edu.iastate.biocyc.dao.txt
Class AbstractBiocycElement

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

All Implemented Interfaces:

BiocycElement

Direct Known Subclasses:

BiocycClass, BiocycCompound, BiocycEnzrxn, BiocycGene, BiocycPathway, BiocycProtein, BiocycReaction

public abstract class AbstractBiocycElement
extends java.lang.Object
implements BiocycElement

Field Summary

(package private) java.util.Map

dataMap the attribute value

Constructor Summary

AbstractBiocycElement()
default constructor

AbstractBiocycElement(java.util.Map dataMap)
default constructor

Method Summary

static java.util.Map	adjustName(java.util.Map instanceMap) adjust the name so it is unique in the whole name space.
abstract Blockunit	createBlockunit(java.lang.String organism, java.lang.String username, java.lang.String source) create the blockunit
static java.util.Set	duplicatedName(java.util.Map instanceMap) collect duplicate common name.
java.util.Collection	getCitationList() get the pubmed id list
java.util.Collection	getCommentList() get the comment list
java.lang.String	getCommonName() get the common name
java.util.Map	getDataMap() get the data map
protected java.lang.Object	getFirst(java.util.Map dataMap, java.lang.Object key) get first object in the map.
java.util.Collection	getSynonymList() get the synonym list
java.util.Collection	getTypeList() get the type list
java.lang.String	getUniqueId() get the unique id
static boolean	isNumeric(java.lang.String str) detect if a string is a integer
Blockunit	joinCommonProperties(Blockunit blockunit) join common properties like synonyms, comments and references
Blockunit	joinConfidence(Blockunit blockunit)
void	setDataMap(java.util.Map dataMap) set the data map

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

dataMap

java.util.Map dataMap

the attribute value

Constructor Detail

AbstractBiocycElement

public AbstractBiocycElement()

default constructor

AbstractBiocycElement

public AbstractBiocycElement(java.util.Map dataMap)

default constructor

Parameters:

dataMap - the attribute value map

Method Detail

setDataMap

public void setDataMap(java.util.Map dataMap)

set the data map

Specified by:

setDataMap in interface BiocycElement

Parameters:

dataMap - data map for all attributes

getUniqueId

public java.lang.String getUniqueId()

get the unique id

Specified by:

getUniqueId in interface BiocycElement

Returns:

the unique id

getCommonName

public java.lang.String getCommonName()

get the common name

Specified by:

getCommonName in interface BiocycElement

Returns:

common name

getFirst

protected java.lang.Object getFirst(java.util.Map dataMap,
                                    java.lang.Object key)

get first object in the map. Used for single value attributes

Parameters:

dataMap - the map

key - the key

Returns:

the first object

getSynonymList

public java.util.Collection getSynonymList()

get the synonym list

Specified by:

getSynonymList in interface BiocycElement

Returns:

synonym list

getTypeList

public java.util.Collection getTypeList()

get the type list

Specified by:

getTypeList in interface BiocycElement

Returns:

type list

getDataMap

public java.util.Map getDataMap()

get the data map

Specified by:

getDataMap in interface BiocycElement

Returns:

the data map

getCommentList

public java.util.Collection getCommentList()

get the comment list

Returns:

the comment list

getCitationList

public java.util.Collection getCitationList()

get the pubmed id list

Returns:

the pubmed id list

duplicatedName

public static java.util.Set duplicatedName(java.util.Map instanceMap)

collect duplicate common name. For these names, we should use unique id in database

Parameters:

instanceMap - the instance map

Returns:

the duplicated name set

adjustName

public static java.util.Map adjustName(java.util.Map instanceMap)

adjust the name so it is unique in the whole name space.

Parameters:

instanceMap - the instance map

Returns:

the new map do not contain duplicated common name

createBlockunit

public abstract 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

Returns:

create the blockunit

joinCommonProperties

public Blockunit joinCommonProperties(Blockunit blockunit)

join common properties like synonyms, comments and references

Parameters:

blockunit - the blockunit to be joined.

Returns:

the new blockunit has joined information

joinConfidence

public Blockunit joinConfidence(Blockunit blockunit)

isNumeric

public static boolean isNumeric(java.lang.String str)

detect if a string is a integer

Parameters:

str - string to detect

Returns:

true if it is numeric, I am not sure the semantic of Character.isDigit()