can you save a fasta file without being prompted?

danny_1 · 18 August 2009 10:30

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

jimp · 19 August 2009 10:22

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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