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[Phenoscape-commit] SF.net SVN: phenoscape:[3404] trunk/data/incomplete-files/ Baez_Harrison_2005.nex
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From: <nyc...@us...> - 2012-01-31 19:28:06
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Revision: 3404
http://phenoscape.svn.sourceforge.net/phenoscape/?rev=3404&view=rev
Author: nyctorex831
Date: 2012-01-31 19:27:57 +0000 (Tue, 31 Jan 2012)
Log Message:
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Completed Matrix
Added Paths:
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trunk/data/incomplete-files/Baez_Harrison_2005.nex
Added: trunk/data/incomplete-files/Baez_Harrison_2005.nex
===================================================================
--- trunk/data/incomplete-files/Baez_Harrison_2005.nex (rev 0)
+++ trunk/data/incomplete-files/Baez_Harrison_2005.nex 2012-01-31 19:27:57 UTC (rev 3404)
@@ -0,0 +1,210 @@
+#NEXUS
+[written Tue Jan 31 14:26:15 EST 2012 by Mesquite version 2.74 (build 550) at wl-10-180-71-130.wireless.duke.local/10.180.71.130]
+
+BEGIN TAXA;
+ TITLE Taxa;
+ DIMENSIONS NTAX=19;
+ TAXLABELS
+ Ascaphus Chelomophrynus_ Cordicephalus_ Discoglossus_ Eoxenopoides_ Hymenochirus_ Llankibatrachus_ Pachycentrata_ Palaeobatrachus_ Pipa_ Pseudhymenochirus_ Rhinophrynus_ Saltenia_ ?Shelania?laurenti_ Shelania_pascuali_ Silurana Singidella_ Xenopus_ ?Xenopus?romeri
+ ;
+
+END;
+
+
+BEGIN CHARACTERS;
+ TITLE Character_Matrix;
+ DIMENSIONS NCHAR=56;
+ FORMAT DATATYPE = STANDARD GAP = - MISSING = ? SYMBOLS = " 0 1 2 3 4 5 6 7 8 9 A B C D E F G H J K M N";
+ CHARSTATELABELS
+ 1 skull_shape_in_lateral_profile / rounded_ 'wedge-shaped', 2 nasal_region / 'one-third, or more, of the skull length' 'one-quarter, or less, of the skull length', 3 nasals / paired fused, 4 frontoparietals_?_nasals / not_overlapping overlapping, 5 frontoparietals / paired fused_, 6 frontoparietal_posterolateral_extensions / absent present, 7 anterior_margin_of_the_frontoparietal_fenestra / sphenethmoidal_ossification_surrounds_the_frontoparietal_fenestra_anteriorly sphenethmoidal_ossification_does_not_surround_the_fenestra_anteriorly, 8 olfactory_foramina / bound_completely_or_partially_in_bone bound_in_cartilage, 9 antorbital_plane_of_the_skull / partially_or_completely_cartilaginous ossified_up_to_the_maxillary_arcade, 10 margin_of_the_optic_foramina / not_completely_bound_in_sphenethmoidal_ossification bound_in_sphenethmoidal_ossification, 11 loor_of_the_braincase_in_the_orbital_region / rounded distinctly_angled_, 12 Eustachian_canal / absent 'present, prootic with deep furrow' 'present, prootic with shallow anterior depression', 13 inferior_perilymphatic_foramina / 'present, not ventral to jugular foramina' 'present, ventral to jugular foramina' absent, 14 superior_perilymphatic_foramina / present absent, 15 premaxillary_palatine_process / 'not dagger-like' 'dagger-like', 16 anterior_end_of_the_maxilla / lacking_pointed_process_that_overlaps_premaxilla having_pointed_process_that_overlaps_premaxilla, 17 maxillary_pars_facialis / not_extending_over_premaxilla_anteriorly partially_extending_over_premaxilla_anteriorly nearly_covering_premaxilla_anteriorly, 18 maxillary_antorbital_process / absent present, 19 partes_of_the_maxilla_in_the_orbital_region / distinct not_distinct, 20 maxillary_arcade / complete incomplete, 21 septomaxillae / small_and_complex large_and_accurate_, 22 vomers / medial_to_the_choanae posterior_to_the_choanae absent., 23 parasphenoid_?_braincase / not_fused 'partially^nor com-^npletely fused', 24 alae_of_the_parasphenoid / present absent, 25 anterior_extent_of_the_parasphenoid / not_reaching_maxillary_arcade reaching_maxillary_arcade, 26 posteromedial_extent_of_the_parasphenoid / 'extending near^nthe ventral margin of the foramen magnum' 'ending well^nanterior to the ventral margin of the foramen magnum', 27 squamosal_shape / 'T-shaped without stapedial process' 'T-shaped with stapedial process' 'conch-shaped', 28 zygomatic_ramus_of_the_squamosal / well_developed reduced_or_absent, 29 pterygoid_knob / absent present, 30 position_of_the_anterior_ramus_of_the_pterygoid / medial_tom_axilla abuts_maxilla dorsal_to_maxilla anterior_ramus_absent, 31 medial_ramus_of_the_pterygoid / 'present, lacking indentation' 'present, with indentation' absent, 32 configuration_of_the_pterygoid_in_the_otic_region / not_expanded_ expanded_to_form_an_otic_plate, 33 'pterygoid medial ramus-parasphenoid contact' / limited_or_no_contact extensive_contact, 34 fusion_of_pterygoid_and_otic_capsule / not_fused_ fused_, 35 coronoid_process_of_the_angulosplenial / poorly_developed 'blade-like', 36 relative_position_of_the_lower_jaw_articulation / lateral_to_the_otic_capsule at_the_anterior_margin_of_the_otic_capsule, 37 length_of_the_posteromedial_process_of_the_hyoid / length_less_than_half_the_anteroposterior_length_of_the_lower_jaw length_more_than_half_the_anteroposterior_length_of_the_lower_jaw, 38 anterior_end_of_the_posteromedial_process_of_the_hyoid / wider_than_posterior_end narrower_than_posterior_end, 39 parahyoid_bone / present absent, 40 ceratohyal / not_ossified ossified_, 41 shape_of_the_vertebral_centra / cylindrical depressed_, 42 articulation_facets_of_the_vertebral_centra / notochordal opisthocoelous procoelous, 43 articulation_facets_of_the_postzygapophyses / flat with_grooves_and_ridges curved_ventrally, 44 neural_spines_of_the_presacral_vertebrae / sagittal parasagittal, 45 Vertebrae_I_and_II / 'separate, weak or no imbrication' 'separate, broad imbrication' fused_, 46 ribs / free_ribs_present_in_larvae_and_adults free_ribs_present_in_larvae_and_fused_to_transverse_processes_in_adults ribs_absent_in_larvae_and_adults, 47 sacrum_and_urostyle / not_fused_ fused_, 48 clavicle_?_scapula / 'lateral end contacts medial edge of pars^nacromialis' lateral_end_overlaps_anterior_edge_of_scapula lateral_end_is_fused_to_scapula, 49 medial_end_of_the_clavicle / not_expanded_ expanded_, 50 proportions_of_the_scapula / 'glenoid area one-third of the total length of the scapula' 'glenoid area more than one-third of the total length of the scapula', 51 cleithrum / 'not covering the posterior edge of the supra-scapular cartilage' 'covering part of the posterior edge of^nthe suprascapular cartilage', 52 sternal_expansion_of_the_coracoid_relative_to_its_length / sternal_expansion_less_than_half_the_length_of_the_coracoid sternal_expansion_nearly_half_the_length_of_the_coracoid sternal_expansion_nearly_the_length_of_the_coracoid, 53 'ilial supra-acetabular expansion' / present absent, 54 ilial_preacetabular_expansion / present absent, 55 pubis / cartilaginous ossified_, 56 distal_os_sesamoides_tarsale / absent present ;
+ MATRIX
+ Ascaphus 00000021000020000001000000000000000000000000000101010000
+ Chelomophrynus_ 0?0?10?000?000000000?00100010?????0?010000001201000100??
+ Cordicephalus_ 010010001002??000?01?0011?00?10100000??01100210101000010
+ Discoglossus_ 000000000000000000000000000001000000000001000000010?0000
+ Eoxenopoides_ 010110001111??011011?111102102010010???01100211?00000110
+ Hymenochirus_ 110?1010111120112011121101210301111101111121211200021111
+ Llankibatrachus_ 010110???101??01?1111?1110201211??1011?011002112011011?0
+ Pachycentrata_ 1???11?01111?????????21101??0??110?0???011212?1??0??????
+ Palaeobatrachus_ 01001000001200010001000110101001000000001200210101010010
+ Pipa_ 11011010011120010011121111210201001101101101211100021111
+ Pseudhymenochirus_ 110?1010111120112011121101210301111101111121211200021111
+ Rhinophrynus_ 0001100000100000000000010001012NN?0100000000120100010000
+ Saltenia_ ?10110000101??0101?1?111102110?1001111?01100011101?001??
+ ?Shelania?laurenti_ 0?011000010111???111?111?02?1?????1????011002?12?1??11??
+ Shelania_pascuali_ 011110000101??01?111111110201011001011101100011101101110
+ Silurana 01011011010101010011121110201211001011101110011211101110
+ Singidella_ 110?11?01111??01101112110?21020110?001?011212?12?0?111?1
+ Xenopus_ 01111011010101010011111110201211001011101110?11211101110
+ ?Xenopus?romeri 01111000010111???????111?0??1????0?????011002?12?1??11??
+
+;
+
+END;
+BEGIN ASSUMPTIONS;
+ TYPESET * UNTITLED = unord: 1 - 56;
+
+END;
+
+BEGIN MESQUITECHARMODELS;
+ ProbModelSet * UNTITLED = 'Mk1 (est.)': 1 - 56;
+END;
+
+Begin MESQUITE;
+ MESQUITESCRIPTVERSION 2;
+ TITLE AUTO;
+ tell ProjectCoordinator;
+ timeSaved 1328037975866;
+ getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa;
+ tell It;
+ setID 0 26406373022940126;
+ tell It;
+ setSelected 1 - 19;
+ attachments ;
+ endTell;
+ endTell;
+ getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters;
+ tell It;
+ setID 0 7588572158861693156;
+ mqVersion 274;
+ checksumv 0 2 97128110 null getNumChars 56 numChars 56 getNumTaxa 19 numTaxa 19 short false bits 2097167 states 2097167 sumSquaresStatesOnly 8.79609302542E12 sumSquares 8.79609302542E12 NumFiles 1 NumMatrices 1;
+ mqVersion;
+ endTell;
+ getWindow;
+ tell It;
+ suppress;
+ setResourcesState false false 100;
+ setPopoutState 400;
+ setExplanationSize 0;
+ setAnnotationSize 0;
+ setFontIncAnnot 0;
+ setFontIncExp 0;
+ setSize 640 716;
+ setLocation 640 22;
+ setFont SanSerif;
+ setFontSize 10;
+ getToolPalette;
+ tell It;
+ endTell;
+ desuppress;
+ endTell;
+ getEmployee #mesquite.charMatrices.BasicDataWindowCoord.BasicDataWindowCoord;
+ tell It;
+ showDataWindow #7588572158861693156 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker;
+ tell It;
+ getWindow;
+ tell It;
+ setExplanationSize 30;
+ setAnnotationSize 20;
+ setFontIncAnnot 0;
+ setFontIncExp 0;
+ setSize 540 649;
+ setLocation 640 22;
+ setFont SanSerif;
+ setFontSize 10;
+ getToolPalette;
+ tell It;
+ endTell;
+ setTool mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindow.arrow;
+ colorCells #mesquite.charMatrices.NoColor.NoColor;
+ colorRowNames #mesquite.charMatrices.TaxonGroupColor.TaxonGroupColor;
+ colorColumnNames #mesquite.charMatrices.CharGroupColor.CharGroupColor;
+ colorText #mesquite.charMatrices.NoColor.NoColor;
+ setBackground White;
+ toggleShowNames on;
+ toggleShowTaxonNames on;
+ toggleTight off;
+ toggleThinRows off;
+ toggleShowChanges on;
+ toggleSeparateLines off;
+ toggleShowStates on;
+ toggleAutoWCharNames on;
+ toggleAutoTaxonNames off;
+ toggleShowDefaultCharNames off;
+ toggleConstrainCW on;
+ toggleBirdsEye off;
+ toggleShowPaleGrid off;
+ toggleShowPaleCellColors off;
+ togglePaleInapplicable on;
+ toggleShowBoldCellText off;
+ toggleAllowAutosize on;
+ toggleColorsPanel off;
+ toggleDiagonal on;
+ setDiagonalHeight 80;
+ toggleLinkedScrolling on;
+ toggleScrollLinkedTables off;
+ endTell;
+ showWindow;
+ getWindow;
+ tell It;
+ forceAutosize;
+ endTell;
+ getEmployee #mesquite.charMatrices.ColorByState.ColorByState;
+ tell It;
+ setStateLimit 9;
+ toggleUniformMaximum on;
+ endTell;
+ getEmployee #mesquite.charMatrices.ColorCells.ColorCells;
+ tell It;
+ setColor Red;
+ removeColor off;
+ endTell;
+ getEmployee #mesquite.categ.StateNamesEditor.StateNamesEditor;
+ tell It;
+ makeWindow;
+ tell It;
+ getTable;
+ tell It;
+ rowNamesWidth 104;
+ endTell;
+ setExplanationSize 30;
+ setAnnotationSize 20;
+ setFontIncAnnot 0;
+ setFontIncExp 0;
+ setSize 540 649;
+ setLocation 640 22;
+ setFont SanSerif;
+ setFontSize 10;
+ getToolPalette;
+ tell It;
+ setTool mesquite.categ.StateNamesEditor.StateNamesWindow.ibeam;
+ endTell;
+ setActive;
+ rowsAreCharacters on;
+ toggleConstrainChar on;
+ toggleConstrainCharNum 3;
+ togglePanel off;
+ toggleSummaryPanel off;
+ endTell;
+ showWindow;
+ endTell;
+ getEmployee #mesquite.categ.StateNamesStrip.StateNamesStrip;
+ tell It;
+ showStrip off;
+ endTell;
+ getEmployee #mesquite.charMatrices.AnnotPanel.AnnotPanel;
+ tell It;
+ togglePanel off;
+ endTell;
+ getEmployee #mesquite.charMatrices.CharReferenceStrip.CharReferenceStrip;
+ tell It;
+ showStrip off;
+ endTell;
+ getEmployee #mesquite.charMatrices.QuickKeySelector.QuickKeySelector;
+ tell It;
+ autotabOff;
+ endTell;
+ getEmployee #mesquite.charMatrices.SelSummaryStrip.SelSummaryStrip;
+ tell It;
+ showStrip off;
+ endTell;
+ getEmployee #mesquite.categ.SmallStateNamesEditor.SmallStateNamesEditor;
+ tell It;
+ panelOpen true;
+ endTell;
+ endTell;
+ endTell;
+ endTell;
+end;
+
+
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