Bio::JBrowse::Store::NCList::ArrayRepr - compact array-based serialization of hashrefs
The ArrayRepr class is for operating on indexed representations of objects. For example, if we have a lot of objects with similar attributes, e.g.: [ {start: 1, end: 2, strand: -1}, {start: 5, end: 6, strand: 1}, ... ] we can represent them more compactly (e.g., in JSON) something like this: class = ["start", "end", "strand"] [ [1, 2, -1], [5, 6, 1], ... ] If we want to represent a few different kinds of objects in our big list, we can have multiple "class" arrays, and tag each object to identify which "class" array describes it. For example, if we have a lot of instances of a few types of objects, like this: [ {start: 1, end: 2, strand: 1, id: 1}, {start: 5, end: 6, strand: 1, id: 2}, ... {start: 10, end: 20, chunk: 1}, {start: 30, end: 40, chunk: 2}, ... ] We could use the first array position to indicate the "class" for the object, like this: classes = [["start", "end", "strand", "id"], ["start", "end", "chunk"]] [ [0, 1, 2, 1, 1], [0, 5, 6, 1, 2], ... [1, 10, 20, 1], [1, 30, 40, 1] ] Also, if we occasionally want to add an ad-hoc attribute, we could just stick an optional dictionary onto the end: classes = [["start", "end", "strand", "id"], ["start", "end", "chunk"]] [ [0, 1, 2, 1, 1], [0, 5, 6, 1, 2, {foo: 1}] ] Given that individual objects are being represented by arrays, generic code needs some way to differentiate arrays that are meant to be objects from arrays that are actually meant to be arrays. So for each class, we include a dict with <attribute name>: true mappings for each attribute that is meant to be an array. Also, in cases where some attribute values are the same for all objects in a particular set, it may be convenient to define a prototype ("proto") with default values for all objects in the set In the end, we get something like this: classes = [ { "attributes" : [ "start", "end", "subfeatures" ], "proto" : { "Chrom" : "chr1" }, "isArrayAttr" : { "Subfeatures" : true } } ] That's what this class facilitates.
Robert Buels <rbuels@gmail.com>
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.
To install Bio::JBrowse::Store::NCList, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::JBrowse::Store::NCList
CPAN shell
perl -MCPAN -e shell install Bio::JBrowse::Store::NCList
For more information on module installation, please visit the detailed CPAN module installation guide.