[Biojava-l] Re: Sequence Color Coding

[Matthew Pocock]

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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