Testing for this issue included:

-Verifying that PA was using the native file chooser (tested on Windows, Mac, and Ubuntu).
-Verifying that opening a file using the native file chooser was functioning as expected.
-Verifying that the native file chooser was being used for saving a paxml file.

I am reassigning this to Tarun because it seems that ProtAnnot is still not using the native file chooser in two places:

1) Save Image...
2) Save PAXML...

Re-testing for this issue included:

-Verifying that PA was using the native file chooser (tested on Windows, Mac, and Ubuntu).
-Verifying that opening a file using the native file chooser was functioning as expected (defaulting to user's home folder and remembering last saved location and name).
-Verifying that the native file chooser was being used for saving a paxml file.
-Verifying that the native file chooser was being used for ProtAnnot's Save PAXML feature.
-Verifying that the native file chooser was being used for ProtAnnot's Save Image feature.

The above testing was performed and all checks passed except for one:

ProtAnnot is not remembering the last saved filename when saving a PAXML file.

Also, there is no default name set when saving PAXML files, instead the default filename is just ".paxml".

I say we make the default filename "ProtAnnot.paxml" and then make sure that the file chooser remembers whatever name the user chooses to enter instead.

I am reassigning this issue to John so that changes can be made.

I just noticed that the issue in the above comment preventing me from closing this story has already been tracked in IGBF-1001. Everything else except for that issue passed testing, so this story will now be closed.