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Ace/Sequence/Feature.pm  view on Meta::CPAN

=head1 OBJECT METHODS

Most methods are inherited from I<Ace::Sequence>.  The following
methods are also supported:

=over 4

=item seqname()

  $object = $feature->seqname;

Return the ACeDB Sequence object that this feature is attached to.
The return value is an I<Ace::Object> of the Sequence class.  This
corresponds to the first field of the GFF format and does not
necessarily correspond to the I<Ace::Sequence> object from which the
feature was obtained (use source_seq() for that).

=item source()

=item method()

=item subtype()

  $source = $feature->source;

These three methods are all synonyms for the same thing.  They return
the second field of the GFF format, called "source" in the
documentation.  This is usually the method or algorithm used to
predict the feature, such as "GeneFinder" or "tRNA" scan.  To avoid
ambiguity and enhance readability, the method() and subtype() synonyms
are also recognized.

=item feature()

=item type()

  $type = $feature->type;

These two methods are also synonyms.  They return the type of the
feature, such as "exon", "similarity" or "Predicted_gene".  In the GFF
documentation this is called the "feature" field.  For readability,
you can also use type() to fetch the field.

=item abs_start()

  $start = $feature->abs_start;

This method returns the absolute start of the feature within the
sequence segment indicated by seqname().  As in the I<Ace::Sequence>
method, use start() to obtain the start of the feature relative to its
source.

=item abs_start()

  $start = $feature->abs_start;

This method returns the start of the feature relative to the sequence
segment indicated by seqname().  As in the I<Ace::Sequence> method,
you will more usually use the inherited start() method to obtain the
start of the feature relative to its source sequence (the
I<Ace::Sequence> from which it was originally derived).

=item abs_end()

  $start = $feature->abs_end;

This method returns the end of the feature relative to the sequence
segment indicated by seqname().  As in the I<Ace::Sequence> method,
you will more usually use the inherited end() method to obtain the end
of the feature relative to the I<Ace::Sequence> from which it was
derived.

=item score()

  $score = $feature->score;

For features that are associated with a numeric score, such as
similarities, this returns that value.  For other features, this
method returns undef.

=item strand()

  $strand = $feature->strand;

Returns the strandedness of this feature, either "+1" or "-1".  For
features that are not stranded, returns 0.

=item reversed()

  $reversed = $feature->reversed;

Returns true if the feature is reversed relative to its source
sequence.

=item frame()

  $frame = $feature->frame;

For features that have a frame, such as a predicted coding sequence,
returns the frame, either 0, 1 or 2.  For other features, returns undef.

=item group()

=item info()

=item target()

  $info = $feature->info;

These methods (synonyms for one another) return an Ace::Object
containing other information about the feature derived from the 8th
field of the GFF format, the so-called "group" field.  The type of the
Ace::Object is dependent on the nature of the feature.  The
possibilities are shown in the table below:

  Feature Type           Value of Group Field
  ------------            --------------------
  
  note                   A Text object containing the note.
  
  similarity             An Ace::Sequence::Homology object containing