pid
Class Interaction

java.lang.Object
  extended by pid.Interaction
All Implemented Interfaces:
java.io.Serializable

public class Interaction
extends java.lang.Object
implements java.io.Serializable

Interaction between two entities

Author:
Samuel Croset
See Also:
Serialized Form

Field Summary
private  Abstraction abstraction
           
private  java.util.ArrayList<InteractionComponent> components
           
private  java.util.ArrayList<Condition> conditions
           
private  java.util.ArrayList<java.lang.String> evidences
           
private  java.lang.String id
           
private  java.lang.String interactionType
           
private  java.util.ArrayList<java.lang.Integer> references
           
private  java.lang.String source
           
 
Constructor Summary
Interaction()
          Only constructor, initialise the arrays.
 
Method Summary
 Abstraction getAbstraction()
           
 java.util.ArrayList<InteractionComponent> getComponents()
           
 java.util.ArrayList<Condition> getConditions()
           
 java.util.ArrayList<java.lang.String> getEvidences()
           
 java.lang.String getId()
           
 java.lang.String getInteractionType()
           
 java.util.ArrayList<java.lang.Integer> getReferences()
           
 java.lang.String getSource()
           
 void setAbstraction(Abstraction abstraction)
           
 void setComponents(java.util.ArrayList<InteractionComponent> components)
           
 void setConditions(java.util.ArrayList<Condition> conditions)
           
 void setEvidences(java.util.ArrayList<java.lang.String> evidences)
           
 void setId(java.lang.String id)
           
 void setInteractionType(java.lang.String interactionType)
           
 void setReferences(java.util.ArrayList<java.lang.Integer> references)
           
 void setSource(java.lang.String source)
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

id

private java.lang.String id

interactionType

private java.lang.String interactionType

abstraction

private Abstraction abstraction

source

private java.lang.String source

conditions

private java.util.ArrayList<Condition> conditions

evidences

private java.util.ArrayList<java.lang.String> evidences

references

private java.util.ArrayList<java.lang.Integer> references

components

private java.util.ArrayList<InteractionComponent> components
Constructor Detail

Interaction

public Interaction()
Only constructor, initialise the arrays.

Method Detail

getId

public java.lang.String getId()
Returns:
the ID of the current interaction

setId

public void setId(java.lang.String id)

setInteractionType

public void setInteractionType(java.lang.String interactionType)

getInteractionType

public java.lang.String getInteractionType()
Returns:
the type of interaction. WARNING: this part is odd, because of the original XML

getAbstraction

public Abstraction getAbstraction()
Returns:
the abstraction object, which is a reference to another pathway.

setAbstraction

public void setAbstraction(Abstraction abstraction)

getSource

public java.lang.String getSource()
Returns:
the databse from which the interaction is coming from (only PID at the moment).

setSource

public void setSource(java.lang.String source)

getConditions

public java.util.ArrayList<Condition> getConditions()
Returns:
the condition (Positive or Negative) governing the apparition of this interation.

setConditions

public void setConditions(java.util.ArrayList<Condition> conditions)

getEvidences

public java.util.ArrayList<java.lang.String> getEvidences()
Returns:
the list of evidences. At the moment it is a 3 letters code, should be mapped to human readable via static variable.

setEvidences

public void setEvidences(java.util.ArrayList<java.lang.String> evidences)

getReferences

public java.util.ArrayList<java.lang.Integer> getReferences()
Returns:
the list of PubMed Ids (pmid) describing the interaction.

setReferences

public void setReferences(java.util.ArrayList<java.lang.Integer> references)

getComponents

public java.util.ArrayList<InteractionComponent> getComponents()
Returns:
the list of components interacting in this interaction.

setComponents

public void setComponents(java.util.ArrayList<InteractionComponent> components)