|-source||The sequence source. This must be an Ace::Object of the Sequence class, or be a sequence-like object containing the SMap tag (see below).|
|-offset||An offset from the beginning of the source sequence. The retrieved Ace::Sequence will begin at this position. The offset can be any positive or negative integer. Offets are <B>0-basedB>.|
|-length||The length of the sequence to return. Either a positive or negative integer can be specified. If a negative length is given, the returned sequence will be complemented relative to the source sequence.|
|-refseq||The sequence to use to establish the coordinate system for the returned sequence. Normally the source sequence is used to establish the coordinate system, but this can be used to override that choice. You can provide either an Ace::Object or just a sequence name for this argument. The source and reference sequences must share a common ancestor, but do not have to be directly related. An attempt to use a disjunct reference sequence, such as one on a different chromosome, will fail.|
|-name||As an alternative to using an Ace::Object with the <B>-sourceB> argument, you may specify a source sequence using <B>-nameB> and <B>-dbB>. The Ace::Sequence module will use the provided database accessor to fetch a Sequence object with the specified name. new() will return undef is no Sequence by this name is known.|
|-db||This argument is required if the source sequence is specified by name rather than by object reference. It must be a previously opened handle to the reference database.|
|-secondary||This argument points to one or more previously-opened annotation databases. You may use a scalar if there is only one annotation database. Otherwise, use an array reference. You may add and delete annotation databases after the object is created by using the add_secondary() and delete_secondary() methods.|
Most methods are inherited from Ace::Sequence. The following additional methods are supported:
secondary() @databases = $seq->secondary;
Return a list of the secondary databases currently in use, or an empty list if none.
Add one or more secondary databases to the list of annotation databases. Duplicate databases will be silently ignored.
Delete one or more secondary databases from the list of annotation databases. Databases not already in use will be silently ignored.
Ace, Ace::Object, Ace::Sequence,Ace::Sequence::Homol, Ace::Sequence::FeatureList, Ace::Sequence::Feature, GFF
Lincoln Stein <firstname.lastname@example.org> with extensive help from Jean Thierry-Mieg <email@example.com>
Copyright (c) 1999, Lincoln D. Stein
This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. See DISCLAIMER.txt for disclaimers of warranty.
|perl v5.20.3||ACE::SEQUENCE::MULTI (3)||2001-04-07|