Bio::EnsEMBL::IdMapping::MappingList Class Reference

Inheritance diagram for Bio::EnsEMBL::IdMapping::MappingList:

Public Member Functions
public Bio::EnsEMBL::IdMapping::MappingList	new ()
public void	add_Entry ()
public Arrayref	get_all_Entries ()
public void	add_all ()
public Int	get_entry_count ()
public void	log ()
public String	to_string ()
Public Member Functions inherited from Bio::EnsEMBL::IdMapping::Serialisable
public Bio::EnsEMBL::IdMapping::Serialisable	new ()
public String	write_to_file ()
public Bio::EnsEMBL::IdMapping::Serialisable	read_from_file ()
public String	dump_path ()
public String	cache_file_name ()
public String	cache_file ()
public Boolean	loaded ()

Detailed Description

Synopsis

# create a new MappingList
my $mappings = Bio::EnsEMBL::IdMapping::MappingList->new(
  -DUMP_PATH  => $dump_path,
  -CACHE_FILE => 'gene_mappings.ser',
);
 
# add entries
my $mappings->add_Entry($entry1);
my $mappings->add_all( $entry2, $entry3 );
 
# serialise to file
$mappings->write_to_file;
 
# later, read these mappings from file
my $mappings1 = Bio::EnsEMBL::IdMapping::MappingList->new(
  -DUMP_PATH  => $dump_path,
  -CACHE_FILE => 'gene_mappings.ser',
);
$mappings1->read_from_file;

Description

This object represents a list of Bio::EnsEMBL::IdMapping::Entry
objects. It's essentially an OO wrapper for an array with some type
checking and convenience methods.

Definition at line 38 of file MappingList.pm.

Member Function Documentation

add_all()

public void Bio::EnsEMBL::IdMapping::MappingList::add_all

(

)

  Arg[1]      : List of Bio::EnsEMBL::IdMapping::Entry objects
  Example     :

my @entries = ($entry1, $entry2);
               $mappings->add_all(@entries);

  Description : Adds a list of Entries to the MappingList.
  Return type : none
  Exceptions  : thrown on wrong argument
  Caller      : general
  Status      : At Risk
              : under development

Code:

add_Entry()

public void Bio::EnsEMBL::IdMapping::MappingList::add_Entry

(

)

  Arg[1]      : Bio::EnsEMBL::IdMapping::Entry - Entry to add
  Example     :

$mappings->add_Entry($entry);

  Description : Adds an Entry to the MappingList.
  Return type : none
  Exceptions  : thrown on wrong or missing argument
  Caller      : general
  Status      : At Risk
              : under development

Code:

get_all_Entries()

public Arrayref Bio::EnsEMBL::IdMapping::MappingList::get_all_Entries

(

)

  Example     :

 foreach my $entry (@{ $mappings->get_all_Entries }) {
@section autotoc_md11 do something with the entry
                }

  Description : Gets all Entries in the MappingList.
  Return type : Arrayref of Bio::EnsEMBL::IdMapping::Entry
  Exceptions  : none
  Caller      : general
  Status      : At Risk
              : under development

Code:

get_entry_count()

public Int Bio::EnsEMBL::IdMapping::MappingList::get_entry_count

(

)

  Example     :

my $num_entries = $mappings->get_entry_count;

  Description : Returns the number of Entries in the MappingList.
  Return type : Int
  Exceptions  : none
  Caller      : general
  Status      : At Risk
              : under development

Code:

log()

public void Bio::EnsEMBL::IdMapping::MappingList::log

(

)

  Arg[1]      : String $type - object type (e.g. 'gene')
  Arg[2]      : String $dump_path - path for writing output
  Example     :

$mappings->log('gene', $conf->param('basedir'));

  Description : Logs all Entries in the MappingList to a file. Used for
                debugging.
  Return type : none
  Exceptions  : thrown on I/0 error
  Caller      : general
  Status      : At Risk
              : under development

Code:

new()

public Bio::EnsEMBL::IdMapping::MappingList Bio::EnsEMBL::IdMapping::MappingList::new

(

)

  Arg[1-N]    : see superclass
  Example     :

my $gene_mappings = Bio::EnsEMBL::IdMapping::MappingList->new(
                 -DUMP_PATH   => $dump_path,
                 -CACHE_FILE  => 'gene_mappings.ser',
               );

  Description : Constructor.
  Return type : Bio::EnsEMBL::IdMapping::MappingList
  Exceptions  : none
  Caller      : general
  Status      : At Risk
              : under development

Code:

to_string()

public String Bio::EnsEMBL::IdMapping::MappingList::to_string

(

)

  Example     :

print LOG $mappings->to_string, "\n";

  Description : Returns a string representation of the MappingList. This is
                simply a multi-line string, where each line is a stringified
                Entry.
                Useful for debugging and logging.
  Return type : String
  Exceptions  : none
  Caller      : general
  Status      : At Risk
              : under development

Code:

---

The documentation for this class was generated from the following file:

• ensembl/modules/Bio/EnsEMBL/IdMapping/MappingList.pm