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Bio::EnsEMBL::Compara::Graph::BaseXMLWriter Class Reference
Inheritance diagram for Bio::EnsEMBL::Compara::Graph::BaseXMLWriter:

List of all members.


Class Summary

Description

Used as a base for
 

Definition at line 14 of file BaseXMLWriter.pm.

Available Methods

protected _build_writer ()
protected _write_closing ()
protected _write_opening ()
protected _writer ()
public String file ()
public Nothing finish ()
public IO::Handle handle ()
public namespaces ()
public Instance new ()
public xml_schema_namespace ()

Method Documentation

protected Bio::EnsEMBL::Compara::Graph::BaseXMLWriter::_build_writer ( )
Builds the XML::Writer instance taking into account the handle to use and the
namespaces to register. Override to provide a custom writer instance
 
Code:
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protected Bio::EnsEMBL::Compara::Graph::BaseXMLWriter::_write_closing ( )
Override to write the ending tag along. The writer instance has now been
pushed into $self.
 
Code:
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Reimplemented in Bio::EnsEMBL::Compara::Graph::OrthoXMLWriter, and Bio::EnsEMBL::Compara::Graph::PhyloXMLWriter.

protected Bio::EnsEMBL::Compara::Graph::BaseXMLWriter::_write_opening ( )
Override to write the starting tag along with namespaces if required. Method
takes the writer instance as its first agument (since this is called before
the writer instance is pushed into $self).
 
Code:
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Reimplemented in Bio::EnsEMBL::Compara::Graph::OrthoXMLWriter, and Bio::EnsEMBL::Compara::Graph::PhyloXMLWriter.

protected Bio::EnsEMBL::Compara::Graph::BaseXMLWriter::_writer ( )
Used to get the writer instance to use
 
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public String Bio::EnsEMBL::Compara::Graph::BaseXMLWriter::file ( )
  Arg[0] : Set the file location
  Description : Sets the file location to write to. Will undefine handle
  Returntype : String
  Exceptions : None
  Status     : Stable
 
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public Nothing Bio::EnsEMBL::Compara::Graph::BaseXMLWriter::finish ( )
  Description : An important method which will write the final element. This
  allows you to stream any number of trees into one XML file and then call
  finish once you are done with it. B<Always call this method when you are
  done otherwise your XML will not be valid>.
  Returntype : Nothing
  Exceptions : Thrown if you are not finishing the file off with the correct
  end element
  Status     : Stable
 
Code:
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public IO::Handle Bio::EnsEMBL::Compara::Graph::BaseXMLWriter::handle ( )
  Arg[0] : The handle to set
  Description : Mutator for the handle backing this writer. If invoked without
  giving it an instance of a handler it will use the FILE attribute to open
  an instance of IO::File
  Returntype : IO::Handle
  Exceptions : Thrown if we cannot open a file handle
  Status     : Stable
 
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public Bio::EnsEMBL::Compara::Graph::BaseXMLWriter::namespaces ( )
Alter to return the namespaces to use in this XML file. If specifed
the usage of XSI will be implicit and will mean the 2001 W3C schema. Return
type should be a HashRef keyed by the URI and value should be the prefix
to use. Use an empty prefix to set the namespace as default
 
Code:
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Reimplemented in Bio::EnsEMBL::Compara::Graph::OrthoXMLWriter, and Bio::EnsEMBL::Compara::Graph::PhyloXMLWriter.

public Instance Bio::EnsEMBL::Compara::Graph::BaseXMLWriter::new ( )
  Arg[HANDLE] : IO::Handle; pass in an instance of IO::File or
                an instance of IO::String so long as it behaves
                the same as IO::Handle. Can be left blank in 
                favour of the -FILE parameter
  Arg[FILE]   : Scalar; location of the file to write to                        
  Description : Creates a new writer object. 
  Returntype  : Instance of the writer
  Exceptions  : None
  Status      : Internal
 
Code:
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Reimplemented in Bio::EnsEMBL::Compara::Graph::OrthoXMLWriter, and Bio::EnsEMBL::Compara::Graph::PhyloXMLWriter.

public Bio::EnsEMBL::Compara::Graph::BaseXMLWriter::xml_schema_namespace ( )
Returns the namespace of the XML schema (currently W3C 2001)
 
Code:
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The documentation for this class was generated from the following file: