#!/usr/bin/perl
package Chromosome;

#####################################################################
# Author : Shuai Weng
# Date   : July 2001
# 
# See documentation for the usage details. 
#    
# http:///usr/local/dicty/www_dictybase/db/lib/html/dictyBase/programmer/Chromosome.html
#
#####################################################################

use strict;
use DBI;
use Carp;
use vars qw (@ISA %allowedConstructors);
use dictyBase_Table_LOBInsert;
@ISA = qw (dictyBase_Table_LOBInsert); # base class


# Class Globals

# put column names in the hash below, that are able to uniquely
# specify a row in the table

%allowedConstructors = (chromosome=>undef);
       
####################################################################
sub getORFGeneArrayRef {
####################################################################
    my ($self) = @_;
    my $schema = $self->schema;
    my $sth = $self->dbh->prepare("
        SELECT F.feature_name, L.locus_name
        FROM   $schema.feature F, $schema.locus L
        WHERE  F.chromosome = ?
        AND    F.locus_no = L.locus_no
    ");
    $sth->execute($self->chromosome);
    my $arrayRef = $sth->fetchall_arrayref();
    $sth->finish;
    return $arrayRef;
}

####################################################################
sub DESTROY{
####################################################################
# nothing needs to be done 

}


####################################################################
1; #################################################################
####################################################################

=pod

=head1 Name

Chromosome.pm

=head1 Description

This perl object (Chromosome.pm) acts as container for Chromosome info in oracle database. Once an object has been instantiated, several methods are available to retrieve the attributes of the object. 


=head1 Instantiating a New Chromosome Object

To instantiate a new Chromosome object, you may use following syntax: 

my $Obj = Chromosome->new(dbh=>$dbh,
			  chromosome=>$chrnum);


where $dbh is a valid database handle to either dictyBase or SDEV. All passed in values must be valid values for the columns that were provided, otherwise the script will die, with an appropriate error message.
 

=head1 Accessor Methods


All accessor methods take the form of : 


my $column_value = $Obj->column_name, eg: 


my $dateCreated = $Obj->date_created; 


etc. You can use an accessor for any valid column in the Chromosome table. 


See valid columns in chromosome table:

http:///usr/local/dicty/www_dictybase/db/lib/cgi-bin/dictyBase/tableSpecifications?table=CHROMOSOME

=head2 getRow method

Usage:

my $row = $obj->getRow;

This method returns a tab-delimited row from chromosome table.

=head2 getORFGeneArrayRef

Usage :

foreach my $rowRef (@{$Obj->getORFGeneArrayRef}) {

    my ($featNm, $locusNm) = @$rowRef;

    ....

}

This method returns feature_names and their gene names in a given chromosome. 

=head1 Insert, update and delete Methods

You can also use 'Insert' class method and 'update' and 'delete' 
instance methods for inserting new row into database, updating and 
deleting info for a specified row. 

See dictyBase_Table documentation for usage details :

Update : http:///usr/local/dicty/www_dictybase/db/lib/staff/dictyBase/programmer/dictyBase_Table.html#Update_Method

Insert : http:///usr/local/dicty/www_dictybase/db/lib/staff/dictyBase/programmer/dictyBase_Table.html#Insert_Method

Delete : http:///usr/local/dicty/www_dictybase/db/lib/staff/dictyBase/programmer/dictyBase_Table.html#Delete_Method


=head1 Author

Shuai Weng

shuai@genome.stanford.edu

=cut