[Biojava-l] Help needed for a GUI

mark.schreiber at novartis.com mark.schreiber at novartis.com
Tue Jul 25 01:26:20 UTC 2006

General Plea -

Could someone add some examples of these to the biojava cook book in the 
wiki. I'm not really familiar with the GUI classes so I wouldn't be the 
best person to put up demo code.

- Mark

Mark Schreiber
Research Investigator (Bioinformatics)

Novartis Institute for Tropical Diseases (NITD)
10 Biopolis Road
#05-01 Chromos
Singapore 138670

phone +65 6722 2973
fax  +65 6722 2910

Russ Kepler <russ at kepler-eng.com>
Sent by: biojava-l-bounces at lists.open-bio.org
07/25/2006 05:38 AM

        To:     biojava-l at biojava.org
        cc:     (bcc: Mark Schreiber/GP/Novartis)
        Subject:        Re: [Biojava-l] Help needed for a GUI

On Monday 24 July 2006 03:16 pm, Dr. Christoph Gille wrote:
> >I am new to BioJava and am exploring its features. I am planning to 
> > a simple editor for alignments(something like a wordpad, but to handle
> > alignments).Does Biojava support this? Could someone please show me 
> > pointers for this?
> Using the classes /interfaces
> - MultiLineRenderer
> - FeatureRenderer
> - SequenceRenderer
> - SequencePanel
> - FeatureBlockSequenceRenderer
> one can easily display a gapped sequence with annotations.
> Perhaps one could place several SequencePanels over each other and put
> everything in one scroll-panel?

Better to put the alignment into a TranslatedSequencePanel, and populate 
panel with AlignmentRenderers, one per aligned sequence.  The 
AlignmentRenderer accepts a label that it uses to extract the "current" 
sequence from the alignment that the TranslatedSequencePanel has.  Below 
AlignmentRenderer are the MultiLineRenderers, etc.
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