edu.iastate.biocyc.dao.txt
Class BiocycProtein

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

All Implemented Interfaces:

BiocycElement

public class BiocycProtein
extends AbstractBiocycElement

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

BiocycProtein(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
int	getCoefficient(java.lang.String component)
java.util.Collection	getComplexList() get the complex list that this is a component of
java.util.Collection	getComponentList() get the component list
java.util.Collection	getDblinkList() get the external database link
java.util.Collection	getEnzrxnList() get the catalyzed enzrxn reaction list
java.util.Collection	getGeneList() get the gene list
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

BiocycProtein

public BiocycProtein(java.util.Map dataMap)

default constructor

Parameters:

dataMap - the attribute value map

Method Detail

getDblinkList

public java.util.Collection getDblinkList()

get the external database link

Returns:

the external database link

getEnzrxnList

public java.util.Collection getEnzrxnList()

get the catalyzed enzrxn reaction list

Returns:

the enzrxn list

getGeneList

public java.util.Collection getGeneList()

get the gene list

Returns:

the gene list

getComplexList

public java.util.Collection getComplexList()

get the complex list that this is a component of

Returns:

the complex list

getComponentList

public java.util.Collection getComponentList()

get the component list

Returns:

the component list

getCoefficient

public int getCoefficient(java.lang.String component)

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

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