Package org.biojavax.bio.seq

Interface RichSequenceHandler

  • All Known Implementing Classes:
    BioSQLRichSequenceHandler, DummyRichSequenceHandler
    public interface RichSequenceHandler
    An interface for classes that know how to handle subsequence operations. Implementations may be optimized so that they perform more efficiently in certain conditions. For example a subsequence operation on a huge BioSQL backed RichSequence could be optimized so that the operation is performed more efficiently than dragging the whole sequence to memory and then doing the operation. Implementations of RichSequence should generally delegate symbolAt(int index), subStr(int start, int end), subList(int start, int end) and subSequence(int start, int end) to some implementation of this interface.
    Since:
    1.5
    Author:
    Mark Schreiber, Richard Holland

    • Method Detail

      • edit

        void edit​(RichSequence seq,
          Edit edit)
   throws IndexOutOfBoundsException,
          IllegalAlphabetException,
          ChangeVetoException
        Apply an edit to the Sequence 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

         RichSequence seq = //code to initialize RichSequence
 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());
        Parameters:
        edit - the Edit to perform
        Throws:
        IndexOutOfBoundsException - if the edit does not lie within the SymbolList
        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

      • toList

        List<Symbol> toList​(RichSequence seq)
        Returns a List of symbols.

        This should be an immutable list of symbols or a copy.

        Returns:
        a List of Symbols

      • subStr

        String subStr​(RichSequence seq,
              int start,
              int end)
       throws IndexOutOfBoundsException
        Return a region of this sequence as a String.

        This should use the same rules as seqString.

        Parameters:
        start - the first symbol to include
        end - the last symbol to include
        Returns:
        the string representation
        Throws:
        IndexOutOfBoundsException - if either start or end are not within the SymbolList

      • subList

        SymbolList subList​(RichSequence seq,
                   int start,
                   int end)
            throws IndexOutOfBoundsException
        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.

        Parameters:
        start - the first symbol of the new SymbolList
        end - the last symbol (inclusive) of the new SymbolList
        Throws:
        IndexOutOfBoundsException

      • seqString

        String seqString​(RichSequence seq)
        Stringify this Sequences.

        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.

        Returns:
        a string representation of the symbol list

      • iterator

        Iterator<Symbol> iterator​(RichSequence seq)
        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.

        Returns:
        an iterator