[Biojava-l] Newbie questions

[Michael Giddings]

Hello all,
I have been looking at BioJava to see if it would be of benefit for some of
our work here (and whether we could contribute).  I have some newbie type
questions:

1. I'm looking for a fast DNA sequence implementation for things like
sequence searches, Smith-Waterman alignments, etc.  It seems to me that even
SimpleSequence, being based on SimpleSymbolList, would not be as efficient
as what I'm looking for, since it must create and manage in memory a whole
list of Symbol objects (tell me if I'm wrong).  What I'm thinking of (and I
have such a beast implemented in Objective-C already*) is essentially a
wrapper around a String object (or some kind of contiguous, linear memory
block).  It would have functionality such as reverse, complement, and could
be extended with tools to do SmithWaterman searches against other sequences,
etc. (I also have Objective-C code for SW alignments).  It would be easy to
then have a constructor for the heavier-weight Sequence objects which would
accept one of these "LightweightSequence" objects as input.

2. Why doesn't SimpleSequence or SimpleSymbolList have a constructor which
takes a string as input to initialize the sequence?  Was this intentional
(i.e. am I missing something), or just a feature nobody has needed yet?

3. It would be really nice if there was an overview document for all the
classes, giving a basic rundown on the class hierarchy, where to find
various types of Objects, what the philosophy is behind the inheritance
structure, and so on.  For example, it seems like there is a dual
inheritance structure, one for interfaces an one for the implementations
themselves.  This makes figuring out what's going on doubly complicated to a
newbie.


4. Does anyone on this list know about the Bio-OpenSource meeting at ISMB
'00, and what will be taking place there?  The ISMB web-site is kind of
vague about it, but the registration deadline is fast approaching.

Thanks in advance,

Michael Giddings, Ph.D.
University of Utah, Dept. of Human Genetics


* For those not familiar, Objective-C inherits most (if not all) it's
semantics from Smalltalk, and it is also semantically quite similar to Java.