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 _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
