nexus_parser 1.0.0 → 1.1.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (9) hide show
  1. data/VERSION +1 -1
  2. data/lib/lexer.rb +4 -4
  3. data/lib/{nexus_file.rb → nexus_parser.rb} +20 -21
  4. data/lib/parser.rb +92 -92
  5. data/lib/tokens.rb +40 -40
  6. data/nexus_parser.gemspec +61 -0
  7. data/test/MX_test_03.nex +234 -234
  8. data/test/test_nexus_parser.rb +210 -213
  9. metadata +5 -4
data/lib/tokens.rb CHANGED
@@ -1,4 +1,4 @@
1
- module NexusFile::Tokens
1
+ module NexusParser::Tokens
2
2
 
3
3
  class Token
4
4
  # this allows access the the class attribute regexp, without using a class variable
@@ -220,48 +220,48 @@ module NexusFile::Tokens
220
220
  end
221
221
  end
222
222
 
223
- # NexusFile::Tokens::NexusComment
223
+ # NexusParser::Tokens::NexusComment
224
224
 
225
225
  # this list also defines priority, i.e. if tokens have overlap (which they shouldn't!!) then the earlier indexed token will match first
226
226
  def self.nexus_file_token_list
227
- [ NexusFile::Tokens::NexusStart,
228
- NexusFile::Tokens::BeginBlk,
229
- NexusFile::Tokens::EndBlk,
230
- NexusFile::Tokens::AuthorsBlk,
231
- NexusFile::Tokens::SetsBlk,
232
- NexusFile::Tokens::MqCharModelsBlk,
233
- NexusFile::Tokens::AssumptionsBlk,
234
- NexusFile::Tokens::CodonsBlk,
235
- NexusFile::Tokens::MesquiteBlk,
236
- NexusFile::Tokens::TreesBlk,
237
- NexusFile::Tokens::LabelsBlk,
238
- NexusFile::Tokens::TaxaBlk,
239
- NexusFile::Tokens::NotesBlk,
240
- NexusFile::Tokens::Title,
241
- NexusFile::Tokens::Taxlabels,
242
- NexusFile::Tokens::Dimensions,
243
- NexusFile::Tokens::FileLbl,
244
- NexusFile::Tokens::Format,
245
- NexusFile::Tokens::Equals,
246
- NexusFile::Tokens::ValuePair, # this has bad overlap with Label and likely IDs (need to kill the latter, its a lesser Label)
247
- NexusFile::Tokens::CharStateLabels,
248
- NexusFile::Tokens::ChrsBlk,
249
- NexusFile::Tokens::Number,
250
- NexusFile::Tokens::Matrix,
251
- NexusFile::Tokens::SemiColon,
252
- NexusFile::Tokens::MesquiteIDs,
253
- NexusFile::Tokens::MesquiteBlockID,
254
- NexusFile::Tokens::BlkEnd,
255
- NexusFile::Tokens::Colon,
256
- NexusFile::Tokens::BckSlash,
257
- NexusFile::Tokens::Comma,
258
- NexusFile::Tokens::LParen,
259
- NexusFile::Tokens::RParen,
260
- NexusFile::Tokens::LBracket,
261
- NexusFile::Tokens::RBracket,
262
- NexusFile::Tokens::Label, # must be before RowVec
263
- NexusFile::Tokens::RowVec,
264
- NexusFile::Tokens::ID # need to trash this
227
+ [ NexusParser::Tokens::NexusStart,
228
+ NexusParser::Tokens::BeginBlk,
229
+ NexusParser::Tokens::EndBlk,
230
+ NexusParser::Tokens::AuthorsBlk,
231
+ NexusParser::Tokens::SetsBlk,
232
+ NexusParser::Tokens::MqCharModelsBlk,
233
+ NexusParser::Tokens::AssumptionsBlk,
234
+ NexusParser::Tokens::CodonsBlk,
235
+ NexusParser::Tokens::MesquiteBlk,
236
+ NexusParser::Tokens::TreesBlk,
237
+ NexusParser::Tokens::LabelsBlk,
238
+ NexusParser::Tokens::TaxaBlk,
239
+ NexusParser::Tokens::NotesBlk,
240
+ NexusParser::Tokens::Title,
241
+ NexusParser::Tokens::Taxlabels,
242
+ NexusParser::Tokens::Dimensions,
243
+ NexusParser::Tokens::FileLbl,
244
+ NexusParser::Tokens::Format,
245
+ NexusParser::Tokens::Equals,
246
+ NexusParser::Tokens::ValuePair, # this has bad overlap with Label and likely IDs (need to kill the latter, its a lesser Label)
247
+ NexusParser::Tokens::CharStateLabels,
248
+ NexusParser::Tokens::ChrsBlk,
249
+ NexusParser::Tokens::Number,
250
+ NexusParser::Tokens::Matrix,
251
+ NexusParser::Tokens::SemiColon,
252
+ NexusParser::Tokens::MesquiteIDs,
253
+ NexusParser::Tokens::MesquiteBlockID,
254
+ NexusParser::Tokens::BlkEnd,
255
+ NexusParser::Tokens::Colon,
256
+ NexusParser::Tokens::BckSlash,
257
+ NexusParser::Tokens::Comma,
258
+ NexusParser::Tokens::LParen,
259
+ NexusParser::Tokens::RParen,
260
+ NexusParser::Tokens::LBracket,
261
+ NexusParser::Tokens::RBracket,
262
+ NexusParser::Tokens::Label, # must be before RowVec
263
+ NexusParser::Tokens::RowVec,
264
+ NexusParser::Tokens::ID # need to trash this
265
265
  ]
266
266
  end
267
267
 
data/nexus_parser.gemspec ADDED
@@ -0,0 +1,61 @@
1
+ # Generated by jeweler
2
+ # DO NOT EDIT THIS FILE DIRECTLY
3
+ # Instead, edit Jeweler::Tasks in Rakefile, and run the gemspec command
4
+ # -*- encoding: utf-8 -*-
5
+
6
+ Gem::Specification.new do |s|
7
+ s.name = %q{nexus_parser}
8
+ s.version = "1.1.0"
9
+
10
+ s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
11
+ s.authors = ["mjy"]
12
+ s.date = %q{2010-03-18}
13
+ s.description = %q{A full featured and extensible Nexus file parser in Ruby. }
14
+ s.email = %q{diapriid@gmail.com}
15
+ s.extra_rdoc_files = [
16
+ "LICENSE",
17
+ "README",
18
+ "README.rdoc"
19
+ ]
20
+ s.files = [
21
+ ".document",
22
+ ".gitignore",
23
+ "LICENSE",
24
+ "MIT-LICENSE",
25
+ "README",
26
+ "README.rdoc",
27
+ "Rakefile",
28
+ "VERSION",
29
+ "init.rb",
30
+ "install.rb",
31
+ "lib/lexer.rb",
32
+ "lib/nexus_parser.rb",
33
+ "lib/parser.rb",
34
+ "lib/tokens.rb",
35
+ "nexus_parser.gemspec",
36
+ "tasks/nexus_parser_tasks.rake",
37
+ "test/MX_test_03.nex",
38
+ "test/test.nex",
39
+ "test/test_nexus_parser.rb",
40
+ "uninstall.rb"
41
+ ]
42
+ s.homepage = %q{http://github.com/mjy/nexus_parser}
43
+ s.rdoc_options = ["--charset=UTF-8"]
44
+ s.require_paths = ["lib"]
45
+ s.rubygems_version = %q{1.3.6}
46
+ s.summary = %q{A Nexus file format (phylogenetic inference) parser in Ruby.}
47
+ s.test_files = [
48
+ "test/test_nexus_parser.rb"
49
+ ]
50
+
51
+ if s.respond_to? :specification_version then
52
+ current_version = Gem::Specification::CURRENT_SPECIFICATION_VERSION
53
+ s.specification_version = 3
54
+
55
+ if Gem::Version.new(Gem::RubyGemsVersion) >= Gem::Version.new('1.2.0') then
56
+ else
57
+ end
58
+ else
59
+ end
60
+ end
61
+
data/test/MX_test_03.nex CHANGED
@@ -1,234 +1,234 @@
1
- #NEXUS
2
- [written Sun Apr 20 17:45:47 EDT 2008 by Mesquite version 2.0 (build i69) at procto/192.168.0.100]
3
- BEGIN AUTHORS;
4
- AUTHOR NAME = Jonathan_Coddington CODE = JC;
5
- END;
6
-
7
-
8
- BEGIN TAXA;
9
- TITLE 'Scharff&Coddington_1997_Araneidae';
10
- DIMENSIONS NTAX=10;
11
- TAXLABELS
12
- Dictyna Uloborus Deinopis Nephila&Herennia 'Nephilengys_cruentata' Meta Leucauge_venusta Pachygnatha 'Theridiosoma_01' Tetragnatha
13
- ;
14
- IDS JC1191fcddc2b128 JC1191fcddc2b129 JC1191fcddc2b130 JC1191fcddc2b131 JC1191fcddc2b132 JC1191fcddc2b133 JC1191fcddc2b134 JC1191fcddc2b135 JC1191fcddc2b137 JC1191fcddc2b136 ;
15
- BLOCKID JC1191fcddc0c4;
16
-
17
- END;
18
-
19
-
20
- BEGIN CHARACTERS;
21
- TITLE 'Scharff&Coddington_1997_Araneidae';
22
- DIMENSIONS NCHAR=10;
23
- FORMAT DATATYPE = STANDARD GAP = - MISSING = ? SYMBOLS = " 0 1 2 3 4 5 6 7 8 9 A";
24
- CHARSTATELABELS
25
- 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 ;
26
- MATRIX
27
- Dictyna 0?00201001
28
- Uloborus 0?11000000
29
- Deinopis 0?01002???
30
- Nephila&Herennia 0?21010011
31
- 'Nephilengys_cruentata'0?(0,1)1010(0,1,2)11
32
- Meta 0?01A10011
33
- Leucauge_venusta ???--?-??-
34
- Pachygnatha 0?210(0,1)0011
35
- 'Theridiosoma_01' ??????????
36
- Tetragnatha 0?01011011
37
-
38
- ;
39
- IDS JC1191fcddc3b425 JC1191fcddc3b426 JC1191fcddc3b427 JC1191fcddc3b428 JC1191fcddc3b429 JC1191fcddc3b430 JC1191fcddc3b431 JC1191fcddc3b432 JC1191fcddc3b433 JC1191fcddc3b434 ;
40
- BLOCKID JC1191fcddc0c0;
41
-
42
-
43
- END;
44
- BEGIN TREES;
45
- Title Imported_trees;
46
- LINK Taxa = 'Scharff&Coddington_1997_Araneidae';
47
- TRANSLATE
48
- 1 Dictyna,
49
- 2 Uloborus,
50
- 3 Deinopis,
51
- 4 Nephila&Herennia,
52
- 5 'Nephilengys_cruentata',
53
- 6 Meta,
54
- 7 Leucauge_venusta,
55
- 8 Pachygnatha,
56
- 9 'Theridiosoma_01',
57
- 10 Tetragnatha;
58
- TREE 'Imported tree 1+' = (1,((2,3),(((4,5),(6,(7,(8,10)))),9)));
59
- TREE 'Imported tree 2+' = (1,((2,3),(((4,5),(6,(7,(8,10)))),9)));
60
- TREE 'Imported tree 3+' = (1,((2,3),(((6,(4,5)),(7,(8,10))),9)));
61
- TREE 'Imported tree 4+' = (1,((2,3),(((4,5),(6,(7,(8,10)))),9)));
62
- TREE 'Imported tree 5+' = (1,((2,3),(((6,(4,5)),(7,(8,10))),9)));
63
- TREE 'Imported tree 6+' = (1,((2,3),(((4,5),(6,(7,(8,10)))),9)));
64
- TREE 'Imported tree 7+' = (1,((2,3),(((6,(4,5)),(7,(8,10))),9)));
65
- TREE 'Imported tree 8+' = (1,((2,3),(((6,(4,5)),(7,(8,10))),9)));
66
-
67
- END;
68
-
69
-
70
- BEGIN LABELS;
71
- CHARGROUPLABEL MM_Genitalia COLOR = (RGB 1.0 0.4 0.4) ;
72
- CHARGROUPLABEL Somatic COLOR = (RGB 0.6 1.0 0.33333333) ;
73
- CHARGROUPLABEL Spinnerets COLOR = (RGB 0.46666667 0.57254902 1.0) ;
74
- CHARGROUPLABEL Behavior COLOR = (RGB 1.0 0.46666667 1.0) ;
75
-
76
-
77
- END;
78
-
79
- BEGIN SETS;
80
- CHARPARTITION * UNTITLED = Somatic : 1 - 2 4, MM_Genitalia : 5 - 8 10;
81
-
82
- END;
83
-
84
- BEGIN ASSUMPTIONS;
85
- TYPESET * UNTITLED = unord: 1 - 10;
86
-
87
- EXSET * UNTITLED = ;
88
-
89
- WTSET * UNTITLED = 1: 1 - 10 ;
90
-
91
- END;
92
-
93
- BEGIN CODONS;
94
- CODESET * UNTITLED = universal: 1 - 10;
95
-
96
-
97
- END;
98
-
99
- BEGIN MESQUITECHARMODELS;
100
- ProbModelSet * UNTITLED = 'Mk1 (est.)': 1 - 10;
101
- END;
102
-
103
- BEGIN NOTES;
104
-
105
- TEXT TAXA = 'Scharff&Coddington_1997_Araneidae' TAXON = 2 TEXT = 'This is a footnote to taxon 2, Uloborus';
106
-
107
- TEXT TAXON = 4 CHARACTER = 8 TEXT = This_is_a_footnote_to_a_cell.;
108
-
109
- TEXT CHARACTER = 10 TEXT = This_is_footnote_to_char_10;
110
-
111
- TEXT FILE TEXT = 'Scharff, N. and J. A. Coddington. 1997. A phylogenetic analysis of the orb-weaving spider family Araneidae (Arachnida, Araneae). Zool. J. Linn. Soc. 120(4): 355?434';
112
-
113
- AN T = 4 A = JC DC = 2008.4.13.20.31.19 DM = 2008.4.13.20.31.38 ID = 01194a57d0161 I = _ TF = (CM 'This is an "annotation" to taxon 4') ;
114
-
115
- AN C = 4 A = JC DC = 2008.4.13.20.31.50 DM = 2008.4.13.20.32.10 ID = 01194a584b9f2 I = _ TF = (CM 'This is an annotation to charcter 4, that has no name.') ;
116
-
117
- AN T = 9 C = 3 A = 0 DC = 2008.4.20.17.24.36 DM = 2008.4.20.17.25.4 ID = 01196db963874 I = _ TF = (CM 'This is an annotation to chr 3, taxa 9, coded ?') ;
118
-
119
- AN T = 2 C = 6 A = JC DC = 2008.4.13.20.35.20 DM = 2008.4.13.20.35.36 ID = JC1194a5b7e1a3 I = _ TF = (CM 'This is an annotation that haa a hard return in it^n^n^n^nSo there!') ;
120
-
121
- AN T = 7 C = 10 A = 0 DC = 2008.4.20.17.25.11 DM = 2008.4.20.17.26.1 ID = 01196db9ebd25 I = _ TF = (CM 'this is an annotation^nwith several hard returns^nfor a cell of taxa 6, chr 9 (from zero)^ncoded as -') ;
122
-
123
- END;
124
-
125
- Begin MESQUITE;
126
- MESQUITESCRIPTVERSION 2;
127
- TITLE AUTO;
128
- tell ProjectCoordinator;
129
- getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa;
130
- tell It;
131
- setID 0 6498976404544962919 JC1191fcddc0c4;
132
- tell It;
133
- setDefaultOrder 0 1 2 3 4 5 6 7 9 8;
134
- attachments ;
135
- endTell;
136
- endTell;
137
- getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters;
138
- tell It;
139
- setID 0 2280451364422511229 JC1191fcddc0c0;
140
- checksum 0 3839411132 JC1191fcddc0c0;
141
- endTell;
142
- getEmployee #mesquite.charMatrices.BasicDataWindowCoord.BasicDataWindowCoord;
143
- tell It;
144
- showDataWindow #2280451364422511229 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker;
145
- tell It;
146
- getWindow;
147
- tell It;
148
- getTable;
149
- tell It;
150
- columnWidth 6 55;
151
- columnWidth 7 23;
152
- endTell;
153
- setExplanationSize 30;
154
- setAnnotationSize 20;
155
- setFontIncAnnot 0;
156
- setFontIncExp 0;
157
- setSize 925 472;
158
- setLocation 357 294;
159
- setFont SanSerif;
160
- setFontSize 10;
161
- getToolPalette;
162
- tell It;
163
- setTool mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindow.ibeam;
164
- endTell;
165
- setActive;
166
- setTool mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindow.ibeam;
167
- colorCells #mesquite.charMatrices.AnnotPanel.AnnotPanel;
168
- tell It;
169
- togglePanel on;
170
- endTell;
171
- setBackground White;
172
- toggleShowNames off;
173
- toggleTight off;
174
- toggleShowChanges on;
175
- toggleSeparateLines off;
176
- toggleShowStates on;
177
- toggleAutoWCharNames off;
178
- toggleShowDefaultCharNames off;
179
- toggleConstrainCW on;
180
- setColumnWidth 16;
181
- toggleBirdsEye off;
182
- toggleColorsPanel off;
183
- birdsEyeWidth 2;
184
- toggleLinkedScrolling on;
185
- toggleScrollLinkedTables off;
186
- endTell;
187
- showWindow;
188
- getEmployee #mesquite.categ.StateNamesEditor.StateNamesEditor;
189
- tell It;
190
- makeWindow;
191
- tell It;
192
- setExplanationSize 30;
193
- setAnnotationSize 20;
194
- setFontIncAnnot 0;
195
- setFontIncExp 0;
196
- setSize 925 472;
197
- setLocation 357 294;
198
- setFont SanSerif;
199
- setFontSize 10;
200
- getToolPalette;
201
- tell It;
202
- setTool mesquite.categ.StateNamesEditor.StateNamesWindow.ibeam;
203
- endTell;
204
- rowsAreCharacters on;
205
- toggleConstrainChar on;
206
- toggleConstrainCharNum 3;
207
- togglePanel off;
208
- toggleSummaryPanel off;
209
- endTell;
210
- showWindow;
211
- endTell;
212
- getEmployee #mesquite.categ.StateNamesStrip.StateNamesStrip;
213
- tell It;
214
- showStrip off;
215
- endTell;
216
- getEmployee #mesquite.charMatrices.CharReferenceStrip.CharReferenceStrip;
217
- tell It;
218
- showStrip off;
219
- endTell;
220
- getEmployee #mesquite.charMatrices.ColorCells.ColorCells;
221
- tell It;
222
- setColor Red;
223
- removeColor off;
224
- endTell;
225
- getEmployee #mesquite.charMatrices.QuickKeySelector.QuickKeySelector;
226
- tell It;
227
- autotabOff;
228
- endTell;
229
- endTell;
230
- endTell;
231
- endTell;
232
- end;
233
-
234
-
1
+ #NEXUS
2
+ [written Sun Apr 20 17:45:47 EDT 2008 by Mesquite version 2.0 (build i69) at procto/192.168.0.100]
3
+ BEGIN AUTHORS;
4
+ AUTHOR NAME = Jonathan_Coddington CODE = JC;
5
+ END;
6
+
7
+
8
+ BEGIN TAXA;
9
+ TITLE 'Scharff&Coddington_1997_Araneidae';
10
+ DIMENSIONS NTAX=10;
11
+ TAXLABELS
12
+ Dictyna Uloborus Deinopis Nephila&Herennia 'Nephilengys_cruentata' Meta Leucauge_venusta Pachygnatha 'Theridiosoma_01' Tetragnatha
13
+ ;
14
+ IDS JC1191fcddc2b128 JC1191fcddc2b129 JC1191fcddc2b130 JC1191fcddc2b131 JC1191fcddc2b132 JC1191fcddc2b133 JC1191fcddc2b134 JC1191fcddc2b135 JC1191fcddc2b137 JC1191fcddc2b136 ;
15
+ BLOCKID JC1191fcddc0c4;
16
+
17
+ END;
18
+
19
+
20
+ BEGIN CHARACTERS;
21
+ TITLE 'Scharff&Coddington_1997_Araneidae';
22
+ DIMENSIONS NCHAR=10;
23
+ FORMAT DATATYPE = STANDARD GAP = - MISSING = ? SYMBOLS = " 0 1 2 3 4 5 6 7 8 9 A";
24
+ CHARSTATELABELS
25
+ 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 ;
26
+ MATRIX
27
+ Dictyna 0?00201001
28
+ Uloborus 0?11000000
29
+ Deinopis 0?01002???
30
+ Nephila&Herennia 0?21010011
31
+ 'Nephilengys_cruentata'0?(0,1)1010(0,1,2)11
32
+ Meta 0?01A10011
33
+ Leucauge_venusta ???--?-??-
34
+ Pachygnatha 0?210(0,1)0011
35
+ 'Theridiosoma_01' ??????????
36
+ Tetragnatha 0?01011011
37
+
38
+ ;
39
+ IDS JC1191fcddc3b425 JC1191fcddc3b426 JC1191fcddc3b427 JC1191fcddc3b428 JC1191fcddc3b429 JC1191fcddc3b430 JC1191fcddc3b431 JC1191fcddc3b432 JC1191fcddc3b433 JC1191fcddc3b434 ;
40
+ BLOCKID JC1191fcddc0c0;
41
+
42
+
43
+ END;
44
+ BEGIN TREES;
45
+ Title Imported_trees;
46
+ LINK Taxa = 'Scharff&Coddington_1997_Araneidae';
47
+ TRANSLATE
48
+ 1 Dictyna,
49
+ 2 Uloborus,
50
+ 3 Deinopis,
51
+ 4 Nephila&Herennia,
52
+ 5 'Nephilengys_cruentata',
53
+ 6 Meta,
54
+ 7 Leucauge_venusta,
55
+ 8 Pachygnatha,
56
+ 9 'Theridiosoma_01',
57
+ 10 Tetragnatha;
58
+ TREE 'Imported tree 1+' = (1,((2,3),(((4,5),(6,(7,(8,10)))),9)));
59
+ TREE 'Imported tree 2+' = (1,((2,3),(((4,5),(6,(7,(8,10)))),9)));
60
+ TREE 'Imported tree 3+' = (1,((2,3),(((6,(4,5)),(7,(8,10))),9)));
61
+ TREE 'Imported tree 4+' = (1,((2,3),(((4,5),(6,(7,(8,10)))),9)));
62
+ TREE 'Imported tree 5+' = (1,((2,3),(((6,(4,5)),(7,(8,10))),9)));
63
+ TREE 'Imported tree 6+' = (1,((2,3),(((4,5),(6,(7,(8,10)))),9)));
64
+ TREE 'Imported tree 7+' = (1,((2,3),(((6,(4,5)),(7,(8,10))),9)));
65
+ TREE 'Imported tree 8+' = (1,((2,3),(((6,(4,5)),(7,(8,10))),9)));
66
+
67
+ END;
68
+
69
+
70
+ BEGIN LABELS;
71
+ CHARGROUPLABEL MM_Genitalia COLOR = (RGB 1.0 0.4 0.4) ;
72
+ CHARGROUPLABEL Somatic COLOR = (RGB 0.6 1.0 0.33333333) ;
73
+ CHARGROUPLABEL Spinnerets COLOR = (RGB 0.46666667 0.57254902 1.0) ;
74
+ CHARGROUPLABEL Behavior COLOR = (RGB 1.0 0.46666667 1.0) ;
75
+
76
+
77
+ END;
78
+
79
+ BEGIN SETS;
80
+ CHARPARTITION * UNTITLED = Somatic : 1 - 2 4, MM_Genitalia : 5 - 8 10;
81
+
82
+ END;
83
+
84
+ BEGIN ASSUMPTIONS;
85
+ TYPESET * UNTITLED = unord: 1 - 10;
86
+
87
+ EXSET * UNTITLED = ;
88
+
89
+ WTSET * UNTITLED = 1: 1 - 10 ;
90
+
91
+ END;
92
+
93
+ BEGIN CODONS;
94
+ CODESET * UNTITLED = universal: 1 - 10;
95
+
96
+
97
+ END;
98
+
99
+ BEGIN MESQUITECHARMODELS;
100
+ ProbModelSet * UNTITLED = 'Mk1 (est.)': 1 - 10;
101
+ END;
102
+
103
+ BEGIN NOTES;
104
+
105
+ TEXT TAXA = 'Scharff&Coddington_1997_Araneidae' TAXON = 2 TEXT = 'This is a footnote to taxon 2, Uloborus';
106
+
107
+ TEXT TAXON = 4 CHARACTER = 8 TEXT = This_is_a_footnote_to_a_cell.;
108
+
109
+ TEXT CHARACTER = 10 TEXT = This_is_footnote_to_char_10;
110
+
111
+ TEXT FILE TEXT = 'Scharff, N. and J. A. Coddington. 1997. A phylogenetic analysis of the orb-weaving spider family Araneidae (Arachnida, Araneae). Zool. J. Linn. Soc. 120(4): 355?434';
112
+
113
+ AN T = 4 A = JC DC = 2008.4.13.20.31.19 DM = 2008.4.13.20.31.38 ID = 01194a57d0161 I = _ TF = (CM 'This is an "annotation" to taxon 4') ;
114
+
115
+ AN C = 4 A = JC DC = 2008.4.13.20.31.50 DM = 2008.4.13.20.32.10 ID = 01194a584b9f2 I = _ TF = (CM 'This is an annotation to charcter 4, that has no name.') ;
116
+
117
+ AN T = 9 C = 3 A = 0 DC = 2008.4.20.17.24.36 DM = 2008.4.20.17.25.4 ID = 01196db963874 I = _ TF = (CM 'This is an annotation to chr 3, taxa 9, coded ?') ;
118
+
119
+ AN T = 2 C = 6 A = JC DC = 2008.4.13.20.35.20 DM = 2008.4.13.20.35.36 ID = JC1194a5b7e1a3 I = _ TF = (CM 'This is an annotation that haa a hard return in it^n^n^n^nSo there!') ;
120
+
121
+ AN T = 7 C = 10 A = 0 DC = 2008.4.20.17.25.11 DM = 2008.4.20.17.26.1 ID = 01196db9ebd25 I = _ TF = (CM 'this is an annotation^nwith several hard returns^nfor a cell of taxa 6, chr 9 (from zero)^ncoded as -') ;
122
+
123
+ END;
124
+
125
+ Begin MESQUITE;
126
+ MESQUITESCRIPTVERSION 2;
127
+ TITLE AUTO;
128
+ tell ProjectCoordinator;
129
+ getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa;
130
+ tell It;
131
+ setID 0 6498976404544962919 JC1191fcddc0c4;
132
+ tell It;
133
+ setDefaultOrder 0 1 2 3 4 5 6 7 9 8;
134
+ attachments ;
135
+ endTell;
136
+ endTell;
137
+ getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters;
138
+ tell It;
139
+ setID 0 2280451364422511229 JC1191fcddc0c0;
140
+ checksum 0 3839411132 JC1191fcddc0c0;
141
+ endTell;
142
+ getEmployee #mesquite.charMatrices.BasicDataWindowCoord.BasicDataWindowCoord;
143
+ tell It;
144
+ showDataWindow #2280451364422511229 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker;
145
+ tell It;
146
+ getWindow;
147
+ tell It;
148
+ getTable;
149
+ tell It;
150
+ columnWidth 6 55;
151
+ columnWidth 7 23;
152
+ endTell;
153
+ setExplanationSize 30;
154
+ setAnnotationSize 20;
155
+ setFontIncAnnot 0;
156
+ setFontIncExp 0;
157
+ setSize 925 472;
158
+ setLocation 357 294;
159
+ setFont SanSerif;
160
+ setFontSize 10;
161
+ getToolPalette;
162
+ tell It;
163
+ setTool mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindow.ibeam;
164
+ endTell;
165
+ setActive;
166
+ setTool mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindow.ibeam;
167
+ colorCells #mesquite.charMatrices.AnnotPanel.AnnotPanel;
168
+ tell It;
169
+ togglePanel on;
170
+ endTell;
171
+ setBackground White;
172
+ toggleShowNames off;
173
+ toggleTight off;
174
+ toggleShowChanges on;
175
+ toggleSeparateLines off;
176
+ toggleShowStates on;
177
+ toggleAutoWCharNames off;
178
+ toggleShowDefaultCharNames off;
179
+ toggleConstrainCW on;
180
+ setColumnWidth 16;
181
+ toggleBirdsEye off;
182
+ toggleColorsPanel off;
183
+ birdsEyeWidth 2;
184
+ toggleLinkedScrolling on;
185
+ toggleScrollLinkedTables off;
186
+ endTell;
187
+ showWindow;
188
+ getEmployee #mesquite.categ.StateNamesEditor.StateNamesEditor;
189
+ tell It;
190
+ makeWindow;
191
+ tell It;
192
+ setExplanationSize 30;
193
+ setAnnotationSize 20;
194
+ setFontIncAnnot 0;
195
+ setFontIncExp 0;
196
+ setSize 925 472;
197
+ setLocation 357 294;
198
+ setFont SanSerif;
199
+ setFontSize 10;
200
+ getToolPalette;
201
+ tell It;
202
+ setTool mesquite.categ.StateNamesEditor.StateNamesWindow.ibeam;
203
+ endTell;
204
+ rowsAreCharacters on;
205
+ toggleConstrainChar on;
206
+ toggleConstrainCharNum 3;
207
+ togglePanel off;
208
+ toggleSummaryPanel off;
209
+ endTell;
210
+ showWindow;
211
+ endTell;
212
+ getEmployee #mesquite.categ.StateNamesStrip.StateNamesStrip;
213
+ tell It;
214
+ showStrip off;
215
+ endTell;
216
+ getEmployee #mesquite.charMatrices.CharReferenceStrip.CharReferenceStrip;
217
+ tell It;
218
+ showStrip off;
219
+ endTell;
220
+ getEmployee #mesquite.charMatrices.ColorCells.ColorCells;
221
+ tell It;
222
+ setColor Red;
223
+ removeColor off;
224
+ endTell;
225
+ getEmployee #mesquite.charMatrices.QuickKeySelector.QuickKeySelector;
226
+ tell It;
227
+ autotabOff;
228
+ endTell;
229
+ endTell;
230
+ endTell;
231
+ endTell;
232
+ end;
233
+
234
+