I changed the resolution of my screen to 800x600 and this issue was resolved.
Solutions:
1. To set custom icon instead of JOptionPane dialog box creation
2. Change App/Screen resolution through Java code.

Is the issue related to the info icon not displaying correctly, or not displaying the IGB icon? What is the correct behavior? On Mac the IGB icon is shown.

The issue what I see is the info icon not displaying properly.

Next step as per discussion today: Find a way to get Java Swing to stop showing "i" and "?" images.

I found this link that describes the anatomy of a dialog box (also called "popup") in Windows:

• https://docs.microsoft.com/en-us/windows/desktop/uxguide/win-dialog-box

I think we should understand the conventions recommended for Windows applications and do our best to respect them so that Windows users will feel "at home" in IGB.

Same for Mac users.

I'm not sure how to do that, though! Let's do some research into it.

[~aloraine]

Found a link that explains that MAC does not support frame icons: https://stackoverflow.com/questions/23378119/setimageicon-doesnt-set-jframe-icon-on-mac-swing-window

I did some experiments with MAC and Windows

Findings :
1. Whenever a dialog box is created using JOptionPane and a message type is specified such as INFORMATION_MESSAGE, QUESTION_MESSAGE etc, on windows, a dialog opens with appropriate icon but on mac a default java icon appears as they are not supported on MAC.
2. On MAC, we set the dockIcon image using the below code
if (IS_MAC) {
MacIntegration mi = MacIntegration.getInstance();
if (applicationIconImage != null)

}
as mac cannot detect the setIconImage method of JFrame class.Hence, the image appears on the dialog boxand not as a icon.

On the Windows dialogs in the attached images, I see images appearing in two locations:

• upper left corner (IGB logo image)
• an image within the content of the dialog itself – a question mark or lowercase "i" character

On Windows, the images appearing in the content of the dialog are not being rendered correctly.
Why not?

Where are these question mark and lowercase i character images obtained? Are they coming from the IGB project code base?

Please clarify:

"a dialog opens with appropriate icon but on mac a default java icon appears as they are not supported on MAC."

The only icon being shown on the Mac dialog is the IGB logo, which isn't a default java icon.

??????

On windows - The upper left icon on the dialog box appears whenever we are setting the icon using setIconImage method provided by JFrame class. The image that is seen within the dialog box is the one that gets generated according to the message type set while creating the dialog box.(eg 'i' icon for information, '?' for help etc).

On Mac - MAC doesn't show an upper left icon - it shows red, yellow, green circle instead. We are using a class named MacIntegration so that IGB will behave more mac-like on OS X. This class contains a method named setDockIconImage which is a Wrapper around Apple's com.apple.eawt.setDockIconImage. And wherever this method is set in case of mac, the IGB icon is shown else the default java cup image appears.

Note: By default Java icon, I mean the java cup image.

Follow up question:
I'm still confused about what "default java icon" means. (Sorry to be so dense!)
This is what the word "icon" means to me:

• https://www.computerhope.com/jargon/i/icon.htm
  But in Java, seems like the word "icon" can also mean the images (e.g. "i" and "?") appearing in the content area of dialogs:
• http://en-human-begin.blogspot.com/2007/11/javas-icons-by-default.html

Other java GUI-based applications to use as possible examples:

• Cytoscape
• JalView
• IGV
  Are there others?
  We need to research how other Java applications have solved the image resolution problem described above.

I found another link which explains the reason why the icons are getting cropped on Windows 10.The solution is available in JDK 9.

https://stackoverflow.com/questions/33926645/joptionpane-icon-gets-cropped-in-windows-10

https://bugs.openjdk.java.net/browse/JDK-8151385

I went through the code base of cytoscape and couldn't find any solution regarding resolution.
Also I tried implementing the solution suggested on google but doesn't seem to work as we are trying to access a private final class.

Is the bug fixed in open JDK?

I wasn't actually able to track down to that but I have fixed the issue by adding appropriate images from our code base.
That seem to work.

If we move ahead with using our own custom images:

• Please provide step-by-step instructions for testers to open and view dialogs showing each of the new images added. (They will test using installer for the branch)
• Provide a link to each of the images used if obtained from others
• Don't add images to the code base unless they are freely available and OK for sharing in an open source code base

Testers:

• Follow instructions to open & view dialogs showing each image
• Check different screen resolutions on Windows 10
• Check on Mac (should be no difference in behavior)

I downloaded the images online and are free to use them in our code base.

Images Added are - info, help, error and warning .

The links I used to download them -
https://www.iconfinder.com/icons/55188/32_x_32_px_icon
http://www.softicons.com/toolbar-icons/glassy-buttons-icons-by-curtivearticide/question-mark-icon

Testing Instructions:

1. Open each of the dialog box on IGB eg : File -> Open URL and check for the images on the dialog box if they are cropped or not.

Code changes :

https://bitbucket.org/nzahara/integrated-genome-browser-local/branch/IGBF-1552#diff

Tried updating the the jre version to jre1.8.0_211 and the issue seems to be fixed.

Resolution:

• Bug exists in JRE 1.8 - all versions tested.

Will re-visit when we migrate to JRE 10 or later.