bio 1.3.0 → 1.3.1

data/lib/bio/io/biosql/bioentry_dbxref.rb

@@ -1,11 +0,0 @@
-module Bio
-		class SQL
-			class BioentryDbxref < DummyBase
-#delete				set_sequence_name nil
-				set_primary_key nil #bioentry_id,dbxref_id
-				belongs_to :bioentry, :class_name => "Bioentry"
-				belongs_to :dbxref, :class_name => "Dbxref"
-			end
-    		end #SQL
-end #Bio	
-

data/lib/bio/io/biosql/bioentry_path.rb

@@ -1,12 +0,0 @@
-module Bio
-    class SQL
-			class BioentryPath < DummyBase
-				set_primary_key nil
-#delete				set_sequence_name nil
-				belongs_to :term, :class_name => "Term"
-				#da sistemare per poter procedere.
-				belongs_to :object_bioentry, :class_name=>"Bioentry"
-				belongs_to :subject_bioentry, :class_name=>"Bioentry"
-			end #BioentryPath
-		end #SQL
-end #Bio

data/lib/bio/io/biosql/bioentry_qualifier_value.rb

@@ -1,10 +0,0 @@
-module Bio
-  class SQL
-    class BioentryQualifierValue < DummyBase
-      #NOTE: added rank to primary_keys, now it's finished.
-      set_primary_keys :bioentry_id, :term_id, :rank
-      belongs_to :bioentry, :class_name => "Bioentry"
-      belongs_to :term, :class_name => "Term"
-    end #BioentryQualifierValue
-  end #SQL
-end #Bio

data/lib/bio/io/biosql/bioentry_reference.rb

@@ -1,10 +0,0 @@
-module Bio
-    class SQL
-			class BioentryReference < DummyBase
-				set_primary_keys :bioentry_id, :reference_id, :rank
-				belongs_to :bioentry, :class_name => "Bioentry"
-				belongs_to :reference , :class_name => "Reference"
-			end		
-		end #SQL
-end #Bio		
-

data/lib/bio/io/biosql/bioentry_relationship.rb

@@ -1,10 +0,0 @@
-module Bio
-    class SQL
-			class BioentryRelationship < DummyBase
-#delete				set_primary_key "bioentry_relationship_id"
-				set_sequence_name "bieontry_relationship_pk_seq"
-				belongs_to :object_bioentry, :class_name => "Bioentry"
-				belongs_to :subject_bioentry, :class_name => "Bioentry"
-			end
-		end #SQL
-end #Bio		    

data/lib/bio/io/biosql/biosequence.rb

@@ -1,11 +0,0 @@
-module Bio
-    class SQL
-			class Biosequence < DummyBase
-				set_primary_key "bioentry_id"
-#delete				set_sequence_name "biosequence_pk_seq"
-				belongs_to :bioentry, :foreign_key=>"bioentry_id"
-				#has_one :bioentry
-				#, :class_name => "Bioentry"
-			end
-		end #SQL
-end #Bio		   

data/lib/bio/io/biosql/comment.rb

@@ -1,7 +0,0 @@
- module Bio
-    class SQL
-			class Comment < DummyBase
-			      belongs_to :bioentry, :class_name => "Bioentry"
-			end
-		end #SQL
-end #Bio		   

data/lib/bio/io/biosql/dbxref.rb

@@ -1,13 +0,0 @@
- module Bio
-    class SQL
-			class Dbxref < DummyBase
-			      #set_sequence_name "dbxref_pk_seq"
-			      has_many :dbxref_qualifier_values, :class_name => "DbxrefQualifierValue"
-			      has_many :locations, :class_name => "Location"
-			      has_many :references, :class_name=>"Reference"
-			      has_many :term_dbxrefs, :class_name => "TermDbxref"
-			      has_many :bioentry_dbxrefs, :class_name => "BioentryDbxref"
-            #TODO: check is with bioentry there is an has_and_belongs_to_many relationship has specified in schema overview.
-			    end
-    		end #SQL
-end #Bio		

data/lib/bio/io/biosql/dbxref_qualifier_value.rb

@@ -1,12 +0,0 @@
- module Bio
-    class SQL
-			class DbxrefQualifierValue < DummyBase
-				#think to use composite primary key
-			      set_primary_key nil #dbxref_id, term_id, rank
-#delete			      set_sequence_name nil
-			      belongs_to :dbxref, :class_name => "Dbxref"
-			      belongs_to :term, :class_name => "Term"
-			    end		
-		end #SQL
-end #Bio		
-

data/lib/bio/io/biosql/location.rb

@@ -1,32 +0,0 @@
-module Bio
-  class SQL 
-    class Location < DummyBase
-      #set_sequence_name "location_pk_seq"
-      belongs_to :seqfeature, :class_name => "Seqfeature"
-      belongs_to :dbxref, :class_name => "Dbxref"
-      belongs_to :term, :class_name => "Term"
-      has_many :location_qualifier_values, :class_name => "LocationQualifierValue"
-      
-      def to_s
-        if strand==-1
-          str="complement("+start_pos.to_s+".."+end_pos.to_s+")"
-        else
-          str=start_pos.to_s+".."+end_pos.to_s
-        end
-        return str    
-      end
-      
-      def sequence
-        seq=""
-        unless self.seqfeature.bioentry.biosequence.seq.nil?
-          seq=Bio::Sequence::NA.new(self.seqfeature.bioentry.biosequence.seq[start_pos-1..end_pos-1])
-          seq.reverse_complement! if strand==-1
-        end
-        return seq        
-      end
-      
-      
-      
-    end
-  end #SQL
-end #Bio

data/lib/bio/io/biosql/location_qualifier_value.rb

@@ -1,11 +0,0 @@
- module Bio
-    class SQL 
-			class LocationQualifierValue <  DummyBase
-			      set_primary_key nil #location_id, term_id
-#delete			      set_sequence_name nil
-			      belongs_to :location, :class_name => "Location"
-			      belongs_to :term, :class_name => "Term"
-			    end		
-		end #SQL
-end #Bio
-

data/lib/bio/io/biosql/ontology.rb

@@ -1,10 +0,0 @@
-
- module Bio
-    class SQL 
-		    class Ontology < DummyBase
-		      has_many :terms, :class_name => "Term"
-		      has_many :term_paths, :class_name => "TermPath"
-		      has_many :term_relationships, :class_name => "TermRelationship"
-		    end		
-		end #SQL
-end #Bio

data/lib/bio/io/biosql/reference.rb

@@ -1,9 +0,0 @@
-
- module Bio
-    class SQL 
-		    class Reference < DummyBase  
-		      belongs_to :dbxref, :class_name => "Dbxref"
-		      has_many :bioentry_references, :class_name=>"BioentryRefernce"
-		    end		
-		end #SQL
-end #Bio

data/lib/bio/io/biosql/seqfeature.rb

@@ -1,32 +0,0 @@
-
-module Bio
-  class SQL 
-    class Seqfeature <DummyBase  
-      set_sequence_name "seqfeature_pk_seq"
-      belongs_to :bioentry
-      #, :class_name => "Bioentry"
-      belongs_to :type_term, :class_name => "Term", :foreign_key => "type_term_id"
-      belongs_to :source_term, :class_name => "Term", :foreign_key =>"source_term_id"
-      has_many :seqfeature_dbxrefs, :class_name => "SeqfeatureDbxref", :foreign_key => "seqfeature_id"
-      has_many :seqfeature_qualifier_values, :order=>'rank', :foreign_key => "seqfeature_id"
-      #, :class_name => "SeqfeatureQualifierValue"
-      has_many :locations, :class_name => "Location", :order=>'rank'
-      has_many :object_seqfeature_paths, :class_name => "SeqfeaturePath", :foreign_key => "object_seqfeature_id"
-      has_many :subject_seqfeature_paths, :class_name => "SeqfeaturePath", :foreign_key => "subject_seqfeature_id"
-      has_many :object_seqfeature_relationships, :class_name => "SeqfeatureRelationship", :foreign_key => "object_seqfeature_id"
-      has_many :subject_seqfeature_relationships, :class_name => "SeqfeatureRelationship", :foreign_key => "subject_seqfeature_id"
-
-      #get the subsequence described by the locations objects
-      def sequence
-        return self.locations.inject(Bio::Sequence::NA.new("")){|seq, location| seq<<location.sequence}
-    end
-    
-      #translate the subsequences represented by the feature and its locations
-      #not considering the qualifiers 
-      #Return a Bio::Sequence::AA object
-      def translate(*args)
-        self.sequence.translate(*args)
-      end
-      end		
-    end #SQL
-  end #Bio

data/lib/bio/io/biosql/seqfeature_dbxref.rb

@@ -1,11 +0,0 @@
-
- module Bio
-    class SQL 
-		    class SeqfeatureDbxref < DummyBase
-		      set_primary_keys :seqfeature_id, :dbxref_id
-#delete		      set_sequence_name nil
-		      belongs_to :seqfeature, :class_name => "Seqfeature", :foreign_key => "seqfeature_id"
-		      belongs_to :dbxref, :class_name => "Dbxref", :foreign_key => "dbxref_id"
-		    end		
-		end #SQL
-end #Bio

data/lib/bio/io/biosql/seqfeature_path.rb

@@ -1,11 +0,0 @@
- module Bio
-    class SQL 
-			   class SeqfeaturePath < DummyBase
-			      set_primary_keys :object_seqfeature_id, :subject_seqfeature_id, :term_id
-			      set_sequence_name nil
-			      belongs_to :object_seqfeature, :class_name => "Seqfeature", :foreign_key => "object_seqfeature_id"
-			      belongs_to :subject_seqfeature, :class_name => "Seqfeature", :foreign_key => "subject_seqfeature_id"
-            belongs_to :term, :class_name => "Term"
-			    end		
-		end #SQL
-end #Bio

data/lib/bio/io/biosql/seqfeature_qualifier_value.rb

@@ -1,20 +0,0 @@
-
-module Bio
-  class SQL 
-    class SeqfeatureQualifierValue < DummyBase
-      set_primary_keys  :seqfeature_id, :term_id, :rank
-      set_sequence_name nil
-      belongs_to :seqfeature
-      belongs_to :term, :class_name => "Term"
-      
-      def self.find_cluster(query)
-        term_note= Term.find_by_name('note')
-        find(:all, :conditions =>["value like ? and term_id = ?", "cl:#{query}", term_note])
-      end
-      def self.find_cluster_info(query)
-        term_note= Term.find_by_name('note')
-        find(:all, :conditions =>["value like ? and term_id = ?", "cli:#{query}", term_note])
-      end
-    end		
-  end #SQL
-end #Bio

data/lib/bio/io/biosql/seqfeature_relationship.rb

@@ -1,11 +0,0 @@
-
- module Bio
-    class SQL 
-			    class SeqfeatureRelationship <DummyBase
-			      set_sequence_name "seqfeatue_relationship_pk_seq"
-			      belongs_to :term, :class_name => "Term"
-			      belongs_to :object_seqfeature, :class_name => "Seqfeature"
-			      belongs_to :subject_seqfeature, :class_name => "Seqfeature"
-			    end		
-		end #SQL
-end #Bio

data/lib/bio/io/biosql/taxon.rb

@@ -1,12 +0,0 @@
-
- module Bio
-    class SQL 
-			    class Taxon < DummyBase
-			      set_sequence_name "taxon_pk_seq"
-			      has_many :taxon_names, :class_name => "TaxonName"
-		              has_one :taxon_scientific_name, :class_name => "TaxonName", :conditions=>"name_class = 'scientific name'"
-		              has_one :taxon_genbank_common_name, :class_name => "TaxonName", :conditions=>"name_class = 'genbank common name'"
-			      has_one :bioentry, :class_name => "Bioentry"
-			    end		
-		end #SQL
-end #Bio

data/lib/bio/io/biosql/taxon_name.rb

@@ -1,9 +0,0 @@
-
- module Bio
-    class SQL 
-			    class TaxonName < DummyBase
-			      set_primary_keys :taxon_id, :name, :name_class
-			      belongs_to :taxon, :class_name => "Taxon"      
-			    end		
-		end #SQL
-end #Bio

data/lib/bio/io/biosql/term.rb

@@ -1,27 +0,0 @@
-
- module Bio
-    class SQL 
-			    class Term < DummyBase
-			      belongs_to :ontology, :class_name => "Ontology"
-			      has_many :seqfeature_qualifier_values, :class_name => "SeqfeatureQualifierValue"
-			      has_many :dbxref_qualifier_values, :class_name => "DbxrefQualifierValue"
-            has_many :bioentry_qualifer_values, :class_name => "BioentryQualifierValue"
-            has_many :bioentries, :through=>:bioentry_qualifier_values
-			      has_many :locations, :class_name => "Location"
-			      has_many :seqfeature_relationships, :class_name => "SeqfeatureRelationship"
-			      has_many :term_dbxrefs, :class_name => "TermDbxref"
-			      has_many :term_relationship_terms, :class_name => "TermRelationshipTerm"
-			      has_many :term_synonyms, :class_name => "TermSynonym"
-			      has_many :location_qualifier_values, :class_name => "LocationQualifierValue"
-			      has_many :seqfeature_types, :class_name => "Seqfeature", :foreign_key => "type_term_id"			      
-			      has_many :seqfeature_sources, :class_name => "Seqfeature", :foreign_key => "source_term_id"			      
-			      has_many :term_path_subjects, :class_name => "TermPath", :foreign_key => "subject_term_id"
-			      has_many :term_path_predicates, :class_name => "TermPath", :foreign_key => "predicate_term_id"
-			      has_many :term_path_objects, :class_name => "TermPath", :foreign_key => "object_term_id"			      
-			      has_many :term_relationship_subjects, :class_name => "TermRelationship", :foreign_key =>"subject_term_id"
-			      has_many :term_relationship_predicates, :class_name => "TermRelationship", :foreign_key =>"predicate_term_id"
-			      has_many :term_relationship_objects, :class_name => "TermRelationship", :foreign_key =>"object_term_id"
-            has_many :seqfeature_paths, :class_name => "SeqfeaturePath"
-			    end		
-		end #SQL
-end #Bio

data/lib/bio/io/biosql/term_dbxref.rb

@@ -1,11 +0,0 @@
-
- module Bio
-    class SQL 
-			    class TermDbxref < DummyBase
-			      set_primary_key nil #term_id, dbxref_id
-#delete			      set_sequence_name nil
-			      belongs_to :term, :class_name => "Term"
-			      belongs_to :dbxref, :class_name => "Dbxref"
-			    end		
-		end #SQL
-end #Bio

data/lib/bio/io/biosql/term_path.rb

@@ -1,12 +0,0 @@
-
- module Bio
-    class SQL 
-			    class TermPath < DummyBase
-			      set_sequence_name "term_path_pk_seq"
-			      belongs_to :ontology, :class_name => "Ontology"
-			      belongs_to :subject_term, :class_name => "Term"
-			      belongs_to :object_term, :class_name => "Term"
-			      belongs_to :predicate_term, :class_name => "Term"
-			    end		
-		end #SQL
-end #Bio

data/lib/bio/io/biosql/term_relationship.rb

@@ -1,13 +0,0 @@
-
- module Bio
-    class SQL 
-			    class TermRelationship < DummyBase
-			      set_sequence_name "term_relationship_pk_seq"
-			      belongs_to :ontology, :class_name => "Ontology"
-			      belongs_to :subject_term, :class_name => "Term"
-			      belongs_to :predicate_term, :class_name => "Term"
-			      belongs_to :object_term, :class_name => "Term"
-			      has_one :term_relationship_term, :class_name => "TermRelationshipTerm"
-			    end		
-		end #SQL
-end #Bio

data/lib/bio/io/biosql/term_relationship_term.rb

@@ -1,11 +0,0 @@
-
- module Bio
-    class SQL 
-			    class TermRelationshipTerm < DummyBase
-#delete			      set_sequence_name nil
-			      set_primary_key :term_relationship_id
-			      belongs_to :term_relationship, :class_name => "TermRelationship"
-			      belongs_to :term, :class_name => "Term"
-			    end		
-		end #SQL
-end #Bio

data/lib/bio/io/biosql/term_synonym.rb

@@ -1,10 +0,0 @@
-
- module Bio
-    class SQL 
-			    class TermSynonym < DummyBase
-#delete			      set_sequence_name nil
-			      set_primary_key nil
-			      belongs_to :term, :class_name => "Term"
-			    end		
-		end #SQL
-end #Bio