Class: BioInterchange::Genomics::GFF3Reader
- Defined in:
- lib/biointerchange/genomics/gff3_reader.rb
Instance Method Summary collapse
-
#deserialize(inputstream) ⇒ Object
Reads a GFF3 file from the input stream and returns an associated model.
-
#initialize(name = nil, name_uri = nil, date = nil, batch_size = nil) ⇒ GFF3Reader
constructor
Creates a new instance of a Generic Feature Format Version 3 (GFF3) reader.
-
#postponed? ⇒ Boolean
Returns true if the reading of the input was postponed due to a full batch.
Constructor Details
#initialize(name = nil, name_uri = nil, date = nil, batch_size = nil) ⇒ GFF3Reader
Creates a new instance of a Generic Feature Format Version 3 (GFF3) reader.
The reader supports batch processing.
name
-
Optional name of the person who generated the GFF3 file.
name_uri
-
Optional e-mail address of the person who generated the GFF3 file.
date
-
Optional date of when the GFF3 file was produced.
batch_size
-
Optional integer that determines that number of features that
should be processed in one go.
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# File 'lib/biointerchange/genomics/gff3_reader.rb', line 30 def initialize(name = nil, name_uri = nil, date = nil, batch_size = nil) @name = name @name_uri = name_uri @date = date @batch_size = batch_size @linenumber = 0 end |
Instance Method Details
#deserialize(inputstream) ⇒ Object
Reads a GFF3 file from the input stream and returns an associated model.
If this method is called when postponed?
returns true, then the reading will continue from where it has been interrupted beforehand.
inputstream
-
an instance of class IO or String that holds the contents of a GFF3 file
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# File 'lib/biointerchange/genomics/gff3_reader.rb', line 44 def deserialize(inputstream) if inputstream.kind_of?(IO) create_model(inputstream) elsif inputstream.kind_of?(String) then create_model(StringIO.new(inputstream)) else raise BioInterchange::Exceptions::ImplementationReaderError, 'The provided input stream needs to be either of type IO or String.' end end |
#postponed? ⇒ Boolean
Returns true if the reading of the input was postponed due to a full batch.
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# File 'lib/biointerchange/genomics/gff3_reader.rb', line 55 def postponed? @postponed end |