Testing Notes from Mason:

My understanding of the Version Synonyms feature is that it allows IGB to recognize when one genome is the same as another so the data can all be displayed on the same genome version, for example, if someone added a Quickload site with an "A_thaliana_June_2009" folder and a "Arabidopsis9" folder, you could tell IGB to display these files on the same genome. To see what I mean, you can also follow these steps and use them for testing:

1) Start IGB and add the Quickload directory "SmallQuickload" (attached) within the Data Sources tab of IGB Preferences.
*Note: This Quickload contains a folder called "Arabidopsis9" which I made up and is not currently a synonym for any other genome in IGB.

2) Click the Species drop-down menu in the Current Genome tab on the right-side of IGB and scroll to find an entry called "Arabidopsis9". This should be right underneath "Arabidopsis thaliana" and this helps illustrate the problem because imagine that the user just wanted to add his "Arabidopsis9" data to the "Arabidopsis thaliana" genome in IGB, since he knows the genome's are actually the same.
*Observe: If you select the "Arabidopsis9" species and then select "A-thaliana_Jun_2009" as the genome version you will notice two files under Available Data, "Test1" and "Test2". If you switch to the "Arabidopsis thaliana" species and choose "A-thaliana_Jun_2009" as the genome version, you will not see the files mentioned.

3) We need to add the Version synonyms file so IGB can treat these genomes as the same genome, so open the Data Sources tab of IGB Preferences and add the synonyms.txt file (attached) using the Version Synonyms file chooser.

4) Restart IGB, and now click Species drop-down menu in the Current Genome tab on the right-side of IGB
*Observe: You will not see the "Arabidopsis9" entry listed and if you select the "Arabidopsis thaliana" genome and then select "A-thaliana_Jun_2009" as the genome version you will notice that the files Test1 and Test2 are seen under Available Data, indicating that IGB is recognizing "Arabidopsis9" as a synonym.

As for acceptable inputs, I agree with you both in that directories should not be selectable in the file chooser and that all variations of .TXT files should be allowed (.txt, .Txt, .txT, etc.).

Fixed file chooser UI.
fix can be found at
https://bitbucket.org/ashwiniK27/integrated-genome-browser/commits/b533e199091fdfe9bf74ebf59998c74714358f65?at=IGBF-1185

Testing with MacOS and Linux is required.

(In reference to the notes given by Mason)
After discussing with Dr. Loraine and Mason, two new issues has been created.
IGBF-1187 : Display message to user to restart IGB after configuring version synonym or chromosome file (if required).
IGBF1188: Display error message to user when invalid file is selected.
This fix restricted to file chooser UI change only.

Fix is working as expected on MacOS. Window is similar to native OS file chooser window.

Coed review done. Seems fine to me.
Tested on Linux. Working as expected. Moving to Ready to pull request.

After testing this story I can confirm that the Version Synonyms file chooser within the Data Sources tab of IGB Preferences has been changed to the operating system's native file chooser. This has been tested on Mac, Linux, and Windows and is functioning as expected. Synonyms.txt files are being opened properly in IGB using the feature and are working as expected. This issue is resolved and there seem to be no side effects resulting from this change, so this issue will now be closed.