We are using Number Format parse function which parses the string from the beginning and hence when a value like 5x is entered, it gets parsed to 5.
We have to change the logic in setParametersValue(..) : AbstractMathTransform.java to show an error message

[~aloraine] - I have attached the screenshot of the error popup that would be shown in case of invalid entry. Kindly let me know if I have to change the error message.

Code diff - https://bitbucket.org/noorzahara/integrated-genome-browser-local1/branch/IGBF-649#diff

Change requests:

• Please use the following quoted text to report the error to the user:

You entered parameter [fill in what they entered]. Unfortunately, the Track Operation you selected cannot accept this value. More information about this problem may be available in the Console tab.

• Remove link to "IGB Help" page.

• If possible, add a button: "Copy error message". Place it on the far left side of the dialog, if possible. If not, please it to the left of the "OK" button. When the user selects "Copy error message," the error message shown in the box should be copied to the system clipboard.

[~aloraine] - Thanks for the suggestion. I have attached the screenshot with the changes. Kindly let me know if that looks fine.

The code looks good. I did not test the functionality. But I think it is fine to submit the PR now.

A note to tester: Please read before commencing testing:

• Annotation track operations - https://wiki.transvar.org/display/igbman/Annotation+track+operations
• Graph track operations - https://wiki.transvar.org/display/igbman/Graph+operations+and+joining+and+spliting+graphs
• Testing checklist for track operations - https://wiki.transvar.org/display/ITD/Track+Operaters+-+Annotation+Tracks

If you are new to IGB project and to testing, also read:

• How to test IGB - https://wiki.transvar.org/display/ITD/How+to+test+-+read+this+first

Note that some operations but not all can accept arguments. The changes described above handle cases when the user enters a parameter that the operation cannot accept.

Steps to test

1. Select one of the species from IGB home screen and load a graph.
2. Right click on the track and select Track Operations.
3. Enter an invalid value for any of the operations listed.
4. An error message should appear.

PR Submitted - https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/828/igbf-649/diff

Merged and master branch installers are built. Ready for testing.

Testing dmg installer on Mac.

Warning appears for Right-click on Graph > Track Operations... > Add/Subtract when a non integer or - operator.

Warning does not appear for Right-click on Graph > Track Operations... > Divide/Log/Multiply/Power*.

Divide/Log/Multiply throw null pointer exceptions. Power uses the default value of 2.

It also seems odd that the right-click track operation provides a pop-up warning when entering non numeric text, but in the graph tab operations the textbox does not allow non-numeric text. This seems to be the more default behavior as right-clicking on a bam file and selecting Find Junctions and then attempting to enter non-numeric text does not work.

Bug fix - https://bitbucket.org/noorzahara/integrated-genome-browser-local1/branch/IGBF-649-1#diff

Reviewed this ticket. The functionality is working fine.
Followed the following steps to test:
1. Selected from IGB home screen and loaded a graph.
2. Selected Track Operations from the right click menu.
3. Entered an invalid value for operations listed like Add, Subtract, Divide, Inverse log, etc and observed the error message popup.
4. Entered a valid value for those operations and observed a new track being loaded each time.
Please submit a PR for the same.

PR submitted - https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/829/igbf-649-fix-the-bug/diff

Merged. Master branch installers built and ready for testing.

It is working as expected. Moving to closed.