[Biojava-l] lage data sets/filtersByAnnotation ?

Hi, 1. I was wondering if anyone has testet bioJava/Biosql with large data sets - say the human genome? Not any sequence analysis/manipulation, just retrieving data. Is it reasonable fast to retrieve eg. features filtered by type/ancestor in, say 5 times nested features compared to direct db ac

[Biojava-l] NPE from FlatModel. with SimpleModelInState

Hello! This thread appeared about a year ago, but there was no response to it. Is there any now? I'm currently working on a complex HMM with several SimpleModelInStates. When i try to call [code] DP dp=DPFactory.DEFAULT.createDP(outer_Hmm) [/code] , where outer_Hmm is the HMM, I get the following m

[Biojava-l] Term Synonyms

I have added the concept of Synonyms, found in BioSQL, to the BioJava ontology term objects. I have also made the BioSQL interface part of BioJava aware of these synonyms and capable of retrieving/persisting them from the database. This has resulted in the addition of three new methods ( getSyno