Package biana :: Package BianaParser :: Module psi_Mi25Parser :: Class Psi_MiFormattedDBParser

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Class Psi_MiFormattedDBParser

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PSI-MI formatted DB Parser Class

Instance Methods

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__init__(self)
Starts the bianaParser Object

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parse_database(self)
Method that implements the specific operations of PSI-MI formatted database parser

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addNameAttributesToExternalEntityObject(self, objPsi_MiNames, psi_MiFormatted_object, nameAttribute='name', flagIgnoreAlias=False) source code

addXRefAttributesToExternalEntityObject(self, objPsi_MiXRef, psi_MiFormatted_object, flagIgnoreRefSecondary=False, attribute_class=<class 'biana.BianaObjects.ExternalEntityAttribute.ExternalEnt...) source code

decideInteractorTypeSpecificConversions(self, interactorType)

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decideSequenceTypeSpecificConversions(self, sequenceType)

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decideRoleSpecificConversions(self, nameRole)

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decideAliasTypeSpecificConversions(self, type)

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getIndexOfFirstOccurenceOfDigit(self, strDBName)

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decideDBReferenceSpecificConversions(self, objDBReference)

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checkOrInsertDBNamePrefix(self, dbName, prefix)

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Inherited from bianaParser.BianaParser: add_to_log, close, get_log_string, initialize_input_file_descriptor, parseArguments, print_help, start

Inherited from bianaParser.BianaParser (private): _indent, _splitsize

Inherited from object: __delattr__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __str__

Class Variables

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name = 'psi_mi_2.5'

description = 'This parser inserts psi-mi 2.5 formated informa...

external_entity_definition = 'Each relation participant is con...

external_entity_relations = 'External Entity Relations'

dictDBNameToPrefix = {}

Properties

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Inherited from object: __class__

Method Details

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init(self)
(Constructor)

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Starts the bianaParser Object

Overrides: object.__init__: (inherited documentation)

parse_database(self)

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Method that implements the specific operations of PSI-MI formatted database parser

Overrides: bianaParser.BianaParser.parse_database

Class Variable Details

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description

Value:

'This parser inserts psi-mi 2.5 formated information to biana database
'

external_entity_definition

Value:

'Each relation participant is considered as a distinct External Entity
'

Class Psi_MiFormattedDBParser

__init__(self) (Constructor)

parse_database(self)

description

external_entity_definition

init(self)
(Constructor)