Class AbstractSymbolList

java.lang.Object
org.biojava.utils.AbstractChangeable
org.biojava.bio.symbol.AbstractSymbolList
All Implemented Interfaces:
SymbolList, Changeable
Direct Known Subclasses:
AbstractULAlignment, AbstractULAlignment.SubULAlignment, AssembledSymbolList, ChunkedSymbolList, DummySymbolList, NewAssembledSymbolList, PackedSymbolList, SimpleAlignment, SimpleGappedSymbolList, SimpleSymbolList

public abstract class AbstractSymbolList extends AbstractChangeable implements SymbolList

Abstract helper implementation of the SymbolList core interface. To produce a concrete SymbolList implementation, you need only implement the getAlphabet, length and symbolAt methods. Iterators and sublists are handled for you automatically.

This class makes many custom SymbolList implementations very quick to implement. See org.biojava.bio.seq.tools.ComplementSymbolList for an example of this.

To make a mutable SymbolList, override the implementation of edit to perform the apropreate edit. If your implementation of SymbolList is a view onto an underlying SymbolList, then you must forward any apropreate edit requests to that list, and forward all events from the underlying list to your listeners.

Author:
Thomas Down, Matthew Pocock
  • Constructor Details

  • Method Details

    • iterator

      Description copied from interface: SymbolList
      An Iterator over all Symbols in this SymbolList.

      This is an ordered iterator over the Symbols. It cannot be used to edit the underlying symbols.

      Specified by:
      iterator in interface SymbolList
      Returns:
      an iterator
    • 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
      Parameters:
      start - the first symbol of the new SymbolList
      end - the last symbol (inclusive) of the new SymbolList
    • toList

      public List<Symbol> toList()
      Description copied from interface: SymbolList
      Returns a List of symbols.

      This is an immutable list of symbols. Do not edit it.

      Specified by:
      toList in interface SymbolList
      Returns:
      a List of Symbols
    • seqString

      public String seqString()
      Description copied from interface: SymbolList
      Stringify this symbol list.

      It is expected that this will use the symbol's token to render each symbol. It should be parsable back into a SymbolList using the default token parser for this alphabet.

      Specified by:
      seqString in interface SymbolList
      Returns:
      a string representation of the symbol list
    • 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
      Parameters:
      start - the first symbol to include
      end - the last symbol to include
      Returns:
      the string representation
    • edit

      Description copied from interface: SymbolList
      Apply an edit to the SymbolList as specified by the edit object.

      Description

      All edits can be broken down into a series of operations that change contiguous blocks of the sequence. This represent a one of those operations.

      When applied, this Edit will replace 'length' number of symbols starting a position 'pos' by the SymbolList 'replacement'. This allow to do insertions (length=0), deletions (replacement=SymbolList.EMPTY_LIST) and replacements (length>=1 and replacement.length()>=1).

      The pos and pos+length should always be valid positions on the SymbolList to:

      • be edited (between 0 and symL.length()+1).
      • To append to a sequence, pos=symL.length()+1, pos=0.
      • To insert something at the beginning of the sequence, set pos=1 and length=0.

      Examples

       SymbolList seq = DNATools.createDNA("atcaaaaacgctagc");
       System.out.println(seq.seqString());
      
       // delete 5 bases from position 4
       Edit ed = new Edit(4, 5, SymbolList.EMPTY_LIST);
       seq.edit(ed);
       System.out.println(seq.seqString());
      
       // delete one base from the start
       ed = new Edit(1, 1, SymbolList.EMPTY_LIST);
       seq.edit(ed);
      
       // delete one base from the end
       ed = new Edit(seq.length(), 1, SymbolList.EMPTY_LIST);
       seq.edit(ed);
       System.out.println(seq.seqString());
      
       // overwrite 2 bases from position 3 with "tt"
       ed = new Edit(3, 2, DNATools.createDNA("tt"));
       seq.edit(ed);
       System.out.println(seq.seqString());
      
       // add 6 bases to the start
       ed = new Edit(1, 0, DNATools.createDNA("aattgg");
       seq.edit(ed);
       System.out.println(seq.seqString());
      
       // add 4 bases to the end
       ed = new Edit(seq.length() + 1, 0, DNATools.createDNA("tttt"));
       seq.edit(ed);
       System.out.println(seq.seqString());
      
       // full edit
       ed = new Edit(3, 2, DNATools.createDNA("aatagaa");
       seq.edit(ed);
       System.out.println(seq.seqString());
       
      Specified by:
      edit in interface SymbolList
      Parameters:
      edit - the Edit to perform
      Throws:
      IllegalAlphabetException - if the SymbolList to insert has an incompatible alphabet
      ChangeVetoException - if either the SymboList does not support the edit, or if the change was vetoed
    • equals

      public boolean equals(Object o)
      Provides logical equality for two SymbolLists that share the same list of canonical symbols
      Overrides:
      equals in class Object
    • hashCode

      public int hashCode()
      Overrides:
      hashCode in class Object
    • toString

      public String toString()
      Overrides:
      toString in class Object