Testing Notes from Mason:

IGB uses the chromosome synonyms file to display data from Chr1 on the same chromosome as a file that has data from "ChrOne" for example. To see what I mean, you can follow these quick steps and also use these steps for testing:

1) Open IGB, select the A. thaliana genome, and drag the file ChromosomeTest.bed (attached) onto IGB to open it.
*Note: This is a file that has data for "ChrOne" instead of "Chr1", but we want to visualize this data with another file that has Chr1 data.
*Observe: Now that you have opened ChromosomeTest.bed in IGB, you can look at the Current Genome tab on the right-side of IGB and will notice an extra chromosome, "ChrOne", has been added to the list of chromosomes.

2) Now press Load Data on Chr1 to load data
*Observe: The new file contains no data for Chr1, but if you select the "ChrOne" chromosome and Load Data, you will see the file's data. This is a problem though because you cannot compare this data with the data already loaded in Chr1 without switching back and forth between chromsomes in IGB.

3) We need to add the Chromosome synonyms file so IGB can treat "Chr1" and "ChrOne" as the same chromosome, so open the Data Sources tab of IGB Preferences and add the chromsome.txt file (attached) using the Chromosome Synonyms file chooser.

4) Restart IGB, select the A. thaliana genome again, and drag the file ChromosomeTest.bed onto IGB again to open it.
*Observe: This time when you open the file, you will not see the extra "ChrOne" entry listed in the Current Genome tab with the other chromosomes. This is because we have added the Chromosome.txt file.

5) Now press Load Data on Chr1 to load data
Observe: You will see the data from the new file on Chr1, as desired, so you can compare it with the other data much more easily.

Hopefully this will help clear up any confusion about what happens when the user applies a chromosome.txt file in IGB. Also to be clear, nothing should change related to the Species and Genome version tabs.

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/b210473580f068e2a602b4bd2e4350e1f2f55dc1?at=IGBF-1186

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 with MacOS. File chooser window is changed to MacOS native file chooser.
Chromosome file is parsed as expected and functionality seems intact after change. I have followed testing scenario given by Mason in above notes.

After testing this story I can confirm that the Chromosome 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. Chromsome.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.