fixed xml test and removed redundant jar
replaced alignments with taxonset elements.
Updated beast-graphics to handle drawing multiple trees in a grid with user-defined strides in either horizontal or vertical orientation from top left.
Still working on multiple-tree figures in beast-graphics. Getting there slowly.
Still working on multiple-tree figures in beast-graphics.
refactoring beast-graphics
Added support for LaTeX font size rendering hints and created figure for chapter 4.
corrected file name
Now beginning to convert all tree figures to beast-graphics..
corrected file name
Refactored the BranchStyle and the TreeOrientation into separate classes. Much cleaner now and was able to remove quite a few classes and methods. Will handle node shapes tomorrow.
tidying up test scripts
Added NodeDecorator and NodePositioningRule
added font size support for node heights and tree rotation
added triangulated node positioning and captions
Refactored node time decoration options into a separate class NodeTimesDecorator. Updated all figure XMLs. Added Ranked4Trees.xml figure.
Improving figures
Added named colors and corrected colors in serial sample tree xml
Added unrooted tree drawing back to beast-graphics. Moved caption handling to TreeDrawingGrid class (renamed from TikzTreeGrid). Added in unrooted figure example.
Added first pass support for drawing colored trees using trait names. Fixed some problems in Node related to nodes with one child. Added a simple Node Decorator for debugging purposes.