bio 1.4.1 → 1.4.2

data/test/unit/bio/util/restriction_enzyme/test_sorted_num_array.rb

@@ -0,0 +1,281 @@
+#
+# test/unit/bio/util/restriction_enzyme/test_sorted_num_array.rb - Unit test for Bio::RestrictionEnzyme::SortedNumArray
+#
+# Copyright::   Copyright (C) 2011
+#               Naohisa Goto <ng@bioruby.org>
+# License::     The Ruby License
+#
+
+# loading helper routine for testing bioruby
+require 'pathname'
+load Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4,
+                            'bioruby_test_helper.rb')).cleanpath.to_s
+
+# libraries needed for the tests
+require 'test/unit'
+require 'bio/util/restriction_enzyme'
+require 'bio/util/restriction_enzyme/sorted_num_array'
+
+module Bio
+module TestRestrictionEnzyme
+
+  class TestSortedNumArray < Test::Unit::TestCase
+
+    def setup
+      @klass = Bio::RestrictionEnzyme::SortedNumArray
+      @obj = @klass[14, 265, 4626, -1, 358, 159, 979, 3238, 3]
+    end
+
+    def test_self_bracket
+      assert_equal([ -1, 3, 14, 159, 265, 358, 979, 3238, 4626 ],
+                   @obj.to_a)
+    end
+
+    def test_self_new
+      a = @klass.new
+      assert_instance_of(Bio::RestrictionEnzyme::SortedNumArray, a)
+    end
+
+    def test_dup
+      assert_equal(@obj.to_a, @obj.dup.to_a)
+      h_obj = @obj.instance_eval { internal_data_hash }
+      h_dup = @obj.dup.instance_eval { internal_data_hash }
+      assert(h_obj == h_dup)
+      assert_not_equal(h_obj.__id__, h_dup.__id__)
+    end
+
+    def test_internal_data_hash
+      h = @obj.instance_eval { internal_data_hash }
+      expected = { -1 => true,
+        3 => true, 14 => true, 159 => true, 265 => true,
+        358 => true, 979 => true, 3238 => true, 4626 => true }
+      assert_equal(expected, h)
+    end
+
+    def test_internal_data_hash_eq
+      h = { 0 => true, 50 => true, 100 => true }
+      @obj.last # creating cache (if exists)
+      @obj.instance_eval { self.internal_data_hash = h }
+      assert_equal(100, @obj.last)
+      assert_equal([0, 50, 100], @obj.to_a)
+    end
+
+    #def test_private_clear_cache
+    #  assert_nothing_raised {
+    #    @obj.instance_eval { clear_cache }
+    #  }
+    #  @obj.last # creating cache
+    #  @obj.instance_eval { clear_cache }
+    #  assert_nil(@obj.instance_eval { @sorted_keys })
+    #end
+
+    def test_private_sorted_keys
+      a = @obj.instance_eval { sorted_keys }
+      assert_equal([ -1, 3, 14, 159, 265, 358, 979, 3238, 4626 ], a)
+    end
+
+    def test_private_push_element
+      assert_equal(false, @obj.include?(50))
+      @obj.instance_eval {
+        push_element(50)
+      }
+      assert_equal(true, @obj.include?(50))
+    end
+
+    def test_private_push_element_noeffect
+      assert_equal(true, @obj.include?(159))
+      @obj.instance_eval {
+        push_element(159)
+      }
+      assert_equal(true, @obj.include?(159))
+    end
+
+    def test_private_push_element_last
+      @obj.last # creating cache (if exists)
+      @obj.instance_eval {
+        push_element(9999)
+      }
+      assert_equal(true, @obj.include?(9999))
+      assert_equal(9999, @obj.last)
+    end
+
+    def test_private_push_element_intermediate
+      @obj.last # creating cache (if exists)
+      @obj.instance_eval {
+        push_element(100)
+      }
+      assert_equal(true, @obj.include?(100))
+      assert_equal(4626, @obj.last)
+    end
+
+    def test_private_unshift_element
+      assert_equal(false, @obj.include?(50))
+      @obj.instance_eval {
+        unshift_element(50)
+      }
+      assert_equal(true, @obj.include?(50))
+    end
+
+    def test_private_unshift_element_noeffect
+      assert_equal(true, @obj.include?(159))
+      @obj.instance_eval {
+        unshift_element(159)
+      }
+      assert_equal(true, @obj.include?(159))
+    end
+
+    def test_private_unshift_element_first
+      @obj.last # creating cache (if exists)
+      @obj.instance_eval {
+        unshift_element(-999)
+      }
+      assert_equal(true, @obj.include?(-999))
+      assert_equal(-999, @obj.first)
+    end
+
+    def test_private_unshift_element_intermediate
+      @obj.last # creating cache (if exists)
+      @obj.instance_eval {
+        unshift_element(100)
+      }
+      assert_equal(true, @obj.include?(100))
+      assert_equal(-1, @obj.first)
+    end
+
+    def test_bracket
+      assert_equal(-1, @obj[0])
+      assert_equal(159, @obj[3])
+      assert_equal(4626, @obj[-1])
+      assert_equal([14, 159, 265], @obj[2..4])
+      assert_equal([14, 159, 265], @obj[2,3])
+    end
+
+    def test_bracket_eq
+      assert_raise(NotImplementedError) {
+        @obj[3] = 999
+      }
+    end
+
+    def test_each
+      expected_values = [ -1, 3, 14, 159, 265, 358, 979, 3238, 4626 ]
+      @obj.each do |i|
+        assert_equal(expected_values.shift, i)
+      end
+    end
+
+    def test_reverse_each
+      expected_values = [ -1, 3, 14, 159, 265, 358, 979, 3238, 4626 ]
+      @obj.reverse_each do |i|
+        assert_equal(expected_values.pop, i)
+      end
+    end
+
+    def test_plus
+      obj2 = @klass[ 2, 3, 14, 15 ]
+      assert_equal([ -1, 2, 3, 14, 15, 159, 265, 358, 979, 3238, 4626 ],
+                   (@obj + obj2).to_a)
+    end
+
+    def test_plus_error
+      assert_raise(TypeError) {
+        @obj + 2
+      }
+    end
+
+    def test_eqeq
+      obj2 = @klass[ -1, 3, 14, 159, 265, 358, 979, 3238, 4626 ]
+      assert_equal(true, @obj == obj2)
+    end
+
+    def test_eqeq_self
+      assert_equal(true, @obj == @obj)
+    end
+
+    def test_eqeq_false
+      obj2 = @klass[ 2, 3, 14, 15 ]
+      assert_equal(false, @obj == obj2)
+    end
+
+    def test_eqeq_other
+      obj2 = 'test'
+      assert_equal(false, @obj == obj2)
+    end
+
+    def test_concat
+      ary = [ 9999, -2, 14, 15 ]
+      expected = [ -2, -1, 3, 14, 15, 159, 265, 358, 979, 3238, 4626, 9999 ]
+      # checks if the method returns self
+      assert_equal(@obj, @obj.concat(ary))
+      # checks the value
+      assert_equal(expected, @obj.to_a)
+    end
+
+    def test_push
+      expected = [ -2, -1, 3, 14, 15, 159, 265, 358, 979, 3238, 4626, 9999 ]
+      # checks if the method returns self
+      assert_equal(@obj, @obj.push(15, 14, -2, 9999))
+      # checks the value
+      assert_equal(expected, @obj.to_a)
+    end
+
+    def test_unshift
+      expected = [ -2, -1, 3, 14, 15, 159, 265, 358, 979, 3238, 4626, 9999 ]
+      # checks if the method returns self
+      assert_equal(@obj, @obj.unshift(15, 14, -2, 9999))
+      # checks the value
+      assert_equal(expected, @obj.to_a)
+    end
+
+    def test_ltlt
+      expected = [ -1, 3, 14, 15, 159, 265, 358, 979, 3238, 4626 ]
+      # checks if the method returns self
+      assert_equal(@obj, @obj << 15)
+      # checks the value
+      assert_equal(expected, @obj.to_a)
+    end
+
+    def test_ltlt_noeffect
+      expected = [ -1, 3, 14, 159, 265, 358, 979, 3238, 4626 ]
+      # checks if the method returns self
+      assert_equal(@obj, @obj << 159)
+      # checks the value
+      assert_equal(expected, @obj.to_a)
+    end
+
+    def test_include?
+      assert_equal(true, @obj.include?(159))
+      assert_equal(false, @obj.include?(999))
+    end
+
+    def test_size
+      assert_equal(9, @obj.size)
+    end
+
+    def test_length
+      assert_equal(9, @obj.length)
+    end
+
+    def test_delete
+      assert_equal(nil, @obj.delete(100))
+      assert_equal(159, @obj.delete(159))
+    end
+
+    def test_sort!
+      assert_equal(@obj, @obj.sort!)
+    end
+
+    def test_uniq!
+      assert_equal(@obj, @obj.uniq!)
+    end
+
+    def test_to_a
+      expected = [ -1, 3, 14, 159, 265, 358, 979, 3238, 4626 ]
+      assert_equal(expected, @obj.to_a)
+    end
+
+  end #class TestSortedNumArray
+
+end #module TestRestrictionEnzyme
+end #module Bio
+
+

metadata

@@ -1,34 +1,26 @@
---- !ruby/object:Gem::Specification 
+--- !ruby/object:Gem::Specification
 name: bio
-version: !ruby/object:Gem::Version 
-  prerelease: false
-  segments: 
-  - 1
-  - 4
-  - 1
-  version: 1.4.1
+version: !ruby/object:Gem::Version
+  version: 1.4.2
+  prerelease: 
 platform: ruby
-authors: 
+authors:
 - BioRuby project
 autorequire: bio
 bindir: bin
 cert_chain: []
-
-date: 2010-10-22 00:00:00 +09:00
-default_executable: bioruby
+date: 2011-08-26 00:00:00.000000000 Z
 dependencies: []
-
 description: BioRuby is a library for bioinformatics (biology + information science).
 email: staff@bioruby.org
-executables: 
+executables:
 - bioruby
 - br_biofetch.rb
 - br_bioflat.rb
 - br_biogetseq.rb
 - br_pmfetch.rb
 extensions: []
-
-extra_rdoc_files: 
+extra_rdoc_files:
 - ChangeLog
 - KNOWN_ISSUES.rdoc
 - README.rdoc
@@ -36,7 +28,8 @@ extra_rdoc_files:
 - RELEASE_NOTES.rdoc
 - doc/Changes-1.3.rdoc
 - doc/RELEASE_NOTES-1.4.0.rdoc
-files: 
+- doc/RELEASE_NOTES-1.4.1.rdoc
+files:
 - COPYING
 - COPYING.ja
 - ChangeLog
@@ -61,6 +54,7 @@ files:
 - doc/KEGG_API.rd
 - doc/KEGG_API.rd.ja
 - doc/RELEASE_NOTES-1.4.0.rdoc
+- doc/RELEASE_NOTES-1.4.1.rdoc
 - doc/Tutorial.rd
 - doc/Tutorial.rd.html
 - doc/Tutorial.rd.ja
@@ -209,6 +203,7 @@ files:
 - lib/bio/io/biosql/config/database.yml
 - lib/bio/io/das.rb
 - lib/bio/io/dbget.rb
+- lib/bio/io/ddbjrest.rb
 - lib/bio/io/ddbjxml.rb
 - lib/bio/io/ebisoap.rb
 - lib/bio/io/ensembl.rb
@@ -302,6 +297,7 @@ files:
 - lib/bio/util/restriction_enzyme/analysis.rb
 - lib/bio/util/restriction_enzyme/analysis_basic.rb
 - lib/bio/util/restriction_enzyme/cut_symbol.rb
+- lib/bio/util/restriction_enzyme/dense_int_array.rb
 - lib/bio/util/restriction_enzyme/double_stranded.rb
 - lib/bio/util/restriction_enzyme/double_stranded/aligned_strands.rb
 - lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb
@@ -320,6 +316,7 @@ files:
 - lib/bio/util/restriction_enzyme/single_strand.rb
 - lib/bio/util/restriction_enzyme/single_strand/cut_locations_in_enzyme_notation.rb
 - lib/bio/util/restriction_enzyme/single_strand_complement.rb
+- lib/bio/util/restriction_enzyme/sorted_num_array.rb
 - lib/bio/util/restriction_enzyme/string_formatting.rb
 - lib/bio/util/sirna.rb
 - lib/bio/version.rb
@@ -386,6 +383,7 @@ files:
 - sample/ssearch2tab.rb
 - sample/tdiary.rb
 - sample/test_phyloxml_big.rb
+- sample/test_restriction_enzyme_long.rb
 - sample/tfastx2tab.rb
 - sample/vs-genes.rb
 - setup.rb
@@ -425,6 +423,7 @@ files:
 - test/data/command/echoarg2.bat
 - test/data/embl/AB090716.embl
 - test/data/embl/AB090716.embl.rel89
+- test/data/fasta/EFTU_BACSU.fasta
 - test/data/fasta/example1.txt
 - test/data/fasta/example2.txt
 - test/data/fastq/README.txt
@@ -479,12 +478,15 @@ files:
 - test/data/fastq/wrapping_as_solexa.fastq
 - test/data/fastq/wrapping_original_sanger.fastq
 - test/data/gcg/pileup-aa.msf
+- test/data/genbank/CAA35997.gp
+- test/data/genbank/SCU49845.gb
 - test/data/genscan/sample.report
 - test/data/go/selected_component.ontology
 - test/data/go/selected_gene_association.sgd
 - test/data/go/selected_wikipedia2go
 - test/data/iprscan/merged.raw
 - test/data/iprscan/merged.txt
+- test/data/litdb/1717226.litdb
 - test/data/medline/20146148_modified.medline
 - test/data/meme/db
 - test/data/meme/mast
@@ -504,6 +506,7 @@ files:
 - test/data/phyloxml/made_up.xml
 - test/data/phyloxml/ncbi_taxonomy_mollusca_short.xml
 - test/data/phyloxml/phyloxml_examples.xml
+- test/data/pir/CRAB_ANAPL.pir
 - test/data/prosite/prosite.dat
 - test/data/refseq/nm_126355.entret
 - test/data/rpsblast/misc.rpsblast
@@ -516,7 +519,10 @@ files:
 - test/data/soft/GDS100_partial.soft
 - test/data/soft/GSE3457_family_partial.soft
 - test/data/uniprot/p53_human.uniprot
+- test/functional/bio/appl/blast/test_remote.rb
+- test/functional/bio/appl/test_blast.rb
 - test/functional/bio/appl/test_pts1.rb
+- test/functional/bio/io/test_ddbjrest.rb
 - test/functional/bio/io/test_ensembl.rb
 - test/functional/bio/io/test_pubmed.rb
 - test/functional/bio/io/test_soapwsdl.rb
@@ -559,9 +565,13 @@ files:
 - test/unit/bio/db/embl/test_embl_to_bioseq.rb
 - test/unit/bio/db/embl/test_sptr.rb
 - test/unit/bio/db/embl/test_uniprot.rb
+- test/unit/bio/db/embl/test_uniprot_new_part.rb
 - test/unit/bio/db/fasta/test_defline.rb
 - test/unit/bio/db/fasta/test_defline_misc.rb
 - test/unit/bio/db/fasta/test_format_qual.rb
+- test/unit/bio/db/genbank/test_common.rb
+- test/unit/bio/db/genbank/test_genbank.rb
+- test/unit/bio/db/genbank/test_genpept.rb
 - test/unit/bio/db/kegg/test_compound.rb
 - test/unit/bio/db/kegg/test_drug.rb
 - test/unit/bio/db/kegg/test_enzyme.rb
@@ -581,7 +591,9 @@ files:
 - test/unit/bio/db/test_gff.rb
 - test/unit/bio/db/test_go.rb
 - test/unit/bio/db/test_lasergene.rb
+- test/unit/bio/db/test_litdb.rb
 - test/unit/bio/db/test_medline.rb
+- test/unit/bio/db/test_nbrf.rb
 - test/unit/bio/db/test_newick.rb
 - test/unit/bio/db/test_nexus.rb
 - test/unit/bio/db/test_phyloxml.rb
@@ -629,20 +641,20 @@ files:
 - test/unit/bio/util/restriction_enzyme/single_strand/test_cut_locations_in_enzyme_notation.rb
 - test/unit/bio/util/restriction_enzyme/test_analysis.rb
 - test/unit/bio/util/restriction_enzyme/test_cut_symbol.rb
+- test/unit/bio/util/restriction_enzyme/test_dense_int_array.rb
 - test/unit/bio/util/restriction_enzyme/test_double_stranded.rb
 - test/unit/bio/util/restriction_enzyme/test_single_strand.rb
 - test/unit/bio/util/restriction_enzyme/test_single_strand_complement.rb
+- test/unit/bio/util/restriction_enzyme/test_sorted_num_array.rb
 - test/unit/bio/util/restriction_enzyme/test_string_formatting.rb
 - test/unit/bio/util/test_color_scheme.rb
 - test/unit/bio/util/test_contingency_table.rb
 - test/unit/bio/util/test_restriction_enzyme.rb
 - test/unit/bio/util/test_sirna.rb
-has_rdoc: true
 homepage: http://bioruby.org/
 licenses: []
-
 post_install_message: 
-rdoc_options: 
+rdoc_options:
 - --main
 - README.rdoc
 - --title
@@ -651,30 +663,24 @@ rdoc_options:
 - \.yaml\z
 - --line-numbers
 - --inline-source
-require_paths: 
+require_paths:
 - lib
-required_ruby_version: !ruby/object:Gem::Requirement 
+required_ruby_version: !ruby/object:Gem::Requirement
   none: false
-  requirements: 
-  - - ">="
-    - !ruby/object:Gem::Version 
-      segments: 
-      - 0
-      version: "0"
-required_rubygems_version: !ruby/object:Gem::Requirement 
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
-  requirements: 
-  - - ">="
-    - !ruby/object:Gem::Version 
-      segments: 
-      - 0
-      version: "0"
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
 requirements: []
-
 rubyforge_project: bioruby
-rubygems_version: 1.3.7
+rubygems_version: 1.8.10
 signing_key: 
 specification_version: 3
 summary: Bioinformatics library
 test_files: []
-