|$ref= $segment->ref||Return the reference point that establishes the coordinate system for this segment, e.g. chr1.|
|$start = $segment->start||Return the starting coordinate of this segment.|
|$end = $segment->end||Return the ending coordinate of this segment.|
|@features = $segment->features(@filter)|
|@features = $segment->features(-type=>$type,-category=>$category)||
The features() method returns annotations across the length of the
segment. Two forms of this method are recognized. In the first form,
the <B>B>@filter<B>B> argument contains a series of category names to
retrieve. Each category may be further qualified by a regular
expression which will be used to filter features by their type ID.
Filters have the format category:typeID, where the category and type
are separated by a colon. The typeID and category names are treated
as an unanchored regular expression (but see the note below). As a
special cse, you may use a type of transcript to fetch composite
transcript model objects (the union of exons, introns and cds
Example 1: retrieve all the features in the similarity and experimental categories:
Example 2: retrieve all the similarity features of type EST_elegans and EST_GENOME:
Example 3: retrieve all similarity features that have anything to do with ESTs:
Example 4: retrieve all the transcripts and experimental data
In the second form, the type and categories are given as named arguments. You may use regular expressions for either typeID or category. It is also possible to pass an array reference for either argument, in which case the DAS server will return the union of the features.
Example 5: retrieve all the features in the similarity and experimental categories:
Example 6: retrieve all the similarity features of type EST_elegans and EST_GENOME:
|$dna = $segment->dna||Return the DNA corresponding to the segment. The return value is a simple string, and not a Bio::Sequence object. This method may return undef when used with a DAS annotation server that does not maintain a copy of the DNA.|
|@types = $segment->types|
|$count = $segment->types($type)||
This methods summarizes the feature types available across this
segment. The items in this list can be used as arguments to
Called with no arguments, this method returns an array of Das::Segment::Type objects. See the manual page for details. Called with a TypeID, the method will return the number of instances of the named type on the segment, or undef if the type is invalid. Because the list and count of types is cached, there is no penalty for invoking this method several times.
Lincoln Stein <email@example.com>.
Copyright (c) 2003 Cold Spring Harbor Laboratory
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||DAS::SEGMENT (3)||2010-06-29|