Sure thing, [~aloraine].
The IGB icon appears in two places when launched in Windows.
First place: Windows taskbar, which shows all the different applications that are open at the time (typically is present at the bottom of the screen).
Windows taskbar:
Second place: The titlebar of IGB itself. This is the bar that has the label of IGB along with the version, for example: "Integrated Genome Version 9.1.4"
IGB titlebar:

I am comparing the released IGB version (v9.1.4), which is the one downloaded from BioViz.org installer with the unreleased (v9.1.6) on Master branch, which is running on NetBeans IDE 8.2 on my desktop.
I am currently using two monitors, one being an HD monitor (1920x1080 pixels) and another 4K monitor (3840x2560 pixels)

Released Version (9.1.4)

Windows taskbar icon

• The released IGB version (9.1.4) has a Windows taskbar icon that is nice and clear. The taskbar icon is different depending on the resolution of the screen, which is great and allows the taskbar icon to stay at high resolution no matter what monitor resolution a user is using.
  On my HD monitor, the taskbar icon for 9.1.4 looks to be "igb_16.png", which can be found at integrated-genome-browser/distribution/branding/igb_16
  
  On my 4K monitor, the taskbar icon for 9.1.4 looks to be "igb_32.png", which can be found at integrated-genome-browser/distribution/branding/igb_32
  

IGB titlebar icon
However, when it comes to the titlebar icon on the released version, 9.1.4, the icon is very pixelated on both resolutions (HD and 4K)
9.1.4 titlebar icon on my HD monitor looks like:

9.1.4 titlebar icon on my 4K monitor looks like:

As you can see, the titlebar icons are very pixelated compared to the Windows task bar. Therefore, the icons that are used for the Windows taskbar should also be used for the icons on the titlebar of IGB.
The titlebar icons and the taskbar icons, when compared to each other, take up the same height and width on the screen. So there should be no issues with using the icon seen on the Windows taskbar, on the titlebar of IGB.

Unreleased Version (9.1.6)

Windows taskbar icon
v9.1.6 Windows taskbar icon does not seem to be the same "igb_16" and "igb_32" icons as v9.1.4, and the icon looks very pixelated in the Windows taskbar.

• v9.1.6 on HD monitor - Windows taskbar:

• v9.1.6 on 4K monitor - Windows taskbar:

Here is a comparison of the unreleased v9.1.6 (the left icon) and the released v9.1.4 (the right icon) taskbar icons on my HD monitor:

Here is a comparison of the unreleased v9.1.6 (the left icon) and the released v9.1.4 (the right icon) taskbar icons on my 4K monitor:

IGB titlebar icon
The same pixelated icons found in the Windows taskbar of the unreleased v9.1.6 appear in the IGB titlebar of v9.1.6

===================================================================================
Additional notes for igb_16 & igb_32 icons

I checked where these images were being used in our code base, and turns out they are being used in the file: igb_7.install4j
igb_7.install4j can be found at integrated-genome-browser/distribution/igb_7.install4j

Code from igb_7.install4j

======================================================================================

Additional notes for IGB titlebar icon and Windows Taskbar icon:

• The icon being used for the titlebar of IGB and the Windows taskbar of the unreleased version (v9.1.6) is "igb.png", which can be found at
  integrated-genome-browser/core/common/target/classes/images/igb.png

The method that uses this "igb.png" icon and seems to be responsible for changing the icon for both the Windows taskbar and IGB titlebar is getApplicationIcon(), which is found in CommonUtils.java

This getApplicationIcon() method is then being used in IGB.java to initialize the IGB icon in the following code:

This icon is 128x128 pixels, and it is being fit in an area where a 16x16 pixels icon normally is, so I am guessing that that is why the icon looks very pixelated in IGB titlebar and Windows taskbar. So forcing an image of that size to fit into such a small area is what is most likely causing the crazy pixelation.
I am guessing this issue would be solved by simply using the igb_16.png icon instead of the igb.png icon, but I don't know if the image will scale up or down depending on the resolution, in the same way as the Windows taskbar icon did with the released version (v9.1.4).

In order to confirm that getApplicationIcon() method is responsible for changing the icons, I did a quick test of changing the code in getApplicationIcon() from using "igb.png" to "C_porcellus.png", which is found within the same /images folder, and the picture successfully changed in both the titlebar of IGB and the taskbar of Windows.

However, I am very confused on why the released version (v9.1.4) doesn't have the same clear icon for its titlebar compared to its icon in the Windows taskbar, if the getApplicationIcon() controls both the IGB titlebar icon and the IGB icon in the Windows taskbar.

==================================================================================================

Question: I would like to access the igb_16.png (integrated-genome-browser/distribution/branding/igb_16) inside the getApplicationIcon() method, which is using the /images/ folder (integrated-genome-browser/core/common/target/classes/images). I tried to use the file path for igb_16 "integrated-genome-browser/distribution/branding/igb_16" inside the string of getApplicationIcon() method, but that didn't work.
Each time I try to change a file path inside a method, I am limited to only using the icons within the folder that was originally used. Such as "/Images", but I would like to know how I can go beyond that and access any image or icon I would like within the IGB project.

==================================================================================================

Upon your request, [~aloraine], I checked the different applications that Microsoft offers, such as Word, Powerpoint, Excel. Here is what I found:

• 1. Microsoft Office applications have their icons present in the titlebar of the application all the time.
  2. When using the "Save As", "Open", or any File Chooser window, the titlebar of the new windows that popup includes the icon of the application
  3. Windows such as "Options", "Settings", "About" or any window that does not import or export files does not include any icon in the titlebar, but instead it only includes the title of the window.

So following this theme, the "Preferences" panel that IGB uses would not have an icon in the toolbar, but instead it would only have the title.
Additionally, options in IGB that popup a window to either save, export, or open a file, such as "Open File", "Open Genome from File", "Save Image", "Save Session", and "Load Session" should include the IGB icon on the titlebar of the file chooser windows that appears.

For example:
This is the IGB "Open File" popup file-chooser window, which should include the IGB logo if we are going to model this after Microsoft Office.

This is the Microsoft Word "Open" file-chooser window:

==================================================================================================

Please note: any code images linked above are private on imgur.com, so no one without a link can access them.
Please let know if this is an acceptable way of sharing code or not.
Thanks!

Requests:

• Can you revise the above comment to only discuss igb_7.install4j? The other file – igb.install4j – is not being used.

When you refer to versions of IGB, e.g.,

I am comparing the released IGB version (v9.1.4), which is the one downloaded from BioViz.org with the unreleased (v9.1.6), which is the one we are currently working on.

please indicate if you are using an IGB that was installed via the installer (e.g., the 9.1.4 installer or the "master branch" installer) or an IGB that is running via Netbeans on your desktop.

It matters because IGB has slightly different behaviors depending on how it was installed.

Comment revised.

[~aloraine] I downloaded the master.exe from the main repository - https://bitbucket.org/lorainelab/integrated-genome-browser/downloads/ to test how the icons look.

What I found:
Both the Windows Taskbar icon and the IGB titlebar icon look pixelated, which is the same situation as running IGB on NetBeans.

Additionally, I noticed that the install4j installer window for the LorainLab master.exe had the correct icon for both the titlebar and Windows Taskbar.
I'm mentioning this since you may know a way for me to compare the code for that installer window to see which icons are being used and how, which would help with figuring out what to do with the icons for IGB.

Here is how the installer titlebar looked like:

Not sure what to do next. Moving to Closed.