[Biojava-l] Re: Sequence Color Coding

[Jim Johnson]

Matthew Pocock wrote:
> 
> cc: biojava-l
> 
> satyanarayana pasupuleti wrote:
> > Hi Mathew:
> >
> > I am new to this group. I tried mailing to the group using
> > bio-l@biojava.org <mailto:bio-l@biojava.org>  but I couldnt see my mail
> > in the list. Any clue??
> 
> Try biojava-l@biojava.org and if that doesn't work, hunt arround the
> biojava.org web site for a link to mailing list subscription.
> 
> >
> >  Do you know how does different alphabets in a sequence can be color
> > coded? Do I have to use the Color class in java.awt or is there any
> > package in bio-java that is useful?  I am reading a DNA sequence from a
> > FASTA file. I got the sequence using seq.seqString() method.
> >
> 
> In the org.biojava.bio.gui package there is an interface SymbolStyle
> that encapsulates the rendering hints for symbols (e.g. you can set up A
> to be red with black outline and G to be filled with tiled union jacks
> with dashed purple outline). This is used in a few places, but not
> nearly enough (one more thing for the todo list).
> 
> Do you want to print the sequence out as a string to the terminal or
> render it as a graphic into a swing/awt window? Take a look at the
> org.biojava.bio.gui.sequence package. It includes some classes and
> interfaces for rendering sequence information.
> 
> > Also, how do I parse the BLAST output ? How far the bio-java parser is
> > helpful?
> 
> Take a look at org.biojav.bio.search, org.biojava.program.ssbin and
> org.biojava.bio.program.sax - these together give you parsers for lots
> of formats like blast and ways to process hits into biojava objects or
> just intercept the information using eventbased call-backs.
> 
> >
> > I really appreciate any code or pointers in this regard.
> >
> > Thanks a lot
> >
> > --satya
> >
> 
> oh - and route through the demos - they may do stuff similar to what you
> want.
> 
> >
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I worked a bit on rendering styles last spring, 
but haven't had time to pursue it since.

My goal was to introduce color models similar those in Jalview, 
and eventually port Jalview into biojava.
  http://circinus.ebi.ac.uk:6543/jalview/contents.html
  http://mgd.ahc.umn.edu/java/apps/Jalview.jnlp 


I put my example (webstart, screenshots, and some code) in:
http://mgd.ahc.umn.edu/java/apps/biojava/


JJ


-- 
James E. Johnson <jj@mail.ahc.umn.edu> 
Center for Computational Genomics and Bioinformatics
Mayo Mail Code 43, AHC, University of Minnesota
420 Delaware St SE
Minneapolis, MN 55455 
612-626-6937