edu.iastate.biocyc.io
Class BiocycImporter

java.lang.Object
  edu.iastate.biocyc.io.BiocycImporter

public class BiocycImporter
extends java.lang.Object

read the Biocyc flat files

Author:

Jie Li

Field Summary

(package private) static org.apache.log4j.Logger

logger log4j facility

Constructor Summary

BiocycImporter()
initialize the class data

Method Summary

edu.uci.ics.jung.graph.DirectedGraph	convertGraph(org._3pq.jgrapht.DirectedGraph network, java.util.Map dataMap) convert to the JUNG graph
java.util.Map	createBigMap() create a big map containing all instances.
org._3pq.jgrapht.DirectedGraph	createClassNetwork(java.util.Map bigMap) create the class network
org._3pq.jgrapht.DirectedGraph	createClassPathway(java.util.Map bigMap) get the pathway and class relation
org._3pq.jgrapht.DirectedGraph	createNestedNetwork(java.util.Map bigMap) create the super pathway network
java.lang.Object[]	createReactionNetwork(java.util.Map bigMap) create a big network of all Biocyc information
org._3pq.jgrapht.DirectedGraph	decomposePathway(org._3pq.jgrapht.DirectedGraph network, java.util.Map dataMap, java.util.Collection pbidList) get the graph model containing specified pathways
java.lang.String	getClassFilename()
java.lang.String	getCompoundFilename()
java.lang.String	getDirectory()
java.lang.String	getEnzrxnFilename()
java.lang.String	getGeneFilename()
java.lang.String	getPathwayFilename()
java.lang.String	getProteinFilename()
java.lang.String	getReactionFilename()
java.lang.Object[]	rewriteGraph(java.util.Map bigMap, org._3pq.jgrapht.DirectedGraph reactionNet, org.apache.commons.collections.map.MultiKeyMap coeffMap, org._3pq.jgrapht.DirectedGraph classNet, java.lang.String organism, java.lang.String username, java.lang.String source) the most important function in this conversion.
java.util.Map	rewritePathway(org._3pq.jgrapht.DirectedGraph pathwayNet, java.util.Map bigMap, org._3pq.jgrapht.DirectedGraph network, java.util.Map dataMap, java.lang.String organism, java.lang.String username, java.lang.String source) construct pathway blockunit
void	setDirectory(java.lang.String directory)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

logger

static org.apache.log4j.Logger logger

log4j facility

Constructor Detail

BiocycImporter

public BiocycImporter()

initialize the class data

Method Detail

getDirectory

public java.lang.String getDirectory()

Returns:

the directory

setDirectory

public void setDirectory(java.lang.String directory)

Parameters:

directory - the directory to set

getEnzrxnFilename

public java.lang.String getEnzrxnFilename()

Returns:

the enzrxnFilename

getGeneFilename

public java.lang.String getGeneFilename()

Returns:

the geneFilename

getPathwayFilename

public java.lang.String getPathwayFilename()

Returns:

the pathwayFilename

getProteinFilename

public java.lang.String getProteinFilename()

Returns:

the proteinFilename

getReactionFilename

public java.lang.String getReactionFilename()

Returns:

the reactionFilename

getClassFilename

public java.lang.String getClassFilename()

Returns:

the classFilename

getCompoundFilename

public java.lang.String getCompoundFilename()

Returns:

the compoundFilename

createBigMap

public java.util.Map createBigMap()

create a big map containing all instances. Before this is called, setDirectory() must be called

Returns:

the big map of all instances. The key is the unique id, and the value is BiocycElement

createReactionNetwork

public java.lang.Object[] createReactionNetwork(java.util.Map bigMap)

create a big network of all Biocyc information

Parameters:

bigMap - the big map of the instance

Returns:

the big network only containing the unique id

createClassPathway

public org._3pq.jgrapht.DirectedGraph createClassPathway(java.util.Map bigMap)

get the pathway and class relation

Parameters:

bigMap -

Returns:

the class to pathway graph

createClassNetwork

public org._3pq.jgrapht.DirectedGraph createClassNetwork(java.util.Map bigMap)

create the class network

Parameters:

bigMap - the big map of the instance

Returns:

the class network containing the unique id

createNestedNetwork

public org._3pq.jgrapht.DirectedGraph createNestedNetwork(java.util.Map bigMap)

create the super pathway network

Parameters:

Map - the big map of the instance

Returns:

the super pathway containing the unique id

decomposePathway

public org._3pq.jgrapht.DirectedGraph decomposePathway(org._3pq.jgrapht.DirectedGraph network,
                                                       java.util.Map dataMap,
                                                       java.util.Collection pbidList)

get the graph model containing specified pathways

Parameters:

network - the network after rewrite

dataMap - the blockunit map

pbidList - the pathway blockid list

Returns:

the subgraph

rewritePathway

public java.util.Map rewritePathway(org._3pq.jgrapht.DirectedGraph pathwayNet,
                                    java.util.Map bigMap,
                                    org._3pq.jgrapht.DirectedGraph network,
                                    java.util.Map dataMap,
                                    java.lang.String organism,
                                    java.lang.String username,
                                    java.lang.String source)

construct pathway blockunit

Parameters:

pathwayNet - the nested net

bigMap - the big map of biocyc

network - the reaction network

dataMap - the datamap

Returns:

the pathway blockid and blockunit map

rewriteGraph

public java.lang.Object[] rewriteGraph(java.util.Map bigMap,
                                       org._3pq.jgrapht.DirectedGraph reactionNet,
                                       org.apache.commons.collections.map.MultiKeyMap coeffMap,
                                       org._3pq.jgrapht.DirectedGraph classNet,
                                       java.lang.String organism,
                                       java.lang.String username,
                                       java.lang.String source)

the most important function in this conversion. It rewrites the reaction network from BioCyc to a labeled graph model for MetNet.

Parameters:

bigMap - the big map of all information with unique ID

reactionNet - the reaction network from BioCyc

classNet - the class network from BioCyc

Returns:

the labeled graph model and data mapping from the id to the object.

convertGraph

public edu.uci.ics.jung.graph.DirectedGraph convertGraph(org._3pq.jgrapht.DirectedGraph network,
                                                         java.util.Map dataMap)

convert to the JUNG graph

Parameters:

network - the reaction network

dataMap - the blockid and blockunit map

Returns:

the JUNG graph