[Biojava-l] Complement feature in CDS table

[Thomas Down]

Once upon a time, Y D Sun wrote:
> Dear all,
> 
> How to filter the complement feature in CDS? I get the features in a CDS
> table using the following code:
> 
> 	Map m = f.getAnnotation().asMap();		// f is a
> Feature containing a CDS table
>       
>       String ge = m.get("gene").toString();	// ok
>       String pr = m.get("product").toString();  // ok
> 	...
> 	String co = m.get("complement").toString(); // return nothing
> although the CDS table includes complement(int..int).

The complement(xxx..yyy) stuff is the feature's location, rather
than part of the qualifier-value data.  In BioJava, this will
be represented by a feature having a location from xxx to yyy,
and being on the negative strand.

For more information, see:

   http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html

Thomas.