wwood-bioruby 1.2.11
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- data/README.rdoc +205 -0
- data/README_DEV.rdoc +285 -0
- data/VERSION.yml +4 -0
- data/bin/bioruby +44 -0
- data/bin/br_biofetch.rb +47 -0
- data/bin/br_bioflat.rb +293 -0
- data/bin/br_biogetseq.rb +45 -0
- data/bin/br_pmfetch.rb +421 -0
- data/lib/bio.rb +306 -0
- data/lib/bio/alignment.rb +2518 -0
- data/lib/bio/appl/bl2seq/report.rb +334 -0
- data/lib/bio/appl/blast.rb +505 -0
- data/lib/bio/appl/blast/ddbj.rb +142 -0
- data/lib/bio/appl/blast/format0.rb +1438 -0
- data/lib/bio/appl/blast/format8.rb +83 -0
- data/lib/bio/appl/blast/genomenet.rb +263 -0
- data/lib/bio/appl/blast/ncbioptions.rb +220 -0
- data/lib/bio/appl/blast/remote.rb +105 -0
- data/lib/bio/appl/blast/report.rb +767 -0
- data/lib/bio/appl/blast/rexml.rb +144 -0
- data/lib/bio/appl/blast/rpsblast.rb +277 -0
- data/lib/bio/appl/blast/wublast.rb +635 -0
- data/lib/bio/appl/blast/xmlparser.rb +236 -0
- data/lib/bio/appl/blat/report.rb +530 -0
- data/lib/bio/appl/clustalw.rb +219 -0
- data/lib/bio/appl/clustalw/report.rb +152 -0
- data/lib/bio/appl/emboss.rb +203 -0
- data/lib/bio/appl/fasta.rb +235 -0
- data/lib/bio/appl/fasta/format10.rb +325 -0
- data/lib/bio/appl/gcg/msf.rb +212 -0
- data/lib/bio/appl/gcg/seq.rb +195 -0
- data/lib/bio/appl/genscan/report.rb +552 -0
- data/lib/bio/appl/hmmer.rb +126 -0
- data/lib/bio/appl/hmmer/report.rb +683 -0
- data/lib/bio/appl/iprscan/report.rb +374 -0
- data/lib/bio/appl/mafft.rb +259 -0
- data/lib/bio/appl/mafft/report.rb +226 -0
- data/lib/bio/appl/muscle.rb +52 -0
- data/lib/bio/appl/paml/baseml.rb +95 -0
- data/lib/bio/appl/paml/baseml/report.rb +32 -0
- data/lib/bio/appl/paml/codeml.rb +242 -0
- data/lib/bio/appl/paml/codeml/rates.rb +67 -0
- data/lib/bio/appl/paml/codeml/report.rb +67 -0
- data/lib/bio/appl/paml/common.rb +348 -0
- data/lib/bio/appl/paml/common_report.rb +38 -0
- data/lib/bio/appl/paml/yn00.rb +103 -0
- data/lib/bio/appl/paml/yn00/report.rb +32 -0
- data/lib/bio/appl/phylip/alignment.rb +133 -0
- data/lib/bio/appl/phylip/distance_matrix.rb +96 -0
- data/lib/bio/appl/probcons.rb +41 -0
- data/lib/bio/appl/psort.rb +548 -0
- data/lib/bio/appl/psort/report.rb +542 -0
- data/lib/bio/appl/pts1.rb +263 -0
- data/lib/bio/appl/sim4.rb +124 -0
- data/lib/bio/appl/sim4/report.rb +485 -0
- data/lib/bio/appl/sosui/report.rb +151 -0
- data/lib/bio/appl/spidey/report.rb +593 -0
- data/lib/bio/appl/targetp/report.rb +267 -0
- data/lib/bio/appl/tcoffee.rb +55 -0
- data/lib/bio/appl/tmhmm/report.rb +231 -0
- data/lib/bio/command.rb +593 -0
- data/lib/bio/compat/features.rb +157 -0
- data/lib/bio/compat/references.rb +128 -0
- data/lib/bio/data/aa.rb +353 -0
- data/lib/bio/data/codontable.rb +722 -0
- data/lib/bio/data/na.rb +223 -0
- data/lib/bio/db.rb +329 -0
- data/lib/bio/db/aaindex.rb +357 -0
- data/lib/bio/db/biosql/biosql_to_biosequence.rb +67 -0
- data/lib/bio/db/biosql/sequence.rb +508 -0
- data/lib/bio/db/embl/common.rb +352 -0
- data/lib/bio/db/embl/embl.rb +500 -0
- data/lib/bio/db/embl/embl_to_biosequence.rb +85 -0
- data/lib/bio/db/embl/format_embl.rb +190 -0
- data/lib/bio/db/embl/sptr.rb +1283 -0
- data/lib/bio/db/embl/swissprot.rb +42 -0
- data/lib/bio/db/embl/trembl.rb +41 -0
- data/lib/bio/db/embl/uniprot.rb +42 -0
- data/lib/bio/db/fantom.rb +597 -0
- data/lib/bio/db/fasta.rb +410 -0
- data/lib/bio/db/fasta/defline.rb +532 -0
- data/lib/bio/db/fasta/fasta_to_biosequence.rb +63 -0
- data/lib/bio/db/fasta/format_fasta.rb +97 -0
- data/lib/bio/db/genbank/common.rb +307 -0
- data/lib/bio/db/genbank/ddbj.rb +22 -0
- data/lib/bio/db/genbank/format_genbank.rb +187 -0
- data/lib/bio/db/genbank/genbank.rb +250 -0
- data/lib/bio/db/genbank/genbank_to_biosequence.rb +86 -0
- data/lib/bio/db/genbank/genpept.rb +60 -0
- data/lib/bio/db/genbank/refseq.rb +18 -0
- data/lib/bio/db/gff.rb +1846 -0
- data/lib/bio/db/go.rb +481 -0
- data/lib/bio/db/kegg/brite.rb +41 -0
- data/lib/bio/db/kegg/compound.rb +131 -0
- data/lib/bio/db/kegg/drug.rb +98 -0
- data/lib/bio/db/kegg/enzyme.rb +148 -0
- data/lib/bio/db/kegg/expression.rb +155 -0
- data/lib/bio/db/kegg/genes.rb +263 -0
- data/lib/bio/db/kegg/genome.rb +241 -0
- data/lib/bio/db/kegg/glycan.rb +166 -0
- data/lib/bio/db/kegg/keggtab.rb +357 -0
- data/lib/bio/db/kegg/kgml.rb +256 -0
- data/lib/bio/db/kegg/orthology.rb +136 -0
- data/lib/bio/db/kegg/reaction.rb +82 -0
- data/lib/bio/db/kegg/taxonomy.rb +331 -0
- data/lib/bio/db/lasergene.rb +209 -0
- data/lib/bio/db/litdb.rb +107 -0
- data/lib/bio/db/medline.rb +326 -0
- data/lib/bio/db/nbrf.rb +191 -0
- data/lib/bio/db/newick.rb +658 -0
- data/lib/bio/db/nexus.rb +1854 -0
- data/lib/bio/db/pdb.rb +29 -0
- data/lib/bio/db/pdb/atom.rb +77 -0
- data/lib/bio/db/pdb/chain.rb +210 -0
- data/lib/bio/db/pdb/chemicalcomponent.rb +224 -0
- data/lib/bio/db/pdb/model.rb +148 -0
- data/lib/bio/db/pdb/pdb.rb +1911 -0
- data/lib/bio/db/pdb/residue.rb +176 -0
- data/lib/bio/db/pdb/utils.rb +399 -0
- data/lib/bio/db/prosite.rb +597 -0
- data/lib/bio/db/rebase.rb +456 -0
- data/lib/bio/db/soft.rb +404 -0
- data/lib/bio/db/transfac.rb +375 -0
- data/lib/bio/db/url.rb +42 -0
- data/lib/bio/feature.rb +139 -0
- data/lib/bio/io/biosql/biodatabase.rb +64 -0
- data/lib/bio/io/biosql/bioentry.rb +29 -0
- data/lib/bio/io/biosql/bioentry_dbxref.rb +11 -0
- data/lib/bio/io/biosql/bioentry_path.rb +12 -0
- data/lib/bio/io/biosql/bioentry_qualifier_value.rb +10 -0
- data/lib/bio/io/biosql/bioentry_reference.rb +10 -0
- data/lib/bio/io/biosql/bioentry_relationship.rb +10 -0
- data/lib/bio/io/biosql/biosequence.rb +11 -0
- data/lib/bio/io/biosql/comment.rb +7 -0
- data/lib/bio/io/biosql/config/database.yml +20 -0
- data/lib/bio/io/biosql/dbxref.rb +13 -0
- data/lib/bio/io/biosql/dbxref_qualifier_value.rb +12 -0
- data/lib/bio/io/biosql/location.rb +32 -0
- data/lib/bio/io/biosql/location_qualifier_value.rb +11 -0
- data/lib/bio/io/biosql/ontology.rb +10 -0
- data/lib/bio/io/biosql/reference.rb +9 -0
- data/lib/bio/io/biosql/seqfeature.rb +32 -0
- data/lib/bio/io/biosql/seqfeature_dbxref.rb +11 -0
- data/lib/bio/io/biosql/seqfeature_path.rb +11 -0
- data/lib/bio/io/biosql/seqfeature_qualifier_value.rb +20 -0
- data/lib/bio/io/biosql/seqfeature_relationship.rb +11 -0
- data/lib/bio/io/biosql/taxon.rb +12 -0
- data/lib/bio/io/biosql/taxon_name.rb +9 -0
- data/lib/bio/io/biosql/term.rb +27 -0
- data/lib/bio/io/biosql/term_dbxref.rb +11 -0
- data/lib/bio/io/biosql/term_path.rb +12 -0
- data/lib/bio/io/biosql/term_relationship.rb +13 -0
- data/lib/bio/io/biosql/term_relationship_term.rb +11 -0
- data/lib/bio/io/biosql/term_synonym.rb +10 -0
- data/lib/bio/io/das.rb +461 -0
- data/lib/bio/io/dbget.rb +194 -0
- data/lib/bio/io/ddbjxml.rb +638 -0
- data/lib/bio/io/ebisoap.rb +158 -0
- data/lib/bio/io/ensembl.rb +229 -0
- data/lib/bio/io/fastacmd.rb +163 -0
- data/lib/bio/io/fetch.rb +195 -0
- data/lib/bio/io/flatfile.rb +482 -0
- data/lib/bio/io/flatfile/autodetection.rb +545 -0
- data/lib/bio/io/flatfile/bdb.rb +253 -0
- data/lib/bio/io/flatfile/buffer.rb +237 -0
- data/lib/bio/io/flatfile/index.rb +1381 -0
- data/lib/bio/io/flatfile/indexer.rb +805 -0
- data/lib/bio/io/flatfile/splitter.rb +297 -0
- data/lib/bio/io/higet.rb +73 -0
- data/lib/bio/io/hinv.rb +442 -0
- data/lib/bio/io/keggapi.rb +805 -0
- data/lib/bio/io/ncbirest.rb +733 -0
- data/lib/bio/io/ncbisoap.rb +155 -0
- data/lib/bio/io/pubmed.rb +307 -0
- data/lib/bio/io/registry.rb +292 -0
- data/lib/bio/io/soapwsdl.rb +119 -0
- data/lib/bio/io/sql.rb +186 -0
- data/lib/bio/location.rb +867 -0
- data/lib/bio/map.rb +410 -0
- data/lib/bio/pathway.rb +960 -0
- data/lib/bio/reference.rb +602 -0
- data/lib/bio/sequence.rb +456 -0
- data/lib/bio/sequence/aa.rb +152 -0
- data/lib/bio/sequence/adapter.rb +108 -0
- data/lib/bio/sequence/common.rb +310 -0
- data/lib/bio/sequence/compat.rb +123 -0
- data/lib/bio/sequence/dblink.rb +54 -0
- data/lib/bio/sequence/format.rb +358 -0
- data/lib/bio/sequence/format_raw.rb +23 -0
- data/lib/bio/sequence/generic.rb +24 -0
- data/lib/bio/sequence/na.rb +491 -0
- data/lib/bio/shell.rb +44 -0
- data/lib/bio/shell/core.rb +578 -0
- data/lib/bio/shell/demo.rb +146 -0
- data/lib/bio/shell/interface.rb +218 -0
- data/lib/bio/shell/irb.rb +95 -0
- data/lib/bio/shell/object.rb +71 -0
- data/lib/bio/shell/plugin/blast.rb +42 -0
- data/lib/bio/shell/plugin/codon.rb +218 -0
- data/lib/bio/shell/plugin/das.rb +58 -0
- data/lib/bio/shell/plugin/emboss.rb +23 -0
- data/lib/bio/shell/plugin/entry.rb +105 -0
- data/lib/bio/shell/plugin/flatfile.rb +101 -0
- data/lib/bio/shell/plugin/keggapi.rb +181 -0
- data/lib/bio/shell/plugin/midi.rb +430 -0
- data/lib/bio/shell/plugin/obda.rb +45 -0
- data/lib/bio/shell/plugin/psort.rb +56 -0
- data/lib/bio/shell/plugin/seq.rb +247 -0
- data/lib/bio/shell/plugin/soap.rb +87 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/bioruby_generator.rb +29 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_classes.rhtml +4 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_log.rhtml +27 -0
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- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_modules.rhtml +4 -0
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- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby.css +368 -0
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- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby_controller.rb +144 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby_helper.rb +47 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/commands.rhtml +8 -0
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- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/index.rhtml +26 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/spinner.gif +0 -0
- data/lib/bio/shell/script.rb +25 -0
- data/lib/bio/shell/setup.rb +109 -0
- data/lib/bio/shell/web.rb +102 -0
- data/lib/bio/tree.rb +852 -0
- data/lib/bio/util/color_scheme.rb +191 -0
- data/lib/bio/util/color_scheme/buried.rb +59 -0
- data/lib/bio/util/color_scheme/helix.rb +59 -0
- data/lib/bio/util/color_scheme/hydropathy.rb +64 -0
- data/lib/bio/util/color_scheme/nucleotide.rb +31 -0
- data/lib/bio/util/color_scheme/strand.rb +59 -0
- data/lib/bio/util/color_scheme/taylor.rb +50 -0
- data/lib/bio/util/color_scheme/turn.rb +59 -0
- data/lib/bio/util/color_scheme/zappo.rb +50 -0
- data/lib/bio/util/contingency_table.rb +370 -0
- data/lib/bio/util/restriction_enzyme.rb +228 -0
- data/lib/bio/util/restriction_enzyme/analysis.rb +249 -0
- data/lib/bio/util/restriction_enzyme/analysis_basic.rb +217 -0
- data/lib/bio/util/restriction_enzyme/cut_symbol.rb +107 -0
- data/lib/bio/util/restriction_enzyme/double_stranded.rb +321 -0
- data/lib/bio/util/restriction_enzyme/double_stranded/aligned_strands.rb +130 -0
- data/lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb +103 -0
- data/lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair_in_enzyme_notation.rb +38 -0
- data/lib/bio/util/restriction_enzyme/double_stranded/cut_locations.rb +76 -0
- data/lib/bio/util/restriction_enzyme/double_stranded/cut_locations_in_enzyme_notation.rb +107 -0
- data/lib/bio/util/restriction_enzyme/enzymes.yaml +7061 -0
- data/lib/bio/util/restriction_enzyme/range/cut_range.rb +24 -0
- data/lib/bio/util/restriction_enzyme/range/cut_ranges.rb +47 -0
- data/lib/bio/util/restriction_enzyme/range/horizontal_cut_range.rb +67 -0
- data/lib/bio/util/restriction_enzyme/range/sequence_range.rb +257 -0
- data/lib/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb +242 -0
- data/lib/bio/util/restriction_enzyme/range/sequence_range/fragment.rb +51 -0
- data/lib/bio/util/restriction_enzyme/range/sequence_range/fragments.rb +41 -0
- data/lib/bio/util/restriction_enzyme/range/vertical_cut_range.rb +77 -0
- data/lib/bio/util/restriction_enzyme/single_strand.rb +200 -0
- data/lib/bio/util/restriction_enzyme/single_strand/cut_locations_in_enzyme_notation.rb +135 -0
- data/lib/bio/util/restriction_enzyme/single_strand_complement.rb +23 -0
- data/lib/bio/util/restriction_enzyme/string_formatting.rb +111 -0
- data/lib/bio/util/sirna.rb +288 -0
- data/test/data/HMMER/hmmpfam.out +64 -0
- data/test/data/HMMER/hmmsearch.out +88 -0
- data/test/data/SOSUI/sample.report +11 -0
- data/test/data/TMHMM/sample.report +21 -0
- data/test/data/aaindex/DAYM780301 +30 -0
- data/test/data/aaindex/PRAM900102 +20 -0
- data/test/data/bl2seq/cd8a_cd8b_blastp.bl2seq +53 -0
- data/test/data/bl2seq/cd8a_p53_e-5blastp.bl2seq +37 -0
- data/test/data/blast/2.2.15.blastp.m7 +876 -0
- data/test/data/blast/b0002.faa +15 -0
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- data/test/data/blast/b0002.faa.m8 +1 -0
- data/test/data/blast/blastp-multi.m7 +188 -0
- data/test/data/command/echoarg2.bat +1 -0
- data/test/data/embl/AB090716.embl +65 -0
- data/test/data/embl/AB090716.embl.rel89 +63 -0
- data/test/data/fasta/example1.txt +75 -0
- data/test/data/fasta/example2.txt +21 -0
- data/test/data/genscan/sample.report +63 -0
- data/test/data/iprscan/merged.raw +32 -0
- data/test/data/iprscan/merged.txt +74 -0
- data/test/data/paml/codeml/control_file.txt +30 -0
- data/test/data/paml/codeml/output.txt +78 -0
- data/test/data/paml/codeml/rates +217 -0
- data/test/data/prosite/prosite.dat +2233 -0
- data/test/data/refseq/nm_126355.entret +64 -0
- data/test/data/rpsblast/misc.rpsblast +193 -0
- data/test/data/soft/GDS100_partial.soft +92 -0
- data/test/data/soft/GSE3457_family_partial.soft +874 -0
- data/test/data/uniprot/p53_human.uniprot +1456 -0
- data/test/functional/bio/appl/test_pts1.rb +115 -0
- data/test/functional/bio/io/test_ensembl.rb +229 -0
- data/test/functional/bio/io/test_soapwsdl.rb +52 -0
- data/test/functional/bio/sequence/test_output_embl.rb +51 -0
- data/test/functional/bio/test_command.rb +301 -0
- data/test/runner.rb +14 -0
- data/test/unit/bio/appl/bl2seq/test_report.rb +134 -0
- data/test/unit/bio/appl/blast/test_ncbioptions.rb +112 -0
- data/test/unit/bio/appl/blast/test_report.rb +1135 -0
- data/test/unit/bio/appl/blast/test_rpsblast.rb +398 -0
- data/test/unit/bio/appl/genscan/test_report.rb +182 -0
- data/test/unit/bio/appl/hmmer/test_report.rb +342 -0
- data/test/unit/bio/appl/iprscan/test_report.rb +338 -0
- data/test/unit/bio/appl/mafft/test_report.rb +63 -0
- data/test/unit/bio/appl/paml/codeml/test_rates.rb +45 -0
- data/test/unit/bio/appl/paml/codeml/test_report.rb +45 -0
- data/test/unit/bio/appl/paml/test_codeml.rb +174 -0
- data/test/unit/bio/appl/sosui/test_report.rb +81 -0
- data/test/unit/bio/appl/targetp/test_report.rb +146 -0
- data/test/unit/bio/appl/test_blast.rb +277 -0
- data/test/unit/bio/appl/test_fasta.rb +130 -0
- data/test/unit/bio/appl/test_psort.rb +57 -0
- data/test/unit/bio/appl/test_pts1.rb +77 -0
- data/test/unit/bio/appl/tmhmm/test_report.rb +126 -0
- data/test/unit/bio/data/test_aa.rb +90 -0
- data/test/unit/bio/data/test_codontable.rb +107 -0
- data/test/unit/bio/data/test_na.rb +80 -0
- data/test/unit/bio/db/embl/test_common.rb +117 -0
- data/test/unit/bio/db/embl/test_embl.rb +214 -0
- data/test/unit/bio/db/embl/test_embl_rel89.rb +219 -0
- data/test/unit/bio/db/embl/test_embl_to_bioseq.rb +203 -0
- data/test/unit/bio/db/embl/test_sptr.rb +1812 -0
- data/test/unit/bio/db/embl/test_uniprot.rb +31 -0
- data/test/unit/bio/db/kegg/test_genes.rb +45 -0
- data/test/unit/bio/db/pdb/test_pdb.rb +152 -0
- data/test/unit/bio/db/test_aaindex.rb +197 -0
- data/test/unit/bio/db/test_fasta.rb +250 -0
- data/test/unit/bio/db/test_gff.rb +1190 -0
- data/test/unit/bio/db/test_lasergene.rb +95 -0
- data/test/unit/bio/db/test_medline.rb +127 -0
- data/test/unit/bio/db/test_newick.rb +293 -0
- data/test/unit/bio/db/test_nexus.rb +364 -0
- data/test/unit/bio/db/test_prosite.rb +1437 -0
- data/test/unit/bio/db/test_rebase.rb +101 -0
- data/test/unit/bio/db/test_soft.rb +138 -0
- data/test/unit/bio/db/test_url.rb +36 -0
- data/test/unit/bio/io/flatfile/test_autodetection.rb +375 -0
- data/test/unit/bio/io/flatfile/test_buffer.rb +251 -0
- data/test/unit/bio/io/flatfile/test_splitter.rb +369 -0
- data/test/unit/bio/io/test_ddbjxml.rb +80 -0
- data/test/unit/bio/io/test_ensembl.rb +109 -0
- data/test/unit/bio/io/test_fastacmd.rb +42 -0
- data/test/unit/bio/io/test_flatfile.rb +505 -0
- data/test/unit/bio/io/test_soapwsdl.rb +32 -0
- data/test/unit/bio/sequence/test_aa.rb +115 -0
- data/test/unit/bio/sequence/test_common.rb +373 -0
- data/test/unit/bio/sequence/test_compat.rb +69 -0
- data/test/unit/bio/sequence/test_dblink.rb +58 -0
- data/test/unit/bio/sequence/test_na.rb +330 -0
- data/test/unit/bio/shell/plugin/test_seq.rb +185 -0
- data/test/unit/bio/test_alignment.rb +1025 -0
- data/test/unit/bio/test_command.rb +349 -0
- data/test/unit/bio/test_db.rb +96 -0
- data/test/unit/bio/test_feature.rb +144 -0
- data/test/unit/bio/test_location.rb +599 -0
- data/test/unit/bio/test_map.rb +230 -0
- data/test/unit/bio/test_pathway.rb +499 -0
- data/test/unit/bio/test_reference.rb +252 -0
- data/test/unit/bio/test_sequence.rb +329 -0
- data/test/unit/bio/test_shell.rb +18 -0
- data/test/unit/bio/test_tree.rb +593 -0
- data/test/unit/bio/util/restriction_enzyme/analysis/test_calculated_cuts.rb +299 -0
- data/test/unit/bio/util/restriction_enzyme/analysis/test_cut_ranges.rb +103 -0
- data/test/unit/bio/util/restriction_enzyme/analysis/test_sequence_range.rb +240 -0
- data/test/unit/bio/util/restriction_enzyme/double_stranded/test_aligned_strands.rb +101 -0
- data/test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_location_pair.rb +75 -0
- data/test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_location_pair_in_enzyme_notation.rb +73 -0
- data/test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations.rb +53 -0
- data/test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations_in_enzyme_notation.rb +104 -0
- data/test/unit/bio/util/restriction_enzyme/single_strand/test_cut_locations_in_enzyme_notation.rb +83 -0
- data/test/unit/bio/util/restriction_enzyme/test_analysis.rb +246 -0
- data/test/unit/bio/util/restriction_enzyme/test_cut_symbol.rb +44 -0
- data/test/unit/bio/util/restriction_enzyme/test_double_stranded.rb +115 -0
- data/test/unit/bio/util/restriction_enzyme/test_single_strand.rb +147 -0
- data/test/unit/bio/util/restriction_enzyme/test_single_strand_complement.rb +147 -0
- data/test/unit/bio/util/restriction_enzyme/test_string_formatting.rb +60 -0
- data/test/unit/bio/util/test_color_scheme.rb +33 -0
- data/test/unit/bio/util/test_contingency_table.rb +94 -0
- data/test/unit/bio/util/test_restriction_enzyme.rb +42 -0
- data/test/unit/bio/util/test_sirna.rb +245 -0
- metadata +543 -0
@@ -0,0 +1,18 @@
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#
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# test/unit/bio/test_shell.rb - Unit test for Bio::Shell
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#
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# Copyright:: Copyright (C) 2005 Mitsuteru Nakao <n@bioruby.org>
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# License:: The Ruby License
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#
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# $Id: test_shell.rb,v 1.7 2007/04/05 23:35:42 trevor Exp $
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#
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require 'pathname'
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libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 3, 'lib')).cleanpath.to_s
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$:.unshift(libpath) unless $:.include?(libpath)
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require 'test/unit'
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require 'bio/shell'
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module Bio
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end
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#
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# = test/bio/test_tree.rb - unit test for Bio::Tree
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#
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# Copyright:: Copyright (C) 2006
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# Naohisa Goto <ng@bioruby.org>
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# License:: The Ruby License
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#
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# $Id: test_tree.rb,v 1.5 2007/04/05 23:35:42 trevor Exp $
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#
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require 'test/unit'
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require 'pathname'
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libpath = Pathname.new(File.join(File.dirname(__FILE__), [".."] * 3, "lib")).cleanpath.to_s
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$:.unshift(libpath) unless $:.include?(libpath)
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require 'bio'
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require 'bio/tree'
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module Bio
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class TestTreeEdge < Test::Unit::TestCase
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def setup
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@obj = Bio::Tree::Edge.new(123.45)
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end
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def test_initialize
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assert_nothing_raised { Bio::Tree::Edge.new }
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assert_equal(1.23, Bio::Tree::Edge.new(1.23).distance)
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assert_equal(12.3, Bio::Tree::Edge.new('12.3').distance)
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end
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def test_distance
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assert_equal(123.45, @obj.distance)
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end
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def test_distance_string
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assert_equal("123.45", @obj.distance_string)
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end
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def test_distance=()
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@obj.distance = 678.9
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assert_equal(678.9, @obj.distance)
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assert_equal("678.9", @obj.distance_string)
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@obj.distance = nil
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assert_equal(nil, @obj.distance)
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assert_equal(nil, @obj.distance_string)
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end
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def test_distance_string=()
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@obj.distance_string = "678.9"
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assert_equal(678.9, @obj.distance)
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assert_equal("678.9", @obj.distance_string)
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@obj.distance_string = nil
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assert_equal(nil, @obj.distance)
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assert_equal(nil, @obj.distance_string)
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end
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def test_inspect
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assert_equal("<Edge distance=123.45>", @obj.inspect)
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end
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def test_to_s
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assert_equal("123.45", @obj.to_s)
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end
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end #class TestTreeEdge
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class TestTreeNode < Test::Unit::TestCase
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def setup
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@obj = Bio::Tree::Node.new
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end
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def test_initialize
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assert_nothing_raised { Bio::Tree::Node.new }
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a = nil
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assert_nothing_raised { a = Bio::Tree::Node.new('mouse') }
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assert_equal('mouse', a.name)
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end
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def test_name
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assert_equal(nil, @obj.name)
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@obj.name = 'human'
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assert_equal('human', @obj.name)
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end
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def test_bootstrap
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assert_equal(nil, @obj.bootstrap)
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end
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def test_bootstrap_string
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assert_equal(nil, @obj.bootstrap_string)
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end
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def test_bootstrap=()
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@obj.bootstrap = 98
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assert_equal(98, @obj.bootstrap)
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assert_equal('98', @obj.bootstrap_string)
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@obj.bootstrap = nil
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assert_equal(nil, @obj.bootstrap)
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assert_equal(nil, @obj.bootstrap_string)
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end
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def test_bootstrap_string=()
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@obj.bootstrap_string = '98'
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assert_equal(98, @obj.bootstrap)
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assert_equal('98', @obj.bootstrap_string)
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@obj.bootstrap_string = '99.98'
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assert_equal(99.98, @obj.bootstrap)
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assert_equal('99.98', @obj.bootstrap_string)
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@obj.bootstrap = nil
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assert_equal(nil, @obj.bootstrap)
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assert_equal(nil, @obj.bootstrap_string)
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end
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def test_inspect
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@obj.name = 'human'
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assert_equal('(Node:"human")', @obj.inspect)
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@obj.bootstrap = 99.98
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assert_equal('(Node:"human" bootstrap=99.98)', @obj.inspect)
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end
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def test_to_s
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@obj.name = 'human'
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assert_equal('human', @obj.to_s)
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end
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end #class TestTreeNode
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class TestTree < Test::Unit::TestCase
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def setup
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@tree = Bio::Tree.new
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end
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def test_get_edge_distance
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edge = Bio::Tree::Edge.new
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assert_equal(nil, @tree.get_edge_distance(edge))
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edge = Bio::Tree::Edge.new(12.34)
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assert_equal(12.34, @tree.get_edge_distance(edge))
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assert_equal(12.34, @tree.get_edge_distance(12.34))
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end
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def test_get_edge_distance_string
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edge = Bio::Tree::Edge.new
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assert_equal(nil, @tree.get_edge_distance_string(edge))
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edge = Bio::Tree::Edge.new(12.34)
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assert_equal("12.34", @tree.get_edge_distance_string(edge))
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assert_equal("12.34", @tree.get_edge_distance_string(12.34))
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end
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def test_get_node_name
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node = Bio::Tree::Node.new
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assert_equal(nil, @tree.get_node_name(node))
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node.name = 'human'
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assert_equal('human', @tree.get_node_name(node))
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end
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def test_initialize
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assert_nothing_raised { Bio::Tree.new }
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assert_nothing_raised { Bio::Tree.new(@tree) }
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end
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def test_root
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assert_equal(nil, @tree.root)
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end
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def test_root=()
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assert_equal(nil, @tree.root)
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node = Bio::Tree::Node.new
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@tree.root = node
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assert_equal(node, @tree.root)
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end
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def test_options
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assert_equal({}, @tree.options)
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@tree.options[:bootstrap_style] = :traditional
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assert_equal(:traditional, @tree.options[:bootstrap_style])
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end
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end #class TestTree
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class TestTree2 < Test::Unit::TestCase
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def setup
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# Note that below data is NOT real. The distances are random.
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@tree = Bio::Tree.new
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@mouse = Bio::Tree::Node.new('mouse')
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@rat = Bio::Tree::Node.new('rat')
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@rodents = Bio::Tree::Node.new('rodents')
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@human = Bio::Tree::Node.new('human')
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@chimpanzee = Bio::Tree::Node.new('chimpanzee')
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@primates = Bio::Tree::Node.new('primates')
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@mammals = Bio::Tree::Node.new('mammals')
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@nodes =
|
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[ @mouse, @rat, @rodents, @human, @chimpanzee, @primates, @mammals ]
|
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@edge_rodents_mouse = Bio::Tree::Edge.new(0.0968)
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@edge_rodents_rat = Bio::Tree::Edge.new(0.1125)
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@edge_mammals_rodents = Bio::Tree::Edge.new(0.2560)
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@edge_primates_human = Bio::Tree::Edge.new(0.0386)
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@edge_primates_chimpanzee = Bio::Tree::Edge.new(0.0503)
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@edge_mammals_primates = Bio::Tree::Edge.new(0.2235)
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@edges = [
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[ @rodents, @mouse, @edge_rodents_mouse ],
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[ @rodents, @rat, @edge_rodents_rat ],
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[ @mammals, @rodents, @edge_mammals_rodents ],
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[ @primates, @human, @edge_primates_human ],
|
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[ @primates, @chimpanzee, @edge_primates_chimpanzee ],
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[ @mammals, @primates, @edge_mammals_primates ]
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]
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@edges.each do |a|
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@tree.add_edge(*a)
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end
|
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@by_id = Proc.new { |a, b| a.__id__ <=> b.__id__ }
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end
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def test_clear
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assert_nothing_raised { @tree.clear }
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assert_equal(0, @tree.number_of_nodes)
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assert_equal(0, @tree.number_of_edges)
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end
|
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|
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def test_nodes
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nodes = @nodes.sort(&@by_id)
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assert_equal(nodes, @tree.nodes.sort(&@by_id))
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end
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def test_number_of_nodes
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assert_equal(7, @tree.number_of_nodes)
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end
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def test_each_node
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@tree.each_node do |x|
|
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assert_not_nil(@nodes.delete(x))
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end
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assert_equal(true, @nodes.empty?)
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end
|
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|
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def test_each_edge
|
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@tree.each_edge do |source, target, edge|
|
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assert_not_nil(@edges.delete([ source, target, edge ]))
|
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end
|
239
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assert_equal(true, @edges.empty?)
|
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end
|
241
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|
242
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def test_edges
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edges = @edges.sort { |a, b| a[-1].distance <=> b[-1].distance }
|
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assert_equal(edges,
|
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@tree.edges.sort {
|
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|a, b| a[-1].distance <=> b[-1].distance })
|
247
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end
|
248
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|
249
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def test_number_of_edges
|
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assert_equal(@edges.size, @tree.number_of_edges)
|
251
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+
end
|
252
|
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|
253
|
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def test_adjacent_nodes
|
254
|
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assert_equal([ @rodents ], @tree.adjacent_nodes(@mouse))
|
255
|
+
assert_equal([ @rodents ], @tree.adjacent_nodes(@rat))
|
256
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assert_equal([ @primates ], @tree.adjacent_nodes(@human))
|
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assert_equal([ @primates ], @tree.adjacent_nodes(@chimpanzee))
|
258
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assert_equal([ @mouse, @rat, @mammals ].sort(&@by_id),
|
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@tree.adjacent_nodes(@rodents).sort(&@by_id))
|
260
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assert_equal([ @human, @chimpanzee, @mammals ].sort(&@by_id),
|
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@tree.adjacent_nodes(@primates).sort(&@by_id))
|
262
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assert_equal([ @rodents, @primates ].sort(&@by_id),
|
263
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@tree.adjacent_nodes(@mammals).sort(&@by_id))
|
264
|
+
end
|
265
|
+
|
266
|
+
def test_adjacent_nodes_nonexistent
|
267
|
+
# test for not existed nodes
|
268
|
+
assert_equal([], @tree.adjacent_nodes(Bio::Tree::Node.new))
|
269
|
+
end
|
270
|
+
|
271
|
+
def test_out_edges
|
272
|
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assert_equal([[ @mouse, @rodents, @edge_rodents_mouse ]],
|
273
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+
@tree.out_edges(@mouse))
|
274
|
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assert_equal([[ @rat, @rodents, @edge_rodents_rat ]],
|
275
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+
@tree.out_edges(@rat))
|
276
|
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assert_equal([[ @human, @primates, @edge_primates_human ]],
|
277
|
+
@tree.out_edges(@human))
|
278
|
+
assert_equal([[ @chimpanzee, @primates, @edge_primates_chimpanzee ]],
|
279
|
+
@tree.out_edges(@chimpanzee))
|
280
|
+
end
|
281
|
+
|
282
|
+
def test_out_edges_rodents
|
283
|
+
adjacents = [ @mouse, @rat, @mammals ]
|
284
|
+
edges = [ @edge_rodents_mouse, @edge_rodents_rat, @edge_mammals_rodents ]
|
285
|
+
@tree.out_edges(@rodents).each do |a|
|
286
|
+
assert_equal(@rodents, a[0])
|
287
|
+
assert_not_nil(i = adjacents.index(a[1]))
|
288
|
+
assert_equal(edges[i], a[2])
|
289
|
+
adjacents.delete_at(i)
|
290
|
+
edges.delete_at(i)
|
291
|
+
end
|
292
|
+
assert_equal(true, adjacents.empty?)
|
293
|
+
assert_equal(true, edges.empty?)
|
294
|
+
end
|
295
|
+
|
296
|
+
def test_out_edges_primates
|
297
|
+
adjacents = [ @human, @chimpanzee, @mammals ]
|
298
|
+
edges = [ @edge_primates_human, @edge_primates_chimpanzee,
|
299
|
+
@edge_mammals_primates ]
|
300
|
+
@tree.out_edges(@primates).each do |a|
|
301
|
+
assert_equal(@primates, a[0])
|
302
|
+
assert_not_nil(i = adjacents.index(a[1]))
|
303
|
+
assert_equal(edges[i], a[2])
|
304
|
+
adjacents.delete_at(i)
|
305
|
+
edges.delete_at(i)
|
306
|
+
end
|
307
|
+
assert_equal(true, adjacents.empty?)
|
308
|
+
assert_equal(true, edges.empty?)
|
309
|
+
end
|
310
|
+
|
311
|
+
def test_out_edges_mammals
|
312
|
+
adjacents = [ @rodents, @primates ]
|
313
|
+
edges = [ @edge_mammals_rodents, @edge_mammals_primates ]
|
314
|
+
@tree.out_edges(@mammals).each do |a|
|
315
|
+
assert_equal(@mammals, a[0])
|
316
|
+
assert_not_nil(i = adjacents.index(a[1]))
|
317
|
+
assert_equal(edges[i], a[2])
|
318
|
+
adjacents.delete_at(i)
|
319
|
+
edges.delete_at(i)
|
320
|
+
end
|
321
|
+
assert_equal(true, adjacents.empty?)
|
322
|
+
assert_equal(true, edges.empty?)
|
323
|
+
end
|
324
|
+
|
325
|
+
def test_out_edges_nonexistent
|
326
|
+
# test for not existed nodes
|
327
|
+
assert_equal([], @tree.out_edges(Bio::Tree::Node.new))
|
328
|
+
end
|
329
|
+
|
330
|
+
def test_each_out_edge
|
331
|
+
flag = nil
|
332
|
+
r = @tree.each_out_edge(@mouse) do |src, tgt, edge|
|
333
|
+
assert_equal(@mouse, src)
|
334
|
+
assert_equal(@rodents, tgt)
|
335
|
+
assert_equal(@edge_rodents_mouse, edge)
|
336
|
+
flag = true
|
337
|
+
end
|
338
|
+
assert_equal(@tree, r)
|
339
|
+
assert_equal(true, flag)
|
340
|
+
end
|
341
|
+
|
342
|
+
def test_each_out_edge_rat
|
343
|
+
flag = nil
|
344
|
+
r = @tree.each_out_edge(@rat) do |src, tgt, edge|
|
345
|
+
assert_equal(@rat, src)
|
346
|
+
assert_equal(@rodents, tgt)
|
347
|
+
assert_equal(@edge_rodents_rat, edge)
|
348
|
+
flag = true
|
349
|
+
end
|
350
|
+
assert_equal(@tree, r)
|
351
|
+
assert_equal(true, flag)
|
352
|
+
end
|
353
|
+
|
354
|
+
def test_each_out_edge_human
|
355
|
+
flag = nil
|
356
|
+
r = @tree.each_out_edge(@human) do |src, tgt, edge|
|
357
|
+
assert_equal(@human, src)
|
358
|
+
assert_equal(@primates, tgt)
|
359
|
+
assert_equal(@edge_primates_human, edge)
|
360
|
+
flag = true
|
361
|
+
end
|
362
|
+
assert_equal(@tree, r)
|
363
|
+
assert_equal(true, flag)
|
364
|
+
end
|
365
|
+
|
366
|
+
def test_each_out_edge_chimpanzee
|
367
|
+
flag = nil
|
368
|
+
r = @tree.each_out_edge(@chimpanzee) do |src, tgt, edge|
|
369
|
+
assert_equal(@chimpanzee, src)
|
370
|
+
assert_equal(@primates, tgt)
|
371
|
+
assert_equal(@edge_primates_chimpanzee, edge)
|
372
|
+
flag = true
|
373
|
+
end
|
374
|
+
assert_equal(@tree, r)
|
375
|
+
assert_equal(true, flag)
|
376
|
+
end
|
377
|
+
|
378
|
+
def test_each_out_edge_rodents
|
379
|
+
adjacents = [ @mouse, @rat, @mammals ]
|
380
|
+
edges = [ @edge_rodents_mouse, @edge_rodents_rat, @edge_mammals_rodents ]
|
381
|
+
@tree.each_out_edge(@rodents) do |src, tgt, edge|
|
382
|
+
assert_equal(@rodents, src)
|
383
|
+
assert_not_nil(i = adjacents.index(tgt))
|
384
|
+
assert_equal(edges[i], edge)
|
385
|
+
adjacents.delete_at(i)
|
386
|
+
edges.delete_at(i)
|
387
|
+
end
|
388
|
+
assert_equal(true, adjacents.empty?)
|
389
|
+
assert_equal(true, edges.empty?)
|
390
|
+
end
|
391
|
+
|
392
|
+
def test_each_out_edge_primates
|
393
|
+
adjacents = [ @human, @chimpanzee, @mammals ]
|
394
|
+
edges = [ @edge_primates_human, @edge_primates_chimpanzee,
|
395
|
+
@edge_mammals_primates ]
|
396
|
+
@tree.each_out_edge(@primates) do |src, tgt, edge|
|
397
|
+
assert_equal(@primates, src)
|
398
|
+
assert_not_nil(i = adjacents.index(tgt))
|
399
|
+
assert_equal(edges[i], edge)
|
400
|
+
adjacents.delete_at(i)
|
401
|
+
edges.delete_at(i)
|
402
|
+
end
|
403
|
+
assert_equal(true, adjacents.empty?)
|
404
|
+
assert_equal(true, edges.empty?)
|
405
|
+
end
|
406
|
+
|
407
|
+
def test_each_out_edge_mammals
|
408
|
+
adjacents = [ @rodents, @primates ]
|
409
|
+
edges = [ @edge_mammals_rodents, @edge_mammals_primates ]
|
410
|
+
@tree.each_out_edge(@mammals) do |src, tgt, edge|
|
411
|
+
assert_equal(@mammals, src)
|
412
|
+
assert_not_nil(i = adjacents.index(tgt))
|
413
|
+
assert_equal(edges[i], edge)
|
414
|
+
adjacents.delete_at(i)
|
415
|
+
edges.delete_at(i)
|
416
|
+
end
|
417
|
+
assert_equal(true, adjacents.empty?)
|
418
|
+
assert_equal(true, edges.empty?)
|
419
|
+
end
|
420
|
+
|
421
|
+
def test_each_out_edge_nonexistent
|
422
|
+
# test for not existed nodes
|
423
|
+
flag = nil
|
424
|
+
node = Bio::Tree::Node.new
|
425
|
+
r = @tree.each_out_edge(node) do |src, tgt, edge|
|
426
|
+
flag = true
|
427
|
+
end
|
428
|
+
assert_equal(@tree, r)
|
429
|
+
assert_equal(nil, flag)
|
430
|
+
end
|
431
|
+
|
432
|
+
def test_out_degree
|
433
|
+
assert_equal(1, @tree.out_degree(@mouse))
|
434
|
+
assert_equal(1, @tree.out_degree(@rat))
|
435
|
+
assert_equal(3, @tree.out_degree(@rodents))
|
436
|
+
assert_equal(1, @tree.out_degree(@human))
|
437
|
+
assert_equal(1, @tree.out_degree(@chimpanzee))
|
438
|
+
assert_equal(3, @tree.out_degree(@primates))
|
439
|
+
assert_equal(2, @tree.out_degree(@mammals))
|
440
|
+
end
|
441
|
+
|
442
|
+
def test_out_degree_nonexistent
|
443
|
+
assert_equal(0, @tree.out_degree(Bio::Tree::Node.new))
|
444
|
+
end
|
445
|
+
|
446
|
+
def test_get_edge
|
447
|
+
assert_not_nil(@tree.get_edge(@rodents, @mouse))
|
448
|
+
assert_not_nil(@tree.get_edge(@mouse, @rodents))
|
449
|
+
assert_equal(@edge_rodents_mouse, @tree.get_edge(@rodents, @mouse))
|
450
|
+
assert_equal(@edge_rodents_mouse, @tree.get_edge(@mouse, @rodents))
|
451
|
+
|
452
|
+
assert_not_nil(@tree.get_edge(@rodents, @rat))
|
453
|
+
assert_not_nil(@tree.get_edge(@rat, @rodents))
|
454
|
+
assert_equal(@edge_rodents_rat, @tree.get_edge(@rodents, @rat))
|
455
|
+
assert_equal(@edge_rodents_rat, @tree.get_edge(@rat, @rodents))
|
456
|
+
|
457
|
+
assert_not_nil(@tree.get_edge(@mammals, @rodents))
|
458
|
+
assert_not_nil(@tree.get_edge(@rodents, @mammals))
|
459
|
+
assert_equal(@edge_mammals_rodents, @tree.get_edge(@mammals, @rodents))
|
460
|
+
assert_equal(@edge_mammals_rodents, @tree.get_edge(@rodents, @mammals))
|
461
|
+
|
462
|
+
assert_not_nil(@tree.get_edge(@primates, @human))
|
463
|
+
assert_not_nil(@tree.get_edge(@human, @primates))
|
464
|
+
assert_equal(@edge_primates_human, @tree.get_edge(@primates, @human))
|
465
|
+
assert_equal(@edge_primates_human, @tree.get_edge(@human, @primates))
|
466
|
+
|
467
|
+
assert_not_nil(@tree.get_edge(@primates, @chimpanzee))
|
468
|
+
assert_not_nil(@tree.get_edge(@chimpanzee, @primates))
|
469
|
+
assert_equal(@edge_primates_chimpanzee, @tree.get_edge(@primates, @chimpanzee))
|
470
|
+
assert_equal(@edge_primates_chimpanzee, @tree.get_edge(@chimpanzee, @primates))
|
471
|
+
|
472
|
+
assert_not_nil(@tree.get_edge(@mammals, @primates))
|
473
|
+
assert_not_nil(@tree.get_edge(@primates, @mammals))
|
474
|
+
assert_equal(@edge_mammals_primates, @tree.get_edge(@mammals, @primates))
|
475
|
+
assert_equal(@edge_mammals_primates, @tree.get_edge(@primates, @mammals))
|
476
|
+
end
|
477
|
+
|
478
|
+
def test_get_edge_indirect
|
479
|
+
assert_nil(@tree.get_edge(@mouse, @rat))
|
480
|
+
assert_nil(@tree.get_edge(@human, @chimpanzee))
|
481
|
+
end
|
482
|
+
|
483
|
+
def test_get_edge_nonexistent
|
484
|
+
assert_nil(@tree.get_edge(@mouse, Bio::Tree::Node.new))
|
485
|
+
end
|
486
|
+
|
487
|
+
def test_get_node_by_name
|
488
|
+
assert_not_nil(@tree.get_node_by_name('mouse'))
|
489
|
+
assert_not_nil(@tree.get_node_by_name('rat'))
|
490
|
+
assert_not_nil(@tree.get_node_by_name('human'))
|
491
|
+
assert_not_nil(@tree.get_node_by_name('chimpanzee'))
|
492
|
+
assert_equal(@mouse, @tree.get_node_by_name('mouse'))
|
493
|
+
assert_equal(@rat, @tree.get_node_by_name('rat'))
|
494
|
+
assert_equal(@human, @tree.get_node_by_name('human'))
|
495
|
+
assert_equal(@chimpanzee, @tree.get_node_by_name('chimpanzee'))
|
496
|
+
end
|
497
|
+
|
498
|
+
def test_get_node_by_name_noexistent
|
499
|
+
assert_nil(@tree.get_node_by_name('frog'))
|
500
|
+
end
|
501
|
+
|
502
|
+
def test_add_edge
|
503
|
+
amphibian = Bio::Tree::Node.new('amphibian')
|
504
|
+
edge = Bio::Tree::Edge.new(0.3123)
|
505
|
+
assert_equal(edge, @tree.add_edge(@mammals, amphibian, edge))
|
506
|
+
|
507
|
+
frog = Bio::Tree::Node.new('frog')
|
508
|
+
newt = Bio::Tree::Node.new('newt')
|
509
|
+
assert_instance_of(Bio::Tree::Edge, @tree.add_edge(frog, newt))
|
510
|
+
end
|
511
|
+
|
512
|
+
def test_add_node
|
513
|
+
frog = Bio::Tree::Node.new('frog')
|
514
|
+
# the node does not exist
|
515
|
+
assert_nil(@tree.get_node_by_name('frog'))
|
516
|
+
assert_equal(false, @tree.include?(frog))
|
517
|
+
# add node
|
518
|
+
assert_equal(@tree, @tree.add_node(frog))
|
519
|
+
# the node exists
|
520
|
+
assert_equal(frog, @tree.get_node_by_name('frog'))
|
521
|
+
assert_equal(true, @tree.include?(frog))
|
522
|
+
end
|
523
|
+
|
524
|
+
def test_include?
|
525
|
+
assert_equal(true, @tree.include?(@mouse))
|
526
|
+
assert_equal(true, @tree.include?(@rat))
|
527
|
+
assert_equal(true, @tree.include?(@rodents))
|
528
|
+
assert_equal(true, @tree.include?(@human))
|
529
|
+
assert_equal(true, @tree.include?(@chimpanzee))
|
530
|
+
assert_equal(true, @tree.include?(@primates))
|
531
|
+
assert_equal(true, @tree.include?(@mammals))
|
532
|
+
end
|
533
|
+
|
534
|
+
def test_include_nonexistent
|
535
|
+
assert_equal(false, @tree.include?(Bio::Tree::Node.new))
|
536
|
+
end
|
537
|
+
|
538
|
+
def test_clear_node
|
539
|
+
assert_equal(2, @tree.out_degree(@mammals))
|
540
|
+
# clear node
|
541
|
+
assert_equal(@tree, @tree.clear_node(@mammals))
|
542
|
+
# checks
|
543
|
+
assert_equal(true, @tree.include?(@mammals))
|
544
|
+
assert_equal(0, @tree.out_degree(@mammals))
|
545
|
+
assert_equal(2, @tree.out_degree(@rodents))
|
546
|
+
assert_equal(2, @tree.out_degree(@primates))
|
547
|
+
end
|
548
|
+
|
549
|
+
def test_clear_node_nonexistent
|
550
|
+
assert_raise(IndexError) { @tree.clear_node(Bio::Tree::Node.new) }
|
551
|
+
end
|
552
|
+
|
553
|
+
def test_remove_node
|
554
|
+
assert_equal(2, @tree.out_degree(@mammals))
|
555
|
+
# remove node
|
556
|
+
assert_equal(@tree, @tree.remove_node(@mammals))
|
557
|
+
# checks
|
558
|
+
assert_equal(false, @tree.include?(@mammals))
|
559
|
+
assert_equal(0, @tree.out_degree(@mammals))
|
560
|
+
assert_equal(2, @tree.out_degree(@rodents))
|
561
|
+
assert_equal(2, @tree.out_degree(@primates))
|
562
|
+
end
|
563
|
+
|
564
|
+
def test_remove_node_nonexistent
|
565
|
+
assert_raise(IndexError) { @tree.remove_node(Bio::Tree::Node.new) }
|
566
|
+
end
|
567
|
+
|
568
|
+
def test_remove_node_if
|
569
|
+
assert_equal(@tree, @tree.remove_node_if { |node| node == @mouse })
|
570
|
+
assert_equal(false, @tree.include?(@mouse))
|
571
|
+
end
|
572
|
+
|
573
|
+
def test_remove_node_if_false
|
574
|
+
ary = []
|
575
|
+
assert_equal(@tree, @tree.remove_node_if { |node| ary << node; false })
|
576
|
+
nodes = @nodes.sort(&@by_id)
|
577
|
+
assert_equal(nodes, ary.sort(&@by_id))
|
578
|
+
assert_equal(nodes, @tree.nodes.sort(&@by_id))
|
579
|
+
end
|
580
|
+
|
581
|
+
def test_remove_edge
|
582
|
+
assert_not_nil(@tree.get_edge(@mouse, @rodents))
|
583
|
+
assert_equal(@tree, @tree.remove_edge(@mouse, @rodents))
|
584
|
+
assert_nil(@tree.get_edge(@mouse, @rodents))
|
585
|
+
end
|
586
|
+
|
587
|
+
def test_remove_edge_nonexistent
|
588
|
+
assert_raise(IndexError) { @tree.remove_edge(@mouse, @rat) }
|
589
|
+
end
|
590
|
+
end #class TestTree2
|
591
|
+
|
592
|
+
end #module Bio
|
593
|
+
|