Quicklook plugin

[Cody Hinchliff]

Hi, I am curious about the behavior of the quicklook plugin. It seems that it runs in the background on startup and scans the disk (presumably the home directory) for recognized treefiles, generating quicklook thumbnails for the ones it finds. This is an issue for me, because I have a number of very large treefiles. I noticed after my latest reboot that there was a java process using about 200% of my core resources (2/8 cores):

Meconopsis:~ cody$ top -o cpu
[snipped]

PID  COMMAND      %CPU  TIME     #TH   #WQ  #PORT MEM    PURG   CMPR PGRP PPID STATE    BOOSTS         %CPU_ME %CPU_OTHRS UID  FAULTS  COW     MSGSENT  MSGRECV  SYSBSD   SYSMACH  CSW      PAGEIN IDLEW  POWER USER            #MRE

640  java         244.1 54:39.89 26/2  0    256   204M   0B     0B   640  1    running   0[0]          0.00000 0.00000    501  143348+ 388     925916+  8626+    113459+  2744034+ 3156923+ 97     6037+  244.5 cody            N/A

So I checked the process...

Meconopsis:~ cody$ ps 640

  PID   TT  STAT      TIME COMMAND

  640   ??  R     56:51.07 /System/Library/Frameworks/JavaVM.framework/Home/bin/java -Xmx128M -Djava.awt.headless=true -jar /Library/QuickLook/FigTreeQuickLookPlugin.qlgenerator/Contents/Resources/figtree-pdf.jar /Users/cody/Downloads/Fungi_synth_12March2015.tre

Looks like the FigTree qlgenerator is attempting to make a pdf thumbnail of the tree Fungi_synth_12March2015.tre. I'd prefer it didn't, as that tree is quite large (about 300,000 tips), and it seems like it takes a very long time to build the thumbnail. And that's not the only large tree in my filesystem, some of them are well over 1M tips.

Is there some way to disable thumbnail-building for trees over some maximum size? If not, I will just disable the ql plugin entirely.

[Andrew Rambaut]

Hi Cody,

I haven’t had a chance to update the QL plugin for quite a while (it has it’s own embedded FigTree jar file that is much older than the current version). I can’t say I see the behaviour you describe (with a background task occupying a considerable amount of CPU) but perhaps it is getting stuck on these big trees (which I don’t have). It would be possible to get the the embedded command line version of figtree to have an upper limit on tree size. I will add it to my update list. But for now I think you will need to disable the plugin.

Andrew

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Andrew Rambaut 

Institute for Evolutionary Biology | Centre for Infection, Immunity & Evolution 

Ashworth Laboratories, University of Edinburgh, Edinburgh, EH9 3FL, UK

contact – a.ra...@ed.ac.uk | http://tree.bio.ed.ac.uk | tel +44 131 6508624