GOGrapher.Storage.FilebasedStorage.FilebasedStorage Class Reference

Abstract class / Interface for all storage implementations. More...

Inheritance diagram for GOGrapher.Storage.FilebasedStorage.FilebasedStorage:

List of all members.

Public Member Functions
def	__init__
	Constructor Takes two required parameters.
def	saveState
def	loadState
def	parseAssociation
def	parseOwl
def	parseOboXml
def	getTermAssocList
def	makeTerm
def	makeTerms
def	makeProtein
def	makeProteins
def	getTermsProteinIDs
def	getProteinsTermIDs
def	setTermsProteins
def	getProteinsID
def	getTermsID
Public Attributes
	names
	associations_term
	associations_prot
	relationships
	aspects

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Detailed Description

Abstract class / Interface for all storage implementations.

Definition at line 91 of file FilebasedStorage.py.

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Member Function Documentation

def GOGrapher.Storage.FilebasedStorage.FilebasedStorage.__init__	(		self,
			associations,
			owlfile = None,
			oboxmlfile = None,
			hardEvidence = True
	)

Constructor Takes two required parameters.

Parses all files, stores info in memory. One of oboxmlfile or owlfile must be specified.

Parameters:

	associations	An dictionary whose keys are species names and whose values are assocation file locations
	owfile	Location of GO term relationship OWL file - or -
	oboxmlfile	Location of GO term relationship OBO XML file
	hardEvidence	If true, ignore soft evidence for associations (IEA, IEP, ND)

Definition at line 101 of file FilebasedStorage.py.

def GOGrapher.Storage.FilebasedStorage.FilebasedStorage.saveState

(

self

)

Reimplemented from GOGrapher.Storage.StorageInterface.StorageInterface.

Definition at line 119 of file FilebasedStorage.py.

def GOGrapher.Storage.FilebasedStorage.FilebasedStorage.loadState

(

self

)

Reimplemented from GOGrapher.Storage.StorageInterface.StorageInterface.

Definition at line 123 of file FilebasedStorage.py.

def GOGrapher.Storage.FilebasedStorage.FilebasedStorage.parseAssociation	(		self,
			location,
			hardEvidence
	)

Definition at line 127 of file FilebasedStorage.py.

def GOGrapher.Storage.FilebasedStorage.FilebasedStorage.parseOwl	(		self,
			location
	)

Definition at line 150 of file FilebasedStorage.py.

def GOGrapher.Storage.FilebasedStorage.FilebasedStorage.parseOboXml	(		self,
			location
	)

Definition at line 175 of file FilebasedStorage.py.

def GOGrapher.Storage.FilebasedStorage.FilebasedStorage.getTermAssocList	(		self,
			aspect
	)

Reimplemented from GOGrapher.Storage.StorageInterface.StorageInterface.

Definition at line 200 of file FilebasedStorage.py.

def GOGrapher.Storage.FilebasedStorage.FilebasedStorage.makeTerm	(		self,
			term_id
	)

Reimplemented from GOGrapher.Storage.StorageInterface.StorageInterface.

Definition at line 213 of file FilebasedStorage.py.

def GOGrapher.Storage.FilebasedStorage.FilebasedStorage.makeTerms	(		self,
			term_ids
	)

Definition at line 225 of file FilebasedStorage.py.

def GOGrapher.Storage.FilebasedStorage.FilebasedStorage.makeProtein	(		self,
			protein_id
	)

Reimplemented from GOGrapher.Storage.StorageInterface.StorageInterface.

Definition at line 229 of file FilebasedStorage.py.

def GOGrapher.Storage.FilebasedStorage.FilebasedStorage.makeProteins	(		self,
			protein_ids
	)

Reimplemented from GOGrapher.Storage.StorageInterface.StorageInterface.

Definition at line 233 of file FilebasedStorage.py.

def GOGrapher.Storage.FilebasedStorage.FilebasedStorage.getTermsProteinIDs	(		self,
			termnode,
			species
	)

Reimplemented from GOGrapher.Storage.StorageInterface.StorageInterface.

Definition at line 237 of file FilebasedStorage.py.

def GOGrapher.Storage.FilebasedStorage.FilebasedStorage.getProteinsTermIDs	(		self,
			proteinnode,
			species
	)

Reimplemented from GOGrapher.Storage.StorageInterface.StorageInterface.

Definition at line 246 of file FilebasedStorage.py.

def GOGrapher.Storage.FilebasedStorage.FilebasedStorage.setTermsProteins	(		self,
			termlist,
			species
	)

Reimplemented from GOGrapher.Storage.StorageInterface.StorageInterface.

Definition at line 260 of file FilebasedStorage.py.

def GOGrapher.Storage.FilebasedStorage.FilebasedStorage.getProteinsID	(		self,
			symbol
	)

Reimplemented from GOGrapher.Storage.StorageInterface.StorageInterface.

Definition at line 264 of file FilebasedStorage.py.

def GOGrapher.Storage.FilebasedStorage.FilebasedStorage.getTermsID	(		self,
			goid
	)

Reimplemented from GOGrapher.Storage.StorageInterface.StorageInterface.

Definition at line 268 of file FilebasedStorage.py.

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Member Data Documentation

GOGrapher.Storage.FilebasedStorage.FilebasedStorage.names

Definition at line 104 of file FilebasedStorage.py.

GOGrapher.Storage.FilebasedStorage.FilebasedStorage.associations_term

Definition at line 112 of file FilebasedStorage.py.

GOGrapher.Storage.FilebasedStorage.FilebasedStorage.associations_prot

Definition at line 113 of file FilebasedStorage.py.

GOGrapher.Storage.FilebasedStorage.FilebasedStorage.relationships

Definition at line 165 of file FilebasedStorage.py.

GOGrapher.Storage.FilebasedStorage.FilebasedStorage.aspects

Definition at line 171 of file FilebasedStorage.py.

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The documentation for this class was generated from the following file:

• GOGrapher/Storage/FilebasedStorage.py