[Jalview-discuss] can you save a fasta file without being prompted?

[James Procter]

Hello Danny, thanks for your detailed email.

Danny Rice wrote:
^S Save as prompt bug:
<snip> front of it.  I changed it and compiled with ant and it worked.
yes. you are correct - and indeed, the bug has been fixed in the latest 
development and 2.4 build.

> When you do a 'save as', jalview seems to want to add it's own extension 
> if it doesn't like the one you specify.  Is there a way to get jalview 
> to just go with what you type in without adding .fa or whatever?
no - the logic assumes that if you haven't added a .suffix then it 
should add one appropriate to the file format that has been selected. 
Clearly disbling this could be a preference for advanced users, and 
perhaps taking a second look at the implementation is warranted to check 
it is actually behaving as expected.

> When you open a file on the command line the 'current directory' doesn't 
> seem to get updated to the directory from which you just opened the file 
> nor the directory you may be working from.  It seems to use the 
> directory where the last file was saved.  Is this the expected behaviour?
The command line path does not update the last location list in the GUI. 
I can think of cases for and against this behaviour being changed - this 
will be reviewed in the future.

> If I have colour set to nucleotide and set Identity Threshold to > 0, 
> just so I can see the differences, and reload the file, the Identity 
> Threshold toggles back off and has to be toggled back on and the value 
> reset.  Is there a preference or something else where you can set the 
> Identity Threshold to 'on', and set the Threshold value to a preferred 
> default?

There is no preference entry for this, but it has been suggested and is 
on our feature list. This is also a setting which should be specifiable 
in the annotations file (which allows you to define colourschemes for 
regions on the applet).

thanks again for your email. Just to note, in the future - if you 
provide a bug report can you make sure you include the version of 
jalview that you observed the bug in ? (this makes it easier to locate 
the source that should be/was patched).

cheers!
Jim.

-- 
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J. B. Procter  (ENFIN/VAMSAS)  Barton Bioinformatics Research Group
Phone/Fax:+44(0)1382 388734/345764  http://www.compbio.dundee.ac.uk
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