[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

-- 
Bioinformatics Specialist
Institute for Biological Sciences
National Research Council of Canada
[T] 613-990-0561  [F] 613-952-9092
simon.foote at nrc-cnrc.gc.ca



Y D Sun wrote:

>>-----Original Message-----
>>From: Thomas Down [mailto:thomas at derkholm.net] 
>>Sent: 08 July 2003 13:49
>>To: Y D Sun
>>Cc: biojava-l at biojava.org
>>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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