From: Keith James
Date: 12 Nov 2002 10:04:18 +
In-Reply-To: <[EMAIL PROTECTED]>
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> "Matthew" == Matthew Pocock <[EMAIL PROTECTED]> writes:
> "Matthew" == Matthew Pocock <[EMAIL PROTECTED]> writes:
[...]
Matthew> One is legacy but knows that it is indexing
Matthew> sequences. The other is actively supported by me and
Matthew> conforms to the OBDA spec for flat file indexes but
Matthew> doesn't know that it is inde
Keith James wrote:
Ah, I see. I was looking for whether/how I should make the EMBL-CDROM
index access code fit in with the newer interfaces. I think we should
preserve its functionality as it provides direct access to flatfiles
indexed by EMBOSS.
Keith
Fine - I don't have my finger on the puls
I've modified the tag-value embl parser under demos/tagvalue/EmblParser
to tokenize the whole of the document including the feature table and
the feature properties. Take it for a spin. It's running at a reasonable
speed for me (tested on some of the hum*.dat files from embl). To make
this usef
Compile before commit, fellas! :)
[javadoc]
/biojava-live/ant-build/src/main/org/biojava/bio/seq/impl/LazyFilterFeatureHolder.java:38:
duplicate class: ensembl.LazyFilterFeatureHolder
[javadoc] public class LazyFilterFeatureHolder implements FeatureHolder
{
[javadoc]^
[javadoc] 2
I can't find anywhere in the Feature or Location classes where it indicates
the orientation of a feature.
I'm parsing a GenBank file, and some features have complement() for the
location.
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Hi -
Features that have orientation info will be instances of the
StrandedFeature object. StrandedFeature contains static fields called
POSITIVE and NEGATIVE and a method called something like getStrand()
which returns one of these depending on which strand the feature is on.
- Mark
> -Orig
