#NEXUS
[written Sun Sep 21 19:26:59 PDT 2003 by Mesquite  version 1.0 (build e57)]

BEGIN TAXA;
	TITLE Boxes;
	DIMENSIONS NTAX=4;
	TAXLABELS
		Box_1 Box_2 Box_3 Box_4 
	;

END;


BEGIN CHARACTERS;
	TITLE  Landmark_positions;
	DIMENSIONS NCHAR=4;
	FORMAT DATATYPE = CONTINUOUS ITEMS = (x y ) ;
CHARSTATELABELS 
		3 #4,
		4 #3 ; 
	MATRIX
	Box_1   (0.0 0.0) (0.0 1.0) (1.0 1.0) (1.0 0.0)
	Box_2   (0.0 0.0) (0.0 1.0) (1.0 1.0) (1.0 0.0)
	Box_3   (0.0 0.0) (0.0 1.0) (0.8 0.8) (1.0 0.0)
	Box_4   (0.0 0.0) (0.0 1.0) (1.0 1.0) (1.0 0.0)

;

END;

BEGIN ASSUMPTIONS;
	TYPESET * UNTITLED   =  Squared:  1 -  4;

END;

BEGIN MESQUITECHARMODELS;
	ProbModelSet * UNTITLED   =  Brownian_default:  1 -  4;
END;

Begin MESQUITE;
		MESQUITESCRIPTVERSION 2;
		TITLE AUTO;
		tell ProjectCoordinator;
		getEmployee  #mesquite.minimal.ManageTaxa.ManageTaxa;
		tell It;
			setID 0 5420325524222062819;
		endTell;
		getEmployee  #mesquite.charMatrices.ManageCharacters.ManageCharacters;
		tell It;
			setID 0 4430408865877702767;
			checksum 0 4234720301;
		endTell;
		getEmployee  #mesquite.charMatrices.BasicDataWindowCoord.BasicDataWindowCoord;
		tell It;
			showDataWindow #4430408865877702767 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker;
			tell It;
				getWindow;
				tell It;
					setSize 584 159;
					setLocation 10 471;
					setFont SanSerif;
					setFontSize 10;
					offInfoBar;
					setExplanationSize 20;
					setAnnotationSize 20;
					getToolPalette;
					tell It;
					endTell;
					setTool mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindow.arrow;
					toggleShowNames on;
					toggleTight off;
					toggleShowChanges on;
					toggleShowStates on;
					setColumnWidth 72;
				endTell;
				showWindow;
			endTell;
		endTell;
		getEmployee  #mesquite.trees.BasicTreeWindowCoord.BasicTreeWindowCoord;
		tell It;
			makeTreeWindow #5420325524222062819  #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker;
			tell It;
				setTreeSource  #mesquite.trees.DefaultTrees.DefaultTrees;
				setAssignedID 6850.985887405751.627258943310845990;
				getTreeDrawCoordinator #mesquite.trees.BasicTreeDrawCoordinator.BasicTreeDrawCoordinator;
				tell It;
					suppress;
					setTreeDrawer  #mesquite.trees.DiagonalDrawTree.DiagonalDrawTree;
					tell It;
						setEdgeWidth 12;
						orientUp;
						getEmployee #mesquite.trees.NodeLocsStandard.NodeLocsStandard;
						tell It;
							stretchToggle off;
							branchLengthsToggle off;
							toggleScale on;
							toggleCenter off;
							toggleEven off;
							namesAngle ?;
						endTell;
					endTell;
					setBackground White;
					setBranchColor Black;
					desuppress;
					getEmployee #mesquite.trees.BasicDrawTaxonNames.BasicDrawTaxonNames;
					tell It;
						setColor Black;
						toggleColorPartition on;
						toggleNodeLabels on;
						toggleShowNames on;
					endTell;
				endTell;
				getTreeWindow;
				tell It;
					setSize 650 367;
					setLocation 1 22;
					setFont SanSerif;
					setFontSize 10;
					onInfoBar;
					setExplanationSize 20;
					setAnnotationSize 20;
					getToolPalette;
					tell It;
					endTell;
					setTreeNumber 1;
					setTree '((1,2),(3,4));';
					toggleSizeToFit on;
					toggleTextOnTree off;
					newAssistant  #mesquite.rhetenor.LandmarkDrawings.LandmarkDrawings;
				tell It;
					sizeDrawing 100 60;
					setInitialOffsetX -204;
					setInitialOffsetY -145;
					setItems 0 1;
					toggleLastToFirst on;
					getCharacterSource  #mesquite.charMatrices.CharMatrixCoordIndep.CharMatrixCoordIndep;
					tell It;
						setCharacterSource #mesquite.charMatrices.StoredMatrices.StoredMatrices;
						tell It;
							setDataSet #4430408865877702767;
						endTell;
					endTell;
					getReconstructor  #mesquite.ancstates.AncestralStatesAll.AncestralStatesAll;
					tell It;
						setMethod  #mesquite.parsimony.ParsAncestralStates.ParsAncestralStates;
						tell It;
							setModelSource  #mesquite.parsimony.CurrentParsModels.CurrentParsModels;
							getEmployee #mesquite.parsimony.ParsimonySquared.ParsimonySquared;
							tell It;
								toggleWeight on;
							endTell;
						endTell;
					endTell;
				endTell;
				endTell;
				showWindow;
				getEmployee #mesquite.ornamental.BranchNotes.BranchNotes;
				tell It;
					setAlwaysOn off;
				endTell;
				getEmployee #mesquite.trees.ColorBranches.ColorBranches;
				tell It;
					setColor Red;
					removeColor off;
				endTell;
			endTell;
		endTell;
		newAssistant  #mesquite.basic.ExamplesNavigator.ExamplesNavigator;
		tell It;
			setNextFileName '00-introduction.nex';
			setPrevFileName '19-landmarks.nex';
			getWindow;
			tell It;
					setSize 346 422;
					setLocation 656 22;
					setFont SanSerif;
					setFontSize 10;
					offInfoBar;
					setExplanationSize 0;
					setAnnotationSize 0;
					setActive;
				setExplanation 'Once the data matrix was entered, we then selected "Landmark Drawings" from the Analysis menu of the Tree window.  We chose Stored Matrices.^n^nNote that the most recent common ancestor of Box 3 and Box 4 have the corner somewhat punched in, and the change to Box 3 is indicated by the distortion grid calculated by thin plate splines.^n^nYou''ll notice that some of the points are at the edge of the drawings and not easily visible.  The Landmark Drawings module is Mesquite is in its early developmental stages.  We''re planning to allow you to show distortions against immediate ancestor, or against the root of the tree.^n^nBy the way, the pictures of fish in the original Landmark example were shown by the Projector module (see the tool in the tool palette).  The Projector module can associate pictures to taxa if you hold down the Control key while clicking on a taxon name.  It then displays them or turns off display when you use the projector and touch on the taxon name (without Control). ';
				setTitle 'Landmarks cont''d.';
				toggleFileNames off;
				setPrevButtonName Previous;
				setNextButtonName Intro.;
			endTell;
			showWindow;
		endTell;
		endTell;
end;