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Ace/Sequence.pm  view on Meta::CPAN

completely encloses the selected sequence segment.  The "parent"
sequence is the smallest ACeDB sequence object that contains the
"source".  The parent is used to derive the length and orientation of
source sequences that are not directly associated with DNA objects.

In many cases, the source sequence will be identical to the sequence
initially passed to the new() method.  However, there are exceptions
to this rule.  One common exception occurs when the offset and/or
length cross the boundaries of the passed-in sequence.  In this case,
the ACeDB database is searched for the smallest sequence that contains 
both endpoints of the I<Ace::Sequence> object.

The other common exception occurs in Ace 4.8, where there is support
for "sequence-like" objects that contain the C<SMap> ("Sequence Map")
tag.  The C<SMap> tag provides genomic location information for
arbitrary object -- not just those descended from the Sequence class.
This allows ACeDB to perform genome map operations on objects that are
not directly related to sequences, such as genetic loci that have been
interpolated onto the physical map.  When an C<SMap>-containing object
is passed to the I<Ace::Sequence> new() method, the module will again
choose the smallest ACeDB Sequence object that contains both

Ace/Sequence.pm  view on Meta::CPAN

Once an I<Ace::Sequence> object is created, you can query it using the
following methods:

=head2 asString()

  $name = $seq->asString;

Returns a human-readable identifier for the sequence in the form
I<Source/start-end>, where "Source" is the name of the source
sequence, and "start" and "end" are the endpoints of the sequence
relative to the source (using 1-based indexing).  This method is
called automatically when the I<Ace::Sequence> is used in a string
context.

=head2 source_seq()

  $source = $seq->source_seq;

Return the source of the I<Ace::Sequence>.