Bio::Factory SequenceProcessorI
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Summary
Bio::Factory::SequenceProcessorI - Interface for chained sequence
processing algorithms
Package variables
No package variables defined.
Included modules
Bio::Root::RootI
Inherit
Bio::Factory::SequenceStreamI
Synopsis
    use Bio::SeqIO;
use MySeqProcessor; # is-a Bio::Factory::SequenceProcessorI
# obtain your source stream, e.g., an EMBL file my $seqin = Bio::SeqIO->new(-fh => \*STDIN, -format => 'embl'); # create your processor (it must implement this interface) my $seqalgo = MySeqProcessor->new(); # chain together $seqalgo->source_stream($seqin); # you could create more processors and chain them one after another # ... # finally, the last link in the chain is your SeqIO stream my $seqpipe = $seqalgo; # once you've established the pipeline, proceed as if you had a # single SeqIO stream while(my $seq = $seqpipe->next_seq()) { # ... do something ... }
Description
This defines an interface that allows seamless chaining of sequence
processing algorithms encapsulated in modules while retaining the
overall Bio::SeqIO interface at the end of the pipeline.
This is especially useful if you want an easily configurable
processing pipeline of re-usable algorithms as building blocks instead
of (hard-)coding the whole algorithm in a single script.
There are literally no restrictions as to what an individual module
can do with a sequence object it obtains from the source stream before
it makes it available through its own next_seq() method. It can
manipulate the sequence object, but otherwise keep it intact, but it
can also create any number of new sequence objects from it, or it can
discard some, or any combination thereof. The only requirement is that
its next_seq() method return Bio::PrimarySeqI compliant objects. In
order to play nice, if a processor creates new objects it should try
to use the same sequence factory that the source stream uses, but this
is not strongly mandated.
Methods
source_streamDescriptionCode
Methods description
source_streamcode    nextTop
 Title   : source_stream
Usage : $obj->source_stream($newval)
Function: Get/set the source sequence stream for this sequence
processor.
An implementation is not required to allow set, but will usually do so. Example : Returns : A Bio::Factory::SequenceStreamI compliant object Args : on set, new value (a Bio::Factory::SequenceStreamI compliant object)
Methods code
source_streamdescriptionprevnextTop
sub source_stream {
    shift->throw_not_implemented();
}
General documentation
FEEDBACKTop
Mailing ListsTop
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
the Bioperl mailing list. Your participation is much appreciated.
  bioperl-l@bioperl.org                  - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Support Top
Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
Reporting BugsTop
Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via the
web:
  https://redmine.open-bio.org/projects/bioperl/
AUTHOR - Hilmar LappTop
Email hlapp at gmx.net
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
Bio::Factory::SequenceStreamI methodsTop
 The requirement to implement these methods is inherited from
Bio::Factory::SequenceStreamI. An implementation may not
necessarily have to implement all methods in a meaningful way. Which
methods will be necessary very much depends on the context in which
an implementation of this interface is used. E.g., if it is only used
for post-processing sequences read from a SeqIO stream, write_seq()
will not be used and hence does not need to be implemented in a
meaningful way (it may in fact even throw an exception).
Also, since an implementor will already receive built objects from a sequence stream, sequence_factory() may or may not be relevant, depending on whether the processing method does or does not involve creating new objects.
next_seqTop
 Title   : next_seq
Usage : $seq = stream->next_seq
Function: Reads the next sequence object from the stream and returns it.
In the case of a non-recoverable situation an exception will be thrown. Do not assume that you can resume parsing the same stream after catching the exception. Note that you can always turn recoverable errors into exceptions by calling $stream->verbose(2). Returns : a Bio::Seq sequence object Args : none
See Bio::Root::RootI
write_seqTop
 Title   : write_seq
Usage : $stream->write_seq($seq)
Function: writes the $seq object into the stream
Returns : 1 for success and 0 for error
Args : Bio::Seq object
sequence_factoryTop
 Title   : sequence_factory
Usage : $seqio->sequence_factory($seqfactory)
Function: Get the Bio::Factory::SequenceFactoryI
Returns : Bio::Factory::SequenceFactoryI
Args : none