Class BasicProtein

  • All Implemented Interfaces:
    Protein

    public class BasicProtein
    extends java.lang.Object
    implements Protein
    • Field Detail

      • DomainMidPositionComparator

        public static java.util.Comparator<Domain> DomainMidPositionComparator
    • Constructor Detail

      • BasicProtein

        public BasicProtein​(java.lang.String id_str,
                            java.lang.String species_str,
                            int length)
    • Method Detail

      • contains

        public boolean contains​(java.util.List<java.lang.String> query_domain_ids,
                                boolean in_nc_order)
        Description copied from interface: Protein
        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).
        Specified by:
        contains in interface Protein
        Parameters:
        query_domain_ids - a list of domain ids in a certain order.
        in_nc_order - to consider order
        Returns:
      • getAccession

        public java.lang.String getAccession()
        Specified by:
        getAccession in interface Protein
      • getDescription

        public java.lang.String getDescription()
        Specified by:
        getDescription in interface Protein
      • getLength

        public int getLength()
        Specified by:
        getLength in interface Protein
      • getName

        public java.lang.String getName()
        Specified by:
        getName in interface Protein
      • getProteinDomainCount

        public int getProteinDomainCount​(java.lang.String domain_id)
        Specified by:
        getProteinDomainCount in interface Protein
      • getProteinDomains

        public java.util.List<Domain> getProteinDomains​(java.lang.String domain_id)
        Specified by:
        getProteinDomains in interface Protein
      • setAccession

        public void setAccession​(java.lang.String accession)
      • setDescription

        public void setDescription​(java.lang.String description)
      • setName

        public void setName​(java.lang.String name)
      • toDomainArchitectureString

        public java.lang.String toDomainArchitectureString​(java.lang.String separator)
      • toDomainArchitectureString

        public java.lang.String toDomainArchitectureString​(java.lang.String separator,
                                                           int repeats_limit,
                                                           java.lang.String repeat_separator)
      • toString

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