nexus_parser 1.2.0 → 1.2.2

data/test/test_nexus_parser.rb

@@ -35,18 +35,18 @@ class Test_Lexer < Test::Unit::TestCase
   def test_lexer
     lexer = NexusParser::Lexer.new("[ foo ] BEGIN taxa; BLORF end;")
     assert lexer.pop(NexusParser::Tokens::LBracket)
-    assert id = lexer.pop(NexusParser::Tokens::ID)
+    assert id = lexer.pop(NexusParser::Tokens::Label)
     assert_equal(id.value, "foo")
     assert lexer.pop(NexusParser::Tokens::RBracket)
     assert lexer.pop(NexusParser::Tokens::BeginBlk)
     assert lexer.pop(NexusParser::Tokens::TaxaBlk)
-    assert foo = lexer.pop(NexusParser::Tokens::ID)
+    assert foo = lexer.pop(NexusParser::Tokens::Label)
     assert_equal("BLORF", foo.value) # truncating whitespace
     assert lexer.pop(NexusParser::Tokens::BlkEnd)
 
     lexer2 = NexusParser::Lexer.new("[ foo ] begin authors; BLORF end; [] ()  some crud here")
     assert lexer2.pop(NexusParser::Tokens::LBracket)
-    assert id = lexer2.pop(NexusParser::Tokens::ID)
+    assert id = lexer2.pop(NexusParser::Tokens::Label)
     assert_equal(id.value, "foo")
     assert lexer2.pop(NexusParser::Tokens::RBracket)
     assert lexer2.pop(NexusParser::Tokens::BeginBlk)
@@ -56,46 +56,52 @@ class Test_Lexer < Test::Unit::TestCase
     assert lexer2.pop(NexusParser::Tokens::LParen)
     assert lexer2.pop(NexusParser::Tokens::RParen)
 
+    lexer2a = NexusParser::Lexer.new("begin authors; BLORF endblock; []")
+    assert lexer2a.pop(NexusParser::Tokens::BeginBlk)
+    assert lexer2a.pop(NexusParser::Tokens::AuthorsBlk)
+    assert lexer2a.pop(NexusParser::Tokens::LBracket)
+    assert lexer2a.pop(NexusParser::Tokens::RBracket)
+
     lexer3 = NexusParser::Lexer.new("[ foo ] Begin Characters; BLORF end; [] ()  some crud here")
     assert lexer3.pop(NexusParser::Tokens::LBracket)
-    assert id = lexer3.pop(NexusParser::Tokens::ID)
+    assert id = lexer3.pop(NexusParser::Tokens::Label)
     assert_equal(id.value, "foo")
     assert lexer3.pop(NexusParser::Tokens::RBracket)
     assert lexer3.pop(NexusParser::Tokens::BeginBlk)
     assert lexer3.pop(NexusParser::Tokens::ChrsBlk)
-    assert foo = lexer3.pop(NexusParser::Tokens::ID)
+    assert foo = lexer3.pop(NexusParser::Tokens::Label)
     assert_equal("BLORF", foo.value)
     assert lexer3.pop(NexusParser::Tokens::BlkEnd)
 
     lexer4 = NexusParser::Lexer.new("Begin Characters; 123123123 end; [] ()  some crud here")
     assert lexer4.pop(NexusParser::Tokens::BeginBlk)
     assert lexer4.pop(NexusParser::Tokens::ChrsBlk)
-    assert foo = lexer4.pop(NexusParser::Tokens::Number)
-    assert_equal(123123123, foo.value)
+    assert foo = lexer4.pop(NexusParser::Tokens::PositiveInteger)
+    assert_equal('123123123', foo.value)
     assert lexer4.pop(NexusParser::Tokens::BlkEnd)
 
     lexer5 = NexusParser::Lexer.new("(0,1)")
     assert lexer5.pop(NexusParser::Tokens::LParen)
-    assert foo = lexer5.pop(NexusParser::Tokens::Number)
-    assert_equal(0, foo.value)
+    assert foo = lexer5.pop(NexusParser::Tokens::PositiveInteger)
+    assert_equal('0', foo.value)
     assert lexer5.pop(NexusParser::Tokens::Comma)
-    assert foo = lexer5.pop(NexusParser::Tokens::Number)
-    assert_equal(1, foo.value)
+    assert foo = lexer5.pop(NexusParser::Tokens::PositiveInteger)
+    assert_equal('1', foo.value)
     assert lexer5.pop(NexusParser::Tokens::RParen)
 
     lexer6 =  NexusParser::Lexer.new(" 210(0,1)10A1\n")
     assert foo = lexer6.pop(NexusParser::Tokens::RowVec)
     assert_equal(["2","1","0",["0","1"],"1","0","A","1"], foo.value)
 
-    lexer6a =  NexusParser::Lexer.new("  21a(0 1)0b{3 4 5}(0)(1 a)\n")
+    lexer6a =  NexusParser::Lexer.new("  21a(0 1)0b{345}(0)(1 a)\n")
     assert foo = lexer6a.pop(NexusParser::Tokens::RowVec)
     assert_equal(["2", "1", "a", ["0", "1"], "0", "b", ["3", "4", "5"], "0", ["1", "a"]], foo.value)
 
-    lexer6b =  NexusParser::Lexer.new(" 201{0 1}{0 1}0100)\x0A") # *nix line ending
+    lexer6b =  NexusParser::Lexer.new(" 201(01){0 1}0100\x0A") # *nix line ending
     assert foo = lexer6b.pop(NexusParser::Tokens::RowVec)
     assert_equal(["2", "0", "1", ["0", "1"], ["0", "1"], "0", "1", "0", "0"], foo.value)
 
-    lexer6c =  NexusParser::Lexer.new(" 201{0 1}{0 1}0100)\x0D\x0A") # * dos line ending
+    lexer6c =  NexusParser::Lexer.new(" 201{0 1}{01}0100\x0D\x0A") # * dos line ending
     assert foo = lexer6c.pop(NexusParser::Tokens::RowVec)
     assert_equal(["2", "0", "1", ["0", "1"], ["0", "1"], "0", "1", "0", "0"], foo.value)
 
@@ -120,7 +126,41 @@ class Test_Lexer < Test::Unit::TestCase
   def test_row_vec
     lexer = NexusParser::Lexer.new("0?(0 1)10(A BD , C)1(0,1,2)1-\n")
     assert foo = lexer.pop(NexusParser::Tokens::RowVec)
-    assert_equal(["0", "?", ["0", "1"], "1", "0", ["A", "BD", "C"], "1", ["0", "1", "2"], "1", "-"], foo.value)
+    assert_equal(["0", "?", ["0", "1"], "1", "0", ["A", "B", "D", "C"], "1", ["0", "1", "2"], "1", "-"], foo.value)
+  end
+
+  def test_ungrouped_spaces_in_row_vec
+    lexer = NexusParser::Lexer.new("- A 12(BC) ? \n")
+    assert foo = lexer.pop(NexusParser::Tokens::RowVec)
+    assert_equal(['-', 'A', '1', '2', ['B', 'C'], '?'], foo.value)
+  end
+
+  def test_mismatched_parens_row_vec
+    lexer = NexusParser::Lexer.new("01(12(13\n")
+    assert_raise_with_message(NexusParser::ParseError, /Mismatch/) {
+      lexer.pop(NexusParser::Tokens::RowVec)
+    }
+  end
+
+  def test_mismatched_groupers_row_vec
+    lexer = NexusParser::Lexer.new("01(12}13\n")
+    assert_raise_with_message(NexusParser::ParseError, /Mismatch/) {
+      lexer.pop(NexusParser::Tokens::RowVec)
+    }
+  end
+
+  def test_nested_parens_row_vec
+    lexer = NexusParser::Lexer.new("01(12(34))13\n")
+    assert_raise_with_message(NexusParser::ParseError, /Mismatch/) {
+      lexer.pop(NexusParser::Tokens::RowVec)
+    }
+  end
+
+  def test_unclosed_parens_row_vec
+    lexer = NexusParser::Lexer.new("01(123413\n")
+    assert_raise_with_message(NexusParser::ParseError, /Unclosed/) {
+      lexer.pop(NexusParser::Tokens::RowVec)
+    }
   end
 
   def test_punctuation
@@ -149,7 +189,7 @@ class Test_Lexer < Test::Unit::TestCase
   def test_EndBlk
     lexer = NexusParser::Lexer.new("   \n\n End   ;")
     assert foo = lexer.pop(NexusParser::Tokens::EndBlk)
-    lexer = NexusParser::Lexer.new("\n\nEnd;")
+    lexer = NexusParser::Lexer.new("\n\nEndblock;")
     assert foo = lexer.pop(NexusParser::Tokens::EndBlk)
 
     lexer = NexusParser::Lexer.new("123123  \n\nEnd;")
@@ -401,13 +441,13 @@ class Test_Lexer < Test::Unit::TestCase
         CHARGROUPLABEL Behavior COLOR = (RGB 1.0 0.46666667 1.0) ;
 
 
-      END;
+      ENDBLOCK;
 
     BEGIN some other block;")
 
     assert foo = lexer.pop(NexusParser::Tokens::LabelsBlk)
     assert_equal 'LABELS', foo.value.slice(0,6)
-    assert_equal 'END;', foo.value.slice(-4,4)
+    assert_equal 'ENDBLOCK;', foo.value.slice(-9,9)
   end
 
   def test_SetsBlk
@@ -422,11 +462,6 @@ class Test_Lexer < Test::Unit::TestCase
     assert_equal 'SETS', foo.value.slice(0,4)
     assert_equal 'END;', foo.value.slice(-4,4)
   end
-
-  def test_lexer_errors
-    lexer = NexusParser::Lexer.new("*&")
-    assert_raise(NexusParser::ParseError) {lexer.peek(NexusParser::Tokens::ID)}
-  end
 end
 
 
@@ -513,8 +548,6 @@ class Test_Parser < Test::Unit::TestCase
     assert_equal "Tetragnatha", foo.taxa[9].name
   end
 
-
-
   def test_parse_characters_blk
     input=  "
       TITLE  'Scharff&Coddington_1997_Araneidae';
@@ -570,6 +603,30 @@ class Test_Parser < Test::Unit::TestCase
     assert_equal ["-", "0", "1", "2", "A"], foo.characters[4].state_labels
   end
 
+  def test_matrix_with_short_row
+    input=  "
+      DIMENSIONS  NCHAR=2;
+      FORMAT DATATYPE = STANDARD GAP = - MISSING = ? SYMBOLS = \"  0 1 2 3 4 5 6 7 8 9 A\";
+      CHARSTATELABELS
+        1 Tibia_II /  norm modified, 2 TII_macrosetae /  '= TI' stronger;
+      MATRIX
+      Dictyna                0?
+      Uloborus               ??
+      Deinopis               0
+    ;
+    END;"
+
+    builder = NexusParser::Builder.new
+    @lexer = NexusParser::Lexer.new(input)
+
+    # stub the taxa, they would otherwise get added in dimensions or taxa block
+    (0..2).each{|i| builder.stub_taxon}
+
+    assert_raise_with_message(NexusParser::ParseError, /too short/) {
+      NexusParser::Parser.new(@lexer, builder).parse_characters_blk
+    }
+  end
+
   def test_characters_block_without_IDs_or_title
     input=  "
       DIMENSIONS  NCHAR=10;
@@ -589,7 +646,7 @@ class Test_Parser < Test::Unit::TestCase
       Tetragnatha            0?01011011
 
     ;
-    END;"
+    ENDBLOCK;"
 
     builder = NexusParser::Builder.new
     @lexer = NexusParser::Lexer.new(input)
@@ -619,6 +676,55 @@ class Test_Parser < Test::Unit::TestCase
     assert_equal 10, foo.characters.size
   end
 
+  def test_characters_charlabels_statelabels_block
+    input=  "
+      DIMENSIONS  NCHAR=4;
+      FORMAT DATATYPE = STANDARD GAP = - MISSING = ? SYMBOLS = \"  0 1 2 3 4 5 6 7 8 9 A\";
+      CHARLABELS
+        Tibia_II
+        TII_macrosetae
+        'Femoral tuber'
+        _
+      ;
+      STATELABELS
+      1 norm modified,
+      3 3 3.5 4,
+      4 pres
+      ;
+      MATRIX
+      Dictyna                -?1(01)
+      Uloborus               0321
+    ;
+    ENDBLOCK;"
+
+    builder = NexusParser::Builder.new
+    lexer = NexusParser::Lexer.new(input)
+
+    (0..3).each{|i| builder.stub_taxon}
+
+    NexusParser::Parser.new(lexer,builder).parse_characters_blk
+    foo = builder.nexus_file
+
+    assert_equal 4, foo.characters.size
+    assert_equal "Femoral tuber", foo.characters[2].name
+    assert_equal "Undefined", foo.characters[3].name
+
+    assert_equal "norm", foo.characters[0].states["0"].name
+    assert_equal "modified", foo.characters[0].states["1"].name
+
+    assert_equal "", foo.characters[1].states["3"].name
+
+    assert_equal ["3", "3.5", "4"], foo.characters[2].states.keys.collect{|s| foo.characters[2].states[s].name}.sort
+
+    assert_equal "", foo.characters[1].states["3"].name
+
+    assert_equal ["-"], foo.codings[0][0].states
+    assert_equal ["?"], foo.codings[0][1].states
+    assert_equal ["0", "1"], foo.codings[0][3].states
+
+    assert_equal ["3"], foo.codings[1][1].states
+  end
+
   def test_codings
     foo = parse_nexus_file(@nf)
     assert_equal 100, foo.codings.flatten.size  # two multistates count in single cells
@@ -655,6 +761,82 @@ class Test_Parser < Test::Unit::TestCase
     # add test that nothing is left in lexer
   end
 
+  def test_parse_format_respect_case
+    input = "FORMAT DATATYPE = STANDARD RESPECTCASE GAP = - MISSING = ? SYMBOLS = \"  0 1 2 3 4 5 6 7 8 9 A\";"
+    builder = NexusParser::Builder.new
+    lexer = NexusParser::Lexer.new(input)
+
+    NexusParser::Parser.new(lexer,builder).parse_format
+    foo = builder.nexus_file
+
+    assert_equal "STANDARD", foo.vars[:datatype]
+    assert_equal "-", foo.vars[:gap]
+    assert_equal "?", foo.vars[:missing]
+    assert_equal '0 1 2 3 4 5 6 7 8 9 A', foo.vars[:symbols]
+  end
+
+  # https://github.com/mjy/nexus_parser/issues/9
+  def test_three_both_numeric_and_label_state_names_in_a_row
+    input =" CHARSTATELABELS
+    1 'Metatarsal trichobothria (CodAra.29)' / 3 9 27 asdf;
+    Matrix
+    fooo 01 more stuff here that should not be hit"
+
+    builder = NexusParser::Builder.new
+    lexer = NexusParser::Lexer.new(input)
+
+    builder.stub_chr()
+
+    NexusParser::Parser.new(lexer, builder).parse_chr_state_labels
+
+    foo = builder.nexus_file
+
+    assert_equal "3", foo.characters[0].states['0'].name
+    assert_equal "9", foo.characters[0].states['1'].name
+    assert_equal "27", foo.characters[0].states['2'].name
+    assert_equal "asdf", foo.characters[0].states['3'].name
+  end
+
+  def test_non_label_character_name_character_labels
+    input = 'CHARSTATELABELS
+     1 (intentionally_blank) /,
+     2 /,
+     3 %_coverage /,
+     4 #_of_widgets /,
+     5 !endangered! /,
+     6 @the_front /,
+     7 =antennae,
+     8 `a_=_2` /,
+     9 -35_or-36 ,
+     10 27_or_less /,
+     11 fine_not_fine /,
+     12 3,
+      ;'
+
+    builder = NexusParser::Builder.new
+    lexer = NexusParser::Lexer.new(input)
+
+    (0..11).each{builder.stub_chr()}
+
+    NexusParser::Parser.new(lexer,builder).parse_chr_state_labels
+
+    foo = builder.nexus_file
+
+    assert_equal 12, foo.characters.size
+    assert_equal "(intentionally_blank)", foo.characters[0].name
+    assert_equal "Undefined", foo.characters[1].name
+    assert_equal "%_coverage", foo.characters[2].name
+    assert_equal "#_of_widgets", foo.characters[3].name
+    assert_equal "!endangered!", foo.characters[4].name
+    assert_equal "@the_front", foo.characters[5].name
+    assert_equal "=antennae", foo.characters[6].name # =3
+    assert_equal "`a_=_2`", foo.characters[7].name
+    assert_equal "-35_or-36", foo.characters[8].name
+    assert_equal "27_or_less", foo.characters[9].name
+    assert_equal "fine_not_fine", foo.characters[10].name
+    assert_equal "3", foo.characters[11].name
+  end
+
   def test_parse_chr_state_labels
     input =" CHARSTATELABELS
     1 Tibia_II /  norm modified, 2 TII_macrosetae /  '= TI' stronger, 3 Femoral_tuber /  abs pres 'm-setae', 5 Cymbium /  dorsal mesal lateral, 6 Paracymbium /  abs pres, 7 Globular_tegulum /  abs pres, 8  /  entire w_lobe, 9 Conductor_wraps_embolus, 10 Median_apophysis /  pres abs ;
@@ -736,6 +918,169 @@ class Test_Parser < Test::Unit::TestCase
 
   end
 
+  def test_parse_chr_labels
+    input =" CHARLABELS
+    _
+		'Maxillary teeth'
+    as_df
+		'Highest number of maxillary teeth (or alveoli):';
+    STATELABELS
+    1 more more more,"
+
+    builder = NexusParser::Builder.new
+    lexer = NexusParser::Lexer.new(input)
+
+    (0..3).each{builder.stub_chr()}
+
+    NexusParser::Parser.new(lexer,builder).parse_chr_labels
+
+    foo = builder.nexus_file
+    assert_equal 4, foo.characters.size
+    assert_equal 'Undefined', foo.characters[0].name
+    assert_equal 'Maxillary teeth', foo.characters[1].name
+    assert_equal 'as_df', foo.characters[2].name
+    assert_equal 'Highest number of maxillary teeth (or alveoli):', foo.characters[3].name
+  end
+
+  def test_parse_state_labels
+    input =" STATELABELS
+      1 norm modified,
+      3,
+      4 pres
+    ;
+    CHARLABELS;
+		"
+
+    builder = NexusParser::Builder.new
+    lexer = NexusParser::Lexer.new(input)
+
+    (0..3).each{builder.stub_chr()}
+
+    NexusParser::Parser.new(lexer,builder).parse_state_labels
+
+    foo = builder.nexus_file
+    assert_equal 4, foo.characters.size
+
+    assert_equal "norm", foo.characters[0].states["0"].name
+    assert_equal "modified", foo.characters[0].states["1"].name
+
+    assert_empty foo.characters[1].states
+
+    assert_empty foo.characters[2].states
+
+    assert_equal "pres", foo.characters[3].states["0"].name
+  end
+
+  def test_non_label_character_state_character_labels
+    input = 'CHARSTATELABELS 1 Tibia_II /
+      .5
+      .1.2_form
+      idsimple
+      %_of_length_less_than_10
+      !poisonous!
+      #_is_3_or_4
+      (leave_as_is)
+      @12_o_clock
+      >2
+      ~equal
+      =9
+      ;'
+
+    builder = NexusParser::Builder.new
+    lexer = NexusParser::Lexer.new(input)
+
+    builder.stub_chr()
+
+    NexusParser::Parser.new(lexer,builder).parse_chr_state_labels
+
+    foo = builder.nexus_file
+
+    assert_equal ".5", foo.characters[0].states["0"].name
+    assert_equal ".1.2_form", foo.characters[0].states["1"].name
+    assert_equal "idsimple", foo.characters[0].states["2"].name
+    assert_equal "%_of_length_less_than_10", foo.characters[0].states["3"].name
+    assert_equal "!poisonous!", foo.characters[0].states["4"].name
+    assert_equal "#_is_3_or_4", foo.characters[0].states["5"].name
+    assert_equal "(leave_as_is)", foo.characters[0].states["6"].name
+    assert_equal "@12_o_clock", foo.characters[0].states["7"].name
+    assert_equal ">2", foo.characters[0].states["8"].name
+    assert_equal "~equal", foo.characters[0].states["9"].name
+    assert_equal "=9", foo.characters[0].states["10"].name
+  end
+
+  def test_arbitrary_quote_and_quotelike_character_state_labels
+    # We could tighten up our handling of accidentally unclosed quotes, but
+    # there's pretty much no way to recover in general, so we're not testing
+    # them here.
+    # Things like ""asdf" " failing is a known issue (maybe not solvable with
+    # regular expressions?).
+    input = 'CHARSTATELABELS 1 Tibia_II /
+      "asd, \'f\'"
+      ""a\'sdf  "
+      \'  /as"df/\'
+      \'asdf;\'
+      ""as, df""
+      ;'
+
+    builder = NexusParser::Builder.new
+    lexer = NexusParser::Lexer.new(input)
+
+    builder.stub_chr()
+
+    NexusParser::Parser.new(lexer,builder).parse_chr_state_labels
+
+    foo = builder.nexus_file
+
+    assert_equal 'asd, \'f\'', foo.characters[0].states["0"].name
+    assert_equal '"a\'sdf', foo.characters[0].states["1"].name
+    assert_equal '/as"df/', foo.characters[0].states["2"].name
+    assert_equal 'asdf;', foo.characters[0].states["3"].name
+    assert_equal '"as, df"', foo.characters[0].states["4"].name
+  end
+
+
+  def test_number_label_chr_state_labels
+    # Character state names that start with numbers
+    input = 'CHARSTATELABELS 1 Tibia_II /
+      123abc
+      -1.23abc
+      -3e-3abc
+      25%_or_less_than
+      ;'
+
+    builder = NexusParser::Builder.new
+    lexer = NexusParser::Lexer.new(input)
+
+    (0..3).each{builder.stub_chr()}
+
+    NexusParser::Parser.new(lexer,builder).parse_chr_state_labels
+
+    foo = builder.nexus_file
+
+    assert_equal "123abc", foo.characters[0].states["0"].name
+    assert_equal "-1.23abc", foo.characters[0].states["1"].name
+    assert_equal "-3e-3abc", foo.characters[0].states["2"].name
+    assert_equal "25%_or_less_than", foo.characters[0].states["3"].name
+  end
+
+  def test_value_pair_label_chr_state_labels
+    # Character state names that are ValuePairs
+    input = 'CHARSTATELABELS 1 Tibia_II /
+      234=(a_b_c)
+      ;'
+
+    builder = NexusParser::Builder.new
+    lexer = NexusParser::Lexer.new(input)
+
+    builder.stub_chr()
+
+    NexusParser::Parser.new(lexer,builder).parse_chr_state_labels
+
+    foo = builder.nexus_file
+
+    assert_equal '234=(a_b_c)', foo.characters[0].states["0"].name
+  end
+
   def DONT_test_parse_really_long_string_of_chr_state_labels
     input =" CHARSTATELABELS
     1 Epigynal_ventral_margin /  'entire (Fig. 15G)' 'with scape (Fig. 27D)', 2 Epigynal_external_structure /  openings_on_a_broad_depression 'copulatory openings on plate, flush with abdomen, sometimes slit like', 3 Epigynal_depression /  'round or square, at most slightly wider than high ' 'elongate, at least twice as wide as high ', 4 Epigynal_plate_surface /  'smooth (Fig. 12E)' 'ridged (Fig. 21G)', 5 epignynal_septum /  absent_ present_, 6 Copulatory_bursa_anterior_margin /  'entire, broadly transverse (Fig. 19B)' 'medially acute (Figs. 22G, 40B)', 7 'Copulatory duct: spermathecal junction' /  posterior lateral_or_anterior, 8 Copulatory_duct_loops_relative_to_spermathecae /  apart 'encircling (Fig. 93J)', 9 Copulatory_duct_terminal_sclerotization /  as_rest_of_duct_ 'distinctly sclerotized, clearly more than rest of duct ', 10 Hard_sclerotized_CD_region /  mostly_or_entirely_ectal_to_the_ectal_rim_of_the_spermathecae 'caudal to the spermathecae, mesal to ectal margin of spermathecae', 11 Male_palpal_tibial_rim /  uniform_or_only_slightly_asymmetric 'strongly and asymmetrically protruding, scoop-shaped (Fig 36D)', 12 Male_palpal_tibia_prolateral_trichobothria /  one none, 13 Cymbial_ridge_ectal_setae /  unmodified 'strongly curved towards the palpal bulb (Kochiura, Figs. 51B-C, 52C)', 14 Cymbial_distal_promargin /  entire 'with an apophysis (Argyrodes, Figs.) ', 15 Cymbial_mesal_margin /  entire 'incised (Anelosimus, Figs. 17D, 20A) ' deeply_notched, 16 Cymbial_tip_sclerotization /  like_rest_of_cymbium 'lightly sclerotized, appears white', 17 Cymbial_tip_setae /  like_other_setae 'thick and strongly curved (Kochiura, Figs. 51B, 52C)', 18 Cymbial_sheath /  absent present, 19 Lock_placement /  'distal (Figs. 67B, 92F-G, I, M)' 'central (Fig. 92H)', 20 Lock_mechanism /  'hook (Figs 31F, 60D, 91A, 92D-E, J-L)' 'hood (Figs 18A, 75B, 92F-I, M)' 'Theridula (Fig 81D)', 21 Cymbial_hook_orientation /  'facing downwards (Figs. 91A, 92D-E, J-K)' 'facing upwards (Fig. 60C-D, 92L)', 22 Cymbial_hook_location /  'inside cymbium (Fig. 92D-E, J-K)' 'ectal cymbial margin (Figs. 67B, 92L).', 23 Cymbial_hook_distal_portion /  'blunt (Figs. 31F, 92D-E)' 'tapering to a narrow tongue (Figs. 66B, 67D, 92L)', 24 Cymbial_hood_size /  'narrow (Fig. 92F-H)' 'broad (Fig. 92I)' 'Spintharus (Fig. 92M)', 25 Cymbial_hood_region /  'translucent, hood visible through cymbium (Anelosimus, Figs. 90A, 91C)' 'opaque, hood not visible', 26 Alveolus_shape /  'circular or oval (Fig. 92A-H)' 'with a mesal extension (Fig. 92A)', 27 Tegulum_ectal_margin /  entire 'protruded (Fig. 20D)', 28 Tegular_groove /  absent 'present (Fig. 28B)', 29 SDT_SB_I /  separate touching, 30 'SDT post-SB II turn' /  gradual '90 degrees (Anelosimus, Fig. 93B)', 31 SDT_SB_I_&_II_reservoir_segment_alignment /  divergent parallel, 32 SDT_SB_I_&_II_orientation /  in_plane_of_first_loop_from_fundus 'out of plane of first loop, against tegular wall', 33 SDT_RSB_I_&_II /  absent present, 34 SDT_SB_III /  absent present, 35 SDT_SB_IV /  absent 'present (Fig. 93E)', 36 Conductor_shape /  'simple, round or oval, short' 'fan shaped, narrow base and broad tip (Selkirkiella, Kochiura)' Enoplognatha Argyrodes Achaearanea Theridion '''rupununi''' '''tanzania''' '''cup-shaped''', 37 Conductor /  'with a groove for embolus (Figs. 10A, 28D, 69B)' 'entire (Figs. 13D, 17F, 52C-D)', 38 Conductor_surface /  'smooth (Figs. 75B, 77B-C)' ' heavily ridged (Figs. 10B-C, 44D. 67C, 69D)', 39 Conductor_tip_sclerotization /  like_base more_than_base, 40 Subconductor /  absent present, 41 Subconductor_pit_upper_wall /  'entire, or slightly protruding' forms_a_regular_oval_lip, 42 Subconductor_at_C_base /  narrows_abruptly_before_C_base narrows_gradually_along_its_entire_length broad_at_base, 43 'Embolus tail-SC relation' /  'hooked in, or oriented towards SC' surpasses_SC behind_E_base, 44 Tegulum_ectally_ /  occupying_less_than_half_of_the_cymbial_cavity_ occupying_more_than_half_of_the_cymbial_cavity, 45 MA_and_sperm_duct /  sperm_duct_loop_not_inside_MA 'sperm duct loop inside MA (Figs. 90F, 91B)', 46 'MA-tegular membrane connection' /  broad narrow, 47 MA_form /  unbranched 'two nearly equally sized branches (Fig. 22A-B) ', 48 MA_distal_tip /  entire hooded, 49 MA_hood_form /  'narrow, pit-like (Figs. 31F, 34D)' 'scoop-shaped (Figs. 60D, 66B, 67D)', 50 TTA_form /  entire 'grooved (Fig. 44C)', 51 TTA /  bulky 'prong shaped (vittatus group)', 52 TTA_distal_tip /  entire_or_gently_curved Argyrodes 'hooked (branched)', 53 TTA_hook_distal_branch /  barely_exceeding_lower_branch_ 'extending beyond lower branch (jucundus group) ', 54 TTA_hook_distal_branch /  thick_ 'thin, finger like (domingo, dubiosus)', 55 TTA_hook_proximal_branch /  'blunt, broad' 'flattened, bladelike' 'cylindrical, elongated', 56 TTA_surface_subterminally /  smooth ridged, 57 TTA_tip_surface /  smooth 'ridged (Figs. 7A-B, 17F, 31D, 34D, 54A, 56B, 86A)', 58 Embolus_and_TTA /  loosely_associated_to_or_resting_in_TTA_shallow_groove 'parts of E entirely enclosed in TTA (Figs. 37A-B, 44C, 89C)', 59 Embolus_tip_surface /  smooth denticulate, 60 Embolus_spiral_curviture /  gentle whip_like corkscrew, 61 Embolus_tip /  entire bifid, 62 Embolus_origin /  retroventral_on_tegulum 'retrolateral (ectal), partially or completely hidden by cymbium (Figs 44C, 60A-C, 67B)', 63 Embolus_ridges /  absent present, 64 Embolus_shape /  short_to_moderately_elongate 'extremely long, >2 spirals (Figs. 54D, 73A-E)', 65 Embolus_spiral_width /  'thin, much of E spiral subequal to E tip ' 'thick, entire E spiral much broader than tip ', 66 Embolus_distal_rim /  'entire (normal)' deeply_grooved, 67 Embolic_terminus /  abrupt 'with a distal apophysis (EA, Fig. 34E) ', 68 Embolus_tail /  'entire, smooth' 'distinct, lobed', 69 'Embolus-dh connection grooves' /  absent present, 70 'Embolus-dh grooves' /  'deep, extend into the E base more than twice longer than the distance between them' 'short, extend into the E base about as long, or slightly longer than the distance between them', 71 E_spiral_distally /  'relatively thin or filiform, cylindrical' 'thick, not cylindrical' 'rupununi/lorenzo like', 72 Embolus_spiral /  entire 'biparted (Eb)' pars_pendula, 73 Eb_orientation /  towards_embolus_tip towards_tibia, 74 Embolic_division_b /  separates_early_from_E E_and_Eb_tightly_associated_the_entire_spiral, 75 Embolic_division_b /  broad 'narrow, relative to Eb spiral, snout-like', 76 'Eb distal portion, ectal marginl' /  'level, not raised ' with_a_distinct_ridge_, 77 Eb_form /  flat 'globose, inflated', 78 Eb_form /  'distinct, clearly separate apophysis' 'short, confined to first section of spiral, barely separate', 79 Eb_tip_and_E_tip_association /  separate Eb_and_E_tips_juxtaposed 'E tip rests on Eb ''cup''', 80 Eb_snout /  'short, snug with E spiral ' 'long, separate from E spiral ', 81 Distal_portion_of_Eb /  entire with_a_cup_shaped_apophysis with_a_raised_ridge, 82 E_tail /  lobe_not_reaching_ectal_margin_of_Eb_ lobe_touching_ectal_margin_of_Eb_, 83 Extra_tegular_sclerite /  absent_ present_, 84 'Median eyes (male)' /  flush_with_carapace 'on tubercle (Argyrodes)', 85 'AME size (male)' /  subequal_or_slightly_larger_than_ALE clearly_smaller_than_ALE, 86 Cheliceral_posterior_margin /  toothed smooth, 87 Cheliceral_posterior_tooth_number /  three_or_more two one, 88 Cheliceral_furrow /  smooth denticulate, 89 Carapace_hairiness /  'sparsely or patchily hirsute (Fig. 48D)' 'uniformly hirsute (Fig. 71D)', 90 Carapace_pars_stridens /  irregular regular_parallel_ridges, 91 Interocular_area /  more_or_less_flush_with_clypeus projecting_beyond_clypeus, 92 Clypeus /  concave_or_flat with_a_prominent_projection, 93 'ocular and clypeal region setae distribution (male)' /  sparse 'in a dense field, or fields', 94 'Labium-sternum connection' /  'visible seam  (Fig. 27C)' fused, 95 Sternocoxal_tubercles /  present absent, 96 Pedicel_location /  'anterior (Fig. 94A-D)' 'medial (Fig. 94J-K)', 97 Abdominal_folium_pattern /  bilateral_spots_or_blotches distinct_central_band_, 98 Abdomen_pattern /  Anelosimus_, 99 Dorsal_band /  'dark edged by white (Kochiura, Anelosimus, Fig. 94G, J)' 'light edged by dark (Fig. 94H)' 'Ameridion, light edged by white (Fig. 94I)', 100 Abdominal_dot_pigment /  silver 'non-reflective, dull', 101 SPR_form /  'weakly keeled (Figs. 67F, 74F)' 'strongly keeled and elongate (Figs. 16B-C, 24D-E, 42F)', 102 SPR_pick_number /  '1-4' '6-28' '>30', 103 SPR_insertion /  flush_with_abdominal_surface 'on a ridge (Figs 32D, 72A-B)', 104 'SPR mesally-oriented picks' /  absent present, 105 'SPR mesally-oriented picks relative to sagittal plane' /  angled_dorsally perpendicular_or_angled_ventrally, 106 SPR /  straight_or_slightly_irregular distinctly_curved 'argyrodine, dorsal picks aside others', 107 SPR_dorsal_pick_spacing /  subequal_to_ventral_pick_spacing distinctly_compressed, 108 SPR_relative_to_pedicel /  lateral dorsal, 109 SPR_setae /  separate tight, 110 'Supra pedicillate ventrolateral  (4 o''clock) proprioreceptor' /  absent present, 111 Epiandrous_fusule_arrangement /  in_one_pair_of_sockets in_a_row, 112 Epiandrous_fusule_pair_number /  '=>9' '6-8' '4-5' 1, 113 Colulus /  'present (Figs. 45E, 61F)' 'absent (Figs. 16E, 78A)' 'invaginated (Figs. 9D,  63G)', 114 Colulus_size /  'large and fleshy (Figs. 55H, 61F)' 'small, less than half the length of its setae (Fig. 38B)', 115 Colular_setae /  present absent, 116 'Colular setae number (female)' /  three_or_more two_, 117 'Palpal claw dentition (female)' /  'dense, > half of surface covered by denticles (Figs. 2D, 9E, 11D, 12G, 45G, 47E, 58G, 80D)' 'sparse < half of surface with denticles', 118 'Palpal tibial trichobothria (female)' /  four three two five, 119 Femur_I_relative_to_II /  subequal 'robust, clearly larger than femur II', 120 'Leg IV relative length (male)' /  '3rd longest (typical leg formula 1243)' '2nd longest (typical leg formula 1423)' 'longest (typical leg formula 4123)', 121 'Leg IV relative length (female)' /  3rd_longest 2nd_longest longest_, 122 'Femur vs. metatarsus length (female)' /  metatarsus_longer metatarsus_shorter, 123 'Femur vs. metatarsus length (male)' /  metatarsus_longer metatarsus_shorter, 124 'Metatarsus vs. tibia length (female)' /  metatarsus_longer metatarsus_shorter, 125 'Metatarsus vs. tibia length (male)' /  metatarsus_longer metatarsus_shorter, 126 Metatarsal_ventral_macrosetae /  like_other_macrosetae thickened_ventrally, 127 Tarsus_IV_comb_serrations /  'simple, straight' curved_hooks, 128 Tarsal_organ_size /  'smaller than setal sockets (normal)' enlarged, 129 'Tarsus IV central claw vs. laterals (male)' /  'short, at most subequal' 'elongate, longer (Figs. 19E, 21C, 23D, 32H, 57F, 58F)', 130 'Tarsus IV central claw vs. laterals (female)' /  equal_or_shorter stout_and_distinctly_longer minute, 131 Spinneret_insertion /  abdominal_apex 'subapical, abdomen extending beyond spinnerets', 132 PLS_flagelliform_spigot_length /  subequal_to__PLS_CY 'longer than PLS CY (Figs. 68E, 78B, 82D)', 133 'PLS, PMS CY spigot bases' /  'not modified, subequal or smaller than ampullates' 'huge and elongated, much larger than ampullates ', 134 CY_shaft_surface /  smooth grooved, 135 PLS_AC_spigot_number /  five_or_more four_or_less, 136 PLS_flagelliform_spigot /  present absent, 137 PLS_posterior_AG_spigot_shape /  'normal, round' flattened, 138 PLS_theridiid_type_AG_position /  more_or_less_parallel end_to_end, 139 'PMS minor ampullate (mAP) spigot shaft length' /  'short, subequal to CY shaft' clearly_longer_than_any_CY_shaft, 140 Web_form /  'linyphioid-like sheet web (Fig. 99C)' 'cobweb (Figs. 97G, 99A-B, 100A-F, 101A-E)' 'network mesh web - with foraging field below (rupununi/lorenzo)' 'dry line-web', 141 'Knock-down lines' /  absent present, 142 Sticky_silk_in_web /  present absent, 143 Egg_sac_surface /  spherical_to_lenticular 'stalked (Fig. 88E, 98D).', 144 Egg_case_structure /  suboval_or_roundish basal_knob rhomboid elongated Spiky, 145 Web_construction /  solitary communal, 146 Mating_thread /  present absent, 147 Adult_females_per_nest /  one multiple, 148 cooperative_behavior /  solitary subsocial permanent_sociality ;

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: nexus_parser
 version: !ruby/object:Gem::Version
-  version: 1.2.0
+  version: 1.2.2
 platform: ruby
 authors:
 - mjy
@@ -9,7 +9,7 @@ authors:
 autorequire:
 bindir: exe
 cert_chain: []
-date: 2024-04-03 00:00:00.000000000 Z
+date: 2024-05-15 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler
@@ -128,7 +128,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.5.3
+rubygems_version: 3.5.9
 signing_key:
 specification_version: 4
 summary: A Nexus file format (phylogenetic inference) parser in Ruby.