Full package name: mesquite.ancstates.TraceCharOverTrees.TraceCharOverTrees Duty: Analysis Assistant for Tree Display (mesquite.lib.duties.TreeDisplayAssistantA)
Module Explanation
Summarizes at each node reconstructions of the states of a character over a series of trees. The summary is shown on the current tree; if you want to show it on a consensus of the trees, make sure that the current tree is that consensus.
Author(s): Wayne P. Maddison and David R. Maddison
Version 3.70
Commands of Trace Character Over Trees
setDisplayMode
Explanation: Sets module used to display reconstructed states
Parameters: [name of module]
nextCharacter
Explanation: Goes to next character history
previousCharacter
Explanation: Goes to previous character history
chooseCharacter
Explanation: Queries user about which character history to use
saveNodeValues
Explanation: Queries user about which node number to save values for
toggleShowLegend
Explanation: Sets whether or not the legend is shown
Parameters: [on = show; off]
toggleShowNodeAbsent
Explanation: Sets whether or not the fraction of trees with node absent is shown
Parameters: [on = show; off]
toggleShowEquivocal
Explanation: Sets whether or not the fraction of trees with equivocal states is shown
Parameters: [on = show; off]
setMode
Explanation: Sets how to count ambiguous state assignments at each node for each tree
Parameters: [0 = count state if in optimal state set, or has non-zero likelihood or other score, 1 = count state only if unique in assignment, with no others of non-zero score, 2 = count state if unique in assignment or if uniquely has best score]
setCharacter
Explanation: Sets which character history to use
Parameters: [history number]
setNumTrees
Explanation: Sets the number of trees
Parameters: [number]
setTreeSource
Explanation: Sets the source of trees for comparison
Parameters: [name of module]
setHistorySource
Explanation: Sets module supplying character histories
Parameters: [name of module]
suppress
Explanation: Suppresses calculations
desuppress
Explanation: Desuppresses calculations
getAncStSource
Explanation: Returns ancestral states calculating module
closeTrace
Explanation: Turns off Trace Character Over Trees
setInitialOffsetX
Explanation: Sets initial horizontal offset of legend from home position
Parameters: [offset in pixels]
setInitialOffsetY
Explanation: Sets initial vertical offset of legend from home position
