Unsure if I should post that here or in the bug tracker. I’m using jalview 2.11.2.6 (the download link for the latest jars does not work), and I can search via Ctrl+F in the sequence name and sequence itself for small alignments, but it fails to work for large ones (4700 sequences). Is that a known problem ? Can I do anything about it ?
Thanks
Hi Vincent,
Firstly, I’ve fixed the executable jar link, thanks for reporting that.
There aren’t any active open issues about this, and I am unable to replicate the problem you’re describing in either the current or the 2.11.2.6 release. I was using a Fasta file of 74,000 admittedly shortish (~130aa) sequences. Can you give some more details about the alignment you’re using? If you’re able you could send/attach it for us to try (don’t do this if there are any privacy issues!).
One other thing that occurs to me is the working memory available to Jalview might be restricted.
You can easily see what memory is available by turning on
Tools → Show Memory Usage,
and you can adjust memory settings by going to
Tools → Preferences (or Jalview → Settings on macOS (or Jalview → Preferences on an older macOs)) and find the Startup tab (toward the end of the tabs).
There’s a white box that shows what memory would be set on that compuer, and a percentage setting and an absolute cap setting.
These are by default set to sensible values so I doubt that’s the problem, but it’s worth checking.
Let us know if that does help, or some more details about the alignment.
Ben
Hi … just a quick note… i thimk it unlilely that jalview is running out of memory, since you’d see something to that effect in the console or as a warning dialog.
If you can send us more details … or demo via a jitsi call that would help us help you ! Jalview 2.11.3 has some patches to the find routine, but i can’t think of any that mean large alignments will not be properly searched, only that jalview might take a little longer to do it.
Jim.
Thanks for the updated version !
Upon looking, the problem is indeed not the large alignment, it’s the fact that I had loaded some annotations on the large alignment. I can look for things in a large alignment, but if I load a small alignment and some annotations, I cannot find anymore.
You can try that with the following files:
https://bfs.imm.cnrs.fr/r/Z2xoZkwj#yE5XbFnYSjCDg8mCk1tr0uJBEj9d6UR8p0iD4+bT6mU=
Hope this helps,
Vincent
Hi Vincent,
Thanks for the extra information about the circumstances, and the attached files.
Using the files, the executable jar, I’ve still not been able to replicate the problem (assuming I’m trying the same kind of Find!), but I’ve only been able to try this out on macOS so far, using the Azul Java 8 JRE for Apple Silicon.
I’ve created an issue (https://issues.jalview.org/browse/JAL-4363) where we will investigate further, and added you as a watcher so you should get updates on progress.
In the meantime, it would be great if you can comment on that issue (same login as Discourse) with the type of computer you’re using (OS is the most important to know); anything you can tell us about the JVM you’re running the executable jar is (the output of java -version should be enough); and some example find terms that are failing for you.
Sorry not to have a quick fix! Ben