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?