Hey there, Elaine !
On 08/07/2014 19:29, Elaine Meng wrote:
I'm having a great time playing with Jalview Desktop, but I ran across a couple
of things that may or may not be related.
:)
Starting with a large alignment from Pfam (PF00532 full alignment with >5K
sequences), which apparently includes many blank columns, I get different results
when redundancy-filtering to 90% before and after removing the blank columns.
yes. This is because Jalview isn't excluding gapped columns from the
redundancy calculation. Definitely an oversight (although it *might*
sometime be useful). I also notice the documentation is pretty sparse
on this function:
"Selecting the option in the Alignment window's *Edit* menu or pressing
*'CONTROL+D'* brings up a dialog box asking you to select a threshold.
If the percentage identity between the aligned positions of any two
sequences in the visible alignment exceeds this value, the shorter
sequence is discarded.
/Note:/ The redundancy calculation is done when the dialog box is
opened. For large numbers of sequences this can take a long time as all
pairs have to be compared."
I'll need to check exactly what's going on here though, since I started
to create some more rigorous tests for the PID function because I've
been looking at implementing different measures. Hope I didn't break it
again !
Namely I get only a couple of sequences remaining when I filter before removing
the blank columns, but hundreds remaining if I do it after removing the blank
columns. Could it be due to running out of memory when I still have all the
blank columns, or are blank columns somehow used when calculating % identity?
nothing to do with memory. Just a slightly broken function that needs
fixing!
Suspecting memory issues, I got the launchApp jnlp for 1G from your website
http://www.jalview.org/jvmmemoryparams.html
However, when I use that and then from the Tools menu choose to show memory
usage, the max value is no different than before. Shouldn't the max be 1G?
Also, when I use launchApp it complains it couldn't open the examples file
even though I had earlier specified in my Jalview preferences not to open that
file. I'm a little unclear on whether it should be using the same settings
(apart from memory allocation) as when I start by double-clicking the
jalview.jnlp vs this launchApp file.
this is a tiny but extremely annoying bug in the launchApp servlet that
I've not gotten around to fixing.
Try this link instead: http://www.jalview.org/webstart/jalview_2G.jnlp
Thanks, as you know I'm a newbie but I try to figure it out from the
documentation whenever possible!
Much appreciated !
Jim.
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