Re: [Biojava-l] Complement feature in CDS table

[Simon Foote]

Hi George,

Just check the strand. 
If its StrandedFeature.NEGATIVE then its complement, otherwise it isn't.

examples: feature.getStrand() --> StrandedFeature.NEGATIVE = complement
                feature.getStrand().getValue()  --> -1 = complement
                feature.getStrand().getToken() --> - = complement
Simon

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Bioinformatics Specialist
Institute for Biological Sciences
National Research Council of Canada
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Y D Sun wrote:

-----Original Message-----
From: Thomas Down [mailto:[EMAIL PROTECTED] 
Sent: 08 July 2003 13:49
To: Y D Sun
Cc: [EMAIL PROTECTED]
Subject: Re: [Biojava-l] Complement feature in CDS table

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.

   

I want to check if a CDS contains the keyword "complement". Is there any
method to do so?
George

 

For more information, see:

   

http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.htm
l
Thomas.

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