bio 1.0.0 → 1.1.0

data/test/unit/bio/db/embl/test_uniprot.rb

@@ -1,23 +1,10 @@
 #
 # test/unit/bio/db/embl/test_uniprot.rb - Unit test for Bio::UniProt
 #
-#   Copyright (C) 2005 Mitsuteru Nakao <n@bioruby.org>
+# Copyright::  Copyright (C) 2005 Mitsuteru Nakao <n@bioruby.org>
+# License::    The Ruby License
 #
-#  This library is free software; you can redistribute it and/or
-#  modify it under the terms of the GNU Lesser General Public
-#  License as published by the Free Software Foundation; either
-#  version 2 of the License, or (at your option) any later version.
-#
-#  This library is distributed in the hope that it will be useful,
-#  but WITHOUT ANY WARRANTY; without even the implied warranty of
-#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
-#  Lesser General Public License for more details.
-#
-#  You should have received a copy of the GNU Lesser General Public
-#  License along with this library; if not, write to the Free Software
-#  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307  USA
-#
-#  $Id: test_uniprot.rb,v 1.3 2005/12/18 17:43:51 nakao Exp $
+#  $Id: test_uniprot.rb,v 1.5 2007/04/05 23:35:43 trevor Exp $
 #
 
 require 'pathname'

data/test/unit/bio/db/kegg/test_genes.rb

@@ -1,23 +1,10 @@
 #
 # test/unit/bio/db/kegg/test_genes.rb - Unit test for Bio::KEGG::GENES
 #
-#   Copyright (C) 2005 Mitsuteru Nakao <n@bioruby.org>
+# Copyright::  Copyright (C) 2005 Mitsuteru Nakao <n@bioruby.org>
+# License::    The Ruby License
 #
-#  This library is free software; you can redistribute it and/or
-#  modify it under the terms of the GNU Lesser General Public
-#  License as published by the Free Software Foundation; either
-#  version 2 of the License, or (at your option) any later version.
-#
-#  This library is distributed in the hope that it will be useful,
-#  but WITHOUT ANY WARRANTY; without even the implied warranty of
-#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
-#  Lesser General Public License for more details.
-#
-#  You should have received a copy of the GNU Lesser General Public
-#  License along with this library; if not, write to the Free Software
-#  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307  USA
-#
-#  $Id: test_genes.rb,v 1.3 2005/11/09 13:20:09 nakao Exp $
+#  $Id: test_genes.rb,v 1.5 2007/04/05 23:35:43 trevor Exp $
 #
 
 require 'pathname'

data/test/unit/bio/db/pdb/test_pdb.rb

@@ -4,26 +4,9 @@
 # Copyright:: Copyright (C) 2006
 #             Naohisa Goto <ng@bioruby.org>
 #
-# License:: LGPL
-#
-#  $Id: test_pdb.rb,v 1.1 2006/01/26 16:06:03 ngoto Exp $
-#
-#--
-#  This library is free software; you can redistribute it and/or
-#  modify it under the terms of the GNU Lesser General Public
-#  License as published by the Free Software Foundation; either
-#  version 2 of the License, or (at your option) any later version.
-#
-#  This library is distributed in the hope that it will be useful,
-#  but WITHOUT ANY WARRANTY; without even the implied warranty of
-#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
-#  Lesser General Public License for more details.
-#
-#  You should have received a copy of the GNU Lesser General Public
-#  License along with this library; if not, write to the Free Software
-#  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307  USA
-#++
+# License:: The Ruby License
 #
+#  $Id: test_pdb.rb,v 1.3 2007/04/05 23:35:43 trevor Exp $
 #
 
 require 'pathname'
@@ -57,7 +40,7 @@ module Bio
       end
 
       def test_name
-        assert_equal(' CG2', @atom.name)
+        assert_equal('CG2', @atom.name)
       end
 
       def test_altLoc
@@ -77,7 +60,7 @@ module Bio
       end
 
       def test_iCode
-        assert_equal(' ', @atom.iCode)
+        assert_equal('', @atom.iCode)
       end
 
       def test_x
@@ -101,15 +84,15 @@ module Bio
       end
 
       def test_segID
-        assert_equal('A1  ', @atom.segID)
+        assert_equal('A1', @atom.segID)
       end
 
       def test_element
-        assert_equal(' C', @atom.element)
+        assert_equal('C', @atom.element)
       end
 
       def test_charge
-        assert_equal('  ', @atom.charge)
+        assert_equal('', @atom.charge)
       end
 
       def test_xyz

data/test/unit/bio/db/test_aaindex.rb

@@ -3,9 +3,9 @@
 #
 # Copyright::  Copyright (C) 2006 
 #              Mitsuteru C. Nakao <n@bioruby.org>
-# License::    Ruby's
+# License::    The Ruby License
 #
-# $Id: test_aaindex.rb,v 1.3 2006/02/22 07:35:19 nakao Exp $
+# $Id: test_aaindex.rb,v 1.4 2007/04/05 23:35:43 trevor Exp $
 #
 
 require 'pathname'

data/test/unit/bio/db/test_fasta.rb

@@ -1,23 +1,10 @@
 #
 # test/unit/bio/db/test_fasta.rb - Unit test for Bio::FastaFormat
 #
-#   Copyright (C) 2005 Mitsuteru Nakao <n@bioruby.org>
+# Copyright::  Copyright (C) 2005 Mitsuteru Nakao <n@bioruby.org>
+# License::    The Ruby License
 #
-#  This library is free software; you can redistribute it and/or
-#  modify it under the terms of the GNU Lesser General Public
-#  License as published by the Free Software Foundation; either
-#  version 2 of the License, or (at your option) any later version.
-#
-#  This library is distributed in the hope that it will be useful,
-#  but WITHOUT ANY WARRANTY; without even the implied warranty of
-#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
-#  Lesser General Public License for more details.
-#
-#  You should have received a copy of the GNU Lesser General Public
-#  License along with this library; if not, write to the Free Software
-#  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307  USA
-#
-#  $Id: test_fasta.rb,v 1.3 2005/12/18 17:55:13 k Exp $
+#  $Id: test_fasta.rb,v 1.5 2007/04/05 23:35:43 trevor Exp $
 #
 
 require 'pathname'

data/test/unit/bio/db/test_gff.rb

@@ -1,23 +1,10 @@
 #
 # test/unit/bio/db/test_gff.rb - Unit test for Bio::GFF
 #
-#   Copyright (C) 2005 Mitsuteru Nakao <n@bioruby.org>
+# Copyright::   Copyright (C) 2005 Mitsuteru Nakao <n@bioruby.org>
+# License::     The Ruby License
 #
-#  This library is free software; you can redistribute it and/or
-#  modify it under the terms of the GNU Lesser General Public
-#  License as published by the Free Software Foundation; either
-#  version 2 of the License, or (at your option) any later version.
-#
-#  This library is distributed in the hope that it will be useful,
-#  but WITHOUT ANY WARRANTY; without even the implied warranty of
-#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
-#  Lesser General Public License for more details.
-#
-#  You should have received a copy of the GNU Lesser General Public
-#  License along with this library; if not, write to the Free Software
-#  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307  USA
-#
-#  $Id: test_gff.rb,v 1.4 2005/12/19 01:21:42 k Exp $
+#  $Id: test_gff.rb,v 1.6 2007/04/05 23:35:43 trevor Exp $
 #
 
 require 'pathname'

data/test/unit/bio/db/test_lasergene.rb

@@ -0,0 +1,95 @@
+#
+# test/unit/bio/db/test_rebase.rb - Unit test for Bio::Lasergene
+#
+# Author::    Trevor Wennblom  <mailto:trevor@corevx.com>
+# Copyright:: Copyright (c) 2007 Center for Biomedical Research Informatics, University of Minnesota (http://cbri.umn.edu)
+# License::   The Ruby License
+#
+#  $Id: test_lasergene.rb,v 1.2 2007/04/05 23:35:43 trevor Exp $
+#
+
+require 'pathname'
+libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4, 'lib')).cleanpath.to_s
+$:.unshift(libpath) unless $:.include?(libpath)
+
+require 'test/unit'
+require 'bio'
+require 'bio/db/lasergene'
+
+module Bio #:nodoc:
+  class TestLasergene < Test::Unit::TestCase #:nodoc:
+    
+    def setup
+      file_format_1 = <<END
+"Contig 1" (1,934)
+  Contig Length:                  934 bases
+  Average Length/Sequence:        467 bases
+  Total Sequence Length:         1869 bases
+  Top Strand:                       2 sequences
+  Bottom Strand:                    2 sequences
+  Total:                            4 sequences
+^^
+ATGACGTATCCAAAGAGGCGTTACCGGAGAAGAAGACACCGCCCCCGCAGTCCTCTTGGCCAGATCCTCCGCCGCCGCCCCTGGCTCGTCCACCCCCGCCACAGTTACCGCTGGAGAAGGAAAAATGGCATCTTCAWCACCCGCCTATCCCGCAYCTTCGGAWRTACTATCAAGCGAACCACAGTCAGAACGCCCTCCTGGGCGGTGGACATGATGAGATTCAATATTAATGACTTTCTTCCCCCAGGAGGGGGCTCAAACCCCCGCTCTGTGCCCTTTGAATACTACAGAATAAGAAAGGTTAAGGTTGAATTCTGGCCCTGCTCCCCGATCACCCAGGGTGACAGGGGAATGGGCTCCAGTGCTGWTATTCTAGMTGATRRCTTKGTAACAAAGRCCACAGCCCTCACCTATGACCCCTATGTAAACTTCTCCTCCCGCCATACCATAACCCAGCCCTTCTCCTACCRCTCCCGYTACTTTACCCCCAAACCTGTCCTWGATKCCACTATKGATKACTKCCAACCAAACAACAAAAGAAACCAGCTGTGGSTGAGACTACAWACTGCTGGAAATGTAGACCWCGTAGGCCTSGGCACTGCGTKCGAAAACAGTATATACGACCAGGAATACAATATCCGTGTMACCATGTATGTACAATTCAGAGAATTTAATCTTAAAGACCCCCCRCTTMACCCKTAATGAATAATAAMAACCATTACGAAGTGATAAAAWAGWCTCAGTAATTTATTYCATATGGAAATTCWSGGCATGGGGGGGAAAGGGTGACGAACKKGCCCCCTTCCTCCSTSGMYTKTTCYGTAGCATTCYTCCAMAAYACCWAGGCAGYAMTCCTCCSATCAAGAGcYTSYACAGCTGGGACAGCAGTTGAGGAGGACCATTCAAAGGGGGTCGGATTGCTGGTAATCAGA
+END
+
+      file_format_2 = <<END
+^^:                                  350,935
+Contig 1 (1,935)
+  Contig Length:                  935 bases
+  Average Length/Sequence:        580 bases
+  Total Sequence Length:         2323 bases
+  Top Strand:                       2 sequences
+  Bottom Strand:                    2 sequences
+  Total:                            4 sequences
+^^
+ATGTCGGGGAAATGCTTGACCGCGGGCTACTGCTCATCATTGCTTTCTTTGTGGTATATCGTGCCGTTCTGTTTTGCTGTGCTCGTCAACGCCAGCGGCGACAGCAGCTCTCATTTTCAGTCGATTTATAACTTGACGTTATGTGAGCTGAATGGCACGAACTGGCTGGCAGACAACTTTAACTGGGCTGTGGAGACTTTTGTCATCTTCCCCGTGTTGACTCACATTGTTTCCTATGGTGCACTCACTACCAGTCATTTTCTTGACACAGTTGGTCTAGTTACTGTGTCTACCGCCGGGTTTTATCACGGGCGGTACGTCTTGAGTAGCATCTACGCGGTCTGTGCTCTGGCTGCGTTGATTTGCTTCGCCATCAGGTTTGCGAAGAACTGCATGTCCTGGCGCTACTCTTGCACTAGATACACCAACTTCCTCCTGGACACCAAGGGCAGACTCTATCGTTGGCGGTCGCCTGTCATCATAGAGAAAGGGGGTAAGGTTGAGGTCGAAGGTCATCTGATCGATCTCAAAAGAGTTGTGCTTGATGGCTCTGTGGCGACACCTTTAACCAGAGTTTCAGCGGAACAATGGGGTCGTCCCTAGACGACTTTTGCCATGATAGTACAGCCCCACAGAAGGTGCTCTTGGCGTTTTCCATCACCTACACGCCAGTGATGATATATGCCCTAAAGGTAAGCCGCGGCCGACTTTTGGGGCTTCTGCACCTTTTGATTTTTTTGAACTGTGCCTTTACTTTCGGGTACATGACATTCGTGCACTTTCGGAGCACGAACAAGGTCGCGCTCACTATGGGAGCAGTAGTCGCACTCCTTTGGGGGGTGTACTCAGCCATAGAAACCTGGAAATTCATCACCTCCAGATGCCGTTGTGCTTGCTAGGCCGCAAGTACATTCTGGCCCCTGCCCACCACGTTG
+END
+
+      file_format_3 = <<END
+LOCUS       PRU87392               15411 bp    RNA     linear   VRL 17-NOV-2000
+DEFINITION  Porcine reproductive and respiratory syndrome virus strain VR-2332,
+            complete genome.
+ACCESSION   U87392 AF030244 U00153
+VERSION     U87392.3  GI:11192298
+[...cut...]
+     3'UTR           15261..15411
+     polyA_site      15409
+ORIGIN      
+^^
+atgacgtataggtgttggctctatgccttggcatttgtattgtcaggagctgtgaccattggcacagcccaaaacttgctgcacagaaacacccttctgtgatagcctccttcaggggagcttagggtttgtccctagcaccttgcttccggagttgcactgctttacggtctctccacccctttaaccatgtctgggatacttgatcggtgcacgtgtacccccaatgccagggtgtttatggcggagggccaagtctactgcacacgatgcctcagtgcacggtctctccttcccctgaacctccaagtttctgagctcggggtgctaggcctattctacaggcccgaagagccactccggtggacgttgccacgtgcattccccactgttgagtgctcccccgccggggcctgctggctttctgcaatctttccaatcgcacgaatgaccagtggaaacctgaacttccaacaaagaatggtacgggtcgcagctgagctttacagagccggccagctcacccctgcagtcttgaaggctctacaagtttatgaacggggttgccgctggtaccccattgttggacctgtccctggagtggccgttttcgccaattccctacatgtgagtgataaacctttcccgggagcaactcacgtgttgaccaacctgccgctcccgcagagacccaagcctgaagacttttgcccctttgagtgtgctatggctactgtctatgacattggtcatgacgccgtcatgtatgtggccgaaaggaaagtctcctgggcccctcgtggcggggatgaagtgaaatttgaagctgtccccggggagttgaagttgattgcgaaccggctccgcacctccttcccgccccaccacacagtggacatgtctaagttcgccttcacagcccctgggtgtggtgtttctatgcgggtcgaacgccaacacggctgccttcccgctgacactgtccctgaaggcaactgctggtggagcttgtttgacttgcttccactggaagttcagaacaaagaaattcgccatgctaaccaatttggctaccagaccaagcatggtgtctctggcaagtacctacagcggaggctgca
+END
+
+      @lc = Bio::Lasergene
+      @obj1 = @lc.new(file_format_1)
+      @obj2 = @lc.new(file_format_2)
+      @obj3 = @lc.new(file_format_3)
+    end
+
+    def test_methods
+      a1 = @obj1
+      a1_seq = 'atgacgtatccaaagaggcgttaccggagaagaagacaccgcccccgcagtcctcttggccagatcctccgccgccgcccctggctcgtccacccccgccacagttaccgctggagaaggaaaaatggcatcttcawcacccgcctatcccgcaycttcggawrtactatcaagcgaaccacagtcagaacgccctcctgggcggtggacatgatgagattcaatattaatgactttcttcccccaggagggggctcaaacccccgctctgtgccctttgaatactacagaataagaaaggttaaggttgaattctggccctgctccccgatcacccagggtgacaggggaatgggctccagtgctgwtattctagmtgatrrcttkgtaacaaagrccacagccctcacctatgacccctatgtaaacttctcctcccgccataccataacccagcccttctcctaccrctcccgytactttacccccaaacctgtcctwgatkccactatkgatkactkccaaccaaacaacaaaagaaaccagctgtggstgagactacawactgctggaaatgtagaccwcgtaggcctsggcactgcgtkcgaaaacagtatatacgaccaggaatacaatatccgtgtmaccatgtatgtacaattcagagaatttaatcttaaagaccccccrcttmacccktaatgaataataamaaccattacgaagtgataaaawagwctcagtaatttattycatatggaaattcwsggcatgggggggaaagggtgacgaackkgcccccttcctccstsgmytkttcygtagcattcytccamaayaccwaggcagyamtcctccsatcaagagcytsyacagctgggacagcagttgaggaggaccattcaaagggggtcggattgctggtaatcaga'
+      a2 = @obj2
+      a2_seq = 'atgtcggggaaatgcttgaccgcgggctactgctcatcattgctttctttgtggtatatcgtgccgttctgttttgctgtgctcgtcaacgccagcggcgacagcagctctcattttcagtcgatttataacttgacgttatgtgagctgaatggcacgaactggctggcagacaactttaactgggctgtggagacttttgtcatcttccccgtgttgactcacattgtttcctatggtgcactcactaccagtcattttcttgacacagttggtctagttactgtgtctaccgccgggttttatcacgggcggtacgtcttgagtagcatctacgcggtctgtgctctggctgcgttgatttgcttcgccatcaggtttgcgaagaactgcatgtcctggcgctactcttgcactagatacaccaacttcctcctggacaccaagggcagactctatcgttggcggtcgcctgtcatcatagagaaagggggtaaggttgaggtcgaaggtcatctgatcgatctcaaaagagttgtgcttgatggctctgtggcgacacctttaaccagagtttcagcggaacaatggggtcgtccctagacgacttttgccatgatagtacagccccacagaaggtgctcttggcgttttccatcacctacacgccagtgatgatatatgccctaaaggtaagccgcggccgacttttggggcttctgcaccttttgatttttttgaactgtgcctttactttcgggtacatgacattcgtgcactttcggagcacgaacaaggtcgcgctcactatgggagcagtagtcgcactcctttggggggtgtactcagccatagaaacctggaaattcatcacctccagatgccgttgtgcttgctaggccgcaagtacattctggcccctgcccaccacgttg'
+      a3 = @obj3
+      a3_seq = 'atgacgtataggtgttggctctatgccttggcatttgtattgtcaggagctgtgaccattggcacagcccaaaacttgctgcacagaaacacccttctgtgatagcctccttcaggggagcttagggtttgtccctagcaccttgcttccggagttgcactgctttacggtctctccacccctttaaccatgtctgggatacttgatcggtgcacgtgtacccccaatgccagggtgtttatggcggagggccaagtctactgcacacgatgcctcagtgcacggtctctccttcccctgaacctccaagtttctgagctcggggtgctaggcctattctacaggcccgaagagccactccggtggacgttgccacgtgcattccccactgttgagtgctcccccgccggggcctgctggctttctgcaatctttccaatcgcacgaatgaccagtggaaacctgaacttccaacaaagaatggtacgggtcgcagctgagctttacagagccggccagctcacccctgcagtcttgaaggctctacaagtttatgaacggggttgccgctggtaccccattgttggacctgtccctggagtggccgttttcgccaattccctacatgtgagtgataaacctttcccgggagcaactcacgtgttgaccaacctgccgctcccgcagagacccaagcctgaagacttttgcccctttgagtgtgctatggctactgtctatgacattggtcatgacgccgtcatgtatgtggccgaaaggaaagtctcctgggcccctcgtggcggggatgaagtgaaatttgaagctgtccccggggagttgaagttgattgcgaaccggctccgcacctccttcccgccccaccacacagtggacatgtctaagttcgccttcacagcccctgggtgtggtgtttctatgcgggtcgaacgccaacacggctgccttcccgctgacactgtccctgaaggcaactgctggtggagcttgtttgacttgcttccactggaagttcagaacaaagaaattcgccatgctaaccaatttggctaccagaccaagcatggtgtctctggcaagtacctacagcggaggctgca'
+      
+      assert_equal(a1_seq, a1.seq.seq)
+      assert_equal(a2_seq, a2.seq.seq)
+      assert_equal(a3_seq, a3.seq.seq)
+      
+      assert_equal('"Contig 1"', a1.entry_id)
+      assert_equal('Contig 1', a2.name)
+      assert_equal(nil, a3.name)
+      
+      assert_equal(4, a1.total_sequences)
+      assert_equal(4, a2.total_sequences)
+      assert_equal(nil, a3.total_sequences)
+
+      assert_equal(true, a1.standard_comment?)
+      assert_equal(true, a2.standard_comment?)
+      assert_equal(false, a3.standard_comment?) 
+    end
+
+  end
+
+end

data/test/unit/bio/db/test_newick.rb

@@ -0,0 +1,56 @@
+#
+# = test/bio/db/newick.rb - Unit test for Bio::Newick
+#
+# Copyright::   Copyright (C) 2004-2006
+#               Daniel Amelang <dan@amelang.net>
+#               Naohisa Goto <ng@bioruby.org>
+# License::     The Ruby License
+#
+# $Id: test_newick.rb,v 1.5 2007/04/05 23:35:43 trevor Exp $
+#
+
+require 'test/unit'
+
+require 'pathname'
+libpath = Pathname.new(File.join(File.dirname(__FILE__), [".."] * 4, "lib")).cleanpath.to_s
+$:.unshift(libpath) unless $:.include?(libpath)
+
+require 'bio'
+require 'bio/tree'
+require 'bio/db/newick'
+
+module Bio
+  class TestNewick < Test::Unit::TestCase
+
+    TREE_STRING = <<-END_OF_TREE_STRING
+    (
+      (
+        HexLEZ35:0.00263,
+        HexMCZ42:0.00788
+      ):0.00854,
+      (
+        HexFLZ48:0.00457,
+        (
+          HexFLZ83:0.00217,
+          HexFLZ13:0.00574
+        ):0.00100
+      ):0.04692,
+      HexLEZ73:0.00268
+    )[0.1250];
+    END_OF_TREE_STRING
+
+    def test_string_tree
+      newick = Bio::Newick.new(TREE_STRING)
+      tree = newick.tree
+      assert_equal(3, tree.children(tree.root).size)
+      assert_equal(9, tree.descendents(tree.root).size)
+      assert_equal(6, tree.leaves.size)
+      leaf = tree.get_node_by_name('HexFLZ83')
+      assert_equal(3, tree.ancestors(leaf).size)
+      assert_equal(tree.path(tree.root, leaf)[1], tree.ancestors(leaf)[1])
+      assert_equal(0.00217, tree.get_edge(leaf, tree.parent(leaf)).distance)
+      assert_equal("HexFLZ83", leaf.name)
+    end
+
+  end #class TestNewick
+end #module Bio

data/test/unit/bio/db/test_nexus.rb

@@ -0,0 +1,360 @@
+#
+# = test/bio/db/nexus.rb - Unit test for Bio::Nexus
+#
+# Copyright::  Copyright (C) 2006        Christian M Zmasek <cmzmasek@yahoo.com>
+#
+# License::     The Ruby License
+#
+# $Id: test_nexus.rb,v 1.2 2007/04/05 23:35:43 trevor Exp $
+#
+# == Description
+#
+# This file contains unit tests for Bio::Nexus.
+#
+
+require 'test/unit'
+require 'bio/db/nexus'
+
+module Bio
+  
+  class TestNexus < Test::Unit::TestCase
+
+    NEXUS_STRING_1 = <<-END_OF_NEXUS_STRING
+    #NEXUS
+    Begin Taxa;
+     Dimensions [[comment]] ntax=4;
+     TaxLabels "hag fish" [comment] 'african frog'
+     [lots of different comment follow]
+     [] [a] [[a]] [ a ] [[ a ]] [ [ a ] ] [a ]
+     [[a ]] [ [a ] ] [ a] [[ a]] [ [ a] ] [  ]
+     [[  ]] [ [  ] ] [ a b ] [[ a b ]] [ [ a b ] ]
+     [x[ x [x[ x[[x[[xx[x[  x]] ]x ] []]][x]]x]]]
+     
+     [comment_1 comment_3] "rat    snake" 'red
+     
+     
+     mouse';
+    End;
+    
+    [yet another comment End; ]
+   
+    Begin Characters;
+     Dimensions nchar=20
+                ntax=4;
+             [  ntax=1000; ]
+     Format DataType=DNA
+            Missing=x
+            Gap=- MatchChar=.;
+     Matrix [comment]
+     fish  ACATA GAGGG 
+                       TACCT CTAAG
+     frog  ACTTA GAGGC TACCT CTAGC
+     snake ACTCA CTGGG TACCT TTGCG
+     mouse ACTCA GACGG TACCT TTGCG;
+    End;
+    
+    Begin Trees;
+     [comment]
+     Tree best=(fish,(frog,(snake,mo
+                          use)));
+      [some long comment]                    
+     Tree
+     
+     other=(snake,
+     
+                     (frog,(fish,mo
+                           use
+                           )));
+    End;
+    
+    
+    
+    Begin Trees;
+     [comment]
+     Tree worst=(A,(B,(C,D
+                           )));
+     Tree bad=(a,
+   
+                      (b,(c ,  d
+                           )
+                           
+                           
+                           )     );
+    End; 
+  
+   
+    Begin Distances;
+     Dimensions nchar=20 ntax=5;
+     Format Triangle=Both;
+     Matrix
+     taxon_1 0.0 1.0
+             2.0 4.0 7.0
+     taxon_2 1.0
+             0.0 3.0 5.0 8.0
+     taxon_3 3.0 4.0 0.0 6.0 9.0
+     taxon_4 7.0 3.0 2.0 0.0 9.5
+     taxon_5 1.2 1.3 1.4 1.5 0.0;
+    End;
+  
+    Begin Data;
+     Dimensions ntax=5 nchar=14;
+     Format Datatype=RNA gap=# MISSING=x MatchChar=^;
+     TaxLabels ciona
+                 cow [comment1 commentX] ape
+               'purple urchin' "green lizard";
+     Matrix
+     [ comment [old comment] ]
+     taxon_1    A- CCGTCGA-GTTA
+     taxon_2 T- CCG-CGA-GATC
+     
+     taxon_3 A- C-GTCGA-GATG
+       
+       taxon_4                A-    C   C   TC   G
+         A  -     -G  T         T
+         
+         T
+         
+     taxon_5
+T-CGGTCGT-CTTA;
+    End;
+  
+    Begin Private1;
+     Something foo=5 bar=20;
+     Format Datatype=DNA;
+     Matrix
+      taxon_1 1111 1111111111
+      taxon_2 2222 2222222222
+      taxon_3 3333 3333333333
+      taxon_4 4444 4444444444
+      taxon_5 5555 5555555555;
+    End;
+    
+    Begin Private1;
+     some [boring]
+     interesting [
+      outdated
+     ] data be here
+    End;
+    
+    END_OF_NEXUS_STRING
+    
+    DATA_BLOCK_OUTPUT_STRING = <<-DATA_BLOCK_OUTPUT_STRING
+Begin Data;
+ Dimensions NTax=5 NChar=14;
+ Format DataType=RNA Missing=x Gap=# MatchChar=^;
+ TaxLabels ciona cow ape purple_urchin green_lizard;
+ Matrix
+ taxon_1     A-CCGTCGA-GTTA
+ taxon_2     T-CCG-CGA-GATC
+ taxon_3     A-C-GTCGA-GATG
+ taxon_4     A-CCTCGA--GTTT
+ taxon_5     T-CGGTCGT-CTTA;
+End;
+DATA_BLOCK_OUTPUT_STRING
+
+    def test_nexus
+      
+      nexus = Bio::Nexus.new( NEXUS_STRING_1 )
+      blocks = nexus.get_blocks
+      assert_equal( 8, blocks.size )
+      
+      private_blocks   = nexus.get_blocks_by_name( "private1" )  
+      data_blocks      = nexus.get_data_blocks
+      character_blocks = nexus.get_characters_blocks
+      trees_blocks     = nexus.get_trees_blocks
+      distances_blocks = nexus.get_distances_blocks
+      taxa_blocks      = nexus.get_taxa_blocks
+      
+      assert_equal( 2, private_blocks.size )
+      assert_equal( 1, data_blocks.size )
+      assert_equal( 1, character_blocks.size )
+      assert_equal( 2, trees_blocks.size )
+      assert_equal( 1, distances_blocks.size )
+      assert_equal( 1, taxa_blocks.size )
+      
+      taxa_block = taxa_blocks[ 0 ]
+      assert_equal( taxa_block.get_number_of_taxa.to_i , 4 )
+      assert_equal( taxa_block.get_taxa[ 0 ], "hag_fish" )
+      assert_equal( taxa_block.get_taxa[ 1 ], "african_frog" )
+      assert_equal( taxa_block.get_taxa[ 2 ], "rat_snake" )
+      assert_equal( taxa_block.get_taxa[ 3 ], "red_mouse" )
+      
+      chars_block = character_blocks[ 0 ]
+      assert_equal( chars_block.get_number_of_taxa.to_i, 4 )
+      assert_equal( chars_block.get_number_of_characters.to_i, 20 )
+      assert_equal( chars_block.get_datatype, "DNA" )
+      assert_equal( chars_block.get_match_character, "." )
+      assert_equal( chars_block.get_missing, "x" )
+      assert_equal( chars_block.get_gap_character, "-" )
+      assert_equal( chars_block.get_matrix.get_value( 0, 0 ), "fish" )
+      assert_equal( chars_block.get_matrix.get_value( 1, 0 ), "frog" )
+      assert_equal( chars_block.get_matrix.get_value( 2, 0 ), "snake" )
+      assert_equal( chars_block.get_matrix.get_value( 3, 0 ), "mouse" )
+      assert_equal( chars_block.get_matrix.get_value( 0, 20 ), "G" )
+      assert_equal( chars_block.get_matrix.get_value( 1, 20 ), "C" )
+      assert_equal( chars_block.get_matrix.get_value( 2, 20 ), "G" )
+      assert_equal( chars_block.get_matrix.get_value( 3, 20 ), "G" )
+      assert_equal( chars_block.get_characters_strings_by_name( "fish" )[ 0 ], "ACATAGAGGGTACCTCTAAG" ) 
+      assert_equal( chars_block.get_characters_strings_by_name( "frog" )[ 0 ], "ACTTAGAGGCTACCTCTAGC" ) 
+      assert_equal( chars_block.get_characters_strings_by_name( "snake" )[ 0 ], "ACTCACTGGGTACCTTTGCG" ) 
+      assert_equal( chars_block.get_characters_strings_by_name( "mouse" )[ 0 ], "ACTCAGACGGTACCTTTGCG" ) 
+      
+      assert_equal( chars_block.get_characters_string( 0 ), "ACATAGAGGGTACCTCTAAG" ) 
+      assert_equal( chars_block.get_characters_string( 1 ), "ACTTAGAGGCTACCTCTAGC" ) 
+      assert_equal( chars_block.get_characters_string( 2 ), "ACTCACTGGGTACCTTTGCG" ) 
+      assert_equal( chars_block.get_characters_string( 3 ), "ACTCAGACGGTACCTTTGCG" )
+      
+      assert_equal( chars_block.get_row_name( 1 ), "frog" )
+
+      assert_equal( chars_block.get_sequences_by_name( "fish" )[ 0 ].seq.to_s.downcase, "ACATAGAGGGTACCTCTAAG".downcase ) 
+      assert_equal( chars_block.get_sequences_by_name( "frog" )[ 0 ].seq.to_s.downcase, "ACTTAGAGGCTACCTCTAGC".downcase ) 
+      assert_equal( chars_block.get_sequences_by_name( "snake" )[ 0 ].seq.to_s.downcase, "ACTCACTGGGTACCTTTGCG".downcase ) 
+      assert_equal( chars_block.get_sequences_by_name( "mouse" )[ 0 ].seq.to_s.downcase, "ACTCAGACGGTACCTTTGCG".downcase ) 
+      
+      assert_equal( chars_block.get_sequences_by_name( "fish" )[ 0 ].definition, "fish" )
+      assert_equal( chars_block.get_sequences_by_name( "frog" )[ 0 ].definition, "frog" )
+      assert_equal( chars_block.get_sequences_by_name( "snake" )[ 0 ].definition, "snake" )
+      assert_equal( chars_block.get_sequences_by_name( "mouse" )[ 0 ].definition, "mouse" )
+      
+      assert_equal( chars_block.get_sequence( 0 ).seq.to_s.downcase, "ACATAGAGGGTACCTCTAAG".downcase ) 
+      assert_equal( chars_block.get_sequence( 1 ).seq.to_s.downcase, "ACTTAGAGGCTACCTCTAGC".downcase ) 
+      assert_equal( chars_block.get_sequence( 2 ).seq.to_s.downcase, "ACTCACTGGGTACCTTTGCG".downcase ) 
+      assert_equal( chars_block.get_sequence( 3 ).seq.to_s.downcase, "ACTCAGACGGTACCTTTGCG".downcase ) 
+
+      assert_equal( chars_block.get_sequence( 0 ).definition, "fish" ) 
+      assert_equal( chars_block.get_sequence( 1 ).definition, "frog" ) 
+      assert_equal( chars_block.get_sequence( 2 ).definition, "snake" ) 
+      assert_equal( chars_block.get_sequence( 3 ).definition, "mouse" ) 
+      
+      
+      tree_block_0 = trees_blocks[ 0 ]
+      tree_block_1 = trees_blocks[ 1 ]
+      assert_equal( tree_block_0.get_tree_names[ 0 ], "best" )
+      assert_equal( tree_block_0.get_tree_names[ 1 ], "other" )
+      assert_equal( tree_block_0.get_tree_strings_by_name( "best" )[ 0 ], "(fish,(frog,(snake,mouse)));" )
+      assert_equal( tree_block_0.get_tree_strings_by_name( "other" )[ 0 ], "(snake,(frog,(fish,mouse)));" )
+      
+      best_tree = tree_block_0.get_trees_by_name( "best" )[ 0 ]
+      other_tree = tree_block_0.get_trees_by_name( "other" )[ 0 ]
+      worst_tree = tree_block_1.get_tree( 0 )
+      bad_tree = tree_block_1.get_tree( 1 )
+      assert_equal( 6, best_tree.descendents( best_tree.root ).size )
+      assert_equal( 4, best_tree.leaves.size)
+      assert_equal( 6, other_tree.descendents( other_tree.root ).size )
+      assert_equal( 4, other_tree.leaves.size)
+      fish_leaf_best = best_tree.nodes.find { |x| x.name == 'fish' }
+      assert_equal( 1, best_tree.ancestors(  fish_leaf_best ).size )
+      fish_leaf_other = other_tree.nodes.find { |x| x.name == 'fish' }
+      assert_equal( 3, other_tree.ancestors(  fish_leaf_other ).size )
+
+      a_leaf_worst = worst_tree.nodes.find { |x| x.name == 'A' }
+      assert_equal( 1, worst_tree.ancestors(  a_leaf_worst ).size )
+      c_leaf_bad = bad_tree.nodes.find { |x| x.name == 'c' }
+      assert_equal( 3, bad_tree.ancestors(  c_leaf_bad ).size )
+      
+      
+      dist_block = distances_blocks[ 0 ]
+      assert_equal( dist_block.get_number_of_taxa.to_i, 5 )
+      assert_equal( dist_block.get_number_of_characters.to_i, 20 )
+      assert_equal( dist_block.get_triangle, "Both" )
+      assert_equal( dist_block.get_matrix.get_value( 0, 0 ), "taxon_1" )
+      assert_equal( dist_block.get_matrix.get_value( 1, 0 ), "taxon_2" )
+      assert_equal( dist_block.get_matrix.get_value( 2, 0 ), "taxon_3" )
+      assert_equal( dist_block.get_matrix.get_value( 3, 0 ), "taxon_4" )
+      assert_equal( dist_block.get_matrix.get_value( 4, 0 ), "taxon_5" )
+      assert_equal( dist_block.get_matrix.get_value( 0, 5 ).to_f, 7.0 )
+      assert_equal( dist_block.get_matrix.get_value( 1, 5 ).to_f, 8.0 )
+      assert_equal( dist_block.get_matrix.get_value( 2, 5 ).to_f, 9.0 )
+      assert_equal( dist_block.get_matrix.get_value( 3, 5 ).to_f, 9.5 )
+      assert_equal( dist_block.get_matrix.get_value( 4, 5 ).to_f, 0.0 )
+      
+      data_block = data_blocks[ 0 ]
+      assert_equal( data_block.get_number_of_taxa.to_i, 5 )
+      assert_equal( data_block.get_number_of_characters.to_i, 14 )
+      assert_equal( data_block.get_datatype, "RNA" )
+      assert_equal( data_block.get_match_character, "^" )
+      assert_equal( data_block.get_missing, "x" )
+      assert_equal( data_block.get_gap_character, "#" )
+      assert_equal( data_block.get_matrix.get_value( 0, 0 ), "taxon_1" )
+      assert_equal( data_block.get_matrix.get_value( 1, 0 ), "taxon_2" )
+      assert_equal( data_block.get_matrix.get_value( 2, 0 ), "taxon_3" )
+      assert_equal( data_block.get_matrix.get_value( 3, 0 ), "taxon_4" )
+      assert_equal( data_block.get_matrix.get_value( 4, 0 ), "taxon_5" )
+      assert_equal( data_block.get_matrix.get_value( 0, 14 ), "A" )
+      assert_equal( data_block.get_matrix.get_value( 1, 14 ), "C" )
+      assert_equal( data_block.get_matrix.get_value( 2, 14 ), "G" )
+      assert_equal( data_block.get_matrix.get_value( 3, 14 ), "T" )
+      assert_equal( data_block.get_matrix.get_value( 4, 14 ), "A" )
+      assert_equal( data_block.get_taxa[ 0 ], "ciona" )
+      assert_equal( data_block.get_taxa[ 1 ], "cow" )
+      assert_equal( data_block.get_taxa[ 2 ], "ape" )
+      assert_equal( data_block.get_taxa[ 3 ], "purple_urchin" )
+      assert_equal( data_block.get_taxa[ 4 ], "green_lizard" )
+      
+     
+      assert_equal( data_block.get_characters_strings_by_name( "taxon_1" )[ 0 ], "A-CCGTCGA-GTTA" ) 
+      assert_equal( data_block.get_characters_strings_by_name( "taxon_2" )[ 0 ], "T-CCG-CGA-GATC" ) 
+      assert_equal( data_block.get_characters_strings_by_name( "taxon_3" )[ 0 ], "A-C-GTCGA-GATG" ) 
+      assert_equal( data_block.get_characters_strings_by_name( "taxon_4" )[ 0 ], "A-CCTCGA--GTTT" )
+      assert_equal( data_block.get_characters_strings_by_name( "taxon_5" )[ 0 ], "T-CGGTCGT-CTTA" )     
+      
+      assert_equal( data_block.get_characters_string( 0 ), "A-CCGTCGA-GTTA" ) 
+      assert_equal( data_block.get_characters_string( 1 ), "T-CCG-CGA-GATC" ) 
+      assert_equal( data_block.get_characters_string( 2 ), "A-C-GTCGA-GATG" ) 
+      assert_equal( data_block.get_characters_string( 3 ), "A-CCTCGA--GTTT" )
+      assert_equal( data_block.get_characters_string( 4 ), "T-CGGTCGT-CTTA" )
+      
+      assert_equal( data_block.get_row_name( 0 ), "taxon_1" )
+      assert_equal( data_block.get_row_name( 1 ), "taxon_2" )
+      assert_equal( data_block.get_row_name( 2 ), "taxon_3" )
+      assert_equal( data_block.get_row_name( 3 ), "taxon_4" )
+      assert_equal( data_block.get_row_name( 4 ), "taxon_5" )
+
+      assert_equal( data_block.get_sequences_by_name( "taxon_1" )[ 0 ].seq.to_s.downcase, "A-CCGTCGA-GTTA".downcase ) 
+      assert_equal( data_block.get_sequences_by_name( "taxon_2" )[ 0 ].seq.to_s.downcase, "T-CCG-CGA-GATC".downcase ) 
+      assert_equal( data_block.get_sequences_by_name( "taxon_3" )[ 0 ].seq.to_s.downcase, "A-C-GTCGA-GATG".downcase ) 
+      assert_equal( data_block.get_sequences_by_name( "taxon_4" )[ 0 ].seq.to_s.downcase, "A-CCTCGA--GTTT".downcase ) 
+      assert_equal( data_block.get_sequences_by_name( "taxon_5" )[ 0 ].seq.to_s.downcase, "T-CGGTCGT-CTTA".downcase )
+      
+      assert_equal( data_block.get_sequences_by_name( "taxon_1" )[ 0 ].definition, "taxon_1" )
+      assert_equal( data_block.get_sequences_by_name( "taxon_2" )[ 0 ].definition, "taxon_2" )
+      assert_equal( data_block.get_sequences_by_name( "taxon_3" )[ 0 ].definition, "taxon_3" )
+      assert_equal( data_block.get_sequences_by_name( "taxon_4" )[ 0 ].definition, "taxon_4" )
+      assert_equal( data_block.get_sequences_by_name( "taxon_5" )[ 0 ].definition, "taxon_5" )
+      
+      assert_equal( data_block.get_sequence( 0 ).seq.to_s.downcase, "A-CCGTCGA-GTTA".downcase ) 
+      assert_equal( data_block.get_sequence( 1 ).seq.to_s.downcase, "T-CCG-CGA-GATC".downcase ) 
+      assert_equal( data_block.get_sequence( 2 ).seq.to_s.downcase, "A-C-GTCGA-GATG".downcase ) 
+      assert_equal( data_block.get_sequence( 3 ).seq.to_s.downcase, "A-CCTCGA--GTTT".downcase )
+      assert_equal( data_block.get_sequence( 4 ).seq.to_s.downcase, "T-CGGTCGT-CTTA".downcase ) 
+
+      assert_equal( data_block.get_sequence( 0 ).definition, "taxon_1" ) 
+      assert_equal( data_block.get_sequence( 1 ).definition, "taxon_2" ) 
+      assert_equal( data_block.get_sequence( 2 ).definition, "taxon_3" ) 
+      assert_equal( data_block.get_sequence( 3 ).definition, "taxon_4" )
+      assert_equal( data_block.get_sequence( 4 ).definition, "taxon_5" ) 
+      
+      assert_equal( DATA_BLOCK_OUTPUT_STRING, data_block.to_nexus() ) 
+      
+      generic_0 = private_blocks[ 0 ]
+      generic_1 = private_blocks[ 1 ]
+      assert_equal( generic_0.get_tokens[ 0 ], "Something" )
+      assert_equal( generic_0.get_tokens[ 1 ], "foo" )
+      assert_equal( generic_0.get_tokens[ 2 ], "5" )
+      assert_equal( generic_0.get_tokens[ 3 ], "bar" )
+      assert_equal( generic_0.get_tokens[ 4 ], "20" )
+      assert_equal( generic_0.get_tokens[ 5 ], "Format" )
+      assert_equal( generic_0.get_tokens[ 6 ], "Datatype" )
+      assert_equal( generic_0.get_tokens[ 7 ], "DNA" )
+      assert_equal( generic_0.get_tokens[ 8 ], "Matrix" )
+      assert_equal( generic_0.get_tokens[ 9 ], "taxon_1" )
+      assert_equal( generic_0.get_tokens[10 ], "1111" )
+      assert_equal( generic_1.get_tokens[ 0 ], "some" )
+      assert_equal( generic_1.get_tokens[ 1 ], "interesting" )
+      assert_equal( generic_1.get_tokens[ 2 ], "data" )
+      assert_equal( generic_1.get_tokens[ 3 ], "be" )
+      assert_equal( generic_1.get_tokens[ 4 ], "here" )
+      
+    end # test_nexus
+  end # class TestNexus
+end # module Bio