edu.iastate.biocyc.dao.txt
Class BiocycClass

java.lang.Object
  edu.iastate.biocyc.dao.txt.AbstractBiocycElement
      edu.iastate.biocyc.dao.txt.BiocycClass

All Implemented Interfaces:

BiocycElement

public class BiocycClass
extends AbstractBiocycElement

specialized class

Author:

Jie Li

Field Summary

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

logger log4j facility

Fields inherited from class edu.iastate.biocyc.dao.txt.AbstractBiocycElement

dataMap

Constructor Summary

BiocycClass(java.util.Map dataMap)
default constructor

Method Summary

Blockunit	createBlockunit(java.lang.String organism, java.lang.String username, java.lang.String source) create the blockunit
ClassName	createClassName() get the data object class name
static java.util.Map	getBiologicalType(org._3pq.jgrapht.DirectedGraph classNetwork) this is an extension of protein type detection.
static java.util.Collection	getDescendantList(org._3pq.jgrapht.DirectedGraph network, java.lang.Object node) get descendant list.
static java.util.Map	getProteinType(org._3pq.jgrapht.DirectedGraph classNetwork) get the protein type, either protein complex, or polypeptide or nothing else
static boolean	isRoot(java.lang.String parentType) determine if this is a root class
static java.util.Map	toBiocycMap(java.util.Map dataMap) instance map contains the unique id key and biocyc element value

Methods inherited from class edu.iastate.biocyc.dao.txt.AbstractBiocycElement

adjustName, duplicatedName, getCitationList, getCommentList, getCommonName, getDataMap, getFirst, getSynonymList, getTypeList, getUniqueId, isNumeric, joinCommonProperties, joinConfidence, setDataMap

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

BiocycClass

public BiocycClass(java.util.Map dataMap)

default constructor

Parameters:

dataMap - the data map

Method Detail

isRoot

public static boolean isRoot(java.lang.String parentType)

determine if this is a root class

Parameters:

parentType - the parent class

Returns:

true if this is a root, false if it is not

toBiocycMap

public static java.util.Map toBiocycMap(java.util.Map dataMap)

instance map contains the unique id key and biocyc element value

Parameters:

dataMap - the data map

Returns:

the instance map

getProteinType

public static java.util.Map getProteinType(org._3pq.jgrapht.DirectedGraph classNetwork)

get the protein type, either protein complex, or polypeptide or nothing else

Parameters:

classNetwork - the class network

Returns:

the mapping

getBiologicalType

public static java.util.Map getBiologicalType(org._3pq.jgrapht.DirectedGraph classNetwork)

this is an extension of protein type detection. We need to get any biological type including the entity type, interaction type or pathway

Parameters:

classNetwork - the class network

Returns:

the map between the biocyc type and metnet biological type

getDescendantList

public static java.util.Collection getDescendantList(org._3pq.jgrapht.DirectedGraph network,
                                                     java.lang.Object node)

get descendant list. The self is not a descendant.

Parameters:

network - the class network

node - the node

Returns:

the descendant uniqueId list

createClassName

public ClassName createClassName()

get the data object class name

Returns:

the data object class name

createBlockunit

public Blockunit createBlockunit(java.lang.String organism,
                                 java.lang.String username,
                                 java.lang.String source)

Description copied from interface: BiocycElement

create the blockunit

Specified by:

createBlockunit in interface BiocycElement

Specified by:

createBlockunit in class AbstractBiocycElement

Returns:

create the blockunit