Problem with Cytoscape's interface

[acz...@gmail.com]

Dear All,

I am having the following problem for some time now but lately it has become more persistent. During the Cytoscape session, when I move the mouse over the Cytoscape window it seems like it is dragging the panes along with it. As a result, I cannot have a clear view neither to my network nor to the application commands. This is totally frustrating for me. Cytoscape 3.6.1 previously and now Cytoscape 3.7.1 is running on an ASUS ROG laptop with NVidia 1070GTX 8GB GDDR5 graphics (latest drivers installed), Intel i7 7700 CPU, NVme Samsung 960 Pro 512GB, 32GB 2400 DDR4 RAM and Windows 10 Pro (latest version, all updates installed). The laptop has an embedded 15,6’ 1920x1080 max FHD monitor and it is connected to a 32’ Samsung U32H850 4k monitor via mini DisplayPort at 3840x2160 60Hz or at 1920x1080 60Hz resolution, with the problem appearing on both resolutions. I have tried several different setups regarding the relevance between the 2 monitors (duplicate window, only monitor 1 or 2 active, both monitors active etc) with no lack. This behavior occurs more often when a plugin app is running simultaneously with Cytoscape, like ClueGO 2.5.3 or Enrichment Map 3.1.0, even when no tasks are being performed. I would be very grateful for any recommendations.

Kind Regards,
Athanassios Zees, PhD

[Scooter Morris]

Hi Athanassios,

   I haven't seen anything like this except on my mac when for some reason the network view thinks that button 1 is pressed.  Try this the next time this happens.  Move your mouse (or cursor) over the network panel, then explicitly click in.  Then drag your cursor out making sure that you no longer have button 1 (or the equivalent) pressed.  See if that manages to clear it.

-- scooter

[acz...@gmail.com]

Dear scooter,

Thank you for your prompt reply. I am not sure what you mean by the term "button 1". Is it application interface related or mouse related. Please elucidate me on that in order to try your method. Thank you in advance.

Athanassios

[Scooter Morris]

"Button 1" refers to the select button, or "click" button on your mouse.  This is typically emulated by the click on a trackpad.  In Cytoscape, if nothing is selected and if you hold down (click) on a trackpad or your mouse, it will drag the canvas.

-- scooter

[acz...@gmail.com]

On Tuesday, 22 January 2019 21:25:57 UTC+2, Athanassios Zees wrote:

Dear Scooter,

Thank you for clarifying your answer to me. Unfortunately since your last entry to this post I am trying to apply your suggestion among several other things that come in mind eventually. However the problem persists and it is extremely annoying. It makes Cytoscape almost useless and impossible to operate. The only thing I found that works for a while is emptying CytoscapeConfiguration folder under ".../Users/(user name)and reinstalling the applications, but soon after the problem reappears. I am open to any suggestions, since I am kind of desperate.

Does anyone knows if there is any Cytoscape's incompatibility with specific hardware or software (including Windows versions)? I would be extremely grateful for your feedback. Thank you all in advance.

Athanassios

[acz...@gmail.com]

[acz...@gmail.com]

On Tuesday, 22 January 2019 21:41:41 UTC+2, Athanassios Zees wrote:
> On Tuesday, 22 January 2019 21:25:57 UTC+2, Athanassios Zees wrote:
> > On Thursday, 20 December 2018 18:24:26 UTC+2, Scooter Morris wrote:
> > > "Button 1" refers to the select button, or "click" button on your mouse.  This is typically emulated by the click on a trackpad.  In Cytoscape, if nothing is selected and if you hold down (click) on a trackpad or your mouse, it will drag the canvas.
> > >
> > >
> > > -- scooter
> > >
> > > On Thursday, December 13, 2018 at 8:23:34 AM UTC-8, Athanassios Zees wrote:Dear scooter,
> > >
> > >
> > >
> > > Thank you for your prompt reply. I am not sure what you mean by the term "button 1". Is it application interface related or mouse related. Please elucidate me on that in order to try your method. Thank you in advance.
> > >
> > >
> > >
> > > Athanassios
>
> Dear Scooter,
>

> Thank you for clarifying your answer for me. Since your last entry to this post I am trying to apply your suggestion among several other things that came to mind eventually. However the problem still persists and it is extremely annoying. It makes Cytoscape almost useless and impossible to operate. The only thing I found that works for a while is emptying CytoscapeConfiguration folder under ".../Users/(user name) and reinstalling the applications, but soon after the problem reappears. I am open to any suggestions, since I am kind of desperate.
>
> Does anyone knows if there is any Cytoscape's incompatibility with specific hardware or software configutations (including Windows versions)? I would be extremely grateful for your feedback. Thank you all in advance.
>
> Athanassios

[Scooter Morris]

Sounds to me like there might be an issue with an App interfering.  Try disabling all apps (you can disable them in the App manager without uninstalling them).   If the problem is gone, then try to enable them one at a time until you can track down the culprit.  Let us know if you do and we'll try to figure out what's going on with the app.

-- scooter

[fabiola...@gmail.com]

Hi, I can't select any nodes from the network using the mouse selection. If I click on an empty point on the canvas and try to select nodes/edges by dragging, it simply moves the network canva around, and this renders cytoscape unusable. I can't find a way of changing the way in which the mouse selection interacts with the network, as it seems the api interprets any "long click" as a drag option for the whole image, not a selection option.
I tried changing my trackpad and mouse settings, but to no avail. I'm not sure which apps should be interfering, if any, as it seems nothing is activated in the cytoscape session I'm in.
I used an older version of cytoscape in the past and never experienced any problem, I dowloaded Cytoscape 3.7.1 and trying to use it on Mac OS X 10.13.6 - x86_64

thanks.

[Alex Pico]

Hold shift to perform drag select. Default drag is for pan. This was changed a few versions back to follow the majority of gestures in other applications. … but it takes a while to get used to! :)

 - Alex

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[jinyong1...@gmail.com]

I am also having a similar issue as well which is very frustrating. It goes away when I minimize/maximize a couple of times in a row but comes back the second my mouse crosses over any one of the panes. I also experienced a similar issue with GSEA interface... I have little clue as to what could be the cause of this problem but as OP suggests, I don't think it's a hardware problem. Running on Ryzen 3800X RTX2070S with 32GB RAM and so forth with up-to-date drivers. 

Jin

[acz...@gmail.com]

The problem still persists for me also and none of the solutions given from the community or tried by me worked. I had the same problem with Qiagen's Ingenuity software installed on the same computer and operating system, which is also been using Java to visualize its windows and results. I come to believe that it must be a Java issue, a bug or a conflict with other software or hardware installed on the pc. Should someone has an idea why this is happening, I would be extremely grateful if he or she could share it with us.

Athanassios

[acz...@gmail.com]

The problem still persists for me also and none of the solutions given from the community or tried by me worked. I had the same problem with Qiagen's Ingenuity software installed on the same computer and operating system, which is also been using Java to visualize its windows and results. I come to believe that it must be a Java issue, a bug or a conflict with other software or hardware installed on the pc. Should someone has an idea why this is happening, I would be extremely grateful if he or she could share it with us.

Athanassios

On Thursday, 19 September 2019 19:12:58 UTC+3, jinyong1...@gmail.com wrote:

[acz...@gmail.com]

The problem still persists for me also and none of the solutions given from the community or tried by me worked. I had the same problem with Qiagen's Ingenuity software installed on the same computer and operating system, which is also been using Java to visualize its windows and results. I come to believe that it must be a Java issue, a bug or a conflict with other software or hardware installed on the pc. Should someone has an idea why this is happening, I would be extremely grateful if he or she could share it with us.

Athanassios

On Thursday, 19 September 2019 19:12:58 UTC+3, jinyong1...@gmail.com wrote:

[Scooter Morris]

Can you tell us what version of Java you are running? 

-- scooter

[jinyong1...@gmail.com]

I just updated it to Version 8 build 231(build 1.8.0_231-b11) and the problem persists. I am experiencing broken graphics after selecting GSEA output folders to make enrichmentMap networks. 

Jin

[Scooter Morris]

Hi Jin,

   Sorry that you continue to have problems.  My best guess is that something is interfering with Java's rendering pipeline.  This is particularly true since multiple java applications are showing the same symptoms.  My only suggestion is to see if any other programs are running, but beyond that, I'm sort of at a loss.  You might try to disable all plugins to see if there is a particular plugin that exacerbates the problem.  Sorry I can't be of more help.

-- scooter

[amirnaasser]

Hi, i have the same problem :(.

[Alex Pico]

Please file a bug report with more details. Details about your system, including Java version. Plus details about what exactly you see and how to reproduce it. For example, does it happen every time? Does it happen after reboot?

https://cytoscape.org/bug-report.html

[Alex Pico]

Ah, I see you bug report. Thanks! We will answer there.

[陈杰煌]

Hi. It seems like a problem from years ago. Same problem here.  A display bug or glitch after around 2-3 minutes of normal work. 9700k @4.9 GHz, 16G 4000 DDR4 RAM, AMD 6800xt with the newest released drive 2023.3.1.