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Bio::EnsEMBL::Compara::Production::Projection::Writer::ProjectedFileWriter Class Reference
Inheritance diagram for Bio::EnsEMBL::Compara::Production::Projection::Writer::ProjectedFileWriter:

List of all members.


Class Summary

Description

This class writes out to a file location given at construction time using
Text::CSV. If this is not present this class will not work.
 

Definition at line 19 of file ProjectedFileWriter.pm.

Available Methods

protected _build_file_handle ()
protected _csv_writer ()
protected _projection_to_array ()
public close ()
public DESTROY ()
public file ()
public file_handle ()
public new ()
public projections ()
public write ()
public write_projection ()

Method Documentation

protected Bio::EnsEMBL::Compara::Production::Projection::Writer::ProjectedFileWriter::_build_file_handle ( )

Undocumented method

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protected Bio::EnsEMBL::Compara::Production::Projection::Writer::ProjectedFileWriter::_csv_writer ( )

Undocumented method

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protected Bio::EnsEMBL::Compara::Production::Projection::Writer::ProjectedFileWriter::_projection_to_array ( )

Undocumented method

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public Bio::EnsEMBL::Compara::Production::Projection::Writer::ProjectedFileWriter::close ( )
Used to close down the underlying file handle
 
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public Bio::EnsEMBL::Compara::Production::Projection::Writer::ProjectedFileWriter::DESTROY ( )
Destroys the file handle generated by this object if we were not given 
one during construction
 
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public Bio::EnsEMBL::Compara::Production::Projection::Writer::ProjectedFileWriter::file ( )
  Description : Getter for the file name
 
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public Bio::EnsEMBL::Compara::Production::Projection::Writer::ProjectedFileWriter::file_handle ( )
  
  Description : Getter for the file handle
 
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public Bio::EnsEMBL::Compara::Production::Projection::Writer::ProjectedFileWriter::new ( )
  Arg[-file] : required if file_handle is not given;
  Arg[-file_handle] : required if file is not given; 
  Description : New method used for a new instance of the given object. 
                Required fields are indicated accordingly. Fields are specified
                using the Arguments syntax (case insensitive).
 
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Reimplemented from Bio::EnsEMBL::Compara::Production::Projection::Writer::BaseWriter.

public Bio::EnsEMBL::Compara::Production::Projection::Writer::BaseWriter::projections ( ) [inherited]
  Description : Getter.
 
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public Bio::EnsEMBL::Compara::Production::Projection::Writer::BaseWriter::write ( ) [inherited]
The subroutine we call in order to write projection data out
 
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public Bio::EnsEMBL::Compara::Production::Projection::Writer::ProjectedFileWriter::write_projection ( )
Writes the projection data to configured file handle or to the given 
file location. The output is a CSV of the following columns:
=over 8
=item DBEntry accession
=item Source's stable ID i.e. the object the transferred accession was originally attached to
=item Target's stable ID i.e. the end point for this transfer
=item Source's % identity
=item Target's % identity
=item Type of homology
=back
 
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Reimplemented from Bio::EnsEMBL::Compara::Production::Projection::Writer::BaseWriter.


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