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Bio::EnsEMBL::Utils::IO::ReportSerializer Class Reference
Inheritance diagram for Bio::EnsEMBL::Utils::IO::ReportSerializer:

List of all members.


Class Summary

Synopsis

    use Bio::EnsEMBL::Registry;
    use Bio::EnsEMBL::Utils::IO::ReportSerializer;
    use IO::File;
    
    my $registry = 'Bio::EnsEMBL::Registry';
    $output_fh = IO::File-\>new($config{'output'},'w') or die;
    $serializer = new ReportSerializer($output_fh);
    my $slice_adaptor = $registry-\>get_adaptor( 'Human', 'Core', 'Slice' );
    my $slice = $slice_adaptor-\>fetch_by_toplevel_location("6:1000000..1500000");
    
    $serializer-\>print_section_header($slice);
    $serializer-\>print_feature_list($slice-\>get_all_Genes);

Description

Subclass of Serializer that can turn a feature into a text block
Unsuited to very large slices, because it requires a select-all approach for features.
 

Definition at line 31 of file ReportSerializer.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_iterator ()
public print_feature_list ()
public void print_main_header ()
public print_metadata ()
public void print_section_header ()
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:
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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:
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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:
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Reimplemented in Bio::EnsEMBL::Utils::IO::FASTASerializer, and Bio::EnsEMBL::Utils::IO::GFFSerializer.

public Bio::EnsEMBL::Utils::IO::ReportSerializer::print_feature ( )
    Arg [1]    : Bio::EnsEMBL::Feature, subclass or related pseudo-feature
    Example    : $reporter->print_feature($feature,$slice_start_coordinate,"X")
 
Code:
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Reimplemented from Bio::EnsEMBL::Utils::IO::FeatureSerializer.

public void Bio::EnsEMBL::Utils::IO::FeatureSerializer::print_feature_Iterator ( ) [inherited]
	Arg [1]    : Bio::EnsEMBL::Utils::Iterator
	Description: Automatically spools through an iterator for convenience
	Returntype : None
 
Code:
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public Bio::EnsEMBL::Utils::IO::ReportSerializer::print_feature_iterator ( )

Undocumented method

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public Bio::EnsEMBL::Utils::IO::ReportSerializer::print_feature_list ( )
    Arg [1]    : Listref of Bio::EnsEMBL::Feature, subclass or related pseudo-feature
    Description: Relies on a list of similar features to print in a block together.
                 Overrides superclass method
                 Results are truncated after the first 100 features for brevity.
    Example    : $reporter->print_feature_list(\@features);
 
Code:
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Reimplemented from Bio::EnsEMBL::Utils::IO::FeatureSerializer.

public void Bio::EnsEMBL::Utils::IO::ReportSerializer::print_main_header ( )
    Arg [1]    : Arrayref of slices going into the file.
    Description: Printing the header text for this report
                 Requires a slice list in order to report how many will be printed
    Returntype : None
 
Code:
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Reimplemented from Bio::EnsEMBL::Utils::IO::Serializer.

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

public void Bio::EnsEMBL::Utils::IO::ReportSerializer::print_section_header ( )
    Arg [1]    : Bio::EnsEMBL::Slice
    Description: Prints a summary of the slice
                 Intended to be used prior to print_feature_list()
    Returntype : None
 
Code:
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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:
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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:
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The documentation for this class was generated from the following file: