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)