cls.ReactomeBiopaxParser.CReactomeBiopaxParser Class Reference

Public Member Functions
def	Initialize (self, config, log=False)
	Initialize the parser. More...
def	GetIid2Iids (self)
	Return the iid2iids dictionary. More...
def	GetXref2Iid (self)
	Return the xref2iids dictionary. More...
def	GetData (self)
	Return the data dictionary. More...
def	GetEntries (self)
	Return the ENTRIES object. More...

Public Attributes
	recursions

Static Public Attributes
bool	log = False
	data = None
	iid2iids = defaultdict(set)
	xref2iid = defaultdict(set)
int	recursions = 0
	visitedIds = set()
	config = CPaths()
	react = CReactomeBiopaxParser()
	start = time.time()
	log
int	i = 0
def	i2i = react.GetIid2Iids()
def	x2i = react.GetXref2Iid()

Member Function Documentation

GetData()

def cls.ReactomeBiopaxParser.CReactomeBiopaxParser.GetData

(

self

)

Return the data dictionary.

    @return The dictionary that contains all the bipax pathway data.

GetEntries()

def cls.ReactomeBiopaxParser.CReactomeBiopaxParser.GetEntries

(

self

)

Return the ENTRIES object.

    @return The dictionary that describes the attributes and values for
    each XML element in a Biopax file.

GetIid2Iids()

def cls.ReactomeBiopaxParser.CReactomeBiopaxParser.GetIid2Iids

(

self

)

Return the iid2iids dictionary.

    @return The dictionary that links internal object ids to their
    annotated object ids.

GetXref2Iid()

def cls.ReactomeBiopaxParser.CReactomeBiopaxParser.GetXref2Iid

(

self

)

Return the xref2iids dictionary.

    @return The dictionary that external database references to internal
    object ids.

Initialize()

def cls.ReactomeBiopaxParser.CReactomeBiopaxParser.Initialize	(		self,
			config,
			log = False
	)

Initialize the parser.

    Parse the XML file into an internal representation. then go through
    this representation in order to extract the pathway hierarchy and
    link internal to external ids. Store the resulting data in variables.

    @param config  @ref common.Paths.CPaths object containing paths
    @param log If @c True will output internal logging information. False
    by default.
    @return @c True if all went ok. @c False if there was an error
    (issued by @ref common.ErrorHandler).

Member Data Documentation

config

cls.ReactomeBiopaxParser.CReactomeBiopaxParser.config = CPaths()

static

data

cls.ReactomeBiopaxParser.CReactomeBiopaxParser.data = None

static

i

int cls.ReactomeBiopaxParser.CReactomeBiopaxParser.i = 0

static

i2i

def cls.ReactomeBiopaxParser.CReactomeBiopaxParser.i2i = react.GetIid2Iids()

static

iid2iids

cls.ReactomeBiopaxParser.CReactomeBiopaxParser.iid2iids = defaultdict(set)

static

log [1/2]

bool cls.ReactomeBiopaxParser.CReactomeBiopaxParser.log = False

static

log [2/2]

cls.ReactomeBiopaxParser.CReactomeBiopaxParser.log

static

react

cls.ReactomeBiopaxParser.CReactomeBiopaxParser.react = CReactomeBiopaxParser()

static

recursions [1/2]

int cls.ReactomeBiopaxParser.CReactomeBiopaxParser.recursions = 0

static

recursions [2/2]

cls.ReactomeBiopaxParser.CReactomeBiopaxParser.recursions

start

cls.ReactomeBiopaxParser.CReactomeBiopaxParser.start = time.time()

static

visitedIds

cls.ReactomeBiopaxParser.CReactomeBiopaxParser.visitedIds = set()

static

x2i

def cls.ReactomeBiopaxParser.CReactomeBiopaxParser.x2i = react.GetXref2Iid()

static

xref2iid

cls.ReactomeBiopaxParser.CReactomeBiopaxParser.xref2iid = defaultdict(set)

static

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

• cls/ReactomeBiopaxParser.py