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[Treebase-guts] SF.net SVN: treebase:[377] trunk/treebase-core/lib/examples
|
From: <rv...@us...> - 2009-12-15 18:14:58
|
Revision: 377
http://treebase.svn.sourceforge.net/treebase/?rev=377&view=rev
Author: rvos
Date: 2009-12-15 18:14:51 +0000 (Tue, 15 Dec 2009)
Log Message:
-----------
Adding mesquite classes
Added Paths:
-----------
trunk/treebase-core/lib/examples/Correlation/
trunk/treebase-core/lib/examples/Correlation/00-introduction.nex
trunk/treebase-core/lib/examples/Correlation/00a-FelsensteinsContrasts.nex
trunk/treebase-core/lib/examples/Correlation/00b-pagel94Hominids.nex
trunk/treebase-core/lib/examples/Correlation/00c-pairwiseIntro.nex
trunk/treebase-core/lib/examples/Correlation/01-pairwise.nex
trunk/treebase-core/lib/examples/Correlation/02-pairwiseFig2(1).nex
trunk/treebase-core/lib/examples/Correlation/03-pairwiseFig2(2).nex
trunk/treebase-core/lib/examples/Correlation/04-pairwiseFig2(3).nex
trunk/treebase-core/lib/examples/Correlation/05-pairwiseFig3-6(1).nex
trunk/treebase-core/lib/examples/Correlation/06-pairwiseFig3-6(2).nex
trunk/treebase-core/lib/examples/Correlation/07-pairwiseFig3-6(3).nex
Added: trunk/treebase-core/lib/examples/Correlation/00-introduction.nex
===================================================================
--- trunk/treebase-core/lib/examples/Correlation/00-introduction.nex (rev 0)
+++ trunk/treebase-core/lib/examples/Correlation/00-introduction.nex 2009-12-15 18:14:51 UTC (rev 377)
@@ -0,0 +1,33 @@
+#NEXUS
+[written Mon Sep 03 09:22:06 PDT 2007 by Mesquite version 2.0BETA3 (build i55) at Thrandina.local/127.0.0.1 (Wayne Maddison)]
+Begin MESQUITE;
+ MESQUITESCRIPTVERSION 2;
+ TITLE AUTO;
+ tell ProjectCoordinator;
+ newAssistant #mesquite.basic.ExamplesNavigator.ExamplesNavigator;
+ tell It;
+ setNextFileName '00a-FelsensteinsContrasts.nex';
+ getWindow;
+ tell It;
+ setExplanationSize 0;
+ setAnnotationSize 0;
+ setFontIncAnnot 0;
+ setFontIncExp 0;
+ setSize 429 288;
+ setLocation 5 22;
+ setFont SanSerif;
+ setFontSize 10;
+ setActive;
+ setExplanation 'Phylogenetic tests of whether two characters have correlated evolution can be done in three ways using Mesquite:^n^n(1) Two continuous characters: Felsenstein''s independent contrasts^n^n(2) Two categorical two-state characters: Pagel''s 1994 method.^n^n(3) Two categorical or one categorical and one continuous character: pairwise comparisons.^n^nHere are example files for these various methods^n^nTo go from one file to another, hit the "Next" button';
+ setTitle Character_Correlation;
+ toggleFileNames off;
+ setPrevButtonName Previous;
+ setNextButtonName Next;
+ addFileLink Return_to_main_Introduction '../Introduction.nex';
+ endTell;
+ showWindow;
+ endTell;
+ endTell;
+end;
+
+
Added: trunk/treebase-core/lib/examples/Correlation/00a-FelsensteinsContrasts.nex
===================================================================
--- trunk/treebase-core/lib/examples/Correlation/00a-FelsensteinsContrasts.nex (rev 0)
+++ trunk/treebase-core/lib/examples/Correlation/00a-FelsensteinsContrasts.nex 2009-12-15 18:14:51 UTC (rev 377)
@@ -0,0 +1,373 @@
+#NEXUS
+[written Mon Sep 03 09:22:19 PDT 2007 by Mesquite version 2.0BETA3 (build i55) at Thrandina.local/127.0.0.1 (Wayne Maddison)]
+
+BEGIN TAXA;
+ DIMENSIONS NTAX=49;
+ TAXLABELS
+ Tm Ur Um Nn pl Mp Ml Cp Ct Lp Ca Uc Vf Hh Cc Aj Pp Pt Pq Tb Cs Db Eh Ec Eb Lg Cd Gc Sc Bb To Gg Gt Ac Mk Oa Oc He Am Cu Dl Ab Aa cq Dd Al Rt Ov Oh
+ ;
+ BLOCKID WM114cc2658fc35;
+
+END;
+
+
+BEGIN CHARACTERS;
+ DIMENSIONS NCHAR=2;
+ FORMAT DATATYPE = CONTINUOUS;
+ MATRIX
+ Tm 2.423245874 2.062957834
+ Ur 2.400192489 1.918030337
+ Um 1.970346876 1.754348336
+ Nn 0.6434526765 0.0211892991
+ pl 0.84509804 0.0569048513
+ Mp 0.3979400087 0.3979400087
+ Ml 1.064457989 -0.060480747
+ Cp 1.547774705 2.307067951
+ Ct 1.123851641 1.653212514
+ Lp 1.301029996 2.204119983
+ Ca 0.9444826722 0.9590413923
+ Uc 0.5682017241 0.0413926852
+ Vf 0.6812412374 0.587710965
+ Hh 1.428134794 2.184123354
+ Cc 1.716003344 1.397940009
+ Aj 1.769377326 1.7930916
+ Pp 1.719331287 1.365487985
+ Pt 2.206825876 1.84260924
+ Pq 2.192567453 2.372912003
+ Tb 2.397940009 0.3010299957
+ Cs 3.301029996 0.8228216453
+ Db 3.079181246 1.193124598
+ Eh 2.301029996 1.544068044
+ Ec 2.544068044 1.352182518
+ Eb 2.371067862 2.217483944
+ Lg 1.977723605 -0.301029996
+ Cd 2.740362689 2.0
+ Gc 3.031408464 1.927370363
+ Sc 2.792391689 2.139879086
+ Bb 2.937016107 2.123851641
+ To 2.7084209 1.942008053
+ Gg 1.795880017 1.301029996
+ Gt 1.311753861 0.7242758696
+ Ac 1.574031268 0.8129133566
+ Mk 0.6989700043 -1.36653154
+ Oa 2.054995862 1.356981401
+ Oc 1.929418926 1.15624619
+ He 2.355068206 1.903089987
+ Am 1.726319612 0.5797835966
+ Cu 2.334453751 1.875061263
+ Dl 2.113943352 0.3424226808
+ Ab 2.133538908 0.6989700043
+ Aa 1.698970004 1.0
+ cq 2.477121255 1.111598525
+ Dd 1.740362689 0.1139433523
+ Al 2.584331224 1.206825876
+ Rt 2.0 1.477121255
+ Ov 1.755874856 0.2922560714
+ Oh 1.86923172 0.45484486
+
+;
+ BLOCKID WM114cc26593f0;
+
+
+END;
+BEGIN TREES;
+ TRANSLATE
+ 1 Tm,
+ 2 Ur,
+ 3 Um,
+ 4 Nn,
+ 5 pl,
+ 6 Mp,
+ 7 Ml,
+ 8 Cp,
+ 9 Ct,
+ 10 Lp,
+ 11 Ca,
+ 12 Uc,
+ 13 Vf,
+ 14 Hh,
+ 15 Cc,
+ 16 Aj,
+ 17 Pp,
+ 18 Pt,
+ 19 Pq,
+ 20 Tb,
+ 21 Cs,
+ 22 Db,
+ 23 Eh,
+ 24 Ec,
+ 25 Eb,
+ 26 Lg,
+ 27 Cd,
+ 28 Gc,
+ 29 Sc,
+ 30 Bb,
+ 31 To,
+ 32 Gg,
+ 33 Gt,
+ 34 Ac,
+ 35 Mk,
+ 36 Oa,
+ 37 Oc,
+ 38 He,
+ 39 Am,
+ 40 Cu,
+ 41 Dl,
+ 42 Ab,
+ 43 Aa,
+ 44 cq,
+ 45 Dd,
+ 46 Al,
+ 47 Rt,
+ 48 Ov,
+ 49 Oh;
+ TREE Untitled_Tree = ((((((1:2000000.0,2:2000000.0)n95:3000000.0,3:5000000.0)n31:3.9E7,((4:5000000.0,5:5000000.0)n92:2.6E7,(6:2.0E7,7:2.0E7)n07:1.1E7)n93:1.3E7)n06:8000000.0,(((((8:2500000.0,9:2500000.0)n34:500000.0,10:3000000.0)n32:3000000.0,11:6000000.0)n28:3000000.0,12:9000000.0)n22:500000.0,13:9500000.0)n21:4.25E7)n05:6000000.0,((14:5000000.0,15:5000000.0)n18:2.1E7,(16:9000000.0,(17:2500000.0,(18:2000000.0,19:2000000.0)n36:500000.0)n35:6500000.0)n23:1.7E7)n10:3.2E7)n03:1.2E7,(((20:5.0E7,(21:1.3E7,22:1.3E7)n16:3.7E7)n99:6000000.0,(23:7000000.0,(24:6000000.0,25:6000000.0)n29:1000000.0)n26:4.9E7)n04:1.0E7,((26:1.75E7,27:1.75E7)n77:2.55E7,(28:2.05E7,((((29:1.0E7,30:1.0E7)n98:9000000.0,31:1.9E7)n24:500000.0,((((32:2500000.0,33:2500000.0)n27:4500000.0,34:7000000.0)n90:4000000.0,35:1.1E7)n19:5000000.0,((36:4000000.0,37:4000000.0)n97:1.15E7,(38:9000000.0,(39:6500000.0,(40:5500000.0,(41:3500000.0,42:3500000.0)n33:2000000.0)n30:1000000.0)n20:2500000.0)n91:6500000.0)n14:500000.0)n13:3500000.0)n12:500000.0,(43:1.95E7,((44:4000000.0,45:4000000.0)n96:7000000.0,(46:5500000.0,(47:5000000.0,(48:1000000.0,49:1000000.0)n39:4000000.0)n38:500000.0)n37:5500000.0)n17:8500000.0)n11:500000.0)n09:500000.0)n08:2.25E7)n88:2.3E7)n02:4000000.0)n01:0.0;
+
+END;
+
+
+BEGIN ASSUMPTIONS;
+ TYPESET * UNTITLED = Squared: 1 - 2;
+
+END;
+
+BEGIN MESQUITECHARMODELS;
+ ProbModelSet * UNTITLED = Brownian_default: 1 - 2;
+END;
+
+Begin MESQUITE;
+ MESQUITESCRIPTVERSION 2;
+ TITLE AUTO;
+ tell ProjectCoordinator;
+ getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa;
+ tell It;
+ setID 0 7933746709840163491 WM114cc2658fc35;
+ endTell;
+ getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters;
+ tell It;
+ setID 0 4190772235764235829 WM114cc26593f0;
+ checksum 0 2240152432 WM114cc26593f0;
+ endTell;
+ getEmployee #mesquite.trees.BasicTreeWindowCoord.BasicTreeWindowCoord;
+ tell It;
+ makeTreeWindow #7933746709840163491 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker;
+ tell It;
+ setTreeSource #mesquite.trees.StoredTrees.StoredTrees;
+ tell It;
+ setTreeBlock 1;
+ toggleUseWeights off;
+ endTell;
+ setAssignedID 404.985450020823.5565377021587689415;
+ getTreeWindow;
+ tell It;
+ setExplanationSize 30;
+ setAnnotationSize 20;
+ setFontIncAnnot 0;
+ setFontIncExp 0;
+ setSize 570 329;
+ setLocation 5 22;
+ setFont SanSerif;
+ setFontSize 10;
+ getToolPalette;
+ tell It;
+ endTell;
+ getTreeDrawCoordinator #mesquite.trees.BasicTreeDrawCoordinator.BasicTreeDrawCoordinator;
+ tell It;
+ suppress;
+ setTreeDrawer #mesquite.trees.SquareTree.SquareTree;
+ tell It;
+ setNodeLocs #mesquite.trees.NodeLocsStandard.NodeLocsStandard;
+ tell It;
+ stretchToggle off;
+ branchLengthsToggle on;
+ toggleScale on;
+ toggleBroadScale off;
+ toggleCenter on;
+ toggleEven on;
+ namesAngle ?;
+ endTell;
+ setEdgeWidth 2;
+ orientRight;
+ toggleCorners off;
+ endTell;
+ setBackground White;
+ setBranchColor Black;
+ showNodeNumbers off;
+ showBranchColors on;
+ labelBranchLengths off;
+ desuppress;
+ getEmployee #mesquite.trees.BasicDrawTaxonNames.BasicDrawTaxonNames;
+ tell It;
+ setColor Black;
+ toggleColorPartition on;
+ toggleShadePartition off;
+ toggleNodeLabels on;
+ toggleCenterNodeNames off;
+ toggleShowNames on;
+ endTell;
+ endTell;
+ setTreeNumber 1;
+ useSuggestedSize off;
+ toggleSizeToFit on;
+ toggleTextOnTree off;
+ newWindowAssistant #mesquite.trees.MirrorTreeWindowMaker.MirrorTreeWindowMaker;
+ tell It;
+ getWindow;
+ tell It;
+ popOut;
+ setExplanationSize 30;
+ setAnnotationSize 0;
+ setFontIncAnnot 0;
+ setFontIncExp 0;
+ setSize 543 446;
+ setLocation 614 29;
+ setFont SanSerif;
+ setFontSize 10;
+ newAssistantLeft #mesquite.ancstates.TraceCharacterHistory.TraceCharacterHistory;
+ tell It;
+ suspend ;
+ setDisplayMode #mesquite.ancstates.ShadeStatesOnTree.ShadeStatesOnTree;
+ tell It;
+ toggleLabels off;
+ toggleGray off;
+ endTell;
+ setHistorySource #mesquite.ancstates.RecAncestralStates.RecAncestralStates;
+ tell It;
+ getCharacterSource #mesquite.charMatrices.CharSrcCoordObed.CharSrcCoordObed;
+ tell It;
+ setCharacterSource #mesquite.charMatrices.StoredCharacters.StoredCharacters;
+ tell It;
+ setDataSet #4190772235764235829;
+ endTell;
+ endTell;
+ setMethod #mesquite.parsimony.ParsAncestralStates.ParsAncestralStates;
+ tell It;
+ setModelSource #mesquite.parsimony.CurrentParsModels.CurrentParsModels;
+ getEmployee #mesquite.parsimony.ParsimonySquared.ParsimonySquared;
+ tell It;
+ toggleWeight on;
+ endTell;
+ endTell;
+ endTell;
+ setCharacter 1;
+ setMapping 1;
+ toggleShowLegend off;
+ toggleGray off;
+ toggleWeights on;
+ resume ;
+ endTell;
+ newAssistantRight #mesquite.ancstates.TraceCharacterHistory.TraceCharacterHistory;
+ tell It;
+ suspend ;
+ setDisplayMode #mesquite.ancstates.ShadeStatesOnTree.ShadeStatesOnTree;
+ tell It;
+ toggleLabels off;
+ toggleGray off;
+ endTell;
+ setHistorySource #mesquite.ancstates.RecAncestralStates.RecAncestralStates;
+ tell It;
+ getCharacterSource #mesquite.charMatrices.CharSrcCoordObed.CharSrcCoordObed;
+ tell It;
+ setCharacterSource #mesquite.charMatrices.StoredCharacters.StoredCharacters;
+ tell It;
+ setDataSet #4190772235764235829;
+ endTell;
+ endTell;
+ setMethod #mesquite.parsimony.ParsAncestralStates.ParsAncestralStates;
+ tell It;
+ setModelSource #mesquite.parsimony.CurrentParsModels.CurrentParsModels;
+ getEmployee #mesquite.parsimony.ParsimonySquared.ParsimonySquared;
+ tell It;
+ toggleWeight on;
+ endTell;
+ endTell;
+ endTell;
+ setCharacter 2;
+ setMapping 1;
+ toggleShowLegend off;
+ toggleGray off;
+ toggleWeights on;
+ resume ;
+ endTell;
+ endTell;
+ getTreeDrawCoordinator #mesquite.trees.BasicTreeDrawCoordinator.BasicTreeDrawCoordinator;
+ tell It;
+ suppress;
+ setTreeDrawer #mesquite.trees.DiagonalDrawTree.DiagonalDrawTree;
+ tell It;
+ setNodeLocs #mesquite.trees.NodeLocsStandard.NodeLocsStandard;
+ tell It;
+ stretchToggle off;
+ branchLengthsToggle off;
+ toggleScale on;
+ toggleBroadScale off;
+ toggleCenter off;
+ toggleEven off;
+ namesAngle ?;
+ endTell;
+ setEdgeWidth 12;
+ orientLeft;
+ endTell;
+ setBackground White;
+ setBranchColor Black;
+ showNodeNumbers off;
+ showBranchColors on;
+ labelBranchLengths off;
+ desuppress;
+ getEmployee #mesquite.trees.BasicDrawTaxonNames.BasicDrawTaxonNames;
+ tell It;
+ setColor Black;
+ toggleColorPartition on;
+ toggleShadePartition off;
+ toggleNodeLabels off;
+ toggleCenterNodeNames off;
+ toggleShowNames on;
+ endTell;
+ endTell;
+ showWindow;
+ endTell;
+ endTell;
+ showWindow;
+ getEmployee #mesquite.trees.ColorBranches.ColorBranches;
+ tell It;
+ setColor Red;
+ removeColor off;
+ endTell;
+ getEmployee #mesquite.ornamental.BranchNotes.BranchNotes;
+ tell It;
+ setAlwaysOn off;
+ endTell;
+ getEmployee #mesquite.ornamental.ColorTreeByPartition.ColorTreeByPartition;
+ tell It;
+ colorByPartition off;
+ endTell;
+ endTell;
+ endTell;
+ newAssistant #mesquite.basic.ExamplesNavigator.ExamplesNavigator;
+ tell It;
+ setNextFileName '00b-pagel94Hominids.nex';
+ setPrevFileName '00-introduction.nex';
+ getWindow;
+ tell It;
+ setExplanationSize 0;
+ setAnnotationSize 0;
+ setFontIncAnnot 0;
+ setFontIncExp 0;
+ setSize 570 379;
+ setLocation 5 22;
+ setFont SanSerif;
+ setFontSize 10;
+ setActive;
+ setExplanation 'This example file shows the distribution of two continuous characters on a tree. To test whether there is a significant association, Felsenstein''s Independent Contrasts can be used. ^n^nCalculation of Felsenstein''s independent contrasts is not part of the basic version of Mesquite, but rather is available in the PDAP package of modules for Mesquite. It is available at http://mesquiteproject.org/pdap_mesquite (see link below). ^n^nTo learn more about Felsenstein''s contrast calculations, download PDAP and explore its example files.';
+ setTitle 'Felsenstein''s independent contrasts';
+ toggleFileNames off;
+ setPrevButtonName Previous;
+ setNextButtonName Next;
+ addWebLink Mesquite_PDAP_website 'http://mesquiteproject.org/pdap_mesquite';
+ endTell;
+ showWindow;
+ endTell;
+ endTell;
+end;
+
+
Added: trunk/treebase-core/lib/examples/Correlation/00b-pagel94Hominids.nex
===================================================================
--- trunk/treebase-core/lib/examples/Correlation/00b-pagel94Hominids.nex (rev 0)
+++ trunk/treebase-core/lib/examples/Correlation/00b-pagel94Hominids.nex 2009-12-15 18:14:51 UTC (rev 377)
@@ -0,0 +1,319 @@
+#NEXUS
+[written Mon Sep 03 09:16:16 PDT 2007 by Mesquite version 2.0BETA3 (build i55) at Thrandina.local/127.0.0.1 (Wayne Maddison)]
+
+BEGIN TAXA;
+ DIMENSIONS NTAX=9;
+ TAXLABELS
+ Homo_sapiens Pan_troglodytes Pan_paniscus Gorilla_gorilla Pongo_pygmaeus Hylobates_syndactylus Hylobates_sp. Colobus_guereza Colobus_badius
+ ;
+ IDS 010a627b503f49 010a627b503f50 010a627b503f51 010a627b503f52 010a627b503f53 010a627b504054 010a627b504055 010a627b504056 010a627fb2ef57 ;
+ BLOCKID 010a627b503c3;
+
+END;
+
+
+BEGIN CHARACTERS;
+ DIMENSIONS NCHAR=2;
+ FORMAT DATATYPE = STANDARD GAP = - MISSING = ? SYMBOLS = " 0 1";
+ CHARSTATELABELS
+ 1 advertisement / absent present, 2 mating_system / one_male 'multi-male' ;
+ MATRIX
+ Homo_sapiens 00
+ Pan_troglodytes 11
+ Pan_paniscus 11
+ Gorilla_gorilla 00
+ Pongo_pygmaeus 10
+ Hylobates_syndactylus 00
+ Hylobates_sp. 00
+ Colobus_guereza 00
+ Colobus_badius 11
+
+;
+ IDS 010a627b503f4 010a627b503f5 ;
+ BLOCKID WM114cc27480d0;
+
+
+END;
+BEGIN TREES;
+ TRANSLATE
+ 1 Homo_sapiens,
+ 2 Pan_troglodytes,
+ 3 Pan_paniscus,
+ 4 Gorilla_gorilla,
+ 5 Pongo_pygmaeus,
+ 6 Hylobates_syndactylus,
+ 7 Hylobates_sp.,
+ 8 Colobus_guereza,
+ 9 Colobus_badius;
+ TREE page_16_example = ((8:2.0,9:2.0):56.0,((5:22.0,(4:20.0,(1:29.0,(2:9.0,3:5.0):15.0):11.0):10.0):18.0,(6:3.0,7:2.0):28.0):10.0):1.0;
+
+END;
+
+
+BEGIN CODONS;
+CODESET * UNTITLED = universal: 1 - 2;
+
+
+END;
+
+BEGIN ASSUMPTIONS;
+ TYPESET * UNTITLED = unord: 1 - 2;
+
+END;
+
+BEGIN MESQUITECHARMODELS;
+ ProbModelSet * UNTITLED = 'Mk1 (est.)': 1 - 2;
+END;
+
+Begin MESQUITE;
+ MESQUITESCRIPTVERSION 2;
+ TITLE AUTO;
+ tell ProjectCoordinator;
+ getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa;
+ tell It;
+ setID 0 878585605735200005 010a627b503c3;
+ endTell;
+ getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters;
+ tell It;
+ setID 0 7359026449824636807 WM114cc27480d0;
+ checksum 0 1601284411 WM114cc27480d0;
+ endTell;
+ getEmployee #mesquite.trees.BasicTreeWindowCoord.BasicTreeWindowCoord;
+ tell It;
+ makeTreeWindow #878585605735200005 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker;
+ tell It;
+ setTreeSource #mesquite.trees.StoredTrees.StoredTrees;
+ tell It;
+ setTreeBlock 1;
+ toggleUseWeights off;
+ endTell;
+ setAssignedID 1199.1144113549683.1862327035904205997;
+ getTreeWindow;
+ tell It;
+ popOut;
+ setExplanationSize 30;
+ setAnnotationSize 20;
+ setFontIncAnnot 0;
+ setFontIncExp 0;
+ setSize 688 483;
+ setLocation 488 22;
+ setFont SanSerif;
+ setFontSize 10;
+ getToolPalette;
+ tell It;
+ setTool mesquite.trees.BranchLengthsAdjust.AdjustToolExtra.adjustor;
+ endTell;
+ setActive;
+ getTreeDrawCoordinator #mesquite.trees.BasicTreeDrawCoordinator.BasicTreeDrawCoordinator;
+ tell It;
+ suppress;
+ setTreeDrawer #mesquite.trees.SquareTree.SquareTree;
+ tell It;
+ setNodeLocs #mesquite.trees.NodeLocsStandard.NodeLocsStandard;
+ tell It;
+ stretchToggle off;
+ branchLengthsToggle on;
+ toggleScale off;
+ toggleBroadScale off;
+ toggleCenter on;
+ toggleEven on;
+ namesAngle ?;
+ endTell;
+ setEdgeWidth 6;
+ orientRight;
+ toggleCorners off;
+ endTell;
+ setBackground White;
+ setBranchColor Black;
+ showNodeNumbers off;
+ showBranchColors on;
+ labelBranchLengths off;
+ desuppress;
+ getEmployee #mesquite.trees.BasicDrawTaxonNames.BasicDrawTaxonNames;
+ tell It;
+ setFontSize 14;
+ setColor Black;
+ toggleColorPartition on;
+ toggleShadePartition off;
+ toggleNodeLabels on;
+ toggleCenterNodeNames off;
+ toggleShowNames on;
+ endTell;
+ endTell;
+ setTreeNumber 1;
+ useSuggestedSize on;
+ toggleTextOnTree off;
+ newWindowAssistant #mesquite.trees.MirrorTreeWindowMaker.MirrorTreeWindowMaker;
+ tell It;
+ getWindow;
+ tell It;
+ popOut;
+ setExplanationSize 30;
+ setAnnotationSize 0;
+ setFontIncAnnot 0;
+ setFontIncExp 0;
+ setSize 476 392;
+ setLocation 12 409;
+ setFont SanSerif;
+ setFontSize 10;
+ newAssistantLeft #mesquite.ancstates.TraceCharacterHistory.TraceCharacterHistory;
+ tell It;
+ suspend ;
+ setDisplayMode #mesquite.ancstates.ShadeStatesOnTree.ShadeStatesOnTree;
+ tell It;
+ toggleLabels off;
+ toggleGray off;
+ endTell;
+ setHistorySource #mesquite.ancstates.RecAncestralStates.RecAncestralStates;
+ tell It;
+ getCharacterSource #mesquite.charMatrices.CharSrcCoordObed.CharSrcCoordObed;
+ tell It;
+ setCharacterSource #mesquite.charMatrices.StoredCharacters.StoredCharacters;
+ tell It;
+ setDataSet #7359026449824636807;
+ endTell;
+ endTell;
+ setMethod #mesquite.parsimony.ParsAncestralStates.ParsAncestralStates;
+ tell It;
+ setModelSource #mesquite.parsimony.CurrentParsModels.CurrentParsModels;
+ endTell;
+ endTell;
+ setCharacter 1;
+ setMapping 1;
+ toggleShowLegend off;
+ toggleGray off;
+ toggleWeights on;
+ resume ;
+ endTell;
+ newAssistantRight #mesquite.ancstates.TraceCharacterHistory.TraceCharacterHistory;
+ tell It;
+ suspend ;
+ setDisplayMode #mesquite.ancstates.ShadeStatesOnTree.ShadeStatesOnTree;
+ tell It;
+ toggleLabels off;
+ toggleGray off;
+ endTell;
+ setHistorySource #mesquite.ancstates.RecAncestralStates.RecAncestralStates;
+ tell It;
+ getCharacterSource #mesquite.charMatrices.CharSrcCoordObed.CharSrcCoordObed;
+ tell It;
+ setCharacterSource #mesquite.charMatrices.StoredCharacters.StoredCharacters;
+ tell It;
+ setDataSet #7359026449824636807;
+ endTell;
+ endTell;
+ setMethod #mesquite.parsimony.ParsAncestralStates.ParsAncestralStates;
+ tell It;
+ setModelSource #mesquite.parsimony.CurrentParsModels.CurrentParsModels;
+ endTell;
+ endTell;
+ setCharacter 2;
+ setMapping 1;
+ toggleShowLegend off;
+ toggleGray off;
+ toggleWeights on;
+ resume ;
+ endTell;
+ endTell;
+ getTreeDrawCoordinator #mesquite.trees.BasicTreeDrawCoordinator.BasicTreeDrawCoordinator;
+ tell It;
+ suppress;
+ setTreeDrawer #mesquite.trees.SquareTree.SquareTree;
+ tell It;
+ setNodeLocs #mesquite.trees.NodeLocsStandard.NodeLocsStandard;
+ tell It;
+ stretchToggle on;
+ branchLengthsToggle off;
+ toggleScale off;
+ toggleBroadScale off;
+ toggleCenter on;
+ toggleEven on;
+ namesAngle ?;
+ endTell;
+ setEdgeWidth 10;
+ orientLeft;
+ toggleCorners off;
+ endTell;
+ setBackground White;
+ setBranchColor Black;
+ showNodeNumbers off;
+ showBranchColors on;
+ labelBranchLengths off;
+ desuppress;
+ getEmployee #mesquite.trees.BasicDrawTaxonNames.BasicDrawTaxonNames;
+ tell It;
+ setFontSize 12;
+ setColor Black;
+ toggleColorPartition on;
+ toggleShadePartition off;
+ toggleNodeLabels on;
+ toggleCenterNodeNames off;
+ toggleShowNames on;
+ endTell;
+ endTell;
+ showWindow;
+ endTell;
+ newWindowAssistant #mesquite.correl.CorrelationViewer.CorrelationViewer;
+ tell It;
+ getCharSource #mesquite.charMatrices.CharSrcCoordObed.CharSrcCoordObed;
+ tell It;
+ setCharacterSource #mesquite.charMatrices.StoredCharacters.StoredCharacters;
+ tell It;
+ setDataSet #7359026449824636807;
+ endTell;
+ endTell;
+ setCorrelationCalculator #mesquite.correl.Pagel94.Pagel94;
+ tell It;
+ setSeed 1188836136528;
+ setSimCount 100;
+ togglePresentPValue off;
+ setNumIterations 10;
+ endTell;
+ setX -1;
+ setY 0;
+ doCounts;
+ endTell;
+ endTell;
+ showWindow;
+ getEmployee #mesquite.trees.ColorBranches.ColorBranches;
+ tell It;
+ setColor Red;
+ removeColor off;
+ endTell;
+ getEmployee #mesquite.ornamental.BranchNotes.BranchNotes;
+ tell It;
+ setAlwaysOn off;
+ endTell;
+ getEmployee #mesquite.ornamental.ColorTreeByPartition.ColorTreeByPartition;
+ tell It;
+ colorByPartition off;
+ endTell;
+ endTell;
+ endTell;
+ newAssistant #mesquite.basic.ExamplesNavigator.ExamplesNavigator;
+ tell It;
+ setNextFileName '00c-pairwiseIntro.nex';
+ setPrevFileName '00a-FelsensteinsContrasts.nex';
+ getWindow;
+ tell It;
+ setExplanationSize 0;
+ setAnnotationSize 0;
+ setFontIncAnnot 0;
+ setFontIncExp 0;
+ setSize 454 246;
+ setLocation 10 22;
+ setFont SanSerif;
+ setFontSize 10;
+ setExplanation 'Pagel''s 1994 method uses likelihood ratio tests to determine if two categorical characters are correlated. Mesquite requires the two characters to be binary (0,1) characters. To turn on an analysis, choose Pagel 94 Analysis from the Analysis menu of the Tree Window.^n^nThis is an example from Pagel''s Discrete manual. Two characters appear to be associated as shown in the Mirror tree window above. At right is the analysis. To estimate the significance value, select Present P value in the Pagel94 menu of the tree window at right. ^n^nBelow is a link to the section in manual describing the method.';
+ setTitle 'Pagel''s method';
+ toggleFileNames off;
+ setPrevButtonName Previous;
+ setNextButtonName Next;
+ addWebLink Page_in_manual 'docs/mesquite/CharacterEvolution/ProcessCharEvol.html#pagel94';
+ endTell;
+ showWindow;
+ endTell;
+ endTell;
+end;
+
+
Added: trunk/treebase-core/lib/examples/Correlation/00c-pairwiseIntro.nex
===================================================================
--- trunk/treebase-core/lib/examples/Correlation/00c-pairwiseIntro.nex (rev 0)
+++ trunk/treebase-core/lib/examples/Correlation/00c-pairwiseIntro.nex 2009-12-15 18:14:51 UTC (rev 377)
@@ -0,0 +1,34 @@
+#NEXUS
+[written Mon Sep 03 09:16:57 PDT 2007 by Mesquite version 2.0BETA3 (build i55) at Thrandina.local/127.0.0.1 (Wayne Maddison)]
+Begin MESQUITE;
+ MESQUITESCRIPTVERSION 2;
+ TITLE AUTO;
+ tell ProjectCoordinator;
+ newAssistant #mesquite.basic.ExamplesNavigator.ExamplesNavigator;
+ tell It;
+ setNextFileName '01-pairwise.nex';
+ setPrevFileName '00b-pagel94Hominids.nex';
+ getWindow;
+ tell It;
+ setExplanationSize 0;
+ setAnnotationSize 0;
+ setFontIncAnnot 0;
+ setFontIncExp 0;
+ setSize 429 310;
+ setLocation 318 26;
+ setFont SanSerif;
+ setFontSize 10;
+ setActive;
+ setExplanation 'The following examples concern pairwise tests of character association^n^nThey illustrate the methods described in: ^n^nMaddison, W.P. 2000. Testing character correlation using pairwise comparisons on a phylogeny. Journal of Theoretical Biology. 202: 195-204.^n^nThis paper describes methods to choose pairs of taxa for comparative method calculations (tests of character association). The corresponding Mesquite modules automatically find phylogenetically separate pairs of taxa according to specific criteria. ^n^nThe example files begin with a fairly complex example, then proceed through the examples of the figures of the paper cited above.^n';
+ setTitle Pairwise_comparison_examples;
+ toggleFileNames off;
+ setPrevButtonName Previous;
+ setNextButtonName Next;
+ setEditorsVisible;
+ endTell;
+ showWindow;
+ endTell;
+ endTell;
+end;
+
+
Added: trunk/treebase-core/lib/examples/Correlation/01-pairwise.nex
===================================================================
--- trunk/treebase-core/lib/examples/Correlation/01-pairwise.nex (rev 0)
+++ trunk/treebase-core/lib/examples/Correlation/01-pairwise.nex 2009-12-15 18:14:51 UTC (rev 377)
@@ -0,0 +1,409 @@
+#NEXUS
+[written Mon Sep 03 09:17:33 PDT 2007 by Mesquite version 2.0BETA3 (build i55) at Thrandina.local/127.0.0.1 (Wayne Maddison)]
+
+BEGIN TAXA;
+ DIMENSIONS NTAX=24;
+ TAXLABELS
+ species_0 species_1 species_2 species_3 species_4 species_5 species_6 species_7 species_8 species_9 species_10 species_11 species_12 species_13 species_14 species_15 species_16 species_17 species_18 species_19 species_20 species_21 species_22 species_23
+ ;
+ BLOCKID WM114cc2916be37;
+
+END;
+
+
+BEGIN CHARACTERS;
+ TITLE habitat;
+ DIMENSIONS NCHAR=1;
+ FORMAT DATATYPE = STANDARD GAP = - MISSING = ? SYMBOLS = " 0 1";
+ CHARSTATELABELS
+ 1 habitat / aquatic terrestrial ;
+ MATRIX
+ species_0 0
+ species_1 1
+ species_2 0
+ species_3 0
+ species_4 1
+ species_5 1
+ species_6 0
+ species_7 0
+ species_8 1
+ species_9 1
+ species_10 0
+ species_11 0
+ species_12 0
+ species_13 0
+ species_14 0
+ species_15 1
+ species_16 1
+ species_17 1
+ species_18 0
+ species_19 0
+ species_20 1
+ species_21 0
+ species_22 0
+ species_23 0
+
+;
+ BLOCKID WM114cc2916ef0;
+
+
+END;
+BEGIN CHARACTERS;
+ TITLE physiology;
+ DIMENSIONS NCHAR=2;
+ FORMAT DATATYPE = CONTINUOUS;
+CHARSTATELABELS
+ 1 metabolic_rate,
+ 2 sprint_speed ;
+ MATRIX
+ species_0 1.219 11.3
+ species_1 3.56 17.98
+ species_2 0.98 15.16
+ species_3 2.341 19.53
+ species_4 1.998 23.07
+ species_5 2.951 20.78
+ species_6 0.5681 20.44
+ species_7 1.153 17.82
+ species_8 2.713 22.37
+ species_9 5.673 20.12
+ species_10 0.112 13.0
+ species_11 0.6743 15.91
+ species_12 0.9881 16.19
+ species_13 1.231 20.35
+ species_14 1.987 20.32
+ species_15 1.7 18.87
+ species_16 2.987 22.82
+ species_17 3.209 29.87
+ species_18 0.456 19.53
+ species_19 0.9868 16.07
+ species_20 1.233 24.62
+ species_21 0.871 21.01
+ species_22 0.3451 12.83
+ species_23 0.795 13.99
+
+;
+ BLOCKID WM114cc2917030;
+
+
+END;
+BEGIN TREES;
+ TRANSLATE
+ 1 species_0,
+ 2 species_1,
+ 3 species_2,
+ 4 species_3,
+ 5 species_4,
+ 6 species_5,
+ 7 species_6,
+ 8 species_7,
+ 9 species_8,
+ 10 species_9,
+ 11 species_10,
+ 12 species_11,
+ 13 species_12,
+ 14 species_13,
+ 15 species_14,
+ 16 species_15,
+ 17 species_16,
+ 18 species_17,
+ 19 species_18,
+ 20 species_19,
+ 21 species_20,
+ 22 species_21,
+ 23 species_22,
+ 24 species_23;
+ TREE mtDNA_phylogeny = (((((1,16),((9,17),14)),(((6,20),(((8,24),(15,(18,21))),(10,((11,22),12)))),(7,(2,19)))),4),((3,(13,23)),5));
+
+END;
+
+
+BEGIN CODONS;
+CODESET * UNTITLED (CHARACTERS = habitat) = universal: 1;
+
+
+END;
+
+BEGIN ASSUMPTIONS;
+ TYPESET * UNTITLED (CHARACTERS = habitat) = unord: 1;
+TYPESET Current_Parsimony_Models (CHARACTERS = habitat) = unord: 1;
+TYPESET * UNTITLED (CHARACTERS = physiology) = Linear: 1 - 2;
+TYPESET Current_Parsimony_Models (CHARACTERS = physiology) = Linear: 1 - 2;
+
+END;
+
+BEGIN MESQUITECHARMODELS;
+ ProbModelSet * UNTITLED (CHARACTERS = habitat) = 'Mk1 (est.)': 1;
+ProbModelSet * UNTITLED (CHARACTERS = physiology) = Brownian_default: 1 - 2;
+ProbModelSet Current_Probability_Models (CHARACTERS = physiology) = Brownian_default: 1 - 2;
+END;
+
+Begin MESQUITE;
+ MESQUITESCRIPTVERSION 2;
+ TITLE AUTO;
+ tell ProjectCoordinator;
+ getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa;
+ tell It;
+ setID 0 5616496406151607698 WM114cc2916be37;
+ endTell;
+ getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters;
+ tell It;
+ setID 0 5359875599842773608 WM114cc2916ef0;
+ checksum 0 2437689620 WM114cc2916ef0;
+ setID 1 1344182101150933612 WM114cc2917030;
+ checksum 1 573191175 WM114cc2917030;
+ endTell;
+ getEmployee #mesquite.trees.BasicTreeWindowCoord.BasicTreeWindowCoord;
+ tell It;
+ makeTreeWindow #5616496406151607698 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker;
+ tell It;
+ setTreeSource #mesquite.trees.StoredTrees.StoredTrees;
+ tell It;
+ setTreeBlock 1;
+ toggleUseWeights off;
+ endTell;
+ setAssignedID 865.967565541874.2516291620293279705;
+ getTreeWindow;
+ tell It;
+ popOut;
+ setExplanationSize 20;
+ setAnnotationSize 20;
+ setFontIncAnnot 0;
+ setFontIncExp 0;
+ setSize 584 546;
+ setLocation 559 22;
+ setFont SanSerif;
+ setFontSize 10;
+ getToolPalette;
+ tell It;
+ endTell;
+ setActive;
+ getTreeDrawCoordinator #mesquite.trees.BasicTreeDrawCoordinator.BasicTreeDrawCoordinator;
+ tell It;
+ suppress;
+ setTreeDrawer #mesquite.trees.DiagonalDrawTree.DiagonalDrawTree;
+ tell It;
+ setNodeLocs #mesquite.trees.NodeLocsStandard.NodeLocsStandard;
+ tell It;
+ stretchToggle off;
+ branchLengthsToggle off;
+ toggleScale on;
+ toggleBroadScale off;
+ toggleCenter off;
+ toggleEven off;
+ namesAngle ?;
+ endTell;
+ setEdgeWidth 12;
+ orientRight;
+ endTell;
+ setBackground White;
+ setBranchColor Black;
+ showNodeNumbers off;
+ showBranchColors on;
+ labelBranchLengths off;
+ desuppress;
+ getEmployee #mesquite.trees.BasicDrawTaxonNames.BasicDrawTaxonNames;
+ tell It;
+ setFont SanSerif;
+ setFontSize 10;
+ setColor Black;
+ toggleColorPartition on;
+ toggleShadePartition off;
+ toggleNodeLabels on;
+ toggleCenterNodeNames off;
+ toggleShowNames on;
+ endTell;
+ endTell;
+ setTreeNumber 1;
+ useSuggestedSize off;
+ toggleSizeToFit on;
+ toggleTextOnTree off;
+ newAssistant #mesquite.pairwise.PairwiseComparison.PairwiseComparison;
+ tell It;
+ requireCalculate;
+ showStates off;
+ setPairSelector #mesquite.pairwise.PairsOneChar.PairsOneChar;
+ tell It;
+ setLimit 5;
+ endTell;
+ getCharacterSourceA #mesquite.charMatrices.CharSrcCoordObed.CharSrcCoordObed;
+ tell It;
+ setCharacterSource #mesquite.charMatrices.StoredCharacters.StoredCharacters;
+ tell It;
+ setDataSet #5359875599842773608;
+ endTell;
+ endTell;
+ getCharacterSourceB #mesquite.charMatrices.CharSrcCoordObed.CharSrcCoordObed;
+ tell It;
+ setCharacterSource #mesquite.charMatrices.StoredCharacters.StoredCharacters;
+ tell It;
+ setDataSet #1344182101150933612;
+ endTell;
+ endTell;
+ setCharacterA 1;
+ setCharacterB 1;
+ setPairing 1;
+ setInitialOffsetX 3;
+ setInitialOffsetY -494;
+ calculate;
+ endTell;
+ newWindowAssistant #mesquite.trees.MirrorTreeWindowMaker.MirrorTreeWindowMaker;
+ tell It;
+ getWindow;
+ tell It;
+ popOut;
+ setExplanationSize 0;
+ setAnnotationSize 0;
+ setFontIncAnnot 0;
+ setFontIncExp 0;
+ setSize 562 470;
+ setLocation 6 336;
+ setFont SanSerif;
+ setFontSize 10;
+ newAssistantLeft #mesquite.ancstates.TraceCharacterHistory.TraceCharacterHistory;
+ tell It;
+ suspend ;
+ setDisplayMode #mesquite.ancstates.ShadeStatesOnTree.ShadeStatesOnTree;
+ tell It;
+ toggleLabels off;
+ toggleGray off;
+ endTell;
+ setHistorySource #mesquite.ancstates.RecAncestralStates.RecAncestralStates;
+ tell It;
+ getCharacterSource #mesquite.charMatrices.CharSrcCoordObed.CharSrcCoordObed;
+ tell It;
+ setCharacterSource #mesquite.charMatrices.StoredCharacters.StoredCharacters;
+ tell It;
+ setDataSet #5359875599842773608;
+ endTell;
+ endTell;
+ setMethod #mesquite.parsimony.ParsAncestralStates.ParsAncestralStates;
+ tell It;
+ setModelSource #mesquite.parsimony.CurrentParsModels.CurrentParsModels;
+ endTell;
+ endTell;
+ setCharacter 1;
+ setMapping 1;
+ toggleShowLegend on;
+ toggleGray off;
+ toggleWeights on;
+ setInitialOffsetX 20;
+ setInitialOffsetY -161;
+ setLegendWidth 142;
+ setLegendHeight 161;
+ resume ;
+ endTell;
+ newAssistantRight #mesquite.ancstates.TraceCharacterHistory.TraceCharacterHistory;
+ tell It;
+ suspend ;
+ setDisplayMode #mesquite.ancstates.ShadeStatesOnTree.ShadeStatesOnTree;
+ tell It;
+ toggleLabels off;
+ toggleGray off;
+ endTell;
+ setHistorySource #mesquite.ancstates.RecAncestralStates.RecAncestralStates;
+ tell It;
+ getCharacterSource #mesquite.charMatrices.CharSrcCoordObed.CharSrcCoordObed;
+ tell It;
+ setCharacterSource #mesquite.charMatrices.StoredCharacters.StoredCharacters;
+ tell It;
+ setDataSet #1344182101150933612;
+ endTell;
+ endTell;
+ setMethod #mesquite.parsimony.ParsAncestralStates.ParsAncestralStates;
+ tell It;
+ setModelSource #mesquite.parsimony.CurrentParsModels.CurrentParsModels;
+ endTell;
+ endTell;
+ setCharacter 1;
+ setMapping 1;
+ toggleShowLegend on;
+ toggleGray off;
+ toggleWeights on;
+ setInitialOffsetX -162;
+ setInitialOffsetY -305;
+ setLegendWidth 142;
+ setLegendHeight 305;
+ resume ;
+ endTell;
+ endTell;
+ getTreeDrawCoordinator #mesquite.trees.BasicTreeDrawCoordinator.BasicTreeDrawCoordinator;
+ tell It;
+ suppress;
+ setTreeDrawer #mesquite.trees.DiagonalDrawTree.DiagonalDrawTree;
+ tell It;
+ setNodeLocs #mesquite.trees.NodeLocsStandard.NodeLocsStandard;
+ tell It;
+ stretchToggle off;
+ branchLengthsToggle off;
+ toggleScale on;
+ toggleBroadScale off;
+ toggleCenter off;
+ toggleEven off;
+ namesAngle ?;
+ endTell;
+ setEdgeWidth 12;
+ orientLeft;
+ endTell;
+ setBackground White;
+ setBranchColor Black;
+ showNodeNumbers off;
+ showBranchColors on;
+ labelBranchLengths off;
+ desuppress;
+ getEmployee #mesquite.trees.BasicDrawTaxonNames.BasicDrawTaxonNames;
+ tell It;
+ setFont SanSerif;
+ setFontSize 10;
+ setColor Black;
+ toggleColorPartition on;
+ toggleShadePartition off;
+ toggleNodeLabels on;
+ toggleCenterNodeNames off;
+ toggleShowNames on;
+ endTell;
+ endTell;
+ showWindow;
+ endTell;
+ endTell;
+ showWindow;
+ getEmployee #mesquite.trees.ColorBranches.ColorBranches;
+ tell It;
+ setColor Red;
+ removeColor off;
+ endTell;
+ getEmployee #mesquite.ornamental.BranchNotes.BranchNotes;
+ tell It;
+ setAlwaysOn off;
+ endTell;
+ getEmployee #mesquite.ornamental.ColorTreeByPartition.ColorTreeByPartition;
+ tell It;
+ colorByPartition off;
+ endTell;
+ endTell;
+ endTell;
+ newAssistant #mesquite.basic.ExamplesNavigator.ExamplesNavigator;
+ tell It;
+ setNextFileName '02-pairwiseFig2(1).nex';
+ setPrevFileName '00-introduction.nex';
+ getWindow;
+ tell It;
+ setExplanationSize 0;
+ setAnnotationSize 0;
+ setFontIncAnnot 0;
+ setFontIncExp 0;
+ setSize 475 188;
+ setLocation 5 22;
+ setFont SanSerif;
+ setFontSize 10;
+ setExplanation 'This file shows the use of pairwise comparisons to test association between characters on a phylogeny. At right are two data matrices, categorical and continuous. The first character of each is compared in the mirror tree window. Above left is an analysis of pairwise comparisons automatically chosen by the algorithm of W. Maddison (2000). There are 3696 pairings of terminal taxa with 7 pairs contrasting the independent (categorical) variable. The first pairing (#1) is shown: all 7 of its pairs have the dependent variable greater in the terrestrial species, significant with p=0.0078. However, among all 3696 pairings, some are not significant (worst p is 0.2265).';
+ setTitle Pairwise_comparison;
+ toggleFileNames off;
+ setPrevButtonName Previous;
+ setNextButtonName Next;
+ endTell;
+ showWindow;
+ endTell;
+ endTell;
+end;
+
+
Added: trunk/treebase-core/lib/examples/Correlation/02-pairwiseFig2(1).nex
===================================================================
--- trunk/treebase-core/lib/examples/Correlation/02-pairwiseFig2(1).nex (rev 0)
+++ trunk/treebase-core/lib/examples/Correlation/02-pairwiseFig2(1).nex 2009-12-15 18:14:51 UTC (rev 377)
@@ -0,0 +1,299 @@
+#NEXUS
+[written Mon Sep 03 09:17:53 PDT 2007 by Mesquite version 2.0BETA3 (build i55) at Thrandina.local/127.0.0.1 (Wayne Maddison)]
+
+BEGIN TAXA;
+ DIMENSIONS NTAX=20;
+ TAXLABELS
+ A B C D E F G H I J K L M N O P Q R S T
+ ;
+ BLOCKID WM114cc29a60438;
+
+END;
+
+
+BEGIN CHARACTERS;
+ DIMENSIONS NCHAR=2;
+ FORMAT DATATYPE = STANDARD GAP = - MISSING = ? SYMBOLS = " 0 1";
+ MATRIX
+ A 00
+ B 11
+ C 00
+ D 00
+ E 11
+ F 11
+ G 01
+ H 00
+ I 00
+ J 00
+ K 11
+ L 11
+ M 00
+ N 00
+ O 11
+ P 11
+ Q 10
+ R 00
+ S 00
+ T 00
+
+;
+ BLOCKID WM114cc29a6140;
+
+
+END;
+BEGIN TREES;
+ TRANSLATE
+ 1 A,
+ 2 B,
+ 3 C,
+ 4 D,
+ 5 E,
+ 6 F,
+ 7 G,
+ 8 H,
+ 9 I,
+ 10 J,
+ 11 K,
+ 12 L,
+ 13 M,
+ 14 N,
+ 15 O,
+ 16 P,
+ 17 Q,
+ 18 R,
+ 19 S,
+ 20 T;
+ TREE UNTITLED = ((9,14),((15,11),(18,(((7,(20,19)),12),(((1,(10,((16,17),6))),(13,8)),(((4,5),2),3))))));
+
+END;
+
+
+BEGIN MACCLADE;
+Version 3.05;
+LastModified - 1306936660;
+Singles 0100& / 0;
+
+END;
+BEGIN CODONS;
+CODESET * UNTITLED = universal: 1 - 2;
+
+
+END;
+
+BEGIN ASSUMPTIONS;
+OPTIONS DEFTYPE = unord PolyTcount = MINSTEPS;
+ TYPESET * UNTITLED = unord: 1 - 2;
+TYPESET Current_Parsimony_Models = unord: 1 - 2;
+
+END;
+
+BEGIN MESQUITECHARMODELS;
+ ProbModelSet * UNTITLED = 'Mk1 (est.)': 1 - 2;
+END;
+
+Begin MESQUITE;
+ MESQUITESCRIPTVERSION 2;
+ TITLE AUTO;
+ tell ProjectCoordinator;
+ getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa;
+ tell It;
+ setID 0 3196237234391053769 WM114cc29a60438;
+ endTell;
+ getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters;
+ tell It;
+ setID 0 2832606891834185499 WM114cc29a6140;
+ checksum 0 4257668035 WM114cc29a6140;
+ endTell;
+ getEmployee #mesquite.trees.BasicTreeWindowCoord.BasicTreeWindowCoord;
+ tell It;
+ makeTreeWindow #3196237234391053769 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker;
+ tell It;
+ setTreeSource #mesquite.trees.StoredTrees.StoredTrees;
+ tell It;
+ setTreeBlock 1;
+ toggleUseWeights off;
+ endTell;
+ setAssignedID 2369.970632536606.3126887053844580137;
+ getTreeWindow;
+ tell It;
+ popOut;
+ setExplanationSize 20;
+ setAnnotationSize 20;
+ setFontIncAnnot 0;
+ setFontIncExp 0;
+ setSize 859 497;
+ setLocation 398 22;
+ setFont SanSerif;
+ setFontSize 10;
+ getToolPalette;
+ tell It;
+ endTell;
+ setActive;
+ getTreeDrawCoordinator #mesquite.trees.BasicTreeDrawCoordinator.BasicTreeDrawCoordinator;
+ tell It;
+ suppress;
+ setTreeDrawer #mesquite.trees.DiagonalDrawTree.DiagonalDrawTree;
+ tell It;
+ setNodeLocs #mesquite.trees.NodeLocsStandard.NodeLocsStandard;
+ tell It;
+ stretchToggle off;
+ branchLengthsToggle off;
+ toggleScale on;
+ toggleBroadScale off;
+ toggleCenter off;
+ toggleEven off;
+ namesAngle ?;
+ endTell;
+ setEdgeWidth 12;
+ orientUp;
+ endTell;
+ setBackground White;
+ setBranchColor Black;
+ showNodeNumbers off;
+ showBranchColors on;
+ labelBranchLengths off;
+ desuppress;
+ getEmployee #mesquite.trees.BasicDrawTaxonNames.BasicDrawTaxonNames;
+ tell It;
+ setFont SanSerif;
+ setFontSize 10;
+ setColor Black;
+ toggleColorPartition on;
+ toggleShadePartition off;
+ toggleNodeLabels on;
+ toggleCenterNodeNames off;
+ toggleShowNames on;
+ endTell;
+ endTell;
+ setTreeNumber 1;
+ useSuggestedSize off;
+ toggleSizeToFit on;
+ toggleTextOnTree off;
+ newAssistant #mesquite.pairwise.PairwiseComparison.PairwiseComparison;
+ tell It;
+ requireCalculate;
+ showStates on;
+ setPairSelector #mesquite.pairwise.PairsNoChars.PairsNoChars;
+ getCharacterSourceA #mesquite.charMatrices.CharSrcCoordObed.CharSrcCoordObed;
+ tell It;
+ setCharacterSource #mesquite.charMatrices.StoredCharacters.StoredCharacters;
+ tell It;
+ setDataSet #2832606891834185499;
+ endTell;
+ endTell;
+ getCharacterSourceB #mesquite.charMatrices.CharSrcCoordObed.CharSrcCoordObed;
+ tell It;
+ setCharacterSource #mesquite.charMatrices.StoredCharacters.StoredCharacters;
+ tell It;
+ setDataSet #2832606891834185499;
+ endTell;
+ endTell;
+ setCharacterA 1;
+ setCharacterB 2;
+ setPairing 1;
+ setInitialOffsetX -200;
+ setInitialOffsetY -340;
+ calculate;
+ endTell;
+ endTell;
+ showWindow;
+ getEmployee #mesquite.trees.ColorBranches.ColorBranches;
+ tell It;
+ setColor Red;
+ removeColor off;
+ endTell;
+ getEmployee #mesquite.ornamental.BranchNotes.BranchNotes;
+ tell It;
+ setAlwaysOn off;
+ endTell;
+ getEmployee #mesquite.ornamental.ColorTreeByPartition.ColorTreeByPartition;
+ tell It;
+ colorByPartition off;
+ endTell;
+ endTell;
+ endTell;
+ getEmployee #mesquite.charMatrices.BasicDataWindowCoord.BasicDataWindowCoord;
+ tell It;
+ showDataWindow #2832606891834185499 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker;
+ tell It;
+ getWindow;
+ tell It;
+ setExplanationSize 20;
+ setAnnotationSize 20;
+ setFontIncAnnot 0;
+ setFontIncExp 0;
+ setSize 386 277;
+ setLocation 6 22;
+ setFont SanSerif;
+ setFontSize 10;
+ getToolPalette;
+ tell It;
+ endTell;
+ setTool mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindow.arrow;
+ colorCells #mesquite.charMatrices.NoColor.NoColor;
+ setBackground White;
+ toggleShowNames on;
+ toggleTight off;
+ toggleShowChanges on;
+ toggleSeparateLines off;
+ toggleShowStates on;
+ toggleAutoWCharNames on;
+ toggleShowDefaultCharNames off;
+ toggleConstrainCW on;
+ setColumnWidth 16;
+ toggleBirdsEye off;
+ toggleColorsPanel off;
+ birdsEyeWidth 2;
+ toggleLinkedScrolling on;
+ toggleScrollLinkedTables off;
+ endTell;
+ showWindow;
+ 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.ColorCells.ColorCells;
+ tell It;
+ setColor Red;
+ removeColor off;
+ endTell;
+ getEmployee #mesquite.charMatrices.QuickKeySelector.QuickKeySelector;
+ tell It;
+ autotabOff;
+ endTell;
+ endTell;
+ endTell;
+ newAssistant #mesquite.basic.ExamplesNavigator.ExamplesNavigator;
+ tell It;
+ setNextFileName '03-pairwiseFig2(2).nex';
+ setPrevFileName '01-pairwise.nex';
+ getWindow;
+ tell It;
+ setExplanationSize 0;
+ setAnnotationSize 0;
+ setFontIncAnnot 0;
+ setFontIncExp 0;
+ setSize 386 317;
+ setLocation 6 22;
+ setFont SanSerif;
+ setFontSize 10;
+ setExplanation 'For figure 2 of Maddison, W.P. 2000. Testing character correlation using pairwise comparisons on a phylogeny. Journal of Theoretical Biology. 202: 195-204.^n^nThis shows choice of pairs without regard to states of characters. The grey boxes over the terminal taxa show in bold what is designated the Independent variable, and below that the dependent variable.';
+ setTitle Pairwise;
+ toggleFileNames off;
+ setPrevButtonName Previous;
+ setNextButtonName Next;
+ endTell;
+ showWindow;
+ endTell;
+ endTell;
+end;
+
+
Added: trunk/treebase-core/lib/examples/Correlation/03-pairwiseFig2(2).nex
===================================================================
--- trunk/treebase-core/lib/examples/Correlation/03-pairwiseFig2(2).nex (rev 0)
+++ trunk/treebase-core/lib/examples/Correlation/03-pairwiseFig2(2).nex 2009-12-15 18:14:51 UTC (rev 377)
@@ -0,0 +1,302 @@
+#NEXUS
+[written Mon Sep 03 09:18:09 PDT 2007 by Mesquite version 2.0BETA3 (build i55) at Thrandina.local/127.0.0.1 (Wayne Maddison)]
+
+BEGIN TAXA;
+ DIMENSIONS NTAX=20;
+ TAXLABELS
+ A B C D E F G H I J K L M N O P Q R S T
+ ;
+ BLOCKID WM114cc29f73d39;
+
+END;
+
+
+BEGIN CHARACTERS;
+ DIMENSIONS NCHAR=2;
+ FORMAT DATATYPE = STANDARD GAP = - MISSING = ? SYMBOLS = " 0 1";
+ MATRIX
+ A 00
+ B 11
+ C 00
+ D 00
+ E 11
+ F 11
+ G 01
+ H 00
+ I 00
+ J 00
+ K 11
+ L 11
+ M 00
+ N 00
+ O 11
+ P 11
+ Q 10
+ R 00
+ S 00
+ T 00
+
+;
+ BLOCKID WM114cc29f77a0;
+
+
+END;
+BEGIN TREES;
+ TRANSLATE
+ 1 A,
+ 2 B,
+ 3 C,
+ 4 D,
+ 5 E,
+ 6 F,
+ 7 G,
+ 8 H,
+ 9 I,
+ 10 J,
+ 11 K,
+ 12 L,
+ 13 M,
+ 14 N,
+ 15 O,
+ 16 P,
+ 17 Q,
+ 18 R,
+ 19 S,
+ 20 T;
+ TREE UNTITLED = ((9,14),((15,11),(18,(((7,(20,19)),12),(((1,(10,((16,17),6))),(13,8)),(((4,5),2),3))))));
+
+END;
+
+
+BEGIN MACCLADE;
+Version 3.05;
+LastModified - 1306936660;
+Singles 0100& / 0;
+
+END;
+BEGIN CODONS;
+CODESET * UNTITLED = universal: 1 - 2;
+
+
+END;
+
+BEGIN ASSUMPTIONS;
+OPTIONS DEFTYPE = unord PolyTcount = MINSTEPS;
+ TYPESET * UNTITLED = unord: 1 - 2;
+TYPESET Current_Parsimony_Models = unord: 1 - 2;
+
+END;
+
+BEGIN MESQUITECHARMODELS;
+ ProbModelSet * UNTITLED = 'Mk1 (est.)': 1 - 2;
+END;
+
+Begin MESQUITE;
+ MESQUITESCRIPTVERSION 2;
+ TITLE AUTO;
+ tell ProjectCoordinator;
+ getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa;
+ tell It;
+ setID 0 6595404229671493286 WM114cc29f73d39;
+ endTell;
+ getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters;
+ tell It;
+ setID 0 8234977281528109195 WM114cc29f77a0;
+ checksum 0 4257668035 WM114cc29f77a0;
+ endTell;
+ getEmployee #mesquite.trees.BasicTreeWindowCoord.BasicTreeWindowCoord;
+ tell It;
+ makeTreeWindow #6595404229671493286 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker;
+ tell It;
+ setTreeSource #mesquite.trees.StoredTrees.StoredTrees;
+ tell It;
+ setTreeBlock 1;
+ toggleUseWeights off;
+ endTell;
+ setAssignedID 2440.970632551984.9050636877436007407;
+ getTreeWindow;
+ tell It;
+ popOut;
+ setExplanationSize 20;
+ setAnnotationSize 20;
+ setFontIncAnnot 0;
+ setFontIncExp 0;
+ setSize 854 499;
+ setLocation 370 22;
+ setFont SanSerif;
+ setFontSize 10;
+ getToolPalette;
+ tell It;
+ endTell;
+ setActive;
+ getTreeDrawCoordinator #mesquite.trees.BasicTreeDrawCoordinator.BasicTreeDrawCoordinator;
+ tell It;
+ suppress;
+ setTreeDrawer #mesquite.trees.DiagonalDrawTree.DiagonalDrawTree;
+ tell It;
+ setNodeLocs #mesquite.trees.NodeLocsStandard.NodeLocsStandard;
+ tell It;
+ stretchToggle off;
+ branchLengthsToggle off;
+ toggleScale on;
+ toggleBroadScale off;
+ toggleCenter off;
+ toggleEven off;
+ namesAngle ?;
+ endTell;
+ setEdgeWidth 12;
+ orientUp;
+ endTell;
+ setBackground White;
+ setBranchColor Black;
+ showNodeNumbers off;
+ showBranchColors on;
+ labelBranchLengths off;
+ desuppress;
+ getEmployee #mesquite.trees.BasicDrawTaxonNames.BasicDrawTaxonNames;
+ tell It;
+ setFont SanSerif;
+ setFontSize 10;
+ setColor Black;
+ toggleColorPartition on;
+ toggleShadePartition off;
+ toggleNodeLabels on;
+ toggleCenterNodeNames off;
+ toggleShowNames on;
+ endTell;
+ endTell;
+ setTreeNumber 1;
+ useSuggestedSize off;
+ toggleSizeToFit on;
+ toggleTextOnTree off;
+ newAssistant #mesquite.pairwise.PairwiseComparison.PairwiseComparison;
+ tell It;
+ requireCalculate;
+ showStates on;
+ setPairSelector #mesquite.pairwise.PairsOneChar.PairsOneChar;
+ tell It;
+ setLimit 5;
+ endTell;
+ getCharacterSourceA #mesquite.charMatrices.CharSrcCoordObed.CharSrcCoordObed;
+ tell It;
+ setCharacterSource #mesquite.charMatrices.StoredCharacters.StoredCharacters;
+ tell It;
+ setDataSet #8234977281528109195;
+ endTell;
+ endTell;
+ getCharacterSourceB #mesquite.charMatrices.CharSrcCoordObed.CharSrcCoordObed;
+ tell It;
+ setCharacterSource #mesquite.charMatrices.StoredCharacters.StoredCharacters;
+ tell It;
+ setDataSet #8234977281528109195;
+ endTell;
+ endTell;
+ setCharacterA 1;
+ setCharacterB 2;
+ setPairing 1;
+ setInitialOffsetX -200;
+ setInitialOffsetY -340;
+ calculate;
+ endTell;
+ endTell;
+ showWindow;
+ getEmployee #mesquite.trees.ColorBranches.ColorBranches;
+ tell It;
+ setColor Red;
+ removeColor off;
+ endTell;
+ getEmployee #mesquite.ornamental.BranchNotes.BranchNotes;
+ tell It;
+ setAlwaysOn off;
+ endTell;
+ getEmployee #mesquite.ornamental.ColorTreeByPartition.ColorTreeByPartition;
+ tell It;
+ colorByPartition off;
+ endTell;
+ endTell;
+ endTell;
+ getEmployee #mesquite.charMatrices.BasicDataWindowCoord.BasicDataWindowCoord;
+ tell It;
+ showDataWindow #8234977281528109195 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker;
+ tell It;
+ getWindow;
+ tell It;
+ setExplanationSize 20;
+ setAnnotationSize 20;
+ setFontIncAnnot 0;
+ setFontIncExp 0;
+ setSize 337 221;
+ setLocation 6 26;
+ setFont SanSerif;
+ setFontSize 10;
+ getToolPalette;
+ tell It;
+ endTell;
+ setTool mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindow.arrow;
+ colorCells #mesquite.charMatrices.NoColor.NoColor;
+ setBackground White;
+ toggleShowNames on;
+ toggleTight off;
+ toggleShowChanges on;
+ toggleSeparateLines off;
+ toggleShowStates on;
+ toggleAutoWCharNames on;
+ toggleShowDefaultCharNames off;
+ toggleConstrainCW on;
+ setColumnWidth 16;
+ toggleBirdsEye off;
+ toggleColorsPanel off;
+ birdsEyeWidth 2;
+ toggleLinkedScrolling on;
+ toggleScrollLinkedTables off;
+ endTell;
+ showWindow;
+ 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.ColorCells.ColorCells;
+ tell It;
+ setColor Red;
+ removeColor off;
+ endTell;
+ getEmployee #mesquite.charMatrices.QuickKeySelector.QuickKeySelector;
+ tell It;
+ autotabOff;
+ endTell;
+ endTell;
+ endTell;
+ newAssistant #mesquite.basic.ExamplesNavigator.ExamplesNavigator;
+ tell It;
+ setNextFileName '04-pairwiseFig2(3).nex';
+ setPrevFileName '02-pairwiseFig2(1).nex';
+ getWindow;
+ tell It;
+ setExplanationSize 0;
+ setAnnotationSize 0;
+ setFontIncAnnot 0;
+ setFontIncExp 0;
+ setSize 337 261;
+ setLocation 6 26;
+ setFont SanSerif;
+ setFontSize 10;
+ setExplanation 'For figure 2 of Maddison, W.P. 2000. Testing character correlation using pairwise comparisons on a phylogeny. Journal of Theoretical Biology. 202: 195-204.^n^nThis shows choice of pairs to contrast the states of character 1.';
+ setTitle Pairwise;
+ toggleFileNames off;
+ setPrevButtonName Previous;
+ setNextButtonName Next;
+ endTell;
+ showWindow;
+ endTell;
+ endTell;
+end;
+
+
Added: trunk/treebase-core/lib/examples/Correlation/04-pairwiseFig2(3).nex
===================================================================
--- trunk/treebase-core/lib/examples/Correlation/04-pairwiseFig2(3).nex (rev 0)
+++ trunk/treebase-core/lib/examples/Correlation/04-pairwiseFig2(3).nex 2009-12-15 18:14:51 UTC (rev 377)
@@ -0,0 +1,302 @@
+#NEXUS
+[written Mon Sep 03 09:18:51 PDT 2007 by Mesquite version 2.0BETA3 (build i55) at Thrandina.local/127.0.0.1 (Wayne Maddison)]
+
+BEGIN TAXA;
+ DIMENSIONS NTAX=20;
+ TAXLABELS
+ A B C D E F G H I J K L M N O P Q R S T
+ ;
+ BLOCKID WM114cc2a351040;
+
+END;
+
+
+BEGIN CHARACTERS;
+ DIMENSIONS NCHAR=2;
+ FORMAT DATATYPE = STANDARD GAP = - MISSING = ? SYMBOLS = " 0 1";
+ MATRIX
+ A 00
+ B 11
+ C 00
+ D 00
+ E 11
+ F 11
+ G 01
+ H 00
+ I 00
+ J 00
+ K 11
+ L 11
+ M 00
+ N 00
+ O 11
+ P 11
+ Q 10
+ R 00
+ S 00
+ T 00
+
+;
+ BLOCKID WM114cc2a35620;
+
+
+END;
+BEGIN TREES;
+ TRANSLATE
+ 1 A,
+ 2 B,
+ 3 C,
+ 4 D,
+ 5 E,
+ 6 F,
+ 7 G,
+ 8 H,
+ 9 I,
+ 10 J,
+ 11 K,
+ 12 L,
+ 13 M,
+ 14 N,
+ 15 O,
+ 16 P,
+ 17 Q,
+ 18 R,
+ 19 S,
+ 20 T;
+ TREE UNTITLED = ((9,14),((15,11),(18,(((7,(20,19)),12),(((1,(10,((16,17),6))),(13,8)),(((4,5),2),3))))));
+
+END;
+
+
+BEGIN MACCLADE;
+Version 3.05;
+LastModified - 1306936660;
+Singles 0100& / 0;
+
+END;
+BEGIN CODONS;
+CODESET * UNTITLED = universal: 1 - 2;
+
+
+END;
+
+BEGIN ASSUMPTIONS;
+OPTIONS DEFTYPE = unord PolyTcount = MINSTEPS;
+ TYPESET * UNTITLED = unord: 1 - 2;
+TYPESET Current_Parsimony_Models = unord: 1 - 2;
+
+END;
+
+BEGIN MESQUITECHARMODELS;
+ ProbModelSet * UNTITLED = 'Mk1 (est.)': 1 - 2;
+END;
+
+Begin MESQUITE;
+ MESQUITESCRIPTVERSION 2;
+ TITLE AUTO;
+ tell ProjectCoordinator;
+ getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa;
+ tell It;
+ setID 0 5715784789562340009 WM114cc2a351040;
+ endTell;
+ getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters;
+ tell It;
+ setID 0 5834500797987800771 WM114cc2a35620;
+ checksum 0 4257668035 WM114cc2a35620;
+ endTell;
+ getEmployee #mesquite.trees.BasicTreeWindowCoord.BasicTreeWindowCoord;
+ tell It;
+ makeTreeWindow #5715784789562340009 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker;
+ tell It;
+ setTreeSource #mesquite.trees.StoredTrees.StoredTrees;
+ tell It;
+ setTreeBlock 1;
+ toggleUseWeights off;
+ endTell;
+ setAssignedID 2511.970632567011.3284971206291078;
+ getTreeWindow;
+ tell It;
+ popOut;
+ setExplanationSize 20;
+ setAnnotationSize 20;
+ setFontIncAnnot 0;
+ setFontIncExp 0;
+ setSize 807 457;
+ setLocation 396 22;
+ setFont SanSerif;
+ setFontSize 10;
+ getToolPalette;
+ tell It;
+ endTell;
+ getTreeDrawCoordinator #mesquite.trees.BasicTreeDrawCoordinator.BasicTreeDrawCoordinator;
+ tell It;
+ suppress;
+ setTreeDrawer #mesquite.trees.DiagonalDrawTree.DiagonalDrawTree;
+ tell It;
+ setNodeLocs #mesquite.trees.NodeLocsStandard.NodeLocsStandard;
+ tell It;
+ stretchToggle off;
+ branchLengthsToggle off;
+ toggleScale on;
+ toggleBroadScale off;
+ toggleCenter off;
+ toggleEven off;
+ namesAngle ?;
+ endTell;
+ setEdgeWidth 12;
+ orientUp;
+ endTell;
+ setBackground White;
+ setBranchColor Black;
+ showNodeNumbers off;
+ showBranchColors on;
+ labelBranchLengths off;
+ desuppress;
+ getEmployee #mesquite.trees.BasicDrawTaxonNames.BasicDrawTaxonNames;
+ tell It;
+ setFont SanSerif;
+ setFontSize 10;
+ setColor Black;
+ toggleColorPartition on;
+ toggleShadePartition off;
+ toggleNodeLabels on;
+ toggleCenterNodeNames off;
+ toggleShowNames on;
+ endTell;
+ endTell;
+ setTreeNumber 1;
+ useSuggestedSize off;
+ toggleSizeToFit on;
+ toggleTextOnTree off;
+ newAssistant #mesquite.pairwise.PairwiseComparison.PairwiseComparison;
+ tell It;
+ requireCalculate;
+ showStates on;
+ setPairSelector #mesquite.pairwise.PairsTwoChars.PairsTwoChars;
+ tell It;
+ setLimit 5;
+ endTell;
+ getCharacterSourceA #mesquite.charMatrices.CharSrcCoordObed.CharSrcCoordObed;
+ tell It;
+ setCharacterSource #mesquite.charMatrices.StoredCharacters.StoredCharacters;
+ tell It;
+ setDataSet #5834500797987800771;
+ endTell;
+ endTell;
+ getCharacterSourceB #mesquite.charMatrices.CharSrcCoordObed.CharSrcCoordObed;
+ tell It;
+ setCharacterSource #mesquite.charMatrices.StoredCharacters.StoredCharacters;
+ tell It;
+ setDataSet #5834500797987800771;
+ endTell;
+ endTell;
+ setCharacterA 1;
+ setCharacterB 2;
+ setPairing 1;
+ setInitialOffsetX -200;
+ setInitialOffsetY -340;
+ calculate;
+ endTell;
+ endTell;
+ showWindow;
+ getEmployee #mesquite.trees.ColorBranches.ColorBranches;
+ tell It;
+ setColor Red;
+ removeColor off;
+ endTell;
+ getEmployee #mesquite.ornamental.BranchNotes.BranchNotes;
+ tell It;
+ setAlwaysOn off;
+ endTell;
+ getEmployee #mesquite.ornamental.ColorTr...
[truncated message content] |
