[Bioperl-l] Bio::Seq documentation?

[Wes Barris]

Hi,

According to the bioperl documentation the Bio::SeqIO genbank method
"next_seq" returns a "Bio::Seq" object.  Where is the documentation
for a "Bio::Seq" object?  In the documentation on the bioperl web site,
if you click on "bioperl-1.2.3::Bio::Seq" I see the following list:

BaseSeqProcessor
EncodedSeq
LargePrimarySeq
LargeSeq
PrimaryQual
PrimedSeq
QualI
RichSeq
RichSeqI
SeqBuilder
SeqFactory
SeqFastaSpeedFactory
SeqWithQuality
SequenceTrace
TraceI

Which one of these do I look under to find out information about what
is returned by "next_seq"?

What I am trying to do is to parse a genbank file and find out the
sequence direction (3 prime or 5 prime).  What I have done is this,
but I am trying to find out if there is a better "built-in" way to do this:

    if ($seq->description =~ /3'/) {
       $direction = '3prime';
       }
    elsif ($seq->description =~ /5'/) {
       $direction = '5prime';
       }

-- 
Wes Barris
E-Mail: Wes.Barris at csiro.au