiEntry
:
Class representing an entry
biana.BianaParser.psi_MiXMLParser.Psi_MiExperiment
:
Class representing an interactor
biana.BianaParser.psi_MiXMLParser.Psi_MiInteraction
:
Class representing an interaction
biana.BianaParser.psi_MiXMLParser.Psi_MiInteractor
:
Class representing an interactor
biana.BianaParser.psi_MiXMLParser.Psi_MiNames
:
Class representing information encapsulated within names XML tags
biana.BianaParser.psi_MiXMLParser.Psi_MiParticipant
:
Class representing a participant
biana.BianaParser.psi_MiXMLParser.Psi_MiXMLParser
:
Class for parsing individual XML files obeying PSI-MI standarts
biana.BianaParser.psi_MiXMLParser.Psi_MiXRef
:
Class representing information encapsulated within xref XML tags
biana.biana_commands'.administration
object
:
The most base type
biana.BianaDB.BianaDBaccess'.BianaDBaccess
:
Class used as an interface with database biana
biana.BianaParser.bianaParser.BianaParser
:
General Parser Class to biana
biana.BianaParser.biopaxLevel2Parser.BiopaxLevel2Parser
biana.BianaParser.cogParser.CogParser
:
COG Parser Class
biana.BianaParser.gooboParser.GOOBOParser
:
GO OBO 1.2 Parser Class
biana.BianaParser.GenericParser.GenericParser
:
Generic Parser Class
biana.BianaParser.hgncParser.HGNCParser
:
HGNC Parser Class
biana.BianaParser.ipiParser.IPIParser
:
IPI Parser Class
biana.BianaParser.keggGeneParser.KeggGeneParser
biana.BianaParser.keggKOParser.KeggKOParser
biana.BianaParser.keggligandParser.KeggLigandParser
:
Uniprot Parser Class
biana.BianaParser.MyDataParser.MyDataParser
:
MyData Parser Class
biana.BianaParser.ncbiGenPeptParser.NcbiGenPeptParserGenpeptParser
:
Genpept Parser class
biana.BianaParser.nrParser.NrParser
:
NCBI nr Parser Class
biana.BianaParser.pfamParser.PFAMParser
:
PFAM Parser Class
biana.BianaParser.psimioboParser.PSIMIOBOParser
:
PSI MI OBO Parser Class
biana.BianaParser.psi_Mi25Parser.Psi_MiFormattedDBParser
:
PSI-MI formatted DB Parser Class
biana.BianaParser.scopParser.SCOPParser
:
SCOP Parser Class
biana.BianaParser.stringParser.STRINGParser
:
STRING Parser Class
biana.BianaParser.taxonomyParser.TaxonomyParser
:
Taxonomy Parser Class
biana.BianaParser.uniprotParser.UniprotParser
:
Uniprot Parser Class
biana.BianaObjects.BianaReport.BianaReport
:
A class to control BIANA reports
biana.BianaObjects.BianaSessionManager.BianaSessionManager
:
A class to represent a BianaNetworkManager
biana.BianaParser.biopaxLevel2Parser.BiopaxDataSource
biana.BianaParser.biopaxLevel2Parser.BiopaxEntity
biana.BianaParser.biopaxLevel2Parser.BiopaxBioSource
biana.BianaParser.biopaxLevel2Parser.BiopaxInteraction
biana.BianaParser.biopaxLevel2Parser.BiopaxOpenControlledVocabulary
biana.BianaParser.biopaxLevel2Parser.BiopaxPathway
biana.BianaParser.biopaxLevel2Parser.BiopaxPathwayStep
:
A step in a patwhay Multiple interactions may occur in a pathway step, each should be listed in the STEP-INTERACTIONS property.
biana.BianaParser.biopaxLevel2Parser.BiopaxPhysicalEntity
biana.BianaParser.biopaxLevel2Parser.BiopaxComplex
biana.BianaParser.biopaxLevel2Parser.BiopaxDNA
biana.BianaParser.biopaxLevel2Parser.BiopaxProtein
biana.BianaParser.biopaxLevel2Parser.BiopaxRNA
biana.BianaParser.biopaxLevel2Parser.BiopaxSmallMolecule
biana.BianaParser.biopaxLevel2Parser.BiopaxPhysicalEntityParticipant
:
Biopax definition: any additional special characteristics of a physical entity in the context of an interaction or complex.
biana.BianaParser.biopaxLevel2Parser.BiopaxPhysicalInteraction
biana.BianaParser.biopaxLevel2Parser.BiopaxControl
:
An interaction in which one entity regulates, modifies, or otherwise influences another.
biana.BianaParser.biopaxLevel2Parser.BiopaxCatalysis
:
A control interaction in which a physical entity (a catalyst) increases the rate of a conversion interaction by lowering its activation energy.
biana.BianaParser.biopaxLevel2Parser.BiopaxModulation
biana.BianaParser.biopaxLevel2Parser.BiopaxConversion
biana.BianaParser.biopaxLevel2Parser.BiopaxBiochemicalReaction
biana.BianaParser.biopaxLevel2Parser.BiopaxComplexAssembly
biana.BianaParser.biopaxLevel2Parser.BiopaxTransport
biana.BianaParser.biopaxLevel2Parser.BiopaxXREF
biana.BianaParser.biopaxLevel2Parser.BiopaxLevel2Parser.BiopaxLevel2XMLParser
:
Class for parsing individual XML files obeying BIOPAX Level 2 standards
biana.BianaObjects.BlastResult.BlastResult
:
Object to store blast results
biana.BianaObjects.sequenceUtilities.BlastallParserIterator
biana.BianaDB.ConnectorDB.Buffer
:
Class used as an buffer for piana Inserts
biana.BianaDB.ConnectorDB.BufferElement
:
Class used in Buffer object to store a buffer element
biana.BianaObjects.CDHIT.CDHITCluster
biana.BianaObjects.CDHIT.CDHITMatch
biana.BianaDB.ConnectorDB.DB
:
Class for establishing conexions to pianaDB and handling inserts and selects
biana.BianaDB.database.Database
:
Class to represent a relational database
biana.BianaDB.BianaDatabaseDefinition.BianaDatabase
biana.BianaObjects.BianaSessionManager.Enum
biana.BianaObjects.ExternalDatabase'.ExternalDatabase
:
Class to represent an external database (any database giving biologic relevant information)
biana.BianaObjects.ExternalEntity'.ExternalEntity
:
This general object represents an entry in an external database
biana.BianaObjects.ExternalEntityRelation'.ExternalEntityRelation
:
This general object represents an entry represeting a relation between external entities in an external database
biana.BianaObjects.Ontology'.Ontology
:
Class to represent a general ontology
biana.BianaObjects.ExternalEntityAttribute'.ExternalEntityAttribute
:
Class that represents an external entity attribute
biana.BianaObjects.ExternalEntityRelationAttribute'.ExternalEntityRelationAttribute
biana.BianaObjects.ExternalEntityRelationParticipantAttribute'.ExternalEntityRelationParticipantAttribute
biana.utilities.FastaWriter.FastaWriter
:
FastaWriter class to handle outputting sequences in fasta format with customized header
biana.BianaDB.database.FieldDB
:
Class to represent a field in a database
biana.utilities.FormattedFileProcessor.FormattedFileProcessor
:
Wrapper around reading/processing various formatted input streams
biana.utilities.TsvReader.TsvReader
:
Read/process TSV (tab seperated) formatted files
biana.OutBianaInterface'.OutBianaInterface
biana.BianaObjects.PDB'.PDB
biana.BianaObjects.PDB'.PDBAtom
biana.BianaObjects.PDB'.PDBFragment
:
Class to represent a pdb fragment
biana.BianaObjects.PDB'.PDBResidue
biana.BianaDB.database.SQLSelectStatement
biana.BianaObjects.Sequence.Sequence
:
Class to represent a biologic sequencial entity, as nucleotide sequences, protein sequences, etc
biana.BianaObjects.Sequence.DNASequence
biana.BianaObjects.Sequence.ProteinSequence
biana.BianaObjects.Sequence.RNASequence
biana.BianaObjects.SequenceAlignment'.SequenceAlignment
:
Object to represent a sequence alignment, multiple or not
biana.BianaDB.database.TableDB
:
This object will implement a database table
biana.BianaObjects.UnificationProtocol'.UnificationAtomElement
:
Class to represent a condition of unification
biana.BianaObjects.UnificationProtocol'.UnificationProtocol
:
Class to represent
biana.BianaObjects.UserEntity'.UserEntity
:
A container class to represent a User Entity
biana.BianaObjects.UserEntityExpandedRelation'.UserEntityExpandedRelation
:
A class to represent expanded relations between two user entities
biana.BianaObjects.UserEntityRelation'.UserEntityRelation
:
A class to represent a relation between user entities
biana.BianaObjects.UserEntitySet.UserEntitySet
:
Class that represents a set of user entities.
biana.BianaParser.XMLNode.XMLNode
biana.utilities.autoincrement'.autoincrement
Home
Trees
Indices
Help
BIANA
Generated by Epydoc 3.0.1 on Tue May 26 17:06:23 2009
http://epydoc.sourceforge.net