public class SimpleTextInfluenceToBioPAX
extends java.lang.Object
Modifier and Type | Field and Description |
---|---|
BioPAX |
biopax |
java.lang.String |
ChemType |
java.lang.String |
Comments |
java.lang.String |
Confidence |
java.lang.String |
Delay |
java.util.HashMap |
families |
java.util.HashMap |
mapFromTokenToFamily |
java.util.HashMap |
nameElements |
java.util.HashMap |
nameEntity |
java.util.HashMap |
nameFeatures |
java.util.HashMap |
nameParticipant |
java.util.HashMap |
nameReactions |
java.util.HashMap |
phenotypes |
java.lang.String |
pub1 |
java.lang.String |
pub2 |
java.util.HashMap |
publications |
java.lang.String |
Tissue |
java.util.Vector |
tissueTypes |
java.util.Vector |
tokens |
java.util.HashMap |
userDefinedFamilies |
java.util.HashMap |
userDefinedFamiliesExpand |
java.util.HashMap |
userDefinedFamiliesNonSelectedMembers |
Constructor and Description |
---|
SimpleTextInfluenceToBioPAX() |
Modifier and Type | Method and Description |
---|---|
void |
addComplex_(java.lang.String name) |
void |
addComplex(java.lang.String name) |
void |
addComplexBioPAX(java.lang.String name) |
void |
addElementaryReaction(java.lang.String id,
java.lang.String link) |
void |
addEntityBioPAX(java.lang.String name) |
void |
addFamilies(java.util.Vector newFamilies) |
void |
addFamily_(java.lang.String name) |
void |
addFamily(java.lang.String name) |
void |
addIntersectingFamilies() |
void |
addMolecule_(java.lang.String name) |
void |
addMolecule(java.lang.String name) |
void |
addPathwayInfluence(java.lang.String id,
java.lang.String link) |
void |
addPathwayInfluenceBioPAX(java.lang.String id,
java.lang.String link) |
void |
addPhenotype_(java.lang.String name) |
void |
addPhenotype(java.lang.String name) |
void |
addPhenotypeBioPAX(java.lang.String name) |
void |
addPublication(BiochemicalReaction r,
java.lang.String pub) |
void |
addPublicationBioPAX(BiochemicalReaction r,
java.lang.String pub) |
void |
addReaction(java.lang.String id,
java.lang.String link) |
void |
addReactionBioPAX(java.lang.String id,
java.lang.String link) |
void |
checkUserFamiliesForConsistency() |
java.util.Vector |
constitutiveReactions() |
static void |
deleteInstance() |
java.util.Vector |
entitiesForToken(java.lang.String token) |
void |
extractReactionParts_(java.lang.String link,
java.lang.StringBuffer pleft,
java.lang.StringBuffer pright,
java.lang.StringBuffer activation) |
void |
extractReactionParts(java.lang.String link,
java.lang.StringBuffer pleft,
java.lang.StringBuffer pright,
java.lang.StringBuffer activation) |
void |
findAllMembers_(java.lang.String sname,
java.util.Vector members) |
void |
findAllMembers(java.lang.String sname,
java.util.Vector members) |
java.util.Vector |
getAllComplexes(java.util.Vector comps) |
static SimpleTextInfluenceToBioPAX |
getInstance() |
void |
makeBioPAX(java.lang.String text,
java.util.Vector constitutiveReactions)
Construct BioPAX object from AIN data.
|
void |
makeMemberFamilyMap() |
java.util.Vector |
makeReactionListFromLink(java.lang.String reaction) |
void |
mergeFamilies() |
void |
prepareFamilies(java.lang.String text) |
java.lang.String |
preprocessText(java.lang.String text) |
java.util.Vector |
reactionList(java.lang.String text,
java.util.HashMap reactionBackLinks) |
public BioPAX biopax
public java.util.HashMap nameEntity
public java.util.HashMap nameParticipant
public java.util.HashMap nameElements
public java.util.HashMap nameFeatures
public java.util.HashMap nameReactions
public java.util.HashMap families
public java.util.HashMap phenotypes
public java.util.Vector tokens
public java.util.Vector tissueTypes
public java.util.HashMap publications
public java.util.HashMap userDefinedFamilies
public java.util.HashMap mapFromTokenToFamily
public java.util.HashMap userDefinedFamiliesExpand
public java.util.HashMap userDefinedFamiliesNonSelectedMembers
public java.lang.String pub1
public java.lang.String pub2
public java.lang.String ChemType
public java.lang.String Delay
public java.lang.String Confidence
public java.lang.String Comments
public java.lang.String Tissue
public static SimpleTextInfluenceToBioPAX getInstance()
public static void deleteInstance()
public void prepareFamilies(java.lang.String text) throws java.lang.Exception
java.lang.Exception
public void addFamilies(java.util.Vector newFamilies) throws java.lang.Exception
java.lang.Exception
public void makeMemberFamilyMap()
public void checkUserFamiliesForConsistency()
public void addIntersectingFamilies()
public void mergeFamilies()
public void addMolecule_(java.lang.String name) throws java.lang.Exception
java.lang.Exception
public void addComplex_(java.lang.String name) throws java.lang.Exception
java.lang.Exception
public void addPhenotype_(java.lang.String name) throws java.lang.Exception
java.lang.Exception
public void addFamily_(java.lang.String name) throws java.lang.Exception
java.lang.Exception
public void findAllMembers_(java.lang.String sname, java.util.Vector members) throws java.lang.Exception
java.lang.Exception
public java.util.Vector reactionList(java.lang.String text, java.util.HashMap reactionBackLinks)
public java.util.Vector makeReactionListFromLink(java.lang.String reaction)
public java.util.Vector entitiesForToken(java.lang.String token)
public void extractReactionParts_(java.lang.String link, java.lang.StringBuffer pleft, java.lang.StringBuffer pright, java.lang.StringBuffer activation)
public java.util.Vector constitutiveReactions()
public java.util.Vector getAllComplexes(java.util.Vector comps)
public void makeBioPAX(java.lang.String text, java.util.Vector constitutiveReactions) throws java.lang.Exception
text
- text extracted from AIN file.constitutiveReactions
- vector of constitutive reactions, e.g. forming a complex.java.lang.Exception
public void addEntityBioPAX(java.lang.String name) throws java.lang.Exception
java.lang.Exception
public void addComplexBioPAX(java.lang.String name) throws java.lang.Exception
java.lang.Exception
public void addPhenotypeBioPAX(java.lang.String name) throws java.lang.Exception
java.lang.Exception
public void addReactionBioPAX(java.lang.String id, java.lang.String link) throws java.lang.Exception
java.lang.Exception
public void addPublicationBioPAX(BiochemicalReaction r, java.lang.String pub) throws java.lang.Exception
java.lang.Exception
public void addPathwayInfluenceBioPAX(java.lang.String id, java.lang.String link) throws java.lang.Exception
java.lang.Exception
public void addMolecule(java.lang.String name) throws java.lang.Exception
java.lang.Exception
public void addComplex(java.lang.String name) throws java.lang.Exception
java.lang.Exception
public void addReaction(java.lang.String id, java.lang.String link) throws java.lang.Exception
java.lang.Exception
public void addPathwayInfluence(java.lang.String id, java.lang.String link) throws java.lang.Exception
java.lang.Exception
public void extractReactionParts(java.lang.String link, java.lang.StringBuffer pleft, java.lang.StringBuffer pright, java.lang.StringBuffer activation)
public void addElementaryReaction(java.lang.String id, java.lang.String link) throws java.lang.Exception
java.lang.Exception
public void addPublication(BiochemicalReaction r, java.lang.String pub) throws java.lang.Exception
java.lang.Exception
public void addPhenotype(java.lang.String name) throws java.lang.Exception
java.lang.Exception
public void addFamily(java.lang.String name) throws java.lang.Exception
java.lang.Exception
public void findAllMembers(java.lang.String sname, java.util.Vector members) throws java.lang.Exception
java.lang.Exception
public java.lang.String preprocessText(java.lang.String text)