NAME

Bio::JBrowse::Store::NCList::IntervalStore

SYNOPSIS

my $is = Bio::JBrowse::Store::NCList::IntervalStore->new({
             urlTemplate => "lf-{Chunk}.jsonz",
         });
my $chunkBytes = 80_000;
$is->startLoad( $measure, $chunkBytes );
$is->addSorted([10, 100, -1])
$is->addSorted([50, 80, 1])
$is->addSorted([90, 150, -1])
$is->finishLoad();
$is->overlap(60, 85)

=> ([10, 100, -1], [50, 80, 1])

NAME

Bio::JBrowse::Store::NCList::IntervalStore - stores a set of intervals (genomic features) in an on-disk lazy nested-containment list

METHODS

new

Title   : new
Usage   : Bio:JBrowse::Store::NCList::IntervalStore->new(
              arrayRepr => {attributes => ["start", "end", "strand"]},
          )
Function: create a new store
Returns : an Bio::JBrowse::Store::NCList::IntervalStore object
Args    : The Bio::JBrowse::Store::NCList::IntervalStore constuctor accepts the named parameters:
          store: optional object with put(path, data) method, will be used to output
                 feature data
          compress: if true, attempt to compress the data on disk
          arrayRepr: Bio::JBrowse::Store::NCList::ArrayRepr object used to represent the feature data
          urlTemplate (optional): template for URLs where chunks of feature
                                  data will be stored.  This is relative to
                                  the directory with the "trackData.json" file
          nclist (optional): the root of the nclist
          count (optional): the number of intervals in this Bio::JBrowse::Store::NCList::IntervalStore
          minStart (optional): the earliest interval start point
          maxEnd (optional): the latest interval end point

          If this Bio::JBrowse::Store::NCList::IntervalStore hasn't been loaded yet, the optional
          parameters aren't necessary.  But to access a previously-loaded
          Bio::JBrowse::Store::NCList::IntervalStore, the optional parameters *are* needed.

startLoad( $measure, $chunkBytes )

addSorted( \@feature )

finishLoad()

overlapCallback( $from, $to, \&func )

Calls the given function once for each of the intervals that overlap the given interval if <$from <= $to>, iterates left-to-right, otherwise iterates right-to-left.

descriptor

Title   : descriptor
Usage   : $list->descriptor
Returns : a hash containing the data needed to re-construct this
          Bio::JBrowse::Store::NCList::IntervalStore, including the
          root of the NCList plus some metadata and configuration.
          The return value can be passed to the constructor later.

AUTHOR

Mitchell Skinner <jbrowse@arctur.us>

Copyright (c) 2007-2011 The Evolutionary Software Foundation

This package and its accompanying libraries are free software; you can redistribute it and/or modify it under the terms of the LGPL (either version 2.1, or at your option, any later version) or the Artistic License 2.0. Refer to LICENSE for the full license text.

AUTHOR

Robert Buels <rbuels@gmail.com>

COPYRIGHT AND LICENSE

This software is copyright (c) 2013 by Robert Buels.

This is free software; you can redistribute it and/or modify it under the same terms as the Perl 5 programming language system itself.