Archive Ensembl HomeArchive Ensembl Home
Bio::EnsEMBL::Utils::IO::FeatureSerializer Class Reference
Inheritance diagram for Bio::EnsEMBL::Utils::IO::FeatureSerializer:

List of all members.


Class Summary

Synopsis

my $serializer = new Bio::EnsEMBL::Utils::IO::FeatureSerializer( $filehandle );
$serializer-\>print_feature_list( \@list_of_features );

Description

Generic class for serializing features Subclass this class to create a 
format-specific serializer. Be sure to implement print_feature at the 
bare minimum
 

Definition at line 19 of file FeatureSerializer.pm.

Available Methods

public DESTROY ()
public void formatted_write ()
public
Bio::EnsEMBL::Utils::IO::Serializer 
new ()
public print_feature ()
public void print_feature_Iterator ()
public print_feature_list ()
public void print_main_header ()
public print_metadata ()
public print_sequence ()
public Boolean printed_something ()

Method Documentation

public Bio::EnsEMBL::Utils::IO::Serializer::DESTROY ( ) [inherited]
	Destructor
	Description: Restores default state of the STDOUT filehandle as it is a copy
	             and may not flush correctly.
 
Code:
click to view
public void Bio::EnsEMBL::Utils::IO::Serializer::formatted_write ( ) [inherited]
   Arg [1]    : Line format, see Perldoc of formline()
   Arg [2]    : Array of arguments to suit the line format in Arg [1]
   Description: Writes data to the filehandle and rigidly formats it.
                Refer to Perldoc on formline() to specify valid formats.
                Useful for fixed-width file formats.
                Suicides in the event of file system issues.
   Example    : my $FORMAT = '^<<<<<<<<<<<<<<<<<<<|<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<\n';
                $serializer->formatted_write($FORMAT,@text_fields);
   Returntype : None
 
Code:
click to view
public Bio::EnsEMBL::Utils::IO::Serializer Bio::EnsEMBL::Utils::IO::Serializer::new ( ) [inherited]
	Constructor
	Arg [1]    : Optional File handle
	Returntype : Bio::EnsEMBL::Utils::IO::Serializer
 
Code:
click to view

Reimplemented in Bio::EnsEMBL::Utils::IO::FASTASerializer, and Bio::EnsEMBL::Utils::IO::GFFSerializer.

public Bio::EnsEMBL::Utils::IO::FeatureSerializer::print_feature ( )

Undocumented method

Code:
click to view

Reimplemented in Bio::EnsEMBL::Utils::IO::GFFSerializer, and Bio::EnsEMBL::Utils::IO::ReportSerializer.

public void Bio::EnsEMBL::Utils::IO::FeatureSerializer::print_feature_Iterator ( )
	Arg [1]    : Bio::EnsEMBL::Utils::Iterator
	Description: Automatically spools through an iterator for convenience
	Returntype : None
 
Code:
click to view
public Bio::EnsEMBL::Utils::IO::FeatureSerializer::print_feature_list ( )
	Arg [1]    : Listref of Features
	Description: Run print_feature on every feature in the list
 
Code:
click to view

Reimplemented in Bio::EnsEMBL::Utils::IO::ReportSerializer.

public void Bio::EnsEMBL::Utils::IO::Serializer::print_main_header ( ) [inherited]
	Arg [1]    : Data for header, depends on serializer
	Description: Printing the header text or metadata required for this file format,
	             Re-implement in the serializer.
	Returntype : None
 
Code:
click to view

Reimplemented in Bio::EnsEMBL::Utils::IO::GFFSerializer, and Bio::EnsEMBL::Utils::IO::ReportSerializer.

public Bio::EnsEMBL::Utils::IO::Serializer::print_metadata ( ) [inherited]
	
	Arg [1]    : String
	Description: Pipes a custom string into the filehandle that the serializer is using
 
Code:
click to view

Reimplemented in Bio::EnsEMBL::Utils::IO::FASTASerializer, and Bio::EnsEMBL::Utils::IO::GFFSerializer.

public Bio::EnsEMBL::Utils::IO::Serializer::print_sequence ( ) [inherited]
	Arg [1]    : Bio::EnsEMBL::Slice
	Description: By default, prints a block of FASTA format sequence from the given slice

Deprecated:
Code:
click to view
public Boolean Bio::EnsEMBL::Utils::IO::Serializer::printed_something ( ) [inherited]
    Description: Check if serializer has printed any useful data. Not accurate with FASTA
                 due to non-reporting dumper.
    Returntype : Boolean
 
Code:
click to view

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