Class NewAssembledSymbolList

All Implemented Interfaces:
SymbolList, Changeable

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, David Huen (support for overlapped features)
  • Constructor Details

  • Method Details

    • setLength

      public void setLength(int len)
    • putComponent

      public void putComponent(ComponentFeature f)
    • removeComponent

    • getComponentLocationSet

    • 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