[Biojava-l] indexdb.Record implementation

Eckhard Lehmann ecky.l at gmx.de
Mon Dec 8 20:58:43 EST 2003


Hi,

I need to create a quick & dirty database from a Genbank File, which
contains many entries. It seems that I can do this with 
org.biojava.bio.program.indexdb.IndexTools.indexGenbank(...).

But how can I get the Entries by ID, once the index is created? It seems
that the following works:

BioStore bst = new BioStore(new java.io.File("/path/to/indexdir"), false);
Record rec = bst.get("id_of_genbank_enty");

But Record is an interface and therefore without the implementation I would
like to have (the implementation to read out the desired Genbank entry and
e.g. have it as a Sequence object) .

Are there somewhere implementations in biojava-1.30 for processing these
Standard Records - resp. is there another way to do it without the need to
extract the record from the file by parsing the byte-oriented RAF that one can get
by rec.getFile()?

Thanks in advance for any help,

Eckhard ;)



More information about the Biojava-l mailing list