edu.iastate.metnet.aracyc
Class AracycEntity

java.lang.Object
  edu.iastate.metnet.aracyc.AracycEntity

public class AracycEntity
extends java.lang.Object

data object to match Blockunit/Entity

compounds.dat
UNIQUE-ID # TYPES # COMMON-NAME # APPEARS-IN-BINDING-REACTIONS # ATOM-CHARGES # CAS-REGISTRY-NUMBERS # CHARGE # CHEMICAL-FORMULA # CITATIONS # COMMENT # DBLINKS # MOLECULAR-WEIGHT # N+1-NAME # N-1-NAME # N-NAME # ORIGINAL-FRAME-TYPE # PKA1 # PKA2 # PKA3 # SMILES # SUPERATOMS # SYNONYMS # SYSTEMATIC-NAME

Author:

Jie Li

Field Summary

(package private) java.lang.String	aracycid UNIQUE-ID
(package private) java.util.ArrayList	citations CITATIONS
(package private) java.util.ArrayList	comments COMMENT # DBLINKS (CAS, TAIR, PIR, WIT-PWY, SWISSPROT, METACYC, LIGAND-CPD, NCI, LIGAND, ENTREZ, SOYBASE, SWISSMODEL, we can not predict all source of dblinks and their format, it's better to put in the comment field.)
(package private) java.lang.String	name COMMON-NAME
(package private) java.util.ArrayList	synonyms UNIQUE-ID # N+1-NAME # N-1-NAME # N-NAME # SMILES # SYNONYMS # SYSTEMATIC-NAME

Constructor Summary

AracycEntity()

Method Summary

void	addCitations(java.util.ArrayList citations) add citations
void	addCitations(java.lang.String citation) add citations
void	addComments(java.util.ArrayList comments) add comments
void	addComments(java.lang.String comment) add comments
void	addSynonyms(java.util.ArrayList synonyms) add new synonym
void	addSynonyms(java.lang.String synonym) add new synonym
java.lang.String	getAracycid() return the aracyc unique id
java.util.ArrayList	getCitations() return the citations
java.util.ArrayList	getComments() return the comments
java.lang.String	getName() return the name
java.util.ArrayList	getSynonyms() return the synonym
void	put(java.lang.String key, java.util.ArrayList values) common interface for all
void	setAracycid(java.lang.String aracycid) set the aracyc id
void	setCitations(java.util.ArrayList citations) set citations
void	setComments(java.util.ArrayList comments) set comment
void	setName(java.lang.String name) set the name
void	setSynonyms(java.util.ArrayList synonyms) set the synonym

Methods inherited from class java.lang.Object

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

Field Detail

name

java.lang.String name

COMMON-NAME

synonyms

java.util.ArrayList synonyms

UNIQUE-ID # N+1-NAME # N-1-NAME # N-NAME # SMILES # SYNONYMS # SYSTEMATIC-NAME

aracycid

java.lang.String aracycid

UNIQUE-ID

citations

java.util.ArrayList citations

CITATIONS

comments

java.util.ArrayList comments

COMMENT # DBLINKS (CAS, TAIR, PIR, WIT-PWY, SWISSPROT, METACYC, LIGAND-CPD, NCI, LIGAND, ENTREZ, SOYBASE, SWISSMODEL, we can not predict all source of dblinks and their format, it's better to put in the comment field.)

Constructor Detail

AracycEntity

public AracycEntity()

Method Detail

getAracycid

public java.lang.String getAracycid()

return the aracyc unique id

Returns:

Returns the aracycid.

setAracycid

public void setAracycid(java.lang.String aracycid)

set the aracyc id

Parameters:

aracycid - The aracycid to set.

getCitations

public java.util.ArrayList getCitations()

return the citations

Returns:

Returns the citations.

setCitations

public void setCitations(java.util.ArrayList citations)

set citations

Parameters:

citations - The citations to set.

addCitations

public void addCitations(java.lang.String citation)

add citations

Parameters:

citation - the citation to be added

addCitations

public void addCitations(java.util.ArrayList citations)

add citations

Parameters:

citations - the citation to be added

addComments

public void addComments(java.lang.String comment)

add comments

Parameters:

comment - the comment to be added

addComments

public void addComments(java.util.ArrayList comments)

add comments

Parameters:

comments - the comment to be added

getComments

public java.util.ArrayList getComments()

return the comments

Returns:

Returns the comments.

setComments

public void setComments(java.util.ArrayList comments)

set comment

Parameters:

comments - The comments to set.

getName

public java.lang.String getName()

return the name

Returns:

Returns the name.

setName

public void setName(java.lang.String name)

set the name

Parameters:

name - The name to set.

getSynonyms

public java.util.ArrayList getSynonyms()

return the synonym

Returns:

Returns the synonyms.

setSynonyms

public void setSynonyms(java.util.ArrayList synonyms)

set the synonym

Parameters:

synonyms - The synonyms to set.

addSynonyms

public void addSynonyms(java.lang.String synonym)

add new synonym

Parameters:

synonym -

addSynonyms

public void addSynonyms(java.util.ArrayList synonyms)

add new synonym

Parameters:

synonyms -

put

public void put(java.lang.String key,
                java.util.ArrayList values)

common interface for all

Parameters:

key - the key from the map

values - the values of the key