[Biojava-l] BioJava-X parsing of RichSequences

[Ola Spjuth]

Hi,

Implementing a Biojava reader/parser for sequences in Bioclipse [1,2] I
have come up with a few questions:

1) I'd like to use Biojava-X with Bioclipse. Are there any problems
running it with Java 1.5 (as is required by Bioclipse)?

2) I would propose the addition of a readStream(...) method in
RichSequence.IOTools in addition to readFile(...). For the Bioclipse
project it would be most useful to be able to guess the format of a
Stream. As IOTools is marked final it cannot be subclassed.

3) Is HashBioEntryDB a suitable base object for storing 1-N
RichSequences in memory or should I use RichSequence[]? Which solution
has the simplest toByte() method for writing to e.g. a File?

So, basically I am looking for the most convenient way of doing:

i)   Read byte[] (from a File containing 1-N sequences) into a base
object in memory (HashBioEntryDB or RichSequence[])
ii) Write the (HashBioEntryDB or RichSequence[]) to byte[] (and then
later to File using Bioclipse-methods)

Cheers,

   .../Ola

[1] http://www.bioclipse.net
[2] http://wiki.bioclipse.net