biointerchange 0.1.0 → 0.1.2

data/docs/exceptions_readme.txt

@@ -1,13 +0,0 @@
-BioInterchange Exception and Error handling. 
-
-All BioInterchange errors come under two main categories:
-1. InputFormatError
-2. ImplementationError
-
-Each of these classes is handled differently within the BioInterchange framework.
-
-InputFormatErrors are those that could be raised at any time (during runtime), and that the user could then be exposed to. Examples include errors relating to missing files, or incorrect file formats. These Errors are rescued at the highest level in our program, and adjusted such that a user friendly error message is displayed without a stacktrace (backtrace). This helps to keep our system more user-friendly. However, this means that we strongly advise that when such an error is raised, that it comes with a user friendly error message, and is as specific as possible.
-
-ImplementationErrors are those that could only be thrown during program implementation and extension. For example, a method is passed something it isn't expecting or can't handle (e.g., a writer is passed an invalid model). These errors are not caught by the main program, instead left to execute in the normal fashion including stacktrace to enable program debugging by a developer.
-
-ImplementationErrors have three sub-categories. They are split into errors being raised from either the Reader (ImplementationReaderError), the Model (ImplementationModelError), or the Writer (ImplementationWriterError). Please use the ImplementationError sub-class consistent with where the error is being raised. This helps provide an easy way to see which stage in program execution an error has occurred. 

data/lib/biointerchange/gff3.rb

@@ -1,135 +0,0 @@
-module BioInterchange
-
-class GFF3
-
-    def self.strand
-      RDF::URI.new('http://www.sequenceontology.org/gff3#GFF3_0010')
-    end
-
-    def self.attributes
-      RDF::URI.new('http://www.sequenceontology.org/gff3#GFF3_0012')
-    end
-
-    def self.parent
-      RDF::URI.new('http://www.sequenceontology.org/gff3#GFF3_0014')
-    end
-
-    def self.contains
-      RDF::URI.new('http://www.sequenceontology.org/gff3#GFF3_0015')
-    end
-
-    def self.seqid
-      RDF::URI.new('http://www.sequenceontology.org/gff3#GFF3_0004')
-    end
-
-    def self.source
-      RDF::URI.new('http://www.sequenceontology.org/gff3#GFF3_0005')
-    end
-
-    def self.type
-      RDF::URI.new('http://www.sequenceontology.org/gff3#GFF3_0006')
-    end
-
-    def self.start
-      RDF::URI.new('http://www.sequenceontology.org/gff3#GFF3_0007')
-    end
-
-    def self.end
-      RDF::URI.new('http://www.sequenceontology.org/gff3#GFF3_0008')
-    end
-
-    def self.score
-      RDF::URI.new('http://www.sequenceontology.org/gff3#GFF3_0009')
-    end
-
-    def self.phase
-      RDF::URI.new('http://www.sequenceontology.org/gff3#GFF3_0011')
-    end
-
-    def self.tag
-      RDF::URI.new('http://www.sequenceontology.org/gff3#GFF3_0013')
-    end
-
-    def self.Set
-      RDF::URI.new('http://www.sequenceontology.org/gff3#GFF3_0001')
-    end
-
-    def self.Feature
-      RDF::URI.new('http://www.sequenceontology.org/gff3#GFF3_0002')
-    end
-
-    def self.Attribute
-      RDF::URI.new('http://www.sequenceontology.org/gff3#GFF3_0003')
-    end
-
-    def self.Strand
-      RDF::URI.new('http://www.sequenceontology.org/gff3#GFF3_0016')
-    end
-
-    def self.Positive
-      RDF::URI.new('http://www.sequenceontology.org/gff3#GFF3_0017')
-    end
-
-    def self.Negative
-      RDF::URI.new('http://www.sequenceontology.org/gff3#GFF3_0018')
-    end
-
-    def self.UnknownStrand
-      RDF::URI.new('http://www.sequenceontology.org/gff3#GFF3_0019')
-    end
-
-    def self.NotStranded
-      RDF::URI.new('http://www.sequenceontology.org/gff3#GFF3_0020')
-    end
-
-    # Determines whether the given URI is an object property.
-    #
-    # +uri+:: URI that is tested for being an object property
-    def self.is_object_property?(uri)
-      return true if uri == RDF::URI.new('http://www.sequenceontology.org/gff3#GFF3_0010')
-      return true if uri == RDF::URI.new('http://www.sequenceontology.org/gff3#GFF3_0012')
-      return true if uri == RDF::URI.new('http://www.sequenceontology.org/gff3#GFF3_0014')
-      return true if uri == RDF::URI.new('http://www.sequenceontology.org/gff3#GFF3_0015')
-      false
-    end
-
-    # Determines whether the given URI is a datatype property.
-    #
-    # +uri+:: URI that is tested for being a datatype property
-    def self.is_datatype_property?(uri)
-      return true if uri == RDF::URI.new('http://www.sequenceontology.org/gff3#GFF3_0004')
-      return true if uri == RDF::URI.new('http://www.sequenceontology.org/gff3#GFF3_0005')
-      return true if uri == RDF::URI.new('http://www.sequenceontology.org/gff3#GFF3_0006')
-      return true if uri == RDF::URI.new('http://www.sequenceontology.org/gff3#GFF3_0007')
-      return true if uri == RDF::URI.new('http://www.sequenceontology.org/gff3#GFF3_0008')
-      return true if uri == RDF::URI.new('http://www.sequenceontology.org/gff3#GFF3_0009')
-      return true if uri == RDF::URI.new('http://www.sequenceontology.org/gff3#GFF3_0011')
-      return true if uri == RDF::URI.new('http://www.sequenceontology.org/gff3#GFF3_0013')
-      false
-    end
-
-    # Determines whether the given URI is a class.
-    #
-    # +uri+:: URI that is tested for being a class
-    def self.is_class?(uri)
-      return true if uri == RDF::URI.new('http://www.sequenceontology.org/gff3#GFF3_0001')
-      return true if uri == RDF::URI.new('http://www.sequenceontology.org/gff3#GFF3_0002')
-      return true if uri == RDF::URI.new('http://www.sequenceontology.org/gff3#GFF3_0003')
-      return true if uri == RDF::URI.new('http://www.sequenceontology.org/gff3#GFF3_0016')
-      false
-    end
-
-    # Determines whether the given URI is a named individual.
-    #
-    # +uri+:: URI that is tested for being a named individual
-    def self.is_named_individual?(uri)
-      return true if uri == RDF::URI.new('http://www.sequenceontology.org/gff3#GFF3_0017')
-      return true if uri == RDF::URI.new('http://www.sequenceontology.org/gff3#GFF3_0018')
-      return true if uri == RDF::URI.new('http://www.sequenceontology.org/gff3#GFF3_0019')
-      return true if uri == RDF::URI.new('http://www.sequenceontology.org/gff3#GFF3_0020')
-      false
-    end
-
-end
-
-end