Package org.biojava.bio.structure

Class 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 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)