nexus_parser 1.0.0

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Files changed (20) hide show
  1. data/.document +5 -0
  2. data/.gitignore +21 -0
  3. data/LICENSE +20 -0
  4. data/MIT-LICENSE +20 -0
  5. data/README +13 -0
  6. data/README.rdoc +17 -0
  7. data/Rakefile +53 -0
  8. data/VERSION +1 -0
  9. data/init.rb +1 -0
  10. data/install.rb +1 -0
  11. data/lib/lexer.rb +66 -0
  12. data/lib/nexus_file.rb +282 -0
  13. data/lib/parser.rb +334 -0
  14. data/lib/tokens.rb +269 -0
  15. data/tasks/nexus_parser_tasks.rake +4 -0
  16. data/test/MX_test_03.nex +234 -0
  17. data/test/test.nex +382 -0
  18. data/test/test_nexus_parser.rb +937 -0
  19. data/uninstall.rb +1 -0
  20. metadata +82 -0
data/tasks/nexus_parser_tasks.rake ADDED
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+ # desc "Explaining what the task does"
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+ # task :nexus_parser do
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+ # # Task goes here
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+ # end
data/test/MX_test_03.nex ADDED
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+ #NEXUS
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+ [written Sun Apr 20 17:45:47 EDT 2008 by Mesquite version 2.0 (build i69) at procto/192.168.0.100]
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+ BEGIN AUTHORS;
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+ AUTHOR NAME = Jonathan_Coddington CODE = JC;
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+ END;
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+
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+
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+ BEGIN TAXA;
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+ TITLE 'Scharff&Coddington_1997_Araneidae';
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+ DIMENSIONS NTAX=10;
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+ TAXLABELS
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+ Dictyna Uloborus Deinopis Nephila&Herennia 'Nephilengys_cruentata' Meta Leucauge_venusta Pachygnatha 'Theridiosoma_01' Tetragnatha
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+ ;
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+ IDS JC1191fcddc2b128 JC1191fcddc2b129 JC1191fcddc2b130 JC1191fcddc2b131 JC1191fcddc2b132 JC1191fcddc2b133 JC1191fcddc2b134 JC1191fcddc2b135 JC1191fcddc2b137 JC1191fcddc2b136 ;
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+ BLOCKID JC1191fcddc0c4;
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+
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+ END;
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+
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+
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+ BEGIN CHARACTERS;
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+ TITLE 'Scharff&Coddington_1997_Araneidae';
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+ DIMENSIONS NCHAR=10;
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+ FORMAT DATATYPE = STANDARD GAP = - MISSING = ? SYMBOLS = " 0 1 2 3 4 5 6 7 8 9 A";
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+ CHARSTATELABELS
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+ 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 ;
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+ MATRIX
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+ Dictyna 0?00201001
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+ Uloborus 0?11000000
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+ Deinopis 0?01002???
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+ Nephila&Herennia 0?21010011
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+ 'Nephilengys_cruentata'0?(0,1)1010(0,1,2)11
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+ Meta 0?01A10011
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+ Leucauge_venusta ???--?-??-
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+ Pachygnatha 0?210(0,1)0011
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+ 'Theridiosoma_01' ??????????
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+ Tetragnatha 0?01011011
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+
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+ ;
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+ IDS JC1191fcddc3b425 JC1191fcddc3b426 JC1191fcddc3b427 JC1191fcddc3b428 JC1191fcddc3b429 JC1191fcddc3b430 JC1191fcddc3b431 JC1191fcddc3b432 JC1191fcddc3b433 JC1191fcddc3b434 ;
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+ BLOCKID JC1191fcddc0c0;
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+
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+
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+ END;
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+ BEGIN TREES;
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+ Title Imported_trees;
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+ LINK Taxa = 'Scharff&Coddington_1997_Araneidae';
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+ TRANSLATE
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+ 1 Dictyna,
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+ 2 Uloborus,
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+ 3 Deinopis,
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+ 4 Nephila&Herennia,
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+ 5 'Nephilengys_cruentata',
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+ 6 Meta,
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+ 7 Leucauge_venusta,
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+ 8 Pachygnatha,
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+ 9 'Theridiosoma_01',
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+ 10 Tetragnatha;
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+ TREE 'Imported tree 1+' = (1,((2,3),(((4,5),(6,(7,(8,10)))),9)));
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+ TREE 'Imported tree 2+' = (1,((2,3),(((4,5),(6,(7,(8,10)))),9)));
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+ TREE 'Imported tree 3+' = (1,((2,3),(((6,(4,5)),(7,(8,10))),9)));
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+ TREE 'Imported tree 4+' = (1,((2,3),(((4,5),(6,(7,(8,10)))),9)));
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+ TREE 'Imported tree 5+' = (1,((2,3),(((6,(4,5)),(7,(8,10))),9)));
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+ TREE 'Imported tree 6+' = (1,((2,3),(((4,5),(6,(7,(8,10)))),9)));
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+ TREE 'Imported tree 7+' = (1,((2,3),(((6,(4,5)),(7,(8,10))),9)));
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+ TREE 'Imported tree 8+' = (1,((2,3),(((6,(4,5)),(7,(8,10))),9)));
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+
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+ END;
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+
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+
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+ BEGIN LABELS;
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+ CHARGROUPLABEL MM_Genitalia COLOR = (RGB 1.0 0.4 0.4) ;
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+ CHARGROUPLABEL Somatic COLOR = (RGB 0.6 1.0 0.33333333) ;
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+ CHARGROUPLABEL Spinnerets COLOR = (RGB 0.46666667 0.57254902 1.0) ;
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+ CHARGROUPLABEL Behavior COLOR = (RGB 1.0 0.46666667 1.0) ;
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+
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+
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+ END;
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+
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+ BEGIN SETS;
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+ CHARPARTITION * UNTITLED = Somatic : 1 - 2 4, MM_Genitalia : 5 - 8 10;
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+
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+ END;
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+
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+ BEGIN ASSUMPTIONS;
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+ TYPESET * UNTITLED = unord: 1 - 10;
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+
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+ EXSET * UNTITLED = ;
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+
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+ WTSET * UNTITLED = 1: 1 - 10 ;
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+
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+ END;
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+
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+ BEGIN CODONS;
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+ CODESET * UNTITLED = universal: 1 - 10;
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+
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+
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+ END;
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+
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+ BEGIN MESQUITECHARMODELS;
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+ ProbModelSet * UNTITLED = 'Mk1 (est.)': 1 - 10;
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+ END;
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+
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+ BEGIN NOTES;
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+
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+ TEXT TAXA = 'Scharff&Coddington_1997_Araneidae' TAXON = 2 TEXT = 'This is a footnote to taxon 2, Uloborus';
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+
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+ TEXT TAXON = 4 CHARACTER = 8 TEXT = This_is_a_footnote_to_a_cell.;
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+
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+ TEXT CHARACTER = 10 TEXT = This_is_footnote_to_char_10;
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+
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+ 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';
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+
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+ 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') ;
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+
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+ 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.') ;
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+
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+ 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 ?') ;
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+
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+ 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!') ;
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+
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+ 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 -') ;
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+
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+ END;
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+
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+ Begin MESQUITE;
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+ MESQUITESCRIPTVERSION 2;
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+ TITLE AUTO;
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+ tell ProjectCoordinator;
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+ getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa;
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+ tell It;
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+ setID 0 6498976404544962919 JC1191fcddc0c4;
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+ tell It;
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+ setDefaultOrder 0 1 2 3 4 5 6 7 9 8;
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+ attachments ;
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+ endTell;
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+ endTell;
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+ getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters;
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+ tell It;
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+ setID 0 2280451364422511229 JC1191fcddc0c0;
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+ checksum 0 3839411132 JC1191fcddc0c0;
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+ endTell;
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+ getEmployee #mesquite.charMatrices.BasicDataWindowCoord.BasicDataWindowCoord;
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+ tell It;
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+ showDataWindow #2280451364422511229 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker;
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+ tell It;
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+ getWindow;
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+ tell It;
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+ getTable;
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+ tell It;
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+ columnWidth 6 55;
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+ columnWidth 7 23;
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+ endTell;
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+ setExplanationSize 30;
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+ setAnnotationSize 20;
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+ setFontIncAnnot 0;
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+ setFontIncExp 0;
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+ setSize 925 472;
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+ setLocation 357 294;
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+ setFont SanSerif;
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+ setFontSize 10;
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+ getToolPalette;
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+ tell It;
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+ setTool mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindow.ibeam;
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+ endTell;
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+ setActive;
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+ setTool mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindow.ibeam;
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+ colorCells #mesquite.charMatrices.AnnotPanel.AnnotPanel;
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+ tell It;
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+ togglePanel on;
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+ endTell;
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+ setBackground White;
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+ toggleShowNames off;
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+ toggleTight off;
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+ toggleShowChanges on;
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+ toggleSeparateLines off;
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+ toggleShowStates on;
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+ toggleAutoWCharNames off;
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+ toggleShowDefaultCharNames off;
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+ toggleConstrainCW on;
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+ setColumnWidth 16;
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+ toggleBirdsEye off;
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+ toggleColorsPanel off;
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+ birdsEyeWidth 2;
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+ toggleLinkedScrolling on;
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+ toggleScrollLinkedTables off;
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+ endTell;
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+ showWindow;
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+ getEmployee #mesquite.categ.StateNamesEditor.StateNamesEditor;
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+ tell It;
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+ makeWindow;
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+ tell It;
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+ setExplanationSize 30;
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+ setAnnotationSize 20;
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+ setFontIncAnnot 0;
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+ setFontIncExp 0;
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+ setSize 925 472;
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+ setLocation 357 294;
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+ setFont SanSerif;
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+ setFontSize 10;
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+ getToolPalette;
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+ tell It;
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+ setTool mesquite.categ.StateNamesEditor.StateNamesWindow.ibeam;
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+ endTell;
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+ rowsAreCharacters on;
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+ toggleConstrainChar on;
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+ toggleConstrainCharNum 3;
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+ togglePanel off;
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+ toggleSummaryPanel off;
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+ endTell;
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+ showWindow;
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+ endTell;
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+ getEmployee #mesquite.categ.StateNamesStrip.StateNamesStrip;
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+ tell It;
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+ showStrip off;
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+ endTell;
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+ getEmployee #mesquite.charMatrices.CharReferenceStrip.CharReferenceStrip;
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+ tell It;
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+ showStrip off;
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+ endTell;
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+ getEmployee #mesquite.charMatrices.ColorCells.ColorCells;
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+ tell It;
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+ setColor Red;
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+ removeColor off;
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+ endTell;
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+ getEmployee #mesquite.charMatrices.QuickKeySelector.QuickKeySelector;
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+ tell It;
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+ autotabOff;
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+ endTell;
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+ endTell;
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+ endTell;
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+ endTell;
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+ end;
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+
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+
data/test/test.nex ADDED
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+ #NEXUS
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+ [written Sun Apr 13 13:59:23 EDT 2008 by Mesquite version 2.01+ (build j52) at NMNHN-CODDINGT/172.17.227.145 (Jonathan Coddington)]
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+
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+ BEGIN TAXA;
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+ TITLE 'Scharff&Coddington_1997_Araneidae';
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+ DIMENSIONS NTAX=70;
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+ TAXLABELS
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+ Dictyna Uloborus Deinopis Nephila Nephilengys Meta Leucauge Pachygnatha Tetragnatha Theridiosoma Linyphia Pimoa Theridion Chorizopes Gasteracantha Aetrocantha Togacantha Gastroxya Augusta Isoxya Austracantha Macracantha Aspidolasius Caerostris Hypognatha Arkys Archemorus Encyosaccus Xylethrus Chaetacis Micrathena Mastophora Cyrtarachne Pasilobus Arachnura Witica Mecynogea Cyrtophora Neogea Argiope Gea Scoloderus Acanthepeira Anepsion Dolophone Hypsosinga Zygiella Kaira Metepeira Singa Larinia Neoscona Mangora Cercidia Pronous Aculepeira Araneus Bertrana Alpaida Enacrosoma Wixia Acacesia Metazygia Eustala Cyclosa Nuctenea Colphepeira Araniella Eriophora Verrucosa
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+ ;
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+ IDS JC1191fcddc2b128 JC1191fcddc2b129 JC1191fcddc2b130 JC1191fcddc2b131 JC1191fcddc2b132 JC1191fcddc2b133 JC1191fcddc2b134 JC1191fcddc2b135 JC1191fcddc2b136 JC1191fcddc2b137 JC1191fcddc2b138 JC1191fcddc2b139 JC1191fcddc2b140 JC1191fcddc2b141 JC1191fcddc2b142 JC1191fcddc2b143 JC1191fcddc2b144 JC1191fcddc2b145 JC1191fcddc2b146 JC1191fcddc2b147 JC1191fcddc2b148 JC1191fcddc2b149 JC1191fcddc2b150 JC1191fcddc2b151 JC1191fcddc2b152 JC1191fcddc2b153 JC1191fcddc2b154 JC1191fcddc2b155 JC1191fcddc2b156 JC1191fcddc2b157 JC1191fcddc2b158 JC1191fcddc2b159 JC1191fcddc2b160 JC1191fcddc2b161 JC1191fcddc2b162 JC1191fcddc2b163 JC1191fcddc2b164 JC1191fcddc2b165 JC1191fcddc2b166 JC1191fcddc2b167 JC1191fcddc2b168 JC1191fcddc2b169 JC1191fcddc2b170 JC1191fcddc2b171 JC1191fcddc2b172 JC1191fcddc2b173 JC1191fcddc2b174 JC1191fcddc2b175 JC1191fcddc2b176 JC1191fcddc2b177 JC1191fcddc2b178 JC1191fcddc2b179 JC1191fcddc2b180 JC1191fcddc2b181 JC1191fcddc2b182 JC1191fcddc2b183 JC1191fcddc2b184 JC1191fcddc2b185 JC1191fcddc2b186 JC1191fcddc2b187 JC1191fcddc2b188 JC1191fcddc2b189 JC1191fcddc2b190 JC1191fcddc2b191 JC1191fcddc2b192 JC1191fcddc2b193 JC1191fcddc2b194 JC1191fcddc2b195 JC1191fcddc2b196 JC1191fcddc2b197 ;
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+ BLOCKID JC1191fcddc0c4;
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+
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+ END;
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+
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+
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+ BEGIN CHARACTERS;
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+ TITLE 'Scharff&Coddington_1997_Araneidae';
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+ DIMENSIONS NCHAR=82;
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+ FORMAT DATATYPE = STANDARD GAP = - MISSING = ? SYMBOLS = " 0 1 2 3 4 5 6";
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+ CHARSTATELABELS
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+ 1 Tibia_II / norm modified, 2 TII_macrosetae / '= TI' stronger, 3 Femoral_tuber / abs pres 'm-setae', 4 'Palp patellar m-setae' / abs pres, 5 Cymbium / dorsal mesal lateral, 6 Paracymbium / abs pres, 7 Globular_tegulum / abs pres, 8 Conductor_shape / entire w_lobe, 9 Conductor_wraps_embolus / abs pres, 10 Median_apophysis / pres abs, 11 MA_bifid_prong / abs pres, 12 MA_threadlike_spur / abs pres, 13 MA_w_transparent_flap / abs pres, 14 MA_large_w_fork / abs pres, 15 MA_ant_margin / smooth toothed, 16 Radix / abs pres, 17 Distal_hematodocha / abs pres, 18 Paramedian_apophysis / abs pres, 19 Stipes / abs pres, 20 Subterminal_apophysis / abs pres, 21 Subterm_apophysis / norm bubble, 22 Terminal_apophysis / abs pres, 23 Embolus_tip / simple w_cap, 24 Embolus / clockwise anticlockwise, 25 F_genitalia / entelogyne haplogyne, 26 Epigynum / pres abs, 27 Genital_tubercle / abs pres, 28 Scape / abs pres, 29 Scape / normal elongate, 30 Scape_w_pocket_tip / abs pres, 31 Scape / smooth wrinkled, 32 'M Coxa + TrIV setae' / normal stout, 33 Coxa_I_hook / abs pres, 34 Femur_II_w_groove / abs pres, 35 Femur_IV_trichobothria / abs pres, 36 'Pat-tibial autospasy' / abs pres, 37 MtIV_trichobothria / 0_or_1 many, 38 'Tibia-Metatarsus' / norm flattened, 39 Serrate_accessory_claw_setae / a p, 40 Sustentaculum / abs pres, 41 Carapace / hirsute glabrous, 42 F_carapace_shape / 'L>W' 'W(L', 43 M_carapace_shape / oval Gast wide, 44 Cheliceral_margin / smooth strid, 45 Endite_tooth / abs pres, 46 Clypeal_tooth / abs pres, 47 F_Cephalon / norm enlarged, 48 Cephalon_height / normal high, 49 'Anterior:Posterior MOA (m72)' / '<1' '>1', 50 'Lat.-median eye separation' / '<1' '>1', 51 PME_canoe_tapetum / abs pres, 52 PME_narrow_tapetum / abs pres, 53 PLE_canoe_tapetum / norm red abs, 54 PE_row / str_to_recurved procurved, 55 Feathery_hairs / abs pres, 56 Abdominal_sigillae / abs pres, 57 Abd._sigillae / scatt 1_row 2_rows, 58 F_abd_w_ventral_condyles / abs pres, 59 M_abd._shape / norm Gast U 3 4 5 6, 60 Abdominal_shape / 'L>W' 'W>L', 61 'F-M size' / '<2x' '>2x', 62 Gast_abdominal_spines / abs pres, 63 Booklung_cover / smooth strid, 64 Booklung_cover / norm grooved, 65 Sclerotized_ring / abs scl solid, 66 Spiracle / normal sclerotized, 67 'Cp + abd setal bases' / normal gast, 68 Cribellum / pres abs, 69 ALS_PY_bases / normal reduced, 70 Narrowed_PY_fields / abs pres, 71 PMS_paracrib / strob deinopoid abs, 72 PMS_mAP_nubbins / abs pres, 73 PMS_AC_brush / pres 'reduced-absent', 74 Orb / abs pres lost, 75 Orb / w_SS no_SS, 76 Radius_behaviour / Ar Ul Cy Ne, 77 'Non-sticky spiral' / temporary perm, 78 SS_localization / oL1 iL1 L4, 79 'Low-shear SS lines' / abs pres, 80 Very_sticky_SS / abs pres, 81 Extreme_L4_combing / abs pres, 82 Rest_posture / L12_flexed L12_extend ;
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+ MATRIX
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+ Dictyna 0000200001-----0-000-0000000---0000000000000000000100000-00000000000000000-------0
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+ Uloborus 0011000000000000-000-0000000---00010001000000000000-2010-0000000000000100101000001
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+ Deinopis 0000000???-----0-000-0000000---00000001000000000000-2010-0000001000000100100000001
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+ Nephila 0001010011-----0-000-0000000---0000000101000000000100000-0001001000100211103120000
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+ Nephilengys 0001010011-----0-000-0000000---0000000100000000100100000-0001001000100211103120000
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+ Meta 0001010011-----0-000-0000000---0000000101000000000100000-0000001000100210100010001
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+ Leucauge 0001010011-----0-000-00000010000001000101000000000100000-0000000000100211100010001
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+ Pachygnatha 0001011011-----0-000-0001100---00010001010000000000-0000-000000000010020110?-?000?
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+ Tetragnatha 0001011011-----0-000-0001100---00010001010000000000-2000-0000000000100211100010001
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+ Theridiosoma 0001010000000000-000-0010000---0000000101000000100100000-0000000000110211100010000
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+ Linyphia 0001010--1-----0-000-00000010100000100101001000000100000-00000000001102012----0000
34
+ Pimoa 0001010000000000-000-0000000---0000100101001000000100000-00000000001102012----0000
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+ Theridion 0000000000000000-000-0000000----000000101000000000100000-00000000001102012----0000
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+ Chorizopes 0001110000000001111101000000---0000000101000000001110000-00000000011002102-------?
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+ Gasteracantha 00001100000000010100-0000011000000001010011000110111000111211101211100210100000000
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+ Aetrocantha 00001100000000010100-0000010---0000010100110001101110001112111011111002?01???000??
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+ Togacantha 00001100000000010100-0000000---0000010110110001101110001111111011111002?01????00??
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+ Gastroxya 00201100000010010100-0000000---0000000100010001101110001211111010111002?01????00??
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+ Augusta 00201100000010010100-0000000---0000000100100001101110001203111010111002?01??0?00?0
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+ Isoxya 00001100000000010100-0000000---0110010110120001101110001114101010111002?010?0?00?0
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+ Austracantha 01101100000000010100-0000000---0110010100020101101110001111101010111002101????????
44
+ Macracantha 00001100000000010100-0000000---0000010110110001101110001101111012111002?0100??00?0
45
+ Aspidolasius 0001110000000000-000-0000000---00000001101200011011100011051100100?10021010?0?000?
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+ Caerostris 0001100000000000-000-0000000---00000111101000111011100010001100100110021010?000000
47
+ Hypognatha 00011100000000010000-0000000---01100001010200011111100011051000101?100211100000000
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+ Arkys 0001110000000000-000-000000101000000001010200011011?0101206000010011002112????????
49
+ Archemorus 0001110000000000-000-0000000---00000011010000011011?0101206100010011002012????????
50
+ Encyosaccus 00011101000000010000-00000010000000000101000001111110001100110010011002?010?0?00??
51
+ Xylethrus 00011101000000010000-00000010000000000101000000001110001100110011111002?010?0?00?0
52
+ Chaetacis 00011101000000010000-00000010000000000101000000001110001000000112111002?010??00000
53
+ Micrathena 00011101000000010000-0000001000011000011100000000111000100000011211100210100000000
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+ Mastophora 00001100000000010000-0000000---0000010111000000001110000?00110010001002?02-----11-
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+ Cyrtarachne 00011100000000010000-0000000---0000000101000000000110001000110010001002?01000?111?
56
+ Pasilobus 0001110000000001?0?0-0000000---0000000101000000001110001100110010001002?010??-111?
57
+ Arachnura 00001100000000010000-0000000---0000000110000000011110000-00010010001002?0100000000
58
+ Witica 0000110001-----10000-0010000---0000010110000000001110000-00010010001002?0100000000
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+ Mecynogea 0001110001-----10000-1010000---0000000110000000000110000-000000100010121011?1----0
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+ Cyrtophora 000?1100000000010000-0010000---0000000110000000010110000-00010010001012101121----0
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+ Neogea 0001110000010000-000-0000000---0000000110000000000111100-000100100010021010???00??
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+ Argiope 00011100000100010010-0100000---0000000110000000000111100-0001001000100210100000000
63
+ Gea 00011100000100010010-0000000---0000000110000000000111100-0000001000100210100000000
64
+ Scoloderus 01111100000000010000-00000010000110000111000000001110000-0000001000100210100000000
65
+ Acanthepeira 00111100000000010100-00000010000000000110000100101110000-0000001000100210100000000
66
+ Anepsion 0011110000000001?100-10000010000110000111000100000110000-000000100?100210?????000?
67
+ Dolophone 0011110001000--11100-100000100100000111100001100001100011001000100?10021010?0?????
68
+ Hypsosinga 00111100000000011010-10?00010000000000110000100100110000-000000100010021010???00??
69
+ Zygiella 00011100000000011010-1010000---0000000110000000010110000-000000100010021010???00??
70
+ Kaira 00001100001000111000-10000010000000000110000000010110000-00010010001002101-------?
71
+ Metepeira 00011100001000111000-11000010010000000110000100010110000-0000001000100210100000000
72
+ Singa 00111100000000011011010000010100000000110000000010110000-000000100010021010???00?0
73
+ Larinia 00111100000000011011011000010110000000110000100010110000-000000100010021010?000001
74
+ Neoscona 01111100000000011011010000010100110000111000100010110000-0000001000100210100000000
75
+ Mangora 01111100000000011001010000010110110000110000100010110000-0000001000100210100000000
76
+ Cercidia 01011100000000011001010000010110110000110000100010110000-000000100010021110???00??
77
+ Pronous 0101110000000001000???000000---01100001?0000100000??0000-000000100010021110??0000?
78
+ Aculepeira 11111100001000111011011000010010110000110000100010110000-000000100010021010???00?0
79
+ Araneus 11111100001000011011011000010110110000110000100010110000-0000001000100210100000000
80
+ Bertrana 01111101000000010001010000010100110000100000100010110000-0010001000100210100000000
81
+ Alpaida 00111101000000010001010000010000110010110000100011110000-000000100010021010000000?
82
+ Enacrosoma 00111101000000010000-10000010100110000110000100110110000-001000100010021010??0000?
83
+ Wixia 01111101000001011001010000010001110000110000100000110000-000000100010021010000000?
84
+ Acacesia 01111100000001011001010000010001110000110000100000110000-0000001000100210100000000
85
+ Metazygia 01111100000000011001110000010000110000110000100010110000-0000001000100210100000000
86
+ Eustala 01111101000000011011110000010010110000110000100000110000-0000001000100210100000000
87
+ Cyclosa 01111101000000011000-10000010010110010110000100010110000-0000001000100210100000000
88
+ Nuctenea 00011100000000011000-10000010010110000110000100010110000-0000001000100210100000000
89
+ Colphepeira 00111100000000011000-100000100101100001?0000100000110000-00000010001??2??10???00??
90
+ Araniella 10111101000000010000-10000010110110000110000100011110000-000000100010021010?0?00?0
91
+ Eriophora 11111100000000011110-10000011010110010110000100011110000-0000001000100210100000000
92
+ Verrucosa 11111101000000011000-10000011010110000110000100111110000-001000100010021010?000000
93
+
94
+ ;
95
+ IDS JC1191fcddc3b425 JC1191fcddc3b426 JC1191fcddc3b427 JC1191fcddc3b428 JC1191fcddc3b429 JC1191fcddc3b430 JC1191fcddc3b431 JC1191fcddc3b432 JC1191fcddc3b433 JC1191fcddc3b434 JC1191fcddc3b435 JC1191fcddc3b436 JC1191fcddc3b437 JC1191fcddc3b438 JC1191fcddc3b439 JC1191fcddc3b440 JC1191fcddc3b441 JC1191fcddc3b442 JC1191fcddc3b443 JC1191fcddc3b444 JC1191fcddc3b445 JC1191fcddc3b446 JC1191fcddc3b447 JC1191fcddc3b448 JC1191fcddc3b449 JC1191fcddc3b450 JC1191fcddc3b451 JC1191fcddc3b452 JC1191fcddc3b453 JC1191fcddc3b454 JC1191fcddc3b455 JC1191fcddc3b456 JC1191fcddc3b457 JC1191fcddc3b458 JC1191fcddc3b459 JC1191fcddc3b460 JC1191fcddc3b461 JC1191fcddc3b462 JC1191fcddc3b463 JC1191fcddc3b464 JC1191fcddc3b465 JC1191fcddc3b466 JC1191fcddc3b467 JC1191fcddc3b468 JC1191fcddc3b469 JC1191fcddc3b470 JC1191fcddc3b471 JC1191fcddc3b472 JC1191fcddc3b473 JC1191fcddc3b474 JC1191fcddc3b475 JC1191fcddc3b476 JC1191fcddc3b477 JC1191fcddc3b478 JC1191fcddc3b479 JC1191fcddc3b480 JC1191fcddc3b481 JC1191fcddc3b482 JC1191fcddc3b483 JC1191fcddc3b484 JC1191fcddc3b485 JC1191fcddc3b486 JC1191fcddc3b487 JC1191fcddc3b488 JC1191fcddc3b489 JC1191fcddc3b490 JC1191fcddc3b491 JC1191fcddc3b492 JC1191fcddc3b493 JC1191fcddc3b494 JC1191fcddc3b495 JC1191fcddc3b496 JC1191fcddc3b497 JC1191fcddc3b498 JC1191fcddc3b499 JC1191fcddc3b500 JC1191fcddc3b501 JC1191fcddc3b502 JC1191fcddc3b503 JC1191fcddc3b504 JC1191fcddc3b505 JC1191fcddc3b506 ;
96
+ BLOCKID JC1191fcddc0c0;
97
+
98
+
99
+ END;
100
+ BEGIN TREES;
101
+ Title Imported_trees;
102
+ LINK Taxa = 'Scharff&Coddington_1997_Araneidae';
103
+ TRANSLATE
104
+ 1 Dictyna,
105
+ 2 Uloborus,
106
+ 3 Deinopis,
107
+ 4 Nephila,
108
+ 5 Nephilengys,
109
+ 6 Meta,
110
+ 7 Leucauge,
111
+ 8 Pachygnatha,
112
+ 9 Tetragnatha,
113
+ 10 Theridiosoma,
114
+ 11 Linyphia,
115
+ 12 Pimoa,
116
+ 13 Theridion,
117
+ 14 Chorizopes,
118
+ 15 Gasteracantha,
119
+ 16 Aetrocantha,
120
+ 17 Togacantha,
121
+ 18 Gastroxya,
122
+ 19 Augusta,
123
+ 20 Isoxya,
124
+ 21 Austracantha,
125
+ 22 Macracantha,
126
+ 23 Aspidolasius,
127
+ 24 Caerostris,
128
+ 25 Hypognatha,
129
+ 26 Arkys,
130
+ 27 Archemorus,
131
+ 28 Encyosaccus,
132
+ 29 Xylethrus,
133
+ 30 Chaetacis,
134
+ 31 Micrathena,
135
+ 32 Mastophora,
136
+ 33 Cyrtarachne,
137
+ 34 Pasilobus,
138
+ 35 Arachnura,
139
+ 36 Witica,
140
+ 37 Mecynogea,
141
+ 38 Cyrtophora,
142
+ 39 Neogea,
143
+ 40 Argiope,
144
+ 41 Gea,
145
+ 42 Scoloderus,
146
+ 43 Acanthepeira,
147
+ 44 Anepsion,
148
+ 45 Dolophone,
149
+ 46 Hypsosinga,
150
+ 47 Zygiella,
151
+ 48 Kaira,
152
+ 49 Metepeira,
153
+ 50 Singa,
154
+ 51 Larinia,
155
+ 52 Neoscona,
156
+ 53 Mangora,
157
+ 54 Cercidia,
158
+ 55 Pronous,
159
+ 56 Aculepeira,
160
+ 57 Araneus,
161
+ 58 Bertrana,
162
+ 59 Alpaida,
163
+ 60 Enacrosoma,
164
+ 61 Wixia,
165
+ 62 Acacesia,
166
+ 63 Metazygia,
167
+ 64 Eustala,
168
+ 65 Cyclosa,
169
+ 66 Nuctenea,
170
+ 67 Colphepeira,
171
+ 68 Araniella,
172
+ 69 Eriophora,
173
+ 70 Verrucosa;
174
+ TREE Imported_tree_1 = (1,((2,3),((((4,5),(6,(7,(8,9)))),(10,(13,(11,12)))),(14,(((((((18,19),(22,((17,(15,16)),(20,21)))),(23,24)),((25,(26,27)),(28,(29,(30,31))))),(32,(33,34))),((35,36),((37,38),(39,(40,41))))),(42,(43,((46,((47,(48,49)),(50,51))),(45,((66,((65,(68,(69,70))),((63,((59,(58,60)),(64,(61,62)))),((52,(56,57)),(53,(54,55)))))),(44,67)))))))))));
175
+ TREE Imported_tree_2 = (1,((2,3),((((4,5),(6,(7,(8,9)))),(10,(13,(11,12)))),(14,(((((((18,19),(22,((17,(15,16)),(20,21)))),(23,24)),((25,(26,27)),(28,(29,(30,31))))),(32,(33,34))),((35,36),((37,38),(39,(40,41))))),(42,(43,((46,(50,(47,(48,49)))),(45,((66,((65,(68,(69,70))),((63,((59,(58,60)),(64,(61,62)))),((52,(51,(56,57))),(53,(54,55)))))),(44,67)))))))))));
176
+ TREE Imported_tree_3 = (1,((2,3),((((6,(4,5)),(7,(8,9))),(10,(13,(11,12)))),(14,(((((((18,19),(22,((17,(15,16)),(20,21)))),(23,24)),((25,(26,27)),(28,(29,(30,31))))),(32,(33,34))),((35,36),((37,38),(39,(40,41))))),(42,(43,((46,((47,(48,49)),(50,51))),(45,((66,((65,(68,(69,70))),((63,((59,(58,60)),(64,(61,62)))),((52,(56,57)),(53,(54,55)))))),(44,67)))))))))));
177
+ TREE Imported_tree_4 = (1,((2,3),((((4,5),(6,(7,(8,9)))),(10,(13,(11,12)))),(14,(((((((18,19),(22,((17,(15,16)),(20,21)))),(23,24)),((25,(26,27)),(28,(29,(30,31))))),(32,(33,34))),((35,36),((37,38),(39,(40,41))))),(42,(43,((44,(67,(66,((65,(68,(69,70))),((63,((59,(58,60)),(64,(61,62)))),((52,(56,57)),(53,(54,55)))))))),(45,(46,((47,(48,49)),(50,51))))))))))));
178
+ TREE Imported_tree_5 = (1,((2,3),((((6,(4,5)),(7,(8,9))),(10,(13,(11,12)))),(14,(((((((18,19),(22,((17,(15,16)),(20,21)))),(23,24)),((25,(26,27)),(28,(29,(30,31))))),(32,(33,34))),((35,36),((37,38),(39,(40,41))))),(42,(43,((46,(50,(47,(48,49)))),(45,((66,((65,(68,(69,70))),((63,((59,(58,60)),(64,(61,62)))),((52,(51,(56,57))),(53,(54,55)))))),(44,67)))))))))));
179
+ TREE Imported_tree_6 = (1,((2,3),((((4,5),(6,(7,(8,9)))),(10,(13,(11,12)))),(14,(((((((18,19),(22,((17,(15,16)),(20,21)))),(23,24)),((25,(26,27)),(28,(29,(30,31))))),(32,(33,34))),((35,36),((37,38),(39,(40,41))))),(42,(43,((44,(67,(66,((65,(68,(69,70))),((63,((59,(58,60)),(64,(61,62)))),((52,(51,(56,57))),(53,(54,55)))))))),(45,(46,(50,(47,(48,49)))))))))))));
180
+ TREE Imported_tree_7 = (1,((2,3),((((6,(4,5)),(7,(8,9))),(10,(13,(11,12)))),(14,(((((((18,19),(22,((17,(15,16)),(20,21)))),(23,24)),((25,(26,27)),(28,(29,(30,31))))),(32,(33,34))),((35,36),((37,38),(39,(40,41))))),(42,(43,((44,(67,(66,((65,(68,(69,70))),((63,((59,(58,60)),(64,(61,62)))),((52,(56,57)),(53,(54,55)))))))),(45,(46,((47,(48,49)),(50,51))))))))))));
181
+ TREE Imported_tree_8 = (1,((2,3),((((6,(4,5)),(7,(8,9))),(10,(13,(11,12)))),(14,(((((((18,19),(22,((17,(15,16)),(20,21)))),(23,24)),((25,(26,27)),(28,(29,(30,31))))),(32,(33,34))),((35,36),((37,38),(39,(40,41))))),(42,(43,((44,(67,(66,((65,(68,(69,70))),((63,((59,(58,60)),(64,(61,62)))),((52,(51,(56,57))),(53,(54,55)))))))),(45,(46,(50,(47,(48,49)))))))))))));
182
+
183
+ END;
184
+
185
+
186
+ BEGIN LABELS;
187
+ CHARGROUPLABEL MM_Genitalia COLOR = (RGB 1.0 0.4 0.4) ;
188
+ CHARGROUPLABEL Somatic COLOR = (RGB 0.6 1.0 0.33333333) ;
189
+ CHARGROUPLABEL Spinnerets COLOR = (RGB 0.46666667 0.57254902 1.0) ;
190
+ CHARGROUPLABEL Behavior COLOR = (RGB 1.0 0.46666667 1.0) ;
191
+
192
+
193
+ END;
194
+
195
+ BEGIN SETS;
196
+ CHARPARTITION * UNTITLED = Somatic : 1 - 4 32 - 67, MM_Genitalia : 5 - 31, Spinnerets : 68 - 73, Behavior : 74 - 82;
197
+
198
+ END;
199
+
200
+ BEGIN ASSUMPTIONS;
201
+ TYPESET * UNTITLED = unord: 1 - 82;
202
+
203
+ EXSET * UNTITLED = ;
204
+
205
+ WTSET * UNTITLED = 1: 1 - 82 ;
206
+
207
+ END;
208
+
209
+ BEGIN CODONS;
210
+ CODESET * UNTITLED = universal: 1 - 82;
211
+
212
+
213
+ END;
214
+
215
+ BEGIN MESQUITECHARMODELS;
216
+ ProbModelSet * UNTITLED = 'Mk1 (est.)': 1 - 82;
217
+ END;
218
+
219
+ BEGIN NOTES;
220
+
221
+ 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';
222
+
223
+ END;
224
+
225
+ Begin MESQUITE;
226
+ MESQUITESCRIPTVERSION 2;
227
+ TITLE AUTO;
228
+ tell ProjectCoordinator;
229
+ getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa;
230
+ tell It;
231
+ setID 0 6498976404544962919 JC1191fcddc0c4;
232
+ endTell;
233
+ getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters;
234
+ tell It;
235
+ setID 0 2280451364422511229 JC1191fcddc0c0;
236
+ checksum 0 114188958 JC1191fcddc0c0;
237
+ endTell;
238
+ getEmployee #mesquite.charMatrices.BasicDataWindowCoord.BasicDataWindowCoord;
239
+ tell It;
240
+ showDataWindow #2280451364422511229 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker;
241
+ tell It;
242
+ getWindow;
243
+ tell It;
244
+ setExplanationSize 30;
245
+ setAnnotationSize 20;
246
+ setFontIncAnnot 0;
247
+ setFontIncExp 0;
248
+ setSize 707 998;
249
+ setLocation 734 14;
250
+ setFont SanSerif;
251
+ setFontSize 10;
252
+ getToolPalette;
253
+ tell It;
254
+ endTell;
255
+ setTool mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindow.arrow;
256
+ colorCells #mesquite.charMatrices.NoColor.NoColor;
257
+ setBackground White;
258
+ toggleShowNames off;
259
+ toggleShowTaxonNames on;
260
+ toggleTight off;
261
+ toggleShowChanges on;
262
+ toggleSeparateLines off;
263
+ toggleShowStates on;
264
+ toggleAutoWCharNames off;
265
+ toggleShowDefaultCharNames off;
266
+ toggleConstrainCW on;
267
+ toggleBirdsEye off;
268
+ toggleAllowAutosize on;
269
+ toggleColorsPanel off;
270
+ toggleDiagonal off;
271
+ toggleLinkedScrolling on;
272
+ toggleScrollLinkedTables off;
273
+ endTell;
274
+ showWindow;
275
+ getWindow;
276
+ tell It;
277
+ forceAutosize;
278
+ endTell;
279
+ getEmployee #mesquite.categ.StateNamesStrip.StateNamesStrip;
280
+ tell It;
281
+ showStrip off;
282
+ endTell;
283
+ getEmployee #mesquite.charMatrices.AnnotPanel.AnnotPanel;
284
+ tell It;
285
+ togglePanel off;
286
+ endTell;
287
+ getEmployee #mesquite.charMatrices.CharReferenceStrip.CharReferenceStrip;
288
+ tell It;
289
+ showStrip off;
290
+ endTell;
291
+ getEmployee #mesquite.charMatrices.ColorCells.ColorCells;
292
+ tell It;
293
+ setColor Red;
294
+ removeColor off;
295
+ endTell;
296
+ getEmployee #mesquite.charMatrices.QuickKeySelector.QuickKeySelector;
297
+ tell It;
298
+ autotabOff;
299
+ endTell;
300
+ getEmployee #mesquite.collab.ChgHistoryInfo.ChgHistoryInfo;
301
+ tell It;
302
+ togglePanel off;
303
+ endTell;
304
+ getEmployee #mesquite.silk.AnnotSummary.AnnotSummary;
305
+ tell It;
306
+ togglePanel off;
307
+ endTell;
308
+ getEmployee #mesquite.silk.CellImages.CellImages;
309
+ tell It;
310
+ showColors off;
311
+ togglePanel off;
312
+ toggleAnnotations off;
313
+ toggleSums off;
314
+ toggleHistory off;
315
+ toggleLocations off;
316
+ endTell;
317
+ getEmployee #mesquite.silk.StateImages.StateImages;
318
+ tell It;
319
+ showColors off;
320
+ togglePanel off;
321
+ toggleStateAnnotations off;
322
+ toggleCharAnnotations off;
323
+ toggleLocations off;
324
+ endTell;
325
+ getEmployee #mesquite.silk.aaManageImageIndices.aaManageImageIndices;
326
+ tell It;
327
+ setLocal;
328
+ setPrevIndexBase 'http://salticus.zoology.ubc.ca/ATOLSpiders/ATOLImages';
329
+ reset;
330
+ endTell;
331
+ endTell;
332
+ endTell;
333
+ getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters;
334
+ tell It;
335
+ showCharacters #2280451364422511229 #mesquite.lists.CharacterList.CharacterList;
336
+ tell It;
337
+ setData 0;
338
+ getWindow;
339
+ tell It;
340
+ newAssistant #mesquite.lists.DefaultCharOrder.DefaultCharOrder;
341
+ newAssistant #mesquite.lists.CharListInclusion.CharListInclusion;
342
+ newAssistant #mesquite.lists.CharListPartition.CharListPartition;
343
+ newAssistant #mesquite.stochchar.CharListProbModels.CharListProbModels;
344
+ setExplanationSize 30;
345
+ setAnnotationSize 20;
346
+ setFontIncAnnot 0;
347
+ setFontIncExp 0;
348
+ setSize 707 998;
349
+ setLocation 734 14;
350
+ setFont SanSerif;
351
+ setFontSize 10;
352
+ getToolPalette;
353
+ tell It;
354
+ endTell;
355
+ endTell;
356
+ showWindow;
357
+ getEmployee #mesquite.lists.CharListAnnotPanel.CharListAnnotPanel;
358
+ tell It;
359
+ togglePanel off;
360
+ endTell;
361
+ endTell;
362
+ endTell;
363
+ getEmployee #mesquite.basic.ManageFileComments.ManageFileComments;
364
+ tell It;
365
+ editFileComment 0;
366
+ tell It;
367
+ setExplanationSize 0;
368
+ setAnnotationSize 0;
369
+ setFontIncAnnot 0;
370
+ setFontIncExp 0;
371
+ setSize 707 1048;
372
+ setLocation 734 14;
373
+ setFont SanSerif;
374
+ setFontSize 10;
375
+ setActive;
376
+ showWindow;
377
+ endTell;
378
+ endTell;
379
+ endTell;
380
+ end;
381
+
382
+