Package psidev.psi.mi.jami.model

Interface Organism

  • All Known Implementing Classes:
    DefaultOrganism, HostOrganism, HostOrganism, HostOrganism, MitabOrganism, XmlOrganism, XmlOrganism, XmlOrganism
    public interface Organism
    The organism is defined by a taxonomy identifier. It can be used to describe the source organism of an interactor, the organism in which the experiment has been performed or the organism where the participants of an interaction have been expressed in.
    Since:
    22/11/12
    Version:
    $Id$
    Author:
    Marine Dumousseau (marine@ebi.ac.uk)

    • Method Detail

      • getCommonName

        String getCommonName()
        The common name of an organism. It can be null. Ex: human, mouse, ...
        Returns:
        the mnemonic, common name if there is no mnemonic, scientific name if no common names/mnemonic

      • setCommonName

        void setCommonName​(String name)
        Set the common name
        Parameters:
        name - : common name or mnemonic (or scientific name if no common names/mnemonic)

      • getScientificName

        String getScientificName()
        The scientific name of the organism. It can be null Ex: Homo sapiens, Mus musculus, ...
        Returns:
        the scientific name

      • setScientificName

        void setScientificName​(String name)
        Set the scientific name
        Parameters:
        name - : scientific name

      • getTaxId

        int getTaxId()
        The taxonomy identifier of the organism. It should be : - '-1' for 'in vitro' - '-2' for 'chemical synthesis' - '-3' for unknown - '-4' for in vivo - valid NCBI taxonomy identifier (Ex: 9606 for human)
        Returns:
        the taxonomy identifier

      • setTaxId

        void setTaxId​(int id)
        Sets the taxonomy identifier of the organism. It should be : - '-1' for 'in vitro' - '-2' for 'chemical synthesis' - '-3' for unknown - '-4' for in vivo - valid NCBI taxonomy identifier (Ex: 9606 for human)
        Parameters:
        id - a int.
        Throws:
        IllegalArgumentException - if taxid is not valid

      • getAliases

        <A extends Alias> Collection<A> getAliases()
        The other names of the organism. It cannot be null and should return an emtpy Collection if no aliases are attached to this organism Ex: Mus muscaris, transgenic mice and house mouse are mouse synonyms/aliases.
        Type Parameters:
        A - an A object
        Returns:
        the aliases

      • getCellType

        CvTerm getCellType()
        Cell type of the organism. It can be null for the interactor source organisms Ex: Human RCH_ACV -cALL ( B cell precursor) cell line
        Returns:
        the celltype

      • setCellType

        void setCellType​(CvTerm cellType)
        Sets the cell type
        Parameters:
        cellType - : cell type

      • getCompartment

        CvTerm getCompartment()
        The subcellular compartment of the organism. It can be null for the interactor source organisms Ex: nuclear
        Returns:
        the compartment

      • setCompartment

        void setCompartment​(CvTerm compartment)
        Sets the compartment.
        Parameters:
        compartment - : the compartment

      • getTissue

        CvTerm getTissue()
        The source tissue. It can be null for the interacator source organisms Ex: non pigmented ciliary epithelium
        Returns:
        the tissue

      • setTissue

        void setTissue​(CvTerm tissue)
        Sets the tissue
        Parameters:
        tissue - : tissue