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

[Danny Rice]

On 08/16/2009 03:41 AM, Danny Rice wrote:

When I choose the Save menu item or hit ctrl-s a prompt always comes up for
me to enter a file name.  I would have thought that 'save' would just
overwrite the file that is currently open with the latest edits.  Is there a
way to get this behaviour?


This seems to be a bug.  In gui/AlignFrame.java --> save_actionPerformed
there is a check with isValidFormat.  If it returns true (which it will if
the current format is fasta, jalview, clustal, etc) then
saveAs_actionPerformed is called.  The isValidFormat should have a ! in
front of it.  I changed it and compiled with ant and it worked.

A couple more questions:

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?

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?

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?



-Danny
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