[Biojava-l] Editing SymbolLists

[David Waring]

Perhaps I am missing something big here, but I can not figure out how in the
world I can edit a Sequence or a SymbolList.

There is a class Edit, and there seems to be strong support for handling
changes and passing them to anything that is listening, but SimpleSymbolList
is immutable (even the addSymbol method is deprecated). SimpleSequence wraps
a SimpleSymbolist so that is immutable (at least the SymbolList is). The
other subclasses of SymbolList don't seem to be the appropriate. As best I
can tell if I wanted to be able to read a fasta file, and make a change to
the sequence, I would have to.

Create an EditableSymbolList.
Create a FastaSequenceBuilder that used this.
Write a new method or two in SeqIOTools to read my file into my new Sequence
that has an EditableSymbolList.

Is this correct? Does no one else have any desire to edit a SymbolList?

David

PS: ChunkedSymbolList does not appear in the javadoc anywhere, what gives?


|||||||||||||||||||||||||||||||||||||||||||||||||||||||
|   David Waring
|   Systems Programmer
|   University of Washington Genome Center
|   dwaring@u.washington.edu
|   (206) 221-6902
|||||||||||||||||||||||||||||||||||||||||||||||||||||||