Hello
Is there a maximum file size (fasta format) that Jalview will accept? If so, what is it? I cant increase java/virtual memory - no access to this at my university. So curious to know what the max file size is for running alignments on the “launch anywhere” downloadable version of Jalview.
Finishing up my co-op and want to know if I can align a HUGE file, (i dont know what size it would be yet since I have not made it). Basically looking to make a neigbour joining tree in jalview with about 15 different species (ranging from 10 sequences for one species up to about 800 for another). Dont want to waste my time making this huge file if it wont align/run.
Jess
Is there a maximum file size (fasta format) that Jalview will accept? If so, what is it? I cant increase java/virtual memory - no access to this at my university. So curious to know what the max file size is for running alignments on the “launch anywhere” downloadable version of Jalview.
By ‘Launch anywhere’ I assume you mean the webstart version ? If so, you can tweak virtual memory settings by creating a custom JNLP file (http://www.jalview.org/jvmmemoryparams.html).
If you mean the ‘InstallAnywhere version’ then you may indeed have problems due to admin rights.
Either way, the largest memory allocation you can set is around 50% of the physical memory of your machine (e.g. if you have 2G memory, then you can allocate up to around 1G to Jalview).
Finishing up my co-op and want to know if I can align a HUGE file, (i dont know what size it would be yet since I have not made it). Basically looking to make a neigbour joining tree in jalview with about 15 different species (ranging from 10 sequences for one species up to about 800 for another). Dont want to waste my time making this huge file if it wont align/run.
You aren’t going to be able to align that many sequences with the public web services that Jalview talks to, since there is a physical limit of 1000 sequences of up to 1000 residues each. Tree building will probably take a long time once you’ve computed that alignment, too, since Jalview doesn’t use any tricks like BioNJ to speed up the tree building process. Basically, for very large sequence sets, there are a couple of routes, and all involve downloading and installing additional programs which have to be configured or run from the command line. Email me directly if you’d like to discuss your options - since they don’t necessarily involve Jalview 
Jim.
Hi,
Would like to find out if there are javascript api calls can be utilized to change the Colour and/or flip some of the option such as showConservation or showConsensus. I understand those are available as menu function of the Applet, but some of our users are not very familiar with menus, so we would like to provide some quick setting aid for them.
Regards,
Wei
Hello Wei
Would like to find out if there are javascript api calls can be
utilized to change the Colour and/or flip some of the option such as
showConservation or showConsensus.
I guess that you have already checked the applet javascript API (http://www.jalview.org/examples/jalviewLiteJs.html). There are some methods that could be used, but I haven't exposed them in the Javascript interface. Could you lodge a feature request at issues.jalview.org for the functions you need ? I'll take a look and see if I can sneak a patch into v2.8 that will expose the ones you need.
I understand those are available as
menu function of the Applet, but some of our users are not very
familiar with menus, so we would like to provide some quick setting
aid for them.
One of my dreams is to have full programmatic control of the interface functions - but we first have to complete our current milestone which is to merge the applet and application GUI implementation. Then the same programmatic control will be available for both web and stand alone Jalviews!
Thanks for the email - I'll keep an eye on issues.jalview.org and message you via your feature request!
Jim.
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On Wed May 9 06:04:21 2012, Wei Jen wrote: