Package org.biojava.bio.symbol

Class AbstractSymbolList

  • All Implemented Interfaces:
    SymbolList, Changeable
    Direct Known Subclasses:
    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

    • Method Detail

      • iterator

        public Iterator<Symbol> 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

        public void edit​(Edit edit)
          throws IllegalAlphabetException,
                 ChangeVetoException
        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