public class BioPAXGraphMapper
extends java.lang.Object
Modifier and Type | Field and Description |
---|---|
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<java.lang.String,Edge> |
edges
Map from edge ids to Edge objects
|
java.util.HashMap<java.lang.String,java.lang.String> |
entityToReferenceUris
Map from entity uris to reference uris
|
Graph |
graph
Resulting GraphDocument object
|
java.util.HashMap<java.lang.String,Interaction> |
interactions
Map from complete uris to interaction objects
|
java.util.HashMap<java.lang.String,Node> |
nodes
Map from node ids and object uris to Node objects
|
java.util.HashMap<java.lang.String,Pathway> |
pathways
Map from complete uris to pathway objects
|
java.util.Vector<java.lang.String> |
pathwaysAdded |
java.util.HashMap<java.lang.String,PathwayStep> |
pathwaySteps
Map from complete uris to pathwaySteps objects
|
Constructor and Description |
---|
BioPAXGraphMapper() |
Modifier and Type | Method and Description |
---|---|
void |
map()
The mapping implementation
|
static void |
setReactionEffectAttribute(Interaction in,
GraphicNode node,
java.lang.String substring) |
static void |
setReactionEffectAttribute(Interaction in,
Node 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
|
public java.util.HashMap<java.lang.String,Node> nodes
public java.util.HashMap<java.lang.String,java.lang.String> entityToReferenceUris
public java.util.HashMap<java.lang.String,Interaction> interactions
public java.util.HashMap<java.lang.String,PathwayStep> pathwaySteps
public java.util.HashMap<java.lang.String,Pathway> pathways
public java.util.HashMap<java.lang.String,Edge> edges
public BioPAXNamingService biopaxNaming
public BioPAX biopax
public BioPAXToSBMLConverter bsc
public Graph graph
public java.util.Vector<java.lang.String> pathwaysAdded
public void map() throws java.lang.Exception
java.lang.Exception
public static void setReactionEffectAttribute(Interaction in, Node node, java.lang.String substring) throws java.lang.Exception
java.lang.Exception
public static void setReactionEffectAttribute(Interaction in, GraphicNode node, java.lang.String substring) throws java.lang.Exception
java.lang.Exception