RubyGems - bio - Versions diffs - 1.3.1 → 1.4.0 - Mend

bio 1.3.1 → 1.4.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (303) hide show

data/ChangeLog +2105 -3728
data/KNOWN_ISSUES.rdoc +35 -3
data/README.rdoc +8 -2
data/RELEASE_NOTES.rdoc +166 -0
data/bin/bioruby +4 -1
data/bioruby.gemspec +146 -1
data/bioruby.gemspec.erb +3 -1
data/doc/ChangeLog-before-1.3.1 +3961 -0
data/doc/Tutorial.rd +154 -22
data/doc/Tutorial.rd.html +125 -68
data/lib/bio.rb +21 -6
data/lib/bio/appl/bl2seq/report.rb +11 -202
data/lib/bio/appl/blast/format0.rb +0 -193
data/lib/bio/appl/blast/report.rb +2 -147
data/lib/bio/appl/blast/wublast.rb +0 -208
data/lib/bio/appl/fasta.rb +4 -19
data/lib/bio/appl/fasta/format10.rb +0 -14
data/lib/bio/appl/genscan/report.rb +0 -176
data/lib/bio/appl/hmmer.rb +1 -15
data/lib/bio/appl/hmmer/report.rb +0 -100
data/lib/bio/appl/meme/mast.rb +156 -0
data/lib/bio/appl/meme/mast/report.rb +91 -0
data/lib/bio/appl/meme/motif.rb +48 -0
data/lib/bio/appl/psort.rb +0 -111
data/lib/bio/appl/psort/report.rb +1 -45
data/lib/bio/appl/pts1.rb +2 -4
data/lib/bio/appl/sosui/report.rb +5 -54
data/lib/bio/appl/targetp/report.rb +1 -104
data/lib/bio/appl/tmhmm/report.rb +0 -36
data/lib/bio/command.rb +94 -10
data/lib/bio/data/aa.rb +1 -77
data/lib/bio/data/codontable.rb +1 -95
data/lib/bio/data/na.rb +1 -26
data/lib/bio/db/aaindex.rb +1 -38
data/lib/bio/db/fasta.rb +1 -134
data/lib/bio/db/fasta/format_qual.rb +204 -0
data/lib/bio/db/fasta/qual.rb +102 -0
data/lib/bio/db/fastq.rb +645 -0
data/lib/bio/db/fastq/fastq_to_biosequence.rb +40 -0
data/lib/bio/db/fastq/format_fastq.rb +175 -0
data/lib/bio/db/genbank/genbank.rb +1 -86
data/lib/bio/db/gff.rb +0 -17
data/lib/bio/db/go.rb +4 -72
data/lib/bio/db/kegg/common.rb +112 -0
data/lib/bio/db/kegg/compound.rb +29 -20
data/lib/bio/db/kegg/drug.rb +74 -34
data/lib/bio/db/kegg/enzyme.rb +26 -5
data/lib/bio/db/kegg/genes.rb +128 -15
data/lib/bio/db/kegg/genome.rb +3 -41
data/lib/bio/db/kegg/glycan.rb +19 -24
data/lib/bio/db/kegg/orthology.rb +16 -56
data/lib/bio/db/kegg/reaction.rb +81 -28
data/lib/bio/db/kegg/taxonomy.rb +1 -52
data/lib/bio/db/litdb.rb +1 -16
data/lib/bio/db/phyloxml/phyloxml.xsd +582 -0
data/lib/bio/db/phyloxml/phyloxml_elements.rb +1174 -0
data/lib/bio/db/phyloxml/phyloxml_parser.rb +954 -0
data/lib/bio/db/phyloxml/phyloxml_writer.rb +228 -0
data/lib/bio/db/prosite.rb +2 -95
data/lib/bio/db/rebase.rb +5 -6
data/lib/bio/db/sanger_chromatogram/abif.rb +120 -0
data/lib/bio/db/sanger_chromatogram/chromatogram.rb +133 -0
data/lib/bio/db/sanger_chromatogram/chromatogram_to_biosequence.rb +32 -0
data/lib/bio/db/sanger_chromatogram/scf.rb +210 -0
data/lib/bio/io/das.rb +0 -44
data/lib/bio/io/ddbjxml.rb +1 -181
data/lib/bio/io/flatfile.rb +1 -7
data/lib/bio/io/flatfile/autodetection.rb +6 -0
data/lib/bio/io/keggapi.rb +0 -442
data/lib/bio/io/ncbirest.rb +130 -132
data/lib/bio/io/ncbisoap.rb +2 -1
data/lib/bio/io/pubmed.rb +0 -88
data/lib/bio/location.rb +0 -73
data/lib/bio/pathway.rb +0 -171
data/lib/bio/sequence.rb +18 -1
data/lib/bio/sequence/adapter.rb +3 -0
data/lib/bio/sequence/format.rb +16 -0
data/lib/bio/sequence/quality_score.rb +205 -0
data/lib/bio/tree.rb +70 -5
data/lib/bio/util/restriction_enzyme/single_strand.rb +3 -2
data/lib/bio/util/sirna.rb +1 -23
data/lib/bio/version.rb +1 -1
data/sample/demo_aaindex.rb +67 -0
data/sample/demo_aminoacid.rb +101 -0
data/sample/demo_bl2seq_report.rb +220 -0
data/sample/demo_blast_report.rb +285 -0
data/sample/demo_codontable.rb +119 -0
data/sample/demo_das.rb +105 -0
data/sample/demo_ddbjxml.rb +212 -0
data/sample/demo_fasta_remote.rb +51 -0
data/sample/demo_fastaformat.rb +105 -0
data/sample/demo_genbank.rb +132 -0
data/sample/demo_genscan_report.rb +202 -0
data/sample/demo_gff1.rb +49 -0
data/sample/demo_go.rb +98 -0
data/sample/demo_hmmer_report.rb +149 -0
data/sample/demo_kegg_compound.rb +57 -0
data/sample/demo_kegg_drug.rb +65 -0
data/sample/demo_kegg_genome.rb +74 -0
data/sample/demo_kegg_glycan.rb +72 -0
data/sample/demo_kegg_orthology.rb +62 -0
data/sample/demo_kegg_reaction.rb +66 -0
data/sample/demo_kegg_taxonomy.rb +92 -0
data/sample/demo_keggapi.rb +502 -0
data/sample/demo_litdb.rb +42 -0
data/sample/demo_locations.rb +99 -0
data/sample/demo_ncbi_rest.rb +130 -0
data/sample/demo_nucleicacid.rb +49 -0
data/sample/demo_pathway.rb +196 -0
data/sample/demo_prosite.rb +120 -0
data/sample/demo_psort.rb +138 -0
data/sample/demo_psort_report.rb +70 -0
data/sample/demo_pubmed.rb +118 -0
data/sample/demo_sirna.rb +63 -0
data/sample/demo_sosui_report.rb +89 -0
data/sample/demo_targetp_report.rb +135 -0
data/sample/demo_tmhmm_report.rb +68 -0
data/sample/pmfetch.rb +13 -4
data/sample/pmsearch.rb +15 -4
data/sample/test_phyloxml_big.rb +205 -0
data/test/bioruby_test_helper.rb +61 -0
data/test/data/KEGG/1.1.1.1.enzyme +935 -0
data/test/data/KEGG/C00025.compound +102 -0
data/test/data/KEGG/D00063.drug +104 -0
data/test/data/KEGG/G00024.glycan +47 -0
data/test/data/KEGG/G01366.glycan +18 -0
data/test/data/KEGG/K02338.orthology +902 -0
data/test/data/KEGG/R00006.reaction +14 -0
data/test/data/fastq/README.txt +109 -0
data/test/data/fastq/error_diff_ids.fastq +20 -0
data/test/data/fastq/error_double_qual.fastq +22 -0
data/test/data/fastq/error_double_seq.fastq +22 -0
data/test/data/fastq/error_long_qual.fastq +20 -0
data/test/data/fastq/error_no_qual.fastq +20 -0
data/test/data/fastq/error_qual_del.fastq +20 -0
data/test/data/fastq/error_qual_escape.fastq +20 -0
data/test/data/fastq/error_qual_null.fastq +0 -0
data/test/data/fastq/error_qual_space.fastq +21 -0
data/test/data/fastq/error_qual_tab.fastq +21 -0
data/test/data/fastq/error_qual_unit_sep.fastq +20 -0
data/test/data/fastq/error_qual_vtab.fastq +20 -0
data/test/data/fastq/error_short_qual.fastq +20 -0
data/test/data/fastq/error_spaces.fastq +20 -0
data/test/data/fastq/error_tabs.fastq +21 -0
data/test/data/fastq/error_trunc_at_plus.fastq +19 -0
data/test/data/fastq/error_trunc_at_qual.fastq +19 -0
data/test/data/fastq/error_trunc_at_seq.fastq +18 -0
data/test/data/fastq/error_trunc_in_plus.fastq +19 -0
data/test/data/fastq/error_trunc_in_qual.fastq +20 -0
data/test/data/fastq/error_trunc_in_seq.fastq +18 -0
data/test/data/fastq/error_trunc_in_title.fastq +17 -0
data/test/data/fastq/illumina_full_range_as_illumina.fastq +8 -0
data/test/data/fastq/illumina_full_range_as_sanger.fastq +8 -0
data/test/data/fastq/illumina_full_range_as_solexa.fastq +8 -0
data/test/data/fastq/illumina_full_range_original_illumina.fastq +8 -0
data/test/data/fastq/longreads_as_illumina.fastq +40 -0
data/test/data/fastq/longreads_as_sanger.fastq +40 -0
data/test/data/fastq/longreads_as_solexa.fastq +40 -0
data/test/data/fastq/longreads_original_sanger.fastq +120 -0
data/test/data/fastq/misc_dna_as_illumina.fastq +16 -0
data/test/data/fastq/misc_dna_as_sanger.fastq +16 -0
data/test/data/fastq/misc_dna_as_solexa.fastq +16 -0
data/test/data/fastq/misc_dna_original_sanger.fastq +16 -0
data/test/data/fastq/misc_rna_as_illumina.fastq +16 -0
data/test/data/fastq/misc_rna_as_sanger.fastq +16 -0
data/test/data/fastq/misc_rna_as_solexa.fastq +16 -0
data/test/data/fastq/misc_rna_original_sanger.fastq +16 -0
data/test/data/fastq/sanger_full_range_as_illumina.fastq +8 -0
data/test/data/fastq/sanger_full_range_as_sanger.fastq +8 -0
data/test/data/fastq/sanger_full_range_as_solexa.fastq +8 -0
data/test/data/fastq/sanger_full_range_original_sanger.fastq +8 -0
data/test/data/fastq/solexa_full_range_as_illumina.fastq +8 -0
data/test/data/fastq/solexa_full_range_as_sanger.fastq +8 -0
data/test/data/fastq/solexa_full_range_as_solexa.fastq +8 -0
data/test/data/fastq/solexa_full_range_original_solexa.fastq +8 -0
data/test/data/fastq/wrapping_as_illumina.fastq +12 -0
data/test/data/fastq/wrapping_as_sanger.fastq +12 -0
data/test/data/fastq/wrapping_as_solexa.fastq +12 -0
data/test/data/fastq/wrapping_original_sanger.fastq +24 -0
data/test/data/meme/db +0 -0
data/test/data/meme/mast +0 -0
data/test/data/meme/mast.out +13 -0
data/test/data/meme/meme.out +3 -0
data/test/data/phyloxml/apaf.xml +666 -0
data/test/data/phyloxml/bcl_2.xml +2097 -0
data/test/data/phyloxml/made_up.xml +144 -0
data/test/data/phyloxml/ncbi_taxonomy_mollusca_short.xml +65 -0
data/test/data/phyloxml/phyloxml_examples.xml +415 -0
data/test/data/sanger_chromatogram/test_chromatogram_abif.ab1 +0 -0
data/test/data/sanger_chromatogram/test_chromatogram_scf_v2.scf +0 -0
data/test/data/sanger_chromatogram/test_chromatogram_scf_v3.scf +0 -0
data/test/functional/bio/appl/test_pts1.rb +7 -5
data/test/functional/bio/io/test_ensembl.rb +4 -3
data/test/functional/bio/io/test_pubmed.rb +9 -3
data/test/functional/bio/io/test_soapwsdl.rb +5 -4
data/test/functional/bio/io/test_togows.rb +5 -4
data/test/functional/bio/sequence/test_output_embl.rb +6 -4
data/test/functional/bio/test_command.rb +54 -5
data/test/runner.rb +5 -3
data/test/unit/bio/appl/bl2seq/test_report.rb +5 -4
data/test/unit/bio/appl/blast/test_ncbioptions.rb +4 -2
data/test/unit/bio/appl/blast/test_report.rb +5 -4
data/test/unit/bio/appl/blast/test_rpsblast.rb +5 -4
data/test/unit/bio/appl/gcg/test_msf.rb +5 -5
data/test/unit/bio/appl/genscan/test_report.rb +8 -9
data/test/unit/bio/appl/hmmer/test_report.rb +5 -4
data/test/unit/bio/appl/iprscan/test_report.rb +6 -5
data/test/unit/bio/appl/mafft/test_report.rb +6 -5
data/test/unit/bio/appl/meme/mast/test_report.rb +46 -0
data/test/unit/bio/appl/meme/test_mast.rb +103 -0
data/test/unit/bio/appl/meme/test_motif.rb +38 -0
data/test/unit/bio/appl/paml/codeml/test_rates.rb +5 -4
data/test/unit/bio/appl/paml/codeml/test_report.rb +5 -4
data/test/unit/bio/appl/paml/test_codeml.rb +5 -4
data/test/unit/bio/appl/sim4/test_report.rb +5 -4
data/test/unit/bio/appl/sosui/test_report.rb +6 -5
data/test/unit/bio/appl/targetp/test_report.rb +5 -3
data/test/unit/bio/appl/test_blast.rb +5 -4
data/test/unit/bio/appl/test_fasta.rb +4 -2
data/test/unit/bio/appl/test_pts1.rb +4 -2
data/test/unit/bio/appl/tmhmm/test_report.rb +6 -5
data/test/unit/bio/data/test_aa.rb +5 -3
data/test/unit/bio/data/test_codontable.rb +5 -4
data/test/unit/bio/data/test_na.rb +5 -3
data/test/unit/bio/db/biosql/tc_biosql.rb +5 -1
data/test/unit/bio/db/embl/test_common.rb +4 -2
data/test/unit/bio/db/embl/test_embl.rb +6 -6
data/test/unit/bio/db/embl/test_embl_rel89.rb +6 -6
data/test/unit/bio/db/embl/test_embl_to_bioseq.rb +7 -8
data/test/unit/bio/db/embl/test_sptr.rb +6 -8
data/test/unit/bio/db/embl/test_uniprot.rb +6 -5
data/test/unit/bio/db/fasta/test_format_qual.rb +346 -0
data/test/unit/bio/db/kegg/test_compound.rb +146 -0
data/test/unit/bio/db/kegg/test_drug.rb +194 -0
data/test/unit/bio/db/kegg/test_enzyme.rb +241 -0
data/test/unit/bio/db/kegg/test_genes.rb +32 -4
data/test/unit/bio/db/kegg/test_glycan.rb +260 -0
data/test/unit/bio/db/kegg/test_orthology.rb +50 -0
data/test/unit/bio/db/kegg/test_reaction.rb +96 -0
data/test/unit/bio/db/pdb/test_pdb.rb +4 -2
data/test/unit/bio/db/sanger_chromatogram/test_abif.rb +76 -0
data/test/unit/bio/db/sanger_chromatogram/test_scf.rb +98 -0
data/test/unit/bio/db/test_aaindex.rb +6 -6
data/test/unit/bio/db/test_fasta.rb +5 -46
data/test/unit/bio/db/test_fastq.rb +829 -0
data/test/unit/bio/db/test_gff.rb +4 -2
data/test/unit/bio/db/test_lasergene.rb +7 -5
data/test/unit/bio/db/test_medline.rb +4 -2
data/test/unit/bio/db/test_newick.rb +6 -6
data/test/unit/bio/db/test_nexus.rb +4 -2
data/test/unit/bio/db/test_phyloxml.rb +769 -0
data/test/unit/bio/db/test_phyloxml_writer.rb +328 -0
data/test/unit/bio/db/test_prosite.rb +6 -5
data/test/unit/bio/db/test_qual.rb +63 -0
data/test/unit/bio/db/test_rebase.rb +5 -3
data/test/unit/bio/db/test_soft.rb +7 -6
data/test/unit/bio/io/flatfile/test_autodetection.rb +6 -7
data/test/unit/bio/io/flatfile/test_buffer.rb +6 -5
data/test/unit/bio/io/flatfile/test_splitter.rb +4 -4
data/test/unit/bio/io/test_ddbjxml.rb +4 -3
data/test/unit/bio/io/test_ensembl.rb +5 -3
data/test/unit/bio/io/test_fastacmd.rb +4 -3
data/test/unit/bio/io/test_flatfile.rb +6 -5
data/test/unit/bio/io/test_soapwsdl.rb +4 -3
data/test/unit/bio/io/test_togows.rb +4 -2
data/test/unit/bio/sequence/test_aa.rb +5 -3
data/test/unit/bio/sequence/test_common.rb +4 -2
data/test/unit/bio/sequence/test_compat.rb +4 -2
data/test/unit/bio/sequence/test_dblink.rb +5 -3
data/test/unit/bio/sequence/test_na.rb +4 -2
data/test/unit/bio/sequence/test_quality_score.rb +330 -0
data/test/unit/bio/shell/plugin/test_seq.rb +5 -3
data/test/unit/bio/test_alignment.rb +5 -3
data/test/unit/bio/test_command.rb +4 -3
data/test/unit/bio/test_db.rb +5 -3
data/test/unit/bio/test_feature.rb +4 -2
data/test/unit/bio/test_location.rb +4 -2
data/test/unit/bio/test_map.rb +5 -3
data/test/unit/bio/test_pathway.rb +4 -2
data/test/unit/bio/test_reference.rb +4 -2
data/test/unit/bio/test_sequence.rb +5 -3
data/test/unit/bio/test_shell.rb +5 -3
data/test/unit/bio/test_tree.rb +6 -6
data/test/unit/bio/util/restriction_enzyme/analysis/test_calculated_cuts.rb +4 -2
data/test/unit/bio/util/restriction_enzyme/analysis/test_cut_ranges.rb +4 -2
data/test/unit/bio/util/restriction_enzyme/analysis/test_sequence_range.rb +4 -2
data/test/unit/bio/util/restriction_enzyme/double_stranded/test_aligned_strands.rb +4 -2
data/test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_location_pair.rb +4 -2
data/test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_location_pair_in_enzyme_notation.rb +4 -2
data/test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations.rb +4 -2
data/test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations_in_enzyme_notation.rb +4 -2
data/test/unit/bio/util/restriction_enzyme/single_strand/test_cut_locations_in_enzyme_notation.rb +4 -2
data/test/unit/bio/util/restriction_enzyme/test_analysis.rb +4 -2
data/test/unit/bio/util/restriction_enzyme/test_cut_symbol.rb +4 -2
data/test/unit/bio/util/restriction_enzyme/test_double_stranded.rb +4 -2
data/test/unit/bio/util/restriction_enzyme/test_single_strand.rb +17 -13
data/test/unit/bio/util/restriction_enzyme/test_single_strand_complement.rb +17 -13
data/test/unit/bio/util/restriction_enzyme/test_string_formatting.rb +4 -2
data/test/unit/bio/util/test_color_scheme.rb +5 -3
data/test/unit/bio/util/test_contingency_table.rb +5 -3
data/test/unit/bio/util/test_restriction_enzyme.rb +4 -2
data/test/unit/bio/util/test_sirna.rb +6 -4
metadata +147 -2

data/test/unit/bio/shell/plugin/test_seq.rb CHANGED

@@ -5,13 +5,15 @@
 #               Mitsuteru Nakao <n@bioruby.org>
 # License::     The Ruby License
 #
-# $Id: test_seq.rb,v 1.9 2007/04/05 23:35:44 trevor Exp $
+# $Id:$
 #
+# loading helper routine for testing bioruby
 require 'pathname'
-libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 5, 'lib')).cleanpath.to_s
-$:.unshift(libpath) unless $:.include?(libpath)
+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/shell'
 require 'bio/shell/plugin/seq'

data/test/unit/bio/test_alignment.rb CHANGED

@@ -6,13 +6,15 @@
 #              2005 Naohisa Goto <ng@bioruby.org>
 # License::    The Ruby License
 #
-#  $Id: test_alignment.rb,v 1.12 2007/12/26 13:55:40 ngoto Exp $
+#  $Id:$
 #
+# loading helper routine for testing bioruby
 require 'pathname'
-libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 3, 'lib')).cleanpath.to_s
-$:.unshift(libpath) unless $:.include?(libpath)
+load Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 2,
+                            'bioruby_test_helper.rb')).cleanpath.to_s
+# libraries needed for the tests
 require 'test/unit'
 require 'bio/alignment'

data/test/unit/bio/test_command.rb CHANGED

@@ -10,11 +10,12 @@
 #  $Id:$
 #
+# loading helper routine for testing bioruby
 require 'pathname'
-libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 3, 'lib')).cleanpath.to_s
-$:.unshift(libpath) unless $:.include?(libpath)
+load Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 2,
+                            'bioruby_test_helper.rb')).cleanpath.to_s
+# libraries needed for the tests
 require 'test/unit'
 require 'bio/command'

data/test/unit/bio/test_db.rb CHANGED

@@ -4,13 +4,15 @@
 # Copyright::  Copyright (C) 2005 Mitsuteru Nakao <n@bioruby.org>
 # License::    The Ruby License
 #
-#  $Id: test_db.rb,v 1.4 2007/04/05 23:35:42 trevor Exp $
+#  $Id:$
 #
+# loading helper routine for testing bioruby
 require 'pathname'
-libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 3, 'lib')).cleanpath.to_s
-$:.unshift(libpath) unless $:.include?(libpath)
+load Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 2,
+                            'bioruby_test_helper.rb')).cleanpath.to_s
+# libraries needed for the tests
 require 'test/unit'
 require 'bio/db'

data/test/unit/bio/test_feature.rb CHANGED

@@ -8,10 +8,12 @@
 #  $Id:$
 #
+# loading helper routine for testing bioruby
 require 'pathname'
-libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 3 , 'lib')).cleanpath.to_s
-$:.unshift(libpath) unless $:.include?(libpath)
+load Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 2,
+                            'bioruby_test_helper.rb')).cleanpath.to_s
+# libraries needed for the tests
 require 'test/unit'
 require 'bio/feature'
 require 'bio/compat/features'

data/test/unit/bio/test_location.rb CHANGED

@@ -8,10 +8,12 @@
 #  $Id:$
 #
+# loading helper routine for testing bioruby
 require 'pathname'
-libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 3, 'lib')).cleanpath.to_s
-$:.unshift(libpath) unless $:.include?(libpath)
+load Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 2,
+                            'bioruby_test_helper.rb')).cleanpath.to_s
+# libraries needed for the tests
 require 'test/unit'
 require 'bio/location'

data/test/unit/bio/test_map.rb CHANGED

@@ -5,12 +5,14 @@
 #               Jan Aerts <jan.aerts@bbsrc.ac.uk>
 # License::     The Ruby License
 #
-# $Id:
+# $Id:$
+# loading helper routine for testing bioruby
 require 'pathname'
-libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 3, 'lib')).cleanpath.to_s
-$:.unshift(libpath) unless $:.include?(libpath)
+load Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 2,
+                            'bioruby_test_helper.rb')).cleanpath.to_s
+# libraries needed for the tests
 require 'test/unit'
 require 'bio/map'

data/test/unit/bio/test_pathway.rb CHANGED

@@ -8,10 +8,12 @@
 #  $Id:$
 #
+# loading helper routine for testing bioruby
 require 'pathname'
-libpath = Pathname.new(File.join(File.dirname(__FILE__), [".."]*3, "lib")).cleanpath.to_s
-$:.unshift(libpath) unless $:.include?(libpath)
+load Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 2,
+                            'bioruby_test_helper.rb')).cleanpath.to_s
+# libraries needed for the tests
 require 'test/unit'
 require 'bio/pathway'

data/test/unit/bio/test_reference.rb CHANGED

@@ -8,10 +8,12 @@
 # $Id:$
 #
+# loading helper routine for testing bioruby
 require 'pathname'
-libpath = Pathname.new(File.join(File.dirname(__FILE__), [".."] * 3, "lib")).cleanpath.to_s
-$:.unshift(libpath) unless $:.include?(libpath)
+load Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 2,
+                            'bioruby_test_helper.rb')).cleanpath.to_s
+# libraries needed for the tests
 require 'test/unit'
 require 'bio/reference'
 require 'bio/compat/references'

data/test/unit/bio/test_sequence.rb CHANGED

@@ -6,13 +6,15 @@
 #              2006 Mitsuteru C. Nakao <n@bioruby.org>
 # License::    The Ruby License
 #
-#  $Id: test_sequence.rb,v 1.9 2007/04/05 23:35:42 trevor Exp $
+#  $Id:$
 #
+# loading helper routine for testing bioruby
 require 'pathname'
-libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 3, 'lib')).cleanpath.to_s
-$:.unshift(libpath) unless $:.include?(libpath)
+load Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 2,
+                            'bioruby_test_helper.rb')).cleanpath.to_s
+# libraries needed for the tests
 require 'test/unit'
 require 'bio/sequence'

data/test/unit/bio/test_shell.rb CHANGED

@@ -4,13 +4,15 @@
 # Copyright::  Copyright (C) 2005 Mitsuteru Nakao <n@bioruby.org>
 # License::    The Ruby License
 #
-#  $Id: test_shell.rb,v 1.7 2007/04/05 23:35:42 trevor Exp $
+#  $Id:$
 #
+# loading helper routine for testing bioruby
 require 'pathname'
-libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 3, 'lib')).cleanpath.to_s
-$:.unshift(libpath) unless $:.include?(libpath)
+load Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 2,
+                            'bioruby_test_helper.rb')).cleanpath.to_s
+# libraries needed for the tests
 require 'test/unit'
 require 'bio/shell'

data/test/unit/bio/test_tree.rb CHANGED

@@ -5,16 +5,16 @@
 #               Naohisa Goto <ng@bioruby.org>
 # License::     The Ruby License
 #
-# $Id: test_tree.rb,v 1.5 2007/04/05 23:35:42 trevor Exp $
+# $Id:$
 #
-require 'test/unit'
+# loading helper routine for testing bioruby
 require 'pathname'
-libpath = Pathname.new(File.join(File.dirname(__FILE__), [".."] * 3, "lib")).cleanpath.to_s
-$:.unshift(libpath) unless $:.include?(libpath)
+load Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 2,
+                            'bioruby_test_helper.rb')).cleanpath.to_s
-require 'bio'
+# libraries needed for the tests
+require 'test/unit'
 require 'bio/tree'
 module Bio

data/test/unit/bio/util/restriction_enzyme/analysis/test_calculated_cuts.rb CHANGED

@@ -8,10 +8,12 @@
 #  $Id:$
 #
+# loading helper routine for testing bioruby
 require 'pathname'
-libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 6, 'lib')).cleanpath.to_s
-$:.unshift(libpath) unless $:.include?(libpath)
+load Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 5,
+                            'bioruby_test_helper.rb')).cleanpath.to_s
+# libraries needed for the tests
 require 'test/unit'
 require 'bio/util/restriction_enzyme/range/sequence_range/calculated_cuts'
 require 'bio/util/restriction_enzyme/range/cut_range'

data/test/unit/bio/util/restriction_enzyme/analysis/test_cut_ranges.rb CHANGED

@@ -8,10 +8,12 @@
 #  $Id:$
 #
+# loading helper routine for testing bioruby
 require 'pathname'
-libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 6, 'lib')).cleanpath.to_s
-$:.unshift(libpath) unless $:.include?(libpath)
+load Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 5,
+                            'bioruby_test_helper.rb')).cleanpath.to_s
+# libraries needed for the tests
 require 'test/unit'
 require 'bio/util/restriction_enzyme/range/sequence_range'
 require 'bio/util/restriction_enzyme/range/sequence_range/fragments'

data/test/unit/bio/util/restriction_enzyme/analysis/test_sequence_range.rb CHANGED

@@ -8,10 +8,12 @@
 #  $Id:$
 #
+# loading helper routine for testing bioruby
 require 'pathname'
-libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 6, 'lib')).cleanpath.to_s
-$:.unshift(libpath) unless $:.include?(libpath)
+load Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 5,
+                            'bioruby_test_helper.rb')).cleanpath.to_s
+# libraries needed for the tests
 require 'test/unit'
 require 'bio/util/restriction_enzyme/range/sequence_range'
 require 'bio/util/restriction_enzyme/range/sequence_range/fragments'

data/test/unit/bio/util/restriction_enzyme/double_stranded/test_aligned_strands.rb CHANGED

@@ -8,10 +8,12 @@
 #  $Id:$
 #
+# loading helper routine for testing bioruby
 require 'pathname'
-libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 6, 'lib')).cleanpath.to_s
-$:.unshift(libpath) unless $:.include?(libpath)
+load Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 5,
+                            'bioruby_test_helper.rb')).cleanpath.to_s
+# libraries needed for the tests
 require 'test/unit'
 require 'bio/sequence'
 require 'bio/util/restriction_enzyme/double_stranded/aligned_strands'

data/test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_location_pair.rb CHANGED

@@ -8,10 +8,12 @@
 #  $Id:$
 #
+# loading helper routine for testing bioruby
 require 'pathname'
-libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 6, 'lib')).cleanpath.to_s
-$:.unshift(libpath) unless $:.include?(libpath)
+load Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 5,
+                            'bioruby_test_helper.rb')).cleanpath.to_s
+# libraries needed for the tests
 require 'test/unit'
 require 'bio/util/restriction_enzyme/double_stranded/cut_location_pair'

data/test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_location_pair_in_enzyme_notation.rb CHANGED

@@ -8,10 +8,12 @@
 #  $Id:$
 #
+# loading helper routine for testing bioruby
 require 'pathname'
-libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 6, 'lib')).cleanpath.to_s
-$:.unshift(libpath) unless $:.include?(libpath)
+load Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 5,
+                            'bioruby_test_helper.rb')).cleanpath.to_s
+# libraries needed for the tests
 require 'test/unit'
 require 'bio/util/restriction_enzyme/double_stranded/cut_location_pair_in_enzyme_notation'

data/test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations.rb CHANGED

@@ -8,10 +8,12 @@
 #  $Id:$
 #
+# loading helper routine for testing bioruby
 require 'pathname'
-libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 6, 'lib')).cleanpath.to_s
-$:.unshift(libpath) unless $:.include?(libpath)
+load Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 5,
+                            'bioruby_test_helper.rb')).cleanpath.to_s
+# libraries needed for the tests
 require 'test/unit'
 require 'bio/util/restriction_enzyme/double_stranded/cut_locations'

data/test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations_in_enzyme_notation.rb CHANGED

@@ -8,10 +8,12 @@
 #  $Id:$
 #
+# loading helper routine for testing bioruby
 require 'pathname'
-libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 6, 'lib')).cleanpath.to_s
-$:.unshift(libpath) unless $:.include?(libpath)
+load Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 5,
+                            'bioruby_test_helper.rb')).cleanpath.to_s
+# libraries needed for the tests
 require 'test/unit'
 require 'bio/util/restriction_enzyme/double_stranded/cut_locations_in_enzyme_notation'

data/test/unit/bio/util/restriction_enzyme/single_strand/test_cut_locations_in_enzyme_notation.rb CHANGED

@@ -8,10 +8,12 @@
 #  $Id:$
 #
+# loading helper routine for testing bioruby
 require 'pathname'
-libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 6, 'lib')).cleanpath.to_s
-$:.unshift(libpath) unless $:.include?(libpath)
+load Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 5,
+                            'bioruby_test_helper.rb')).cleanpath.to_s
+# libraries needed for the tests
 require 'test/unit'
 require 'bio/util/restriction_enzyme/single_strand/cut_locations_in_enzyme_notation'

data/test/unit/bio/util/restriction_enzyme/test_analysis.rb CHANGED

@@ -8,10 +8,12 @@
 #  $Id:$
 #
+# loading helper routine for testing bioruby
 require 'pathname'
-libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 5, 'lib')).cleanpath.to_s
-$:.unshift(libpath) unless $:.include?(libpath)
+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/analysis'
 require 'bio/sequence'

data/test/unit/bio/util/restriction_enzyme/test_cut_symbol.rb CHANGED

@@ -8,10 +8,12 @@
 #  $Id:$
 #
+# loading helper routine for testing bioruby
 require 'pathname'
-libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 5, 'lib')).cleanpath.to_s
-$:.unshift(libpath) unless $:.include?(libpath)
+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/cut_symbol'

data/test/unit/bio/util/restriction_enzyme/test_double_stranded.rb CHANGED

@@ -8,10 +8,12 @@
 #  $Id:$
 #
+# loading helper routine for testing bioruby
 require 'pathname'
-libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 5, 'lib')).cleanpath.to_s
-$:.unshift(libpath) unless $:.include?(libpath)
+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/double_stranded'
 require 'bio/sequence'

data/test/unit/bio/util/restriction_enzyme/test_single_strand.rb CHANGED

@@ -8,10 +8,12 @@
 #  $Id:$
 #
+# loading helper routine for testing bioruby
 require 'pathname'
-libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 5, 'lib')).cleanpath.to_s
-$:.unshift(libpath) unless $:.include?(libpath)
+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/single_strand'
@@ -128,17 +130,19 @@ class TestSingleStrand < Test::Unit::TestCase #:nodoc:
     assert_raise(ArgumentError) { @t.new('a', [1,1,2]) }
     assert_raise(ArgumentError) { @t.new('a', 1,1,2,2) }
-    assert_raise(ArgumentError) { @t.new(1, [1,2,3]) }
-    assert_raise(ArgumentError) { @t.new('gaat^aca', [1,2,3]) }
-    assert_raise(ArgumentError) { @t.new('gaat^^aca') }
-    assert_raise(ArgumentError) { @t.new('z', [1,2,3]) }
-    assert_raise(ArgumentError) { @t.new('g', [0,1,2]) }
-    assert_raise(ArgumentError) { @t.new('g', 0,1,2,0) }
-    assert_raise(ArgumentError) { @t.new('g', [0,1,1,2]) }
-    assert_raise(ArgumentError) { @t.new('g', 0,1,1,2,2) }
-    assert_raise(ArgumentError) { @t.new(1,2,3) }
-    assert_raise(ArgumentError) { @t.new(1,2,'g') }
+  # NOTE t| 2009-09-19 commented out for library efficiency
+  # re: validate_args(sequence, c) in util/restriction_enzyme/single_strand/single_strand.rb
+    # assert_raise(ArgumentError) { @t.new(1, [1,2,3]) }
+    # assert_raise(ArgumentError) { @t.new('gaat^aca', [1,2,3]) }
+    # assert_raise(ArgumentError) { @t.new('gaat^^aca') }
+    # assert_raise(ArgumentError) { @t.new('z', [1,2,3]) }
+    #
+    # assert_raise(ArgumentError) { @t.new('g', [0,1,2]) }
+    # assert_raise(ArgumentError) { @t.new('g', 0,1,2,0) }
+    # assert_raise(ArgumentError) { @t.new('g', [0,1,1,2]) }
+    # assert_raise(ArgumentError) { @t.new('g', 0,1,1,2,2) }
+    # assert_raise(ArgumentError) { @t.new(1,2,3) }
+    # assert_raise(ArgumentError) { @t.new(1,2,'g') }
   end