These documents are For the HEAD of the CVS repository on July 19, 2007 Api docs for previous releases

Modware

Chromosome

Summary Included libraries Package variables Synopsis Description General documentation Methods
Summary
   Modware::Chromosome - Simple front end class to search and create Modware::Feature::CHROMOSOME objects.
Package variables top
No package variables defined.
Included modulestop
Modware::Root
Modware::Search::Chromosome
Inherit top
Modware::Root
Synopsistop
   # USE CASE: PRINT THE CHROMOSOME SEQUENCE IN FASTA FORMAT
   my $chromosome = new dicty::Chromosome( -name => 'chr1' );
   print $chromosome->sequence( -format => 'fasta' );
Descriptiontop
   This class simply provides a convenient interface to create a chromosome object by passing in the
   chromosome name as the parameter.  The name is often more useful than a feature_id

   The object that is returned is a Modware::Feature::CHROMOSOME object (see those docs for detailed
   information about what methods are available), and 'new' will throw an error
   if there is no chromosome with the name requested.

   See also Modware::Feature and  Modware::Feature::CHROMOSOME
Methodstop
newNo descriptionCode

Methods description

Methods code

newdescriptiontopprevnext
sub new {
   my ($type, @args) = @_;

   my $self = {};
   bless $self, $type;   
  
   my ( $chromosome_name, $name ) =  $self->_rearrange([qw(CHROMOSOME_NAME NAME)], @args);

   $name = $chromosome_name if ($chromosome_name && !$name);

   $self->warn("-chromosome_name argument to Modware::Chromosome constructor is deprecated, use -name\n") if $chromosome_name;

   my ( $chr ) = Modware::Search::Chromosome->Search_chromosome_by_name( $name );


   $self->throw("Cannot find chromosome named $chromosome_name") if !$self;

   return $chr;
}

General documentation

AUTHOR - Eric Just top
   Eric Just e-just@northwestern.edu
APPENDIX top
   The rest of the documentation details each of the object
   methods. Internal methods are usually preceded with a _
seq top
 Title    : new
 Function : creates a new Modware::Feature::CHROMOSOME object from name
 Returns  : Modware::Feature::CHROMOSOME object
 Args     : named arguments
          : -chromosome_name => string