Mouse hovering sometimes not detected

[weevil-see]

I have problems with UI behavior: When hovering over certain elements (like a field in a character matrix) with the annotations panel open, the information from the field in the character matrix is often not visible in the annotations panel even though it should pop up there.

I'm using:
Java 8
Manjaro Linux
KDE with Gnome (X11) as window manager

from the Mesquite output:
Running under Java 1.8.0_452; virtual machine by Arch Linux on Linux 6.12.25-1-MANJARO (architecture: amd64)

I also tried openbox as window manager, but the problem persists. Is this a general problem for all of you, or is it just me?

[wmaddisn]

Hi Jakob, Thanks for the report! Does the annotations panel sometimes show the information, or never? Would you be interested in trying out an alpha test version of Mesquite 4? It has many new things, especially for phylogenomics. Also, it’s been adjusted for the newer Java, which may get around your problem. It’s not generally public yet, but you can try out the version here: https://www.dropbox.com/scl/fo/3ljgy1ccn0tbtznp02m30/AJD39CTPaWSXV_cXfO1ZaFU?rlkey=6bc7czez5az41xxbd3m1vek9n&st=codmgto2&dl=0 (You don’t need to sign up to dropbox to download it, despite the dialog that appears.) You’ll need to get a version of Java, 9 or later. We have been developing it under Java 21 to 24. We’d love your feedback/bug reports on this, because we don’t have much feedback about linux. We have struggled with graphics bugs in Linux-Java, and I’m wondering if they are mostly squashed. Best wishes, Wayne

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On May 6, 2025, at 05:39, Jakob Jilg ***@***.***> wrote: [CAUTION: Non-UBC Email] weevil-see created an issue (MesquiteProject/MesquiteCore#118) I have problems with UI behavior: When hovering over certain elements (like a field in a character matrix) with the annotations panel open, the information from the field in the character matrix is often not visible in the annotations panel even though it should pop up there. I'm using: Java 8 Manjaro Linux KDE with Gnome (X11) as window manager I also tried openbox as window manager, but the problem persists. Is this a general problem for all of you, or is it just me? — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[weevil-see]

Hi @wmaddisn,
the annotations panel sometimes showed the information. Do you need a video (even though it is perhaps a problem of the past)?

Couldn't have wished for a better solution!
I have downloaded Mesquite 4, and at first glance the problem seems to be fixed! I'll use this version to construct my morphological matrix and keep you updated if I encounter any errors.
How stable is the Masquite 4 alpha so far? Is it more or less safe to use it for the construction of a morphological matrix with annotations?

Best
Jakob

[wmaddisn]

Hi Jakob, Mesquite 4 alpha is behaving pretty well. My student and I are using it for our own work, though that is currently with molecular data. There’s nothing dangerous I can think of that we’ve done to the morphological matrices, except possibly things that would cause graphical glitches (but not hurt your data). I think you should be OK to use it, especially if it already solves one problem. Usual recommendation, though, is to save occasionally under different names, or to turn on the backup feature (File>Defaults>Automatic NEXUS backups). Best wishes, Wayne

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On May 19, 2025, at 06:05, Jakob Jilg ***@***.***> wrote: [CAUTION: Non-UBC Email] weevil-see left a comment (MesquiteProject/MesquiteCore#118) Hi Wayne, the annotations panel sometimes showed the information. Couldn't have wished for a better solution! I have downloaded Mesquite 4, and at first glance the problem seems to be fixed! I'll use this version to construct my morphological matrix and keep you updated if I encounter any errors. How stable is the Masquite 4 alpha so far? Is it more or less safe to use it for the construction of a morphological matrix with annotations? Best Jakob — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you commented.Message ID: ***@***.***>

[weevil-see]

Hi,
I came across one issue in the Mesquite 4 alpha:

In Mesquite version 3.81 (build 955), when I hovered with the mouse over a tool in the vertical tool bar, the name of the tool was displayed with additional information in a field at the lower side of the window:

As you can see, not the entire text was visible initially. The "plus" symbol to increase the size of the area was invisible, but working, so I could increase the size.

Sometimes text was shown doubled:

In Mesquite version 4.alpha (build 1067) 14 May 2025, no information on tools is displayed when hovering over the vertical tool bar. Is this a bug or a feature which can be enabled/disabled?
As a new user, I found it quite useful to get immediate information.

All the best,
Jakob

[wmaddisn]

Hi Jakob, Thank you for the report. We very much intend the name of the tool to be displayed, so that’s a bug, either with Java or with Mesquite. (I recently just spent three days dealing with finding and working around a bug in Java on Windows.) I’ll put it in the queue of problems to solve. Thanks, Wayne

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On May 20, 2025, at 03:07, Jakob Jilg ***@***.***> wrote: [CAUTION: Non-UBC Email] weevil-see left a comment (MesquiteProject/MesquiteCore#118) Hi, I came across one issue in the Mesquite 4 alpha: In Mesquite version 3.81 (build 955), when I hovered with the mouse over a tool in the vertical tool bar, the name of the tool was displayed with additional information in a field at the lower side of the window: grafik.png (view on web) As you can see, not the entire text was visible initially. The "plus" symbol to increase the size of the area was invisible, but working, so I could increase the size. Sometimes text was shown doubled: grafik.png (view on web) In Mesquite version 4.alpha (build 1067) 14 May 2025, no information on tools is displayed when hovering over the vertical tool bar. Is this a bug or a feature which can be enabled/disabled? As a new user, I found it quite useful to get immediate information. All the best, Jakob — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you were mentioned.Message ID: ***@***.***>

[weevil-see]

Another small issue:
The number of character states ("states" column) is not updated (here in Mesquite 4):

Actually, character 1 has two states, character 2 has four states, character 3 two states, character 4 two states
The problem persists when restarting the program, and I found the same problem in Mesquite 3.

Edit: Now I got it, its not about the number of states the character has conceptually ("0 without adornment; 1 with thorn; 2 with bump" would be 3) , its about the number of entries in the matrix!

Cheers,
Jakob

[wmaddisn]

Thank you! This concerns me, as it seems more likely to be a calculation problem rather than a display problem. Is there any chance you could send me your data file? I’d keep everything in it entirely confidential. You can send it to ***@***.*** ***@***.***>. Wayne

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On May 20, 2025, at 09:11, Jakob Jilg ***@***.***> wrote: [CAUTION: Non-UBC Email] weevil-see left a comment (MesquiteProject/MesquiteCore#118) Another small issue: The number of character states is not updated (here in Mesquite 4): grafik.png (view on web) Actually, character 1 has two states, character 2 has four states, character 3 two states, character 4 two states The problem persists when restarting the program, and I found the same problem in Mesquite 3. Cheers, Jakob — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you were mentioned.Message ID: ***@***.***>

[weevil-see]

@wmaddisn the email you provided is somehow concealed, I've sent you an email to an adress i found on the internet

Cheers,
Jakob

[weevil-see]

Just a note for others who may read this: As far as I can tell, the mouse hovering bug was fixed in Mesquite 4

Thanks for fixing it!