This was first reported in Feb 2019. Please check to determine if the problem still exists. If it does, modify the code to use the application icon instead. Look for related tickets in Jira for tips on how to make the change.

Commit: https://bitbucket.org/Gchamma/integrated-genome-browser/commits/0a7bd815398172bc3cf2af7e63b913c79b4f3736

There were many more tabs that had a default "Java coffee" icon, and as discussed I updated them as well to the proper icon image.

In total, 8 icon images were updated.
The following had their icons updated:
1. Preferences panel
2. Help option in the Preferences panel
3. Selection Info
4. Add Data Source
5. Add Plugin Repository
6. About Integrated Genome Browser
7. Save Image popup
8. Error popup
===================================================
New icons:

• Preferences panel's icon was changed to the corresponding "gear" icon
• Add Data Source and Add Plugin Repository are within the Preferences panel, therefore they have the same "gear" icon.
• Help option in Preference panel and the Selection Info now have the small blue "i" icon
• Save Image popup now has the corresponding "camera" icon.
• About IGB tab now has the corresponding "bulb" icon.
• The error popup now has the default IGB icon

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To download the changes:
1. Go to https://bitbucket.org/Gchamma/integrated-genome-browser/downloads/
2. Download IGBF-1536.exe

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To test:

(1) To test the Preferences panel:

• Go to File --> Preferences

(2) To test the Help option in the Preferences panel:

• Go to File --> Preferences --> Help --> General Help

(3) To test the Add Data Source:

• Go to File --> Preferences --> Data Sources --> Add..

(4) To test the Add Plugin Repository:

• Go to File --> Preferences --> App Repositories --> Add..

(5) To test the About Integrated Genome Browser:

• Go to Help --> About Integrated Genome Browser

(6) To test the Selection Info:

• Click the blue " i " icon on the top right of IGB, and the window should pop up

(7) To test the Save Image popup:

• Load any genome, click the camera button on the toolbar or go to File --> Save Image

(8) To test the Error popup:

• (1) Go to File --> Open URL --> enter an incorrect URL or random string such as "hello" into the text field, and press OK
  An error page should popup with the default IGB icon
• (2) Go to File --> Open Genome From File --> enter a random string such as "hello" into the Reference Sequence text field, and press OK
  An error page should popup with the default IGB icon

The user has the option to open Console from: Help --> Show Console
The window that pops up still has the default Java icon, because I was not able to import the "CommonUtils" in ConsoleLogPanel.java, which is essential in order to update the Console's titlebar icon.

Note: The default IGB icon that is used as the application icon and used for some of the changes made in this ticket looks a bit blurry compared to the official published version of IGB. I have no idea what is causing this.

Please let me know if anything needs to be changed
Thanks!

Code review:

Attn: Jay Chamma - Please see comments on your branch in Bitbucket.

One thing I am a bit worried about is that it looks like there are many changes to a part of the code that is not supposed to be manually edited. It looks like you only changed whitespace, but I can't tell for certain because every line in several large blocks have been edited. I don't think I can manually inspect every line to make sure there are no functional changes.

That particular file (AddBundleRepositoryFrame.java) was created using the NetBeans GUI builder. When you opened it in Netbeans, it should have shown you the GUI builder graphical editor. I am wondering if you did that and the GUI Builder made all the white space changes? Please check that the changes you made do not break our ability to edit the GUI using the GUI Builder. Even better, make no changes to the file except for the one specific change you wanted, which was to add the settings (sprocket) icon to the upper left corner of the window.

I have read your comments [~aloraine]
1. Changing the methods to private will not be an issue
2. The methods added were created by me and copied to every class that needed it.
3. The white space changes that you mentioned were automatically changed by GUI and not by me. I did not use the GUI Builder at all, but simply added the method to the file. I didn't use or open the "Design" tab until you mentioned it, but after opening the "Design" tab, I received the following error popup:
https://i.imgur.com/9N4AToS.png

• This was not caused by my changes, since that error not only occurs on my "IGBF-1536" branch, but also on my master branch, as well as on a brand new clone of my BitBucket repository.
• The "Generated Code" with the purple background color that is not supposed to be manually altered does not have the uneditable property that it should.
• The same thing can be seen for "// Variables declaration - do not modify " section.
• These two sections of code that are supposed to be uneditable manually, have the same properties as the rest of the code and can be simply deleted and written over by other code.

I am positive that the same error would be seen on other's machines as well.

I looked up the error and the most popular solution is to copy over the GUI elements from the "Design" tab and the methods from the "Source" tab of AddBundleRepositoryFrame.java to a new JFrame class, and delete the old one. The new generated code should be good and should not cause any errors.
I gave this a try on a test branch and it worked. The error was gone and the AddBundleRepositoryFrame.java class and GUI elements worked with no issues.

[~aloraine], please see the following commit:
https://bitbucket.org/Gchamma/integrated-genome-browser/commits/3c86f2ea34313a8a4a7c27b4ccf0113e4045b08a?at=IGBF-1536

Now that I think about it, the changes that we saw in the previous commit for AddBundleRepositoryFrame.java were most likely space changes caused by the shortcut that I used in Netbeans of "alt + shift + f", which basically orders the code in the entire class automatically and adds/deletes spaces in the code.

I use that shortcut after adding code to make sure it looks nice. However, since the section of the code that was automatically generated and that was supposed to be uneditable was actually editable, the shortcut affected these lines of code, which is why these lines of code were updated with white space changes.

So there are no issues when it comes to adding setTitleBarIcon() method to that class.

Can you elaborate on this comment?

Note: The default IGB icon that is used as the application icon and used for some of the changes made in this ticket looks a bit blurry compared to the official published version of IGB. I have no idea what is causing this.

Mac application windows don't contain titlebar icons, but Windows applications (apparently) do.

Question: Do Windows applications typically show the same title bar icon throughout the application, regardless of the what the window is for? What happens in Microsoft Word, Excel, and other Microsoft applications?

I am wondering if we ought to use the IGB icon for all of the windows, instead of varying the icon based on the function of the window? What is the proper approach?

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.

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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.

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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:

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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.