Class DummySymbolList

  • All Implemented Interfaces:
    java.io.Serializable, SymbolList, Changeable

    public class DummySymbolList
    extends AbstractSymbolList
    implements java.io.Serializable
    Symbol list which just consists of non-informative symbols. A DummySymbolList can be constructed over any Alphabet, and may be of any length. Calls to the symbolAt method will always return the non-informative symbol for the alphabet in question (i.e. 'n' for DNA, 'X' for protein, etc.). If you wish to work with Feature objects, but don't have the actual sequence data available, you can construct a SimpleSequence from a DummySequence, and create features. on that.
    Since:
    1.2
    Author:
    Thomas Down, Matthew Pocock
    See Also:
    Serialized Form
    • Method Detail

      • getAlphabet

        public Alphabet getAlphabet()
        Description copied from interface: SymbolList
        The alphabet that this SymbolList is over.

        Every symbol within this SymbolList is a member of this alphabet. alphabet.contains(symbol) == true for each symbol that is within this sequence.

        Specified by:
        getAlphabet in interface SymbolList
        Returns:
        the alphabet
      • length

        public int length()
        Description copied from interface: SymbolList
        The number of symbols in this SymbolList.
        Specified by:
        length in interface SymbolList
        Returns:
        the length
      • symbolAt

        public Symbol symbolAt​(int i)
        Description copied from interface: SymbolList
        Return the symbol at index, counting from 1.
        Specified by:
        symbolAt in interface SymbolList
        Parameters:
        i - the offset into this SymbolList
        Returns:
        the Symbol at that index