Jessica Michelle Severin

NAME - EEDB::Chrom

SYNOPSIS

An object to encapsulate a Chromosome within an Assembly.

DESCRIPTION

An object that corresponds to specific chromosomes within an assembly. Because Chrom is tied to a specific assembly, an instance of a Chrom identifies not only the chromosome, but also the assembly and species

As with all objects in EEDB, Chrom interits from MQdb::DBObject and MQdb::MappedQuery. Please refer to these documents for all superclass methods

CONTACT

Jessica Severin <severin@gsc.riken.jp>

LICENSE

 * Software License Agreement (BSD License)
 * EdgeExpressDB [eeDB] system
 * copyright (c) 2007-2009 Jessica Severin RIKEN OSC
 * All rights reserved.
 * Redistribution and use in source and binary forms, with or without
 * modification, are permitted provided that the following conditions are met:
 *     * Redistributions of source code must retain the above copyright
 *       notice, this list of conditions and the following disclaimer.
 *     * Redistributions in binary form must reproduce the above copyright
 *       notice, this list of conditions and the following disclaimer in the
 *       documentation and/or other materials provided with the distribution.
 *     * Neither the name of Jessica Severin RIKEN OSC nor the
 *       names of its contributors may be used to endorse or promote products
 *       derived from this software without specific prior written permission.
 *
 * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS ''AS IS'' AND ANY
 * EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
 * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
 * DISCLAIMED. IN NO EVENT SHALL COPYRIGHT HOLDERS BE LIABLE FOR ANY
 * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
 * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
 * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
 * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
 * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
 * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

set_cache_behaviour

  Description  : class level method to turn on/off global caching of Chromsome objects
                 since these are very small and used heavily, it is on my default 
                 and it is recommended to not turn it off.
  Parameter[1] : scalar 0/1 to turn the caching off/on
  Returntype   : none
  Exceptions   : none

get_cache_size

  Description : get count of Chroms currently in the memory cache
  Returntype  : scalar count
  Exceptions  : none

init

  Description: initialize a new instance of this object.
               generally not needed for users to call this method
  Returntype : $self
  Exceptions : none

chrom_name

  Description  : simple getter/setter method for the chromosome name
  Parameter[1] : <optional> if specififed it will set the chromsome name
  Returntype   : string
  Exceptions   : none

chrom_type

  Description  : simple getter/setter method for the chromosome type
  Parameter[1] : <optional> if specififed it will set the chromsome type
  Returntype   : string
  Exceptions   : none

description

  Description  : simple getter/setter method for the chromosome description
  Parameter[1] : <optional> if specififed it will set the chromsome description
  Returntype   : string
  Exceptions   : none

assembly

  Description  : simple getter/setter method for the Assembly of this Chrom
  Parameter[1] : <optional> of type EEDB::Assembly. if specififed it will set the assembly
  Returntype   : EEDB::Assembly instance
  Exceptions   : none

chrom_length

  Description  : simple getter/setter method for the chromosome length
  Parameter[1] : <optional scalar> if specififed it will set the chromsome length
  Returntype   : scalar
  Exceptions   : none

display_desc

  Description  : overrides the superclass method.  
                 returns a debugging description of this instance.
                 calling display_info() will print this display_desc to STDOUT
  Returntype   : string
  Exceptions   : none

xml_start

  Description  : overrides the superclass method.  
                 returns the start of the XML description of this instance
  Returntype   : string
  Exceptions   : none

xml_end

  Description  : overrides the superclass method.  
                 returns the end tag of the XML description of this instance
  Returntype   : string
  Exceptions   : none

xml

  Description  : overrides the superclass method.  
                 returns the complete XML description of this instance
  Returntype   : string
  Exceptions   : none

get_subsequence

  Description  : uses ChromChunk objects and the sequence in the database to 
                 return the actual sequence in this region. Since the
                 Chrom is assigned to a specific Assembly one only needs to specify
                 the start/end and an optional strand to fetch the sequence.
  Parameter[1] : chrom_start 
                 the chromosome start of the region to fetch
  Parameter[2] : chrom_end  
                 the chromosome end of the region to fetch
  Parameter[3] : strand <optional> as "-" or "+"
                 the strand of the sequence. if "-" then it will return the sequence 
                 on the reverse strand by reverse complementing the sequence
  Returntype   : Bio::Seq instance or undef if a data error happens
  Errors       : if the region is not valid or if data is not present it will return undef
  Exceptions   : none

store

  Description  : store this instance into an EEDB database
                 on return the instance will have the primary_id() set.
  Parameter[1] : a MQdb::Database to store into
  Returntype   : $self or undef if a problem occurred
  Exceptions   : none

update

  Description  : updates the data of this instance. require the Chrom to have been
                 fetched from database. It must have database() and primary_id()
  Returntype   : $self
  Exceptions   : none