[Mesquitelist] headless version documentation?

[Wayne Maddison]

Apologies for the technically-faint-of-heart:  The menu item selection system is not yet in place for headless.  What you need to do is take direct control over hiring the analysis module for Pairwise Comparison.  If you're already at the stage of commanding the tree window module (e.g. by using sw to show windows and jw to jump to the tree window, then gm to go to its commanding module), then type:

newAssistant PairwiseComparison

This may take you the next step, but given that headless mode is still rough, you may still find some roadblocks. 

Another option is to set up the pairwise comparison analysis the way you want in the GUI version of Mesquite, then use Window>Scripting>Show Snapshot to get the self-scripting commands that would yield the analysis.  You can select out the piece focused on pairwise comparisons and then use these same commands in headless mode.  If you execute them from a script file with a composed Mesquite block, using linkFile, you would need to insert a command to find the tree window to instruct that (since the Mesquite block will be instructing Mesquite or the basic file coordinator by default).

Feel free to ask for more once you hit the next roadblock.

Wayne


On 6 Dec 2010, at 1:32 PM, Alexis Pepper Yelton wrote:

> Thanks in advance for all your help. I am wondering if there is any documentation for the Mesquite headless version? I am trying to load the pairwise comparison module, but it does not step you through the module when I load it by opening the Analysis menu and typing 
> 
> "15", the number corresponding to Pairwise Comparison. I would be happy to run pairwise comparison from the command line as well, if there were some way to call modules directly.
> 
> Best,
> 
> Alexis Yelton
> 
>  
>  
> -- 
> Alexis Pepper Yelton
> Ph.D. Candidate
> Department of Environmental Science, Policy, and Management
> University of California Berkeley
> pyelton at berkeley.edu
> 
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--------------
Wayne Maddison
    Professor and Canada Research Chair, Depts. of Zoology and Botany
    & Director, Beaty Biodiversity Museum
6270 University Boulevard
University of British Columbia
Vancouver, BC  V6T 1Z4   Canada

Home page: http://salticidae.org/wpm/home.html
Mesquite: http://mesquiteproject.org; MacClade: http://macclade.org
Beaty Biodiversity Museum: http://beatymuseum.ubc.ca