spec/gffdb_spec.rb in bio-gff3-0.8.4 vs spec/gffdb_spec.rb in bio-gff3-0.8.5

@@ -40,60 +40,60 @@
     h.keys.sort[0].should == "cds1 Sequence:test01_1:400 (164:190, 192:200)"
     h["cds_short Sequence:test01_1:400 (3:14)"].should == "GAAGATTTGTAT"
   end
 end
 
-describe GFFdb, "GFF3 API (InMemory) with everything in memory" do
+describe GFF3, "GFF3 API (InMemory) with everything in memory" do
 
   before :all do 
     # initialize
-    gffdb = Bio::GFFbrowser::GFFdb.new(TESTGFF1)
-    @gff = gffdb.assembler
+    gff3 = Bio::GFFbrowser::GFF3.new(TESTGFF1)
+    @gff = gff3.assembler
   end
 
   iterators_should_be_implemented
 end
 
-describe GFFdb, "GFF3 API with :cache_components => 1000, :cache_records => :cache_none" do
+describe GFF3, "GFF3 API with :cache_components => 1000, :cache_records => :cache_none" do
   # iterators_should_be_implemented
 end
 
-describe GFFdb, "GFF3 API with :cache_components => 1000, :cache_records => 1000" do
+describe GFF3, "GFF3 API with :cache_components => 1000, :cache_records => 1000" do
   it "should implement real caching"
   # iterators_should_be_implemented
 end
 
-describe GFFdb, "GFF3 API with :cache_records => :cache_none" do
+describe GFF3, "GFF3 API with :cache_records => :cache_none" do
   # iterators_should_be_implemented
 end
 
-describe GFFdb, "GFF3 API (NoCache) with :cache_components => :cache_none, :cache_records => :cache_none" do
+describe GFF3, "GFF3 API (NoCache) with :cache_components => :cache_none, :cache_records => :cache_none" do
   before :all do 
     # initialize
-    gffdb = Bio::GFFbrowser::GFFdb.new(TESTGFF1, :cache_components => :cache_none, :cache_records => :cache_none)
-    @gff = gffdb.assembler
+    gff3 = Bio::GFFbrowser::GFF3.new(TESTGFF1, :cache_components => :cache_none, :cache_records => :cache_none)
+    @gff = gff3.assembler
   end
 
   iterators_should_be_implemented
 end
 
-describe GFFdb, "GFF3 API (InMemory) with external FASTA" do
+describe GFF3, "GFF3 API (InMemory) with external FASTA" do
   before :all do 
-    gffdb = Bio::GFFbrowser::GFFdb.new(TESTGFF1EXT, :fasta_filename => TESTGFF1FASTA)
-    @gff = gffdb.assembler
+    gff3 = Bio::GFFbrowser::GFF3.new(TESTGFF1EXT, :parser => :line, :fasta_filename => TESTGFF1FASTA)
+    @gff = gff3.assembler
   end
 
   it "should have a sequence list" do 
     @gff.parse
     @gff.sequencelist["test02"].should_not == nil
   end
   iterators_should_be_implemented
 end
 
-describe GFFdb, "GFF3 API (NoCache) with external FASTA" do
+describe GFF3, "GFF3 API (NoCache) with external FASTA" do
   before :all do 
-    gffdb = Bio::GFFbrowser::GFFdb.new(TESTGFF1EXT, :fasta_filename => TESTGFF1FASTA, :cache_components => :cache_none, :cache_records => :cache_none)
-    @gff = gffdb.assembler
+    gff3 = Bio::GFFbrowser::GFF3.new(TESTGFF1EXT, :fasta_filename => TESTGFF1FASTA, :cache_components => :cache_none, :cache_records => :cache_none)
+    @gff = gff3.assembler
   end
 
   iterators_should_be_implemented
 end