Package pal.misc

Class Identifier

  • All Implemented Interfaces:
    java.io.Serializable, Nameable, Comparable
    public class Identifier
extends java.lang.Object
implements java.io.Serializable, Comparable, Nameable
    An identifier for some sampled data. This will most often be for example, the accession number of a DNA sequence, or the taxonomic name that the sequence represents, et cetera.
    Version:
    $Id: Identifier.java,v 1.9 2002/11/25 05:40:54 matt Exp $
    Author:
    Alexei Drummond
    See Also:
    Serialized Form

    • Constructor Summary

      Constructors 
      Constructor Description
      Identifier()  
      Identifier​(java.lang.String name)  

    • Method Summary

      All Methods Static Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      int compareTo​(java.lang.Object c)
      Returns a number representing the ordering relationship that the object has with the given object.
      boolean equals​(java.lang.Object c)
      Returns true if this object is equal to the given object.
      static Identifier[] getIdentifiers​(java.lang.String[] names)
      Translates an an array of strings into an array of identifiers
      static Identifier[] getIdentifiers​(IdGroup idGroup)
      Translates an IdGroup into an array of identifiers
      java.lang.String getName()
      get the name of this object.
      static java.lang.String[] getNames​(Identifier[] ids)
      Translates an array of identifiers into an array of strings
      static java.lang.String[] getNames​(Identifier[] ids, int toIgnore)
      Translates an array of identifiers into an array of strings, with optional removal of particular identifier
      static java.lang.String[] getNames​(IdGroup ids)
      Translates an IdGroup into an array of strings
      static java.lang.String[] getNames​(IdGroup ids, int toIgnore)
      Translates an IDgroup into an array of strings, with optional removal of particular identifier
      static java.lang.String[] getNames​(IdGroup ids, int[] toIgnore)
      Translates an IDgroup into an array of strings, with optional removal of particular identifier
      void setName​(java.lang.String s)
      set the name of this object.
      java.lang.String toString()  

      • Methods inherited from class java.lang.Object

        clone, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

    • Field Detail

    • Constructor Detail

      • Identifier

        public Identifier()

      • Identifier

        public Identifier​(java.lang.String name)

    • Method Detail

      • toString

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

      • compareTo

        public int compareTo​(java.lang.Object c)
        Description copied from interface: Comparable
        Returns a number representing the ordering relationship that the object has with the given object. A negative number indicates that the object is "smaller" than the parameter, a positive number means it is "larger" and zero indicates that the objects are equal.
        Specified by:
        compareTo in interface Comparable

      • equals

        public boolean equals​(java.lang.Object c)
        Description copied from interface: Comparable
        Returns true if this object is equal to the given object.
        Specified by:
        equals in interface Comparable
        Overrides:
        equals in class java.lang.Object

      • getName

        public java.lang.String getName()
        Description copied from interface: Nameable
        get the name of this object.
        Specified by:
        getName in interface Nameable
        Returns:
        name of this object.

      • setName

        public void setName​(java.lang.String s)
        Description copied from interface: Nameable
        set the name of this object.
        Specified by:
        setName in interface Nameable
        Parameters:
        s - the new name.

      • getNames

        public static final java.lang.String[] getNames​(Identifier[] ids)
        Translates an array of identifiers into an array of strings

      • getNames

        public static final java.lang.String[] getNames​(Identifier[] ids,
                                                int toIgnore)
        Translates an array of identifiers into an array of strings, with optional removal of particular identifier
        Parameters:
        toIgnoreIndex - the index of an idetifier to ignore, if <0 no element is ignored

      • getIdentifiers

        public static final Identifier[] getIdentifiers​(java.lang.String[] names)
        Translates an an array of strings into an array of identifiers

      • getIdentifiers

        public static final Identifier[] getIdentifiers​(IdGroup idGroup)
        Translates an IdGroup into an array of identifiers

      • getNames

        public static final java.lang.String[] getNames​(IdGroup ids)
        Translates an IdGroup into an array of strings

      • getNames

        public static final java.lang.String[] getNames​(IdGroup ids,
                                                int toIgnore)
        Translates an IDgroup into an array of strings, with optional removal of particular identifier
        Parameters:
        toIgnoreIndex - the index of an idetifier to ignore, if <0 no element is ignored

      • getNames

        public static final java.lang.String[] getNames​(IdGroup ids,
                                                int[] toIgnore)
        Translates an IDgroup into an array of strings, with optional removal of particular identifier
        Parameters:
        toIgnoreIndex - the indexes of an idetifier to ignore, does not need to be sorted