Interface Protein

  • All Known Implementing Classes:
    BasicProtein

    public interface Protein
    • Method Detail

      • addProteinDomain

        void addProteinDomain​(Domain protein_domain)
      • contains

        boolean contains​(java.util.List<java.lang.String> domains,
                         boolean in_nc_order)
        If in_nc_order is set to true, this should return true only and only if the order in List 'domains' and this protein (as determined by the start positions of the domains of this proteins, _not_ by their index) are the same (interspersing, 'other', domains in this are ignored). If in_nc_order is set to false, this should return true only and only if this contains all domains listed in 'domains' (order and count do not matter).
        Parameters:
        domains - a list of domain ids in a certain order.
        in_nc_order - to consider order
        Returns:
      • getAccession

        java.lang.String getAccession()
      • getDescription

        java.lang.String getDescription()
      • getName

        java.lang.String getName()
      • getNumberOfProteinDomains

        int getNumberOfProteinDomains()
      • getProteinDomain

        Domain getProteinDomain​(int index)
      • getProteinDomainCount

        int getProteinDomainCount​(java.lang.String domain_id)
      • getProteinDomains

        java.util.List<Domain> getProteinDomains()
      • getProteinDomains

        java.util.List<Domain> getProteinDomains​(java.lang.String domain_id)
      • getLength

        int getLength()
      • getDomainsSortedByPosition

        java.util.List<Domain> getDomainsSortedByPosition()