[Jalview-discuss] Jalview command line

Julien Roux julien.roux at unil.ch
Mon Feb 7 16:25:53 GMT 2011

Thanks a lot Jim for the very quick answer,
It seems that the applet might actually be a good solution for what I 
need, I guess it is more flexible and complete
I'll have a look at the documentation
I also also registered to "watch" the bug, it may be one day useful to 
use this feature ;)
Have a good week

Le 07.02.11 16:51, Jim Procter a écrit :
> On 07/02/2011 14:31, Julien Roux wrote:
>> Dear Jalview team,
>> I'm new to this mailing list, please excuse me if my question has 
>> already been answered previously.
>> I am trying to create a jalview file (.jar) including an amino-acid 
>> alignment, the associated tree and some annotations.
>> To do this, I want to use the command line. I tried:
>> java -Djava.ext.dirs=/Applications/Jalview/lib -cp 
>> /Applications/Jalview/Jalview.jar jalview.bin.Jalview -open 
>> my_aln.fas -colour ZAPPO -annotations my_annot.jalview -tree 
>> my_tree.nwk -jalview test.jar
>> This works fine and creates the test.jar file correctly. However, 
>> when I add the -nodisplay option to do this without User Interface, 
>> the file test.jar does not include the associated tree. Is this a bug 
>> or I am doing something wrong?
> No  - you aren't doing anything wrong. Including trees in project 
> files whilst in headless mode is actually an 'unimplemented' 
> capability (aka a bug, I guess :) ), and I've recorded it as such 
> here: http://issues.jalview.org/browse/JAL-764
> The reason Jalview fails to write out the tree is because the jalview 
> project IO code is tightly coupled to the Jalview GUI code, and in 
> fact uses the GUI classes to discover what trees are associated with a 
> particular alignment. I do plan to fix up this problem - but not for 
> the next release (ie, not within the next few weeks). I hope that 
> doesn't inconvenience you!
>> I also have 2 other questions:
>> - Is it possible to include (again using the command line) the 
>> nucleotide alignment that corresponds to the AA alignement? I have it 
>> in a separate fasta file.
> not currently, but it's a good feature request. There is a lot of work 
> to be done improving the dna+protein support in Jalview, which is 
> currenty oriented towards working with EMBL/uniprot records, rather 
> than your own nucleotides+translated regions.
>> - Is it possible to export a .html file including the alignment and 
>> the tree and annotations associated? From what I have seen, it seems 
>> that Jalview only exports the AA alignement + annotations. 
> again, a good feature request, although perhaps stepping outside 
> Jalview's remit, since we provide the JalviewLite applet for doing 
> combined alignment and tree visualization on a web page. Jalview only 
> has html generation code for alignments, and doesn't include any means 
> of generating interactive html for the tree (it only supports PNG and 
> EPS generation from the GUI, in fact). What kind of functionality do 
> you need here ?
>> Also, is it possible to wrap the alignement using the command line?
> Only by passing in a custom jalview.properties file, via the 'props' 
> argument. You can prepare one by first quitting all your jalview 
> instances, then making a backup of your current properties file 
> (~/.jalview_properties ), then start jalview and edit the alignment 
> display settings in the preferences dialog from the 'Tools' window. 
> You can test the settings by dragging an alignment into Jalview (after 
> hitting OK to save your preference settings), to see how they have 
> affected the initial alignment display. Then, once you're happy with 
> the default alignment rendering preferences, close jalview, and make a 
> copy of the current ~/.jalview_properties file before re-instating 
> your old preferences file from the backup. You can then use this 
> specially prepared properties file from the command line.
> It sounds a faff, but there are around a dozen options controlling the 
> layout of the alignment, and this is the easiest way to set them all.
> thanks for the email, and I hope you'll keep in touch regarding the 
> bug report about the tree import in headless mode. If you like, you 
> can register on the jalview issues tracker above, and then 'watch' the 
> bug, so you get notified about when I or someone else starts fixing it!
> Jim.

Julien Roux, PhD
Keller group, Department of Ecology and Evolution
Biophore, University of Lausanne, 1015 Lausanne, Switzerland
tel: +41 21 692 4182    fax: +41 21 692 4165

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