Java Treeview Activity
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Activity for Java Treeview
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RICHARD FRIEDMAN posted a comment on ticket #73
Alok, I wasn't referring to third party plugins. I saw several more plugins in the menu than I use. If they are automatically accessed, that's fine. No further work is necessary. Please let me know when the docs are ready and I will review them if you would like me to do so, Thanks and best wishes, Rich From: bugs@jtreeview.p.re.sourceforge.net bugs@jtreeview.p.re.sourceforge.net on behalf of Alok Saldanha alokito@users.sourceforge.net Sent: Monday, September 30, 2024 7:22 PM To: [jtreeview:bugs]...
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Alok Saldanha modified a comment on ticket #73
After testing the Windows install I set 1.2.1 as the default version of Java TreeView. I believe there are very few if any third party plugins, but will try to find some time document how to get them working with the new app bundle layout next weekend.
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I set 1.2.1 as the default version of Java TreeView. I believe there are very few if any third party plugins, but will try to find some time document how to get them working with the new app bundle layout next weekend.
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Java Treeview released /jtreeview/1.2.1/README.md
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Alok, Thank you for the new build. It worked better than expected in that on loading the cdt file I got a heatmap immediately. It is not clear what I should do to get additional plugins or of what use they are. If you would like me to test the pre-relase version once the documentation is ready I will be happy to do so. I will be out of e-mail contact for several Jewish Holidays in October, but I will have an automatic announcement on as to when I will be back and I will be happy to test anything...
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Hi Richard, I believe this issue was caused by AppTranslocation, aka Gatekeeper path randomisation. I have addressed this issue by moving the plugins and coordinates inside of the app bundle. This means that in order to add plugins or coordiantes files you will need to use the Terminal app, but should make JTV easier to use for most people. I'll probably have time to work on the documentation (and general cleanup) the weekend of Oct 5. If you have time, could you try out the newest version? http...
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Alok Saldanha committed [23598e] on Git
Merge branch 'bugs/launch_on_mac'
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Alok Saldanha committed [aba600] on Git
downgraded nanoxml, fix bundle paths
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Alok Saldanha committed [0843a0] on Git
update java application stub
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Alok Saldanha committed [d9f0f4] on Git
comment out registration
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Alok Saldanha committed [3602a5] on Git
Update readme and changelog
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Alok, I am not sure if my previous reply got to you. Dear Alok, First of all, thank you for developing Java Treeview and supporting it over the years. I teach a course in bioinformatics for biologists which only uses GUIs and Java Treeview has been a great asset to my students and in my own work. I am using Version 1.2.0 . It resides in my /Applications directory I launch it by clicking it. I was unable to register, I got a "registration failed" error message. I got it working by allowing treeview...
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Hi Richard, Could you describe the issue a little more fully? 1. Which distribution of Java TreeView are you using, and how are you launching it? 2. What is an example location where you cannot open files? I seem to be able to open files in my Desktop folder on Somoma, Mac OSX 14.6.1 after fixing the bundle launcher. I am prompted to grant Java access when I navigate to that folder, but otherwise it works. There is an additional issue related to finding plugins after AppTranslocation, but after I...
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I have experienced the same problem with Somoma, Mac OSX 14.6.1 . I have tried the workaround above but it did not work. Is there a comparable work around for this OS? Thanks and best wishes, Richard Friedman
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Carson Stacy posted a comment on ticket #73
Here is a work around I found to this issue. Posting here in case it helps anyone. It appears /bin/bash no longer has full disk access on newer versions of MacOS, which I believe the code requires. Following the following steps solved this issue for me: System Settings > Privacy & Security > Full Disk Access If present, click on lock in lower left corner to allow changes Separately, open a new finder window Select Go -> Go to Folder... from the menu bar Type /bin and click Go Drag the /bin/bash icon...
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Jingyi Wu posted a comment on discussion Open Discussion
Yes. I am able to see it in my main user folder but not Desktop, which is more convenient for me. Currently, I grant the full disk access for Java TreeView. So the suggestion from apple is not helpful because you can see the java logo in "Files and Folders" as Full Disk Access. The interesting thing is when I cancel the full disk access for Java TreeView, there is no java logo under "Files and Folders" section for selection. I think there is something wrong.
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The following may help, I will see if I can find a Big Sur machine to test on: https://support.apple.com/guide/mac-help/control-access-to-files-and-folders-on-mac-mchld5a35146/mac
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This seems very similar to the following issue reported a couple weeks back: https://sourceforge.net/p/jtreeview/bugs/73/ Are you able to see files in your main user folder?
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How to run TreeView-1.1.6r4-osx on macOS Catalina?
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Closing since I believe it is fixed in 1.2.0.
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Can Goksal modified a comment on discussion Open Discussion
I am having the same problem. Even when I switch file format to "all files" the folder is still empty. Did you ever figure out what was wrong?
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I am having the same problem. Even when I switch file format to "all files" the folder is still empty.
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Jeffrey Lewis created ticket #73
Problem "Finding" CDT Files Unless in Specific Directory
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I updated my mac system to Big Sur and reinstalled TreeView-1.2.0-osx. However, when I try to open a cdt file in my desktop, I can not. Because when I select the Desktop/Download/Document folder, it is empty from treeview browser. I did grant the full disk permission for treeview.
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Allow Treeview to run on Mac OS X without legacy Java
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Implemented in 1.2.0
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Alok Saldanha committed [138f16]
rename README
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Alok Saldanha committed [a6a0c8]
overwrite with historically working JavaApplicationStub (sigh)
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Alok Saldanha committed [616887]
fixed bug in makeTars.pl
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Alok Saldanha committed [8ef9e9]
#33 updated to universalJavaApplicationStub
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It appears there is a path to a more modern java! I make a ticket for this: https://sourceforge.net/p/jtreeview/feature-requests/33/
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Allow Treeview to run on Mac OS X without legacy Java
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Alok Saldanha committed [de5629]
removed unprintable comments
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Alok Saldanha committed [c216d8]
ignore intellij files
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Alok Saldanha committed [f968a3]
added new HEADER mode for url extractors.
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Alok Saldanha committed [5f352b]
incremented version to 1.2.0
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Anyways, the easy fix (for now) is to remove the com.apple.quarantine attribute. If you open the Terminal app, you can verify that the attribute is present with xattr /Applications/Treeview/Java\ Treeview.app You should see "com.apple.quarantine" as the response. You can then remove the attribute with xattr -d com.apple.quarantine /Applications/Treeview/Java\ Treeview.app
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How to run TreeView-1.1.6r4-osx on macOS Catalina?
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Just a quick update, it seems that "app translocation" was an intentional security feature from OS X: https://www.synack.com/blog/untranslocating-apps/. Also, I notice that this discussion is marked private, but it may be of wide interest. I will mark it public unless you specifically want to keep it private.
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Hi Guri! Sorry for totally dropping the ball on this. Would this kind of script still be useful? Do you already have such a script?
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Problem with "open"
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Closing for now, please file a new ticket if you have an issue.
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Hi Guri! Sorry for totally dropping the ball on this. Would this kind of script still be useful? Do you already have such a script?
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Correlation in gtr file - message 2 (cdt file attached)
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This seems to open fine for me, though you have an extra column on the right.
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Correlation in gtr file - menssage 1 (gtr file attached)
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I'm sorry for the extremely late reply, I didn't notice this tracker until recently. The correlation is merely used to set the height of the branches in the dendrogram, so it's not essential that it be a proper correlation. One thing I noticed is that you have more descriptive text in the first three columns, normally I have identifiers as follows: NODE1X | GENE2X | GENE0X I presume that you've already solved this issue, or no longer care. Please open a new ticket if I'm mistaken.
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I'm sorry for the extremely late reply, I didn't notice this tracker until recently. The correlation is merely used to set the height of the branches in the dendrogram, so it's not essential that it be a proper correlation. I presume that you've already solved this issue, or no longer care. Please open a new ticket if I'm mistaken.
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Dear Jean-Philippe, I apologize for the delay in responding. I have gotten Java Treeview working with Mac OS X 10.15.7. Unfortunately, it requires a bit of hoop jumping. I would like to modernize Java Treeview in the coming months, but I will need to do some prototyping to see what is feasible. In the meantime, I can offer the following workaround: 1) As you correctly noted, Treeview requires Java for OS X 2017, which is available from https://support.apple.com/kb/DL1572?locale=en_US If you try to...
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Dear Jean-Philippe, I apologize for the delay in responding. I have gotten Java Treeview working with Mac OS X 10.15.7. Unfortunately, it requires a bit of hoop jumping. I would like to modernize Java Treeview in the coming months, but I will need to do some prototyping to see what is feasible. In the meantime, I can offer the following workaround: 1) As you correctly noted, Treeview requires Java for OS X 2017, which is available from https://support.apple.com/kb/DL1572?locale=en_US If you try to...
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Jean-Philippe Coppe created ticket #5
How to run TreeView-1.1.6r4-osx on macOS Catalina?
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Hi Sam, most likely java is not installed on your windows machine. You should be able to install the Java JRE from https://java.com/en/. There is no harm in installing the JDK, but the JRE is smaller and should be sufficient. You can also try searching "How to install java on windows 10" to find youtube videos and helpful articles. Please feel free to post again if you run into problems.
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sam fagg modified a comment on discussion Open Discussion
Hi, I am horribly unskilled with Windows machines and I am getting the above-referenced error. The link you provided is now dead. Can you provide a solution? BTW I'm using windows 10, 64-bit
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Hi, I am horribly unskilled with Windows machines and I am getting the above-referenced error. The link you provided is now dead. Can you provide a solution?
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Ewa Wdzieczak-Smering posted a comment on discussion Developers
TreeView-1.1.6r4-osx, 10.13.6 (17G5006), jre-8u191, Java for OS X 2017-001. Upon execution, TreeView caches itself to locations like /private/var/folders/1t/01qptrl5243fqr9l9gjvd5ph0000gn/T/AppTranslocation/4617E906-D77F-4AA1-92A5-A224F9FA5D3D/d/plugins/ and I need to browse to the Plugins folder (/Applications/TreeView-1.1.6r4-osx/TreeView/Plugins) everytime I launch the application. Changing settings in GateKeeper did not work. Oddly enough, TreeView works fine on an older MacBook Air running 10.11.6,...
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Monica Nicolau modified a comment on discussion Developers
This was not a problem before. What has changed? Best I've been able to do was to insert the correct path to plugins every time I start TreeView. Not the best solution. Could there be an option to save the path? It is not clear to me how to control the choice of the working directory when java is launched, as I think Alok Saldanha suggests.
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This was not a problem before. What has changed? Best I've been able to do was to insert the correct path to plugins every time I start TreeView. Not the best solution. Could there be an option to save the path? It is not clear to me how to control the choice of the working directory when java is launched.
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Hi Elizabeth, As you can see from the console message, java treeview is looking for plugins in "C:\Documents and Settings\valvarez\Escritorio\Bio\ProyectoBio\plugins\" and not finding them. This is because the working directory when the program was launched was "C:\Documents and Settings\valvarez\Escritorio\Bio\ProyectoBio". The correct path is likely something like "C:\Documents and Settings\valvarez\Escritorio\Bio\TreeView-1.1.4r3-win\TreeView-1.1.4r3-win\plugins". Manually updating the plugin...
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The important thing is the working directory when java is launched, not the relative location of the application and the plugin folder. The path that is being checked should be printed to standard out.
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Hi Elizabeth, As you can see from the console message, java treeview is looking for plugins in "C:\Documents and Settings\valvarez\Escritorio\Bio\ProyectoBio\plugins\" and not finding them. This is because the working directory when the program was launched was "C:\Documents and Settings\valvarez\Escritorio\Bio\ProyectoBio". The correct path is likely something like "C:\Documents and Settings\valvarez\Escritorio\Bio\TreeView-1.1.4r3-win\TreeView-1.1.4r3-win\plugins". Manually updating the plugin...
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Matthew R Paul posted a comment on discussion Help
Thanks very much. That worked like a charm!
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Thanks very much. That worked like a charm!
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Hi Matt, Sorry for the slow response, I have been on vacation. Evidently when the nanoxml dependency was added, the jar manifest was not updated. You should be able to work around this by doing the following: cd Java\ TreeView.app/Contents/Resources/Java/ java -Xmx1000m -cp TreeView.jar:nanoxml-2.2.2.jar edu.stanford.genetics.treeview.app.LinkedViewApp Hope this helps... java tree view is probably (over)due for some updates. Best, Alok
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Whoops, sent too soon. The problem with the above is that it won't find the plugins folder properly. The following should work, and actually find the plugins: java -Xmx1000m -cp 'Java TreeView.app/Contents/Resources/Java/*' edu.stanford.genetics.treeview.app.LinkedViewApp
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Hi Matt, Sorry for the slow response, I have been on vacation. Evidently when the nanoxml dependency was added, the jar manifest was not updated. You should be able to work around this by doing the following: cd Java\ TreeView.app/Contents/Resources/Java/ java -Xmx1000m -cp TreeView.jar:nanoxml-2.2.2.jar edu.stanford.genetics.treeview.app.LinkedViewApp Hope this helps... java tree view is probably (over)due for some updates. Best, Alok On Thu, Aug 2, 2018 at 11:36 AM Matthew R Paul fatbrian@users.sourceforge.net...
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I am using the 1.1.6r4 osx version. I am trying to upload a large matrix to make heatmaps and am hitting the limit for memory. There are some guidlines for increaisng the memory, by directly running Treeview on the command line. I have tried this out and it errors: command: java -Xmx1000m -jar Java\ TreeView.app/Contents/Resources/Java/TreeView.jar error: Exception in thread "main" java.lang.NoClassDefFoundError: net/n3/nanoxml/IXMLReader at edu.stanford.genetics.treeview.TreeViewApp.<init>(Unknown...
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Taisiia Feoktistova posted a comment on discussion Help
Hi, I am having the same problem. Were you ever able to figure it out? Thank you.
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Alok Saldanha committed [9de913]
Updated link to Treeview 3.0
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Alec Steep posted a comment on discussion Developers
Here's how I fixed it. In the TreeView GUI under the "Help" tab, click "Plugins". You should see a path to the plugins folder, make sure it's accurate. My path was not accurate so I had to chnage it. Then, browse for the plugins in the proper folder and they should be added. Not sure if this is important as I did this beforehand... I located each plugin jar file and granted permission to open it in my Mac's System Preferences under Security and Privacy. I'm runningmac osx 10.12.6 Java version 1.8.0_131...
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Rowan posted a comment on discussion Developers
Hi, I have recently had this problem too. I've tried Jake's adivce of updating Java and ensuring the plugins folder is in the same folder as the application but this hasn't fixed the problem. Any ideas? Thanks
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Hi Chris, Could I know which is the document you follow to solve this problem? I am really stuck here. Thanks!
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Raju Saudagar posted a comment on discussion Developers
How to change the genetree alignment and thickness so that its leaf does not mix up in the wall?
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The tree at the left is mixing up with border. cant view properly. On Mon, Aug 14, 2017 at 12:41 PM, Raju Saudagar rajusaudagar@gmail.com wrote: How to change the genetree alignment and thickness so that its leaf does not mix up in the wall?
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ggiaever posted a comment on ticket #4
thanks alok -- nope, all alone right now...any chance you could point me to how to learn this? many thx for your timely response, treeview rocks, best, guri On Mon, Apr 17, 2017 at 3:08 PM, Alok Saldanha alokito@users.sf.net wrote: That makes sense. Java Treeview does not provide that functionality out of the box. Probably the easiest thing would be to write a script that add a column to the GTR file containing the node structure. The format of the GTR file makes this fairly straightforward. Do you...
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That makes sense. Java Treeview does not provide that functionality out of the box. Probably the easiest thing would be to write a script that add a column to the GTR file containing the node structure. The format of the GTR file makes this fairly straightforward. Do you have someone who is capable of writing something in perl or python? Best, Alok
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i want to annotate the node structure -- e.g. at the first level it would be 1 2 at the second level it would be 1.1 1.2 2.1 2.2 etc. does that make sense? thanks guri On Mon, Apr 17, 2017 at 10:05 AM, Alok Saldanha alokito@users.sf.net wrote: Hello Guri(?), I am afraid I don't fully understand the question. Would you like to be able to select a particular node in the tree, and then extract the subtree below that node? [support-requests:#4] https://sourceforge.net/p/jtreeview/support-requests/4/...
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