The demo programs show how to use some of the BioJava functionality. They are fun prototypes
that are generaly useful in their own right, and are a good starting point for writing your
own code. They are also the bench-mark that I use to check that I haven't broken anything.
Have fun.
- seq demonstrates the basics of the org.biojava.bio.seq package.
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gff shows how to use the GFF parsers to populate sequences
with features, how to filter GFF and how to turn features back into GFF.
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dp contains a working version of the 'occasionaly dishonest cassino' from
the Durbin, Eddie, Krogh & Mitchison book, "Biological Sequence Analysis" (1998). It also
contains programs that search a simple promoter model against some fake DNA, and a simple
profile HMM demo app.
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BioCorba is a working example of a corba client/server that talks
the BioCorba IDL. It uses native BioJava objects to represent both the remote objects, and
also the underlying data for the local server objects.
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SequenceViewer is a JavaWebStart Application that demonstrates a view of features on a sequence.
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FastBeadDemo is a JavaWebStart Application that demonstrates a view of features on a sequence using a org.biojava.bio.gui.sequence.TranslatedSequencePanel for fast rendering.