[Biojava-l] file i/o with ArrayList

[Andreas Prlic]

Hi Stefan,

for your use case (save and load at server start/stop) I'd recommend the
Kryo library.  It will store your data as a binary. Should be only two
lines of code each to persist and load the data.
https://github.com/EsotericSoftware/kryo

You are right, writing is not very well developed, but then there are so
many utility libraries in Java that can be used for efficient
serialization/deserialization in many ways, once you have an object in
memory.

Andreas



On Fri, Jan 30, 2015 at 3:01 AM, stefan harjes <stefanharjes at yahoo.de>
wrote:

> Hi biojava-l
>
>
>
> I have a huge number of small sequences in an Array
> (ListArray<Sequence<?>>) which for server start and stop I would like to
> store on disk. Unfortunately Sequence is not serilizable, so I searched and
> found that GenbankWriterHelper.writeSequences(OutputStream os,
> Collection<Sequence<?>> seqs) should be able to do the job.
> However when looking at GenbankReaderHelper, there are no methods which
> correspond to the above writer method. Am I on the wrong track completely?
>
> When looking at the writer/reader helpers, I think I remember reading that
> they are rudimentary and save only the sequence (fasta)? I would expect in
> such an advanced verision of biojava (4.0 is being prepared?) that there
> must be a standard way to serialize rich sequences/arrays of them in order
> to send them around on streams/Json etc?
>
> Any help would be appreciated
>
> Cheers
> Stefan
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.open-bio.org/pipermail/biojava-l/attachments/20150130/63890c78/attachment.html>