Class AssembledSymbolList

  • All Implemented Interfaces:
    SymbolList, Changeable

    public class AssembledSymbolList
    extends AbstractSymbolList
    Support class for applications which need to patch together sections of sequence into a single SymbolList. This class isn't intended for direct use in user code -- instead, it is a helper for people implementing the full BioJava assembly model. See SimpleAssembly for an example.
    Since:
    1.1
    Author:
    Thomas Down, Greg Cox, Matthew Pocock
    • Method Detail

      • setLength

        public void setLength​(int len)
      • 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.

        Returns:
        the alphabet
      • length

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

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

        public SymbolList subList​(int start,
                                  int end)
        Description copied from interface: SymbolList
        Return a new SymbolList for the symbols start to end inclusive.

        The resulting SymbolList will count from 1 to (end-start + 1) inclusive, and refer to the symbols start to end of the original sequence.

        Specified by:
        subList in interface SymbolList
        Overrides:
        subList in class AbstractSymbolList
        Parameters:
        start - the first symbol of the new SymbolList
        end - the last symbol (inclusive) of the new SymbolList
      • subStr

        public String subStr​(int start,
                             int end)
        Description copied from interface: SymbolList
        Return a region of this symbol list as a String.

        This should use the same rules as seqString.

        Specified by:
        subStr in interface SymbolList
        Overrides:
        subStr in class AbstractSymbolList
        Parameters:
        start - the first symbol to include
        end - the last symbol to include
        Returns:
        the string representation