I often work by mobile computing on a jalview alignment.
At work I have an extra monitor attached to my laptop and after
disconnecting that and putting the whole shebang to sleep some java
programs (LibreOffice, JalView) appear to hang upon resume in absence
of this extra monitor. I do not know whether it has to do with my DE
(xfce, which has recently been upgraded to 8.12, since when these
crashes seem to occur more often), but now I have lost a large portion
of work due to such a java crash. And that when I thought I had saved
my project half an hour before disconnecting at work.
My project had two large alignment files and the one I had been working
on this week has gone, disappeared completely. During resume I got a
blank Jalview frame and I closed the program. The generated java-crash
file starts with:
# A fatal error has been detected by the Java Runtime Environment:
# SIGSEGV (0xb) at pc=0x00007f5a085ddbf4, pid=1281, tid=140024677439296
# JRE version: Java(TM) SE Runtime Environment (8.0_45-b14) (build
1.8.0_45-b14) # Java VM: Java HotSpot(TM) 64-Bit Server VM (25.45-b02
mixed mode linux-amd64 compressed oops)
# Problematic frame:
# C [libpthread.so.0+0x9bf4] pthread_mutex_lock+0x4
What I found though, is that the files within the project
ALSO had not been saved. I had pressed 'Save file' in the menus of
each of the alignment-files to be sure this would happen but this had
not done anything. Or does this only save the file within the jvp
archive??? If so, for me this is not the expected behaviour as I
originally loaded these files into the project from a particular
folder on my disk and when I save these files I expect them to be
written to the same folder as where they originated from....
I find that only by "Save file as", a recent update can get written to
the place of choice from within a project. But this is quite
Am I the only one experiencing this behaviour?
For me expected UI-behaviour would be:
1) Whenever/whatever Safe is chosen the file in question should be
written to disk (outwith the jvp-archive unless the project itself is
saved), overwriting the older version.
2) Also, as a user, when saving a project I assume (wrongly as it turns
out) that with the project the separate files in the project will get
saved too, overwriting the original source files. This does not happen.
Everything, as I understand it, is packed into the jvp archive and only
there. Thus the files in the project are out of sync with the
original files on disk. Thus, if the jvp is corrupted all work is gone.
I think that, when this is the normal behaviour of JalView, a large
improvement is possible here.
What do people think?
Dr. R.W. van Nues
SYNTHETIC and SYSTEMS BIOLOGY at EDINBURGH (SynthSys)
The University of Edinburgh
CH Waddington Building
Max Born Crescent
Edinburgh EH9 3BF
Telephone +44 (0)131 651 9018
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.