fr.curie.BiNoM.pathways.utils
Class BioPAXGraphMapper

java.lang.Object
  fr.curie.BiNoM.pathways.utils.BioPAXGraphMapper

public class BioPAXGraphMapper
extends java.lang.Object

Creates a BioPAX index - mapping of BioPAX content onto an attributed (di)graph

Field Summary

BioPAX	biopax Input BioPAX object
BioPAXNamingService	biopaxNaming Naming service used for the mapping
BioPAXToSBMLConverter	bsc BioPAXToSBML Converter is needed to created the Reaction Network part of the index
java.util.HashMap	edges Map from edge ids to GraphicEdge objects
java.util.HashMap	entities Map from complete uris to entity objects
edu.rpi.cs.xgmml.GraphDocument	graph Resulting GraphDocument object
java.util.HashMap	interactions Map from complete uris to interaction objects
java.util.HashMap	nodes Map from node ids to GraphicNode objects
java.util.HashMap	participants Map from complete uris to physicalEntityParticipants
java.util.HashMap	pathways Map from complete uris to pathway objects
java.util.HashMap	pathwaySteps Map from complete uris to pathwaySteps objects

Constructor Summary

BioPAXGraphMapper()

Method Summary

void	map() The mapping implementation
static void	setReactionEffectAttribute(interaction in, edu.rpi.cs.xgmml.GraphicNode node, java.lang.String substring) If there is a comment with which contains substring+":", this comment is added as a value of an attribute named substring

Methods inherited from class java.lang.Object

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

Field Detail

nodes

public java.util.HashMap nodes

Map from node ids to GraphicNode objects

participants

public java.util.HashMap participants

Map from complete uris to physicalEntityParticipants

entities

public java.util.HashMap entities

Map from complete uris to entity objects

interactions

public java.util.HashMap interactions

Map from complete uris to interaction objects

pathwaySteps

public java.util.HashMap pathwaySteps

Map from complete uris to pathwaySteps objects

pathways

public java.util.HashMap pathways

Map from complete uris to pathway objects

edges

public java.util.HashMap edges

Map from edge ids to GraphicEdge objects

biopaxNaming

public BioPAXNamingService biopaxNaming

Naming service used for the mapping

biopax

public BioPAX biopax

Input BioPAX object

bsc

public BioPAXToSBMLConverter bsc

BioPAXToSBML Converter is needed to created the Reaction Network part of the index

graph

public edu.rpi.cs.xgmml.GraphDocument graph

Resulting GraphDocument object

Constructor Detail

BioPAXGraphMapper

public BioPAXGraphMapper()

Method Detail

map

public void map()
         throws java.lang.Exception

The mapping implementation

Throws:

java.lang.Exception

setReactionEffectAttribute

public static void setReactionEffectAttribute(interaction in,
                                              edu.rpi.cs.xgmml.GraphicNode node,
                                              java.lang.String substring)
                                       throws java.lang.Exception

If there is a comment with which contains substring+":", this comment is added as a value of an attribute named substring

Throws:

java.lang.Exception