org.biojava.bio.structure
Class Compound

java.lang.Object
  extended by org.biojava.bio.structure.Compound
All Implemented Interfaces:
java.lang.Cloneable

public class Compound
extends java.lang.Object
implements java.lang.Cloneable

Created by IntelliJ IDEA. User: jacobsen Date: 22-Jan-2007 Time: 18:14:25


Constructor Summary
Compound()
           
 
Method Summary
 void addChain(Chain chain)
           
 Compound clone()
           
 java.lang.String getAtcc()
           
 java.lang.String getBiologicalUnit()
           
 java.lang.String getCell()
           
 java.lang.String getCellLine()
           
 java.lang.String getCellularLocation()
           
 java.util.List<java.lang.String> getChainId()
          Returns the chain id value.
 java.util.List<Chain> getChains()
          get the chains that are part of this Compound
 java.lang.String getDetails()
           
 java.util.List<java.lang.String> getEcNums()
           
 java.lang.String getEngineered()
           
 java.lang.String getExpressionSystem()
           
 java.lang.String getExpressionSystemAtccNumber()
           
 java.lang.String getExpressionSystemCell()
           
 java.lang.String getExpressionSystemCellLine()
           
 java.lang.String getExpressionSystemCellularLocation()
           
 java.lang.String getExpressionSystemGene()
           
 java.lang.String getExpressionSystemOrgan()
           
 java.lang.String getExpressionSystemOrganelle()
           
 java.lang.String getExpressionSystemOtherDetails()
           
 java.lang.String getExpressionSystemPlasmid()
           
 java.lang.String getExpressionSystemStrain()
           
 java.lang.String getExpressionSystemTaxId()
           
 java.lang.String getExpressionSystemTissue()
           
 java.lang.String getExpressionSystemVariant()
           
 java.lang.String getExpressionSystemVector()
           
 java.lang.String getExpressionSystemVectorType()
           
 java.lang.String getFragment()
           
 java.lang.String getGene()
           
 java.lang.String getHeaderVars()
           
 java.lang.Long getId()
          get the ID used by Hibernate
 java.lang.String getMolId()
          Returns the mol id value.
 java.lang.String getMolName()
           
 java.lang.String getMutation()
           
 java.lang.String getNumRes()
           
 java.lang.String getOrgan()
           
 java.lang.String getOrganelle()
           
 java.lang.String getOrganismCommon()
           
 java.lang.String getOrganismScientific()
           
 java.lang.String getOrganismTaxId()
           
 java.lang.String getRefChainId()
          Returns the ref chain id value.
 java.lang.String getResNames()
           
 java.lang.String getSecretion()
           
 java.lang.String getStrain()
           
 java.util.List<java.lang.String> getSynonyms()
           
 java.lang.String getSynthetic()
           
 java.lang.String getTissue()
           
 java.lang.String getTitle()
           
 java.lang.String getVariant()
           
 void setAtcc(java.lang.String atcc)
           
 void setBiologicalUnit(java.lang.String biologicalUnit)
           
 void setCell(java.lang.String cell)
           
 void setCellLine(java.lang.String cellLine)
           
 void setCellularLocation(java.lang.String cellularLocation)
           
 void setChainId(java.util.List<java.lang.String> chainId)
          Sets the list of chain IDs.
 void setChains(java.util.List<Chain> chains)
           
 void setDetails(java.lang.String details)
           
 void setEcNums(java.util.List<java.lang.String> ecNums)
           
 void setEngineered(java.lang.String engineered)
           
 void setExpressionSystem(java.lang.String expressionSystem)
           
 void setExpressionSystemAtccNumber(java.lang.String expressionSystemAtccNumber)
           
 void setExpressionSystemCell(java.lang.String expressionSystemCell)
           
 void setExpressionSystemCellLine(java.lang.String expressionSystemCellLine)
           
 void setExpressionSystemCellularLocation(java.lang.String expressionSystemCellularLocation)
           
 void setExpressionSystemGene(java.lang.String expressionSystemGene)
           
 void setExpressionSystemOrgan(java.lang.String expressionSystemOrgan)
           
 void setExpressionSystemOrganelle(java.lang.String expressionSystemOrganelle)
           
 void setExpressionSystemOtherDetails(java.lang.String expressionSystemOtherDetails)
           
 void setExpressionSystemPlasmid(java.lang.String expressionSystemPlasmid)
           
 void setExpressionSystemStrain(java.lang.String expressionSystemStrain)
           
 void setExpressionSystemTaxId(java.lang.String expressionSystemTaxId)
           
 void setExpressionSystemTissue(java.lang.String expressionSystemTissue)
           
 void setExpressionSystemVariant(java.lang.String expressionSystemVariant)
           
 void setExpressionSystemVector(java.lang.String expressionSystemVector)
           
 void setExpressionSystemVectorType(java.lang.String expressionSystemVectorType)
           
 void setFragment(java.lang.String fragment)
           
 void setGene(java.lang.String gene)
           
 void setHeaderVars(java.lang.String headerVars)
           
 void setId(java.lang.Long id)
          set the ID used by Hibernate
 void setMolId(java.lang.String molId)
          Set the mol id value.
 void setMolName(java.lang.String molName)
           
 void setMutation(java.lang.String mutation)
           
 void setNumRes(java.lang.String numRes)
           
 void setOrgan(java.lang.String organ)
           
 void setOrganelle(java.lang.String organelle)
           
 void setOrganismCommon(java.lang.String organismCommon)
           
 void setOrganismScientific(java.lang.String organismScientific)
           
 void setOrganismTaxId(java.lang.String organismTaxId)
           
 void setRefChainId(java.lang.String refChainId)
          Returns the ref chain id value.
 void setResNames(java.lang.String resNames)
           
 void setSecretion(java.lang.String secretion)
           
 void setStrain(java.lang.String strain)
           
 void setSynonyms(java.util.List<java.lang.String> synonyms)
           
 void setSynthetic(java.lang.String synthetic)
           
 void setTissue(java.lang.String tissue)
           
 void setTitle(java.lang.String title)
           
 void setVariant(java.lang.String variant)
           
 void showCompound()
           
 void showHeader()
          Print some debug statements to System.out
 void showSource()
           
 java.lang.String toString()
           
 
Methods inherited from class java.lang.Object
equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
 

Constructor Detail

Compound

public Compound()
Method Detail

toString

public java.lang.String toString()
Overrides:
toString in class java.lang.Object

getId

public java.lang.Long getId()
get the ID used by Hibernate

Returns:
the ID used by Hibernate

setId

public void setId(java.lang.Long id)
set the ID used by Hibernate

Parameters:
id -

showHeader

public void showHeader()
Print some debug statements to System.out


showCompound

public void showCompound()

showSource

public void showSource()

getChainId

public java.util.List<java.lang.String> getChainId()
Returns the chain id value.

Returns:
the list of ChainIDs that are described by this Compound
See Also:
setChainId(List)

setChainId

public void setChainId(java.util.List<java.lang.String> chainId)
Sets the list of chain IDs.

Parameters:
chainId - the list of ChainIDs that are described by this Compound
See Also:
getChainId()

getRefChainId

public java.lang.String getRefChainId()
Returns the ref chain id value.

Returns:
the RefChainID
See Also:
setRefChainId(String)

setRefChainId

public void setRefChainId(java.lang.String refChainId)
Returns the ref chain id value.

Parameters:
refChainId - the RefChainID
See Also:
getRefChainId()

getMolId

public java.lang.String getMolId()
Returns the mol id value.

Returns:
the MolId value
See Also:
setMolId(String)

setMolId

public void setMolId(java.lang.String molId)
Set the mol id value.

Parameters:
molId - the MolId value
See Also:
getMolId()

getMolName

public java.lang.String getMolName()

setMolName

public void setMolName(java.lang.String molName)

getTitle

public java.lang.String getTitle()

setTitle

public void setTitle(java.lang.String title)

getSynonyms

public java.util.List<java.lang.String> getSynonyms()

setSynonyms

public void setSynonyms(java.util.List<java.lang.String> synonyms)

getEcNums

public java.util.List<java.lang.String> getEcNums()

setEcNums

public void setEcNums(java.util.List<java.lang.String> ecNums)

getEngineered

public java.lang.String getEngineered()

setEngineered

public void setEngineered(java.lang.String engineered)

getMutation

public java.lang.String getMutation()

setMutation

public void setMutation(java.lang.String mutation)

getBiologicalUnit

public java.lang.String getBiologicalUnit()

setBiologicalUnit

public void setBiologicalUnit(java.lang.String biologicalUnit)

getDetails

public java.lang.String getDetails()

setDetails

public void setDetails(java.lang.String details)

getNumRes

public java.lang.String getNumRes()

setNumRes

public void setNumRes(java.lang.String numRes)

getResNames

public java.lang.String getResNames()

setResNames

public void setResNames(java.lang.String resNames)

getHeaderVars

public java.lang.String getHeaderVars()

setHeaderVars

public void setHeaderVars(java.lang.String headerVars)

getSynthetic

public java.lang.String getSynthetic()

setSynthetic

public void setSynthetic(java.lang.String synthetic)

getFragment

public java.lang.String getFragment()

setFragment

public void setFragment(java.lang.String fragment)

getOrganismScientific

public java.lang.String getOrganismScientific()

setOrganismScientific

public void setOrganismScientific(java.lang.String organismScientific)

getOrganismTaxId

public java.lang.String getOrganismTaxId()

setOrganismTaxId

public void setOrganismTaxId(java.lang.String organismTaxId)

getOrganismCommon

public java.lang.String getOrganismCommon()

setOrganismCommon

public void setOrganismCommon(java.lang.String organismCommon)

getStrain

public java.lang.String getStrain()

setStrain

public void setStrain(java.lang.String strain)

getVariant

public java.lang.String getVariant()

setVariant

public void setVariant(java.lang.String variant)

getCellLine

public java.lang.String getCellLine()

setCellLine

public void setCellLine(java.lang.String cellLine)

getAtcc

public java.lang.String getAtcc()

setAtcc

public void setAtcc(java.lang.String atcc)

getOrgan

public java.lang.String getOrgan()

setOrgan

public void setOrgan(java.lang.String organ)

getTissue

public java.lang.String getTissue()

setTissue

public void setTissue(java.lang.String tissue)

getCell

public java.lang.String getCell()

setCell

public void setCell(java.lang.String cell)

getOrganelle

public java.lang.String getOrganelle()

setOrganelle

public void setOrganelle(java.lang.String organelle)

getSecretion

public java.lang.String getSecretion()

setSecretion

public void setSecretion(java.lang.String secretion)

getGene

public java.lang.String getGene()

setGene

public void setGene(java.lang.String gene)

getCellularLocation

public java.lang.String getCellularLocation()

setCellularLocation

public void setCellularLocation(java.lang.String cellularLocation)

getExpressionSystem

public java.lang.String getExpressionSystem()

getExpressionSystemTaxId

public java.lang.String getExpressionSystemTaxId()

setExpressionSystemTaxId

public void setExpressionSystemTaxId(java.lang.String expressionSystemTaxId)

setExpressionSystem

public void setExpressionSystem(java.lang.String expressionSystem)

getExpressionSystemStrain

public java.lang.String getExpressionSystemStrain()

setExpressionSystemStrain

public void setExpressionSystemStrain(java.lang.String expressionSystemStrain)

getExpressionSystemVariant

public java.lang.String getExpressionSystemVariant()

setExpressionSystemVariant

public void setExpressionSystemVariant(java.lang.String expressionSystemVariant)

getExpressionSystemCellLine

public java.lang.String getExpressionSystemCellLine()

setExpressionSystemCellLine

public void setExpressionSystemCellLine(java.lang.String expressionSystemCellLine)

getExpressionSystemAtccNumber

public java.lang.String getExpressionSystemAtccNumber()

setExpressionSystemAtccNumber

public void setExpressionSystemAtccNumber(java.lang.String expressionSystemAtccNumber)

getExpressionSystemOrgan

public java.lang.String getExpressionSystemOrgan()

setExpressionSystemOrgan

public void setExpressionSystemOrgan(java.lang.String expressionSystemOrgan)

getExpressionSystemTissue

public java.lang.String getExpressionSystemTissue()

setExpressionSystemTissue

public void setExpressionSystemTissue(java.lang.String expressionSystemTissue)

getExpressionSystemCell

public java.lang.String getExpressionSystemCell()

setExpressionSystemCell

public void setExpressionSystemCell(java.lang.String expressionSystemCell)

getExpressionSystemOrganelle

public java.lang.String getExpressionSystemOrganelle()

setExpressionSystemOrganelle

public void setExpressionSystemOrganelle(java.lang.String expressionSystemOrganelle)

getExpressionSystemCellularLocation

public java.lang.String getExpressionSystemCellularLocation()

setExpressionSystemCellularLocation

public void setExpressionSystemCellularLocation(java.lang.String expressionSystemCellularLocation)

getExpressionSystemVectorType

public java.lang.String getExpressionSystemVectorType()

setExpressionSystemVectorType

public void setExpressionSystemVectorType(java.lang.String expressionSystemVectorType)

getExpressionSystemVector

public java.lang.String getExpressionSystemVector()

setExpressionSystemVector

public void setExpressionSystemVector(java.lang.String expressionSystemVector)

getExpressionSystemPlasmid

public java.lang.String getExpressionSystemPlasmid()

setExpressionSystemPlasmid

public void setExpressionSystemPlasmid(java.lang.String expressionSystemPlasmid)

getExpressionSystemGene

public java.lang.String getExpressionSystemGene()

setExpressionSystemGene

public void setExpressionSystemGene(java.lang.String expressionSystemGene)

getExpressionSystemOtherDetails

public java.lang.String getExpressionSystemOtherDetails()

setExpressionSystemOtherDetails

public void setExpressionSystemOtherDetails(java.lang.String expressionSystemOtherDetails)

clone

public Compound clone()
               throws java.lang.CloneNotSupportedException
Overrides:
clone in class java.lang.Object
Throws:
java.lang.CloneNotSupportedException

getChains

public java.util.List<Chain> getChains()
get the chains that are part of this Compound

Returns:
a List of Chain objects

addChain

public void addChain(Chain chain)

setChains

public void setChains(java.util.List<Chain> chains)