No matter what I do, I keep on getting this annoying registration request:
- I registered (even gave my e-mail)
- I pressed "Later"
- I pressed "Never"
It still gets back to me. Shouldn't be hard to fix, I guess :)
Java TreeView 1.1.3, Win XP SP2
Thanks!
I was unable to replicate this problem on Mac OS X. My best guess is that it is trying to store settings in a location for which it does not have write permissions. On windows, which seems to have this problem, it stores in System.getProperty("user.home")\jtview.xml... perhaps with some JVMs user.home is not set? Which java version are you using? You can usually get the java version by typing "java -version" on the command line. Sometimes reinstalling java from Sun fixes the problem http://www.java.com .
If System.getProperty("user.home") maps to C:\Dokumente und Einstellungen\Alex (where Alex is my login), then I find there no jtview.xml. This might be an explanation as to why I don't have a "Recent files" list in JTView either.
Output from java -version
java version "1.6.0_03"
Java(TM) SE Runtime Environment (build 1.6.0_03-b05)
Java HotSpot(TM) Client VM (build 1.6.0_03-b05, mixed mode)
I am a bit reluctant to reinstall Java, as I have other Java apps and I am afraid not to break something else then. Maybe I just could set up the right environment?
Thanks!
If you get a chance, please download the newest version and give it a shot. I tried to make it more aggressive with saving settings, and there is a new Help->Global Prefs Info menuitem that may help diagnose the problem.
Thanks for feedback. It seems that either my system is very reluctant, or aggressive is not aggressive enough. Still same behaviour.
Global Prefs states that the file should be in
C:\Dokumente und Einstellungen\Alex\jtview.xml
There's no file by that name. I created it myself and it still stays at 0 bytes after relaunching JTV a few times.
Do you get any output if you run java treeview from the command line? There is a minimal description of how to do this here:
http://jtreeview.sourceforge.net/docs/JTVUserManual/ch02.html#ch2_flags
Thanks for bearing with me!
Yes, I get, but nothing strange:
C:\Kits\Bio\chip_analysis\TreeView-1.1.4-bin>java -jar TreeView.jar
Plugin Jar jar:file:/C:/Kits/Bio/chip_analysis/TreeView-1.1.4-bin/plugins/Dendrogram.jar!/
Registering Plugin Dendrogram
Registering Plugin Alignment
Registering Plugin KnnDendrogram
Plugin Jar jar:file:/C:/Kits/Bio/chip_analysis/TreeView-1.1.4-bin/plugins/Karyoscope.jar!/
Registering Plugin Karyoscope
Plugin Jar jar:file:/C:/Kits/Bio/chip_analysis/TreeView-1.1.4-bin/plugins/Scatterplot.jar!/
Registering Plugin Scatterplot
Plugin Jar jar:file:/C:/Kits/Bio/chip_analysis/TreeView-1.1.4-bin/plugins/Treeanno.jar!/
Registering Plugin ArrayTreeAnno
Registering Plugin GeneTreeAnno
ViewFrame.dispose
I just put up release 1.1.4r2, which has a button in the"help -> global config info..." dialog that modifies the global config and tries to save it. This code should report any exceptions that are raised in a textbox, please post the output when you get a chance.
Ok, here is the output. What I did: start the program, hit "Later" at registration prompt, went to Global Prefs and hit "Test it!" and quit the program.
C:\Kits\Bio\chip_analysis\TreeView-1.1.4r2-win>java -jar -Xmx500m TreeView.jar
Plugin Jar jar:file:/C:/Kits/Bio/chip_analysis/TreeView-1.1.4r2-win/plugins/Dendrogram.jar!/
Registering Plugin Dendrogram
Registering Plugin Alignment
Registering Plugin KnnDendrogram
Plugin Jar jar:file:/C:/Kits/Bio/chip_analysis/TreeView-1.1.4r2-win/plugins/Karyoscope.jar!/
Registering Plugin Karyoscope
Plugin Jar jar:file:/C:/Kits/Bio/chip_analysis/TreeView-1.1.4r2-win/plugins/Scatterplot.jar!/
Registering Plugin Scatterplot
Plugin Jar jar:file:/C:/Kits/Bio/chip_analysis/TreeView-1.1.4r2-win/plugins/Treeanno.jar!/
Registering Plugin ArrayTreeAnno
Registering Plugin GeneTreeAnno
Not printing config to file, config is unchanged.
Before false
After true
Not printing config to file, config is unchanged.
Before true
After false
ViewFrame.dispose
Not printing config to file, config is unchanged.
this should (finally!) be fixed as of 1.1.4r3, please confirm.
Looks like a toughter nut...
C:\Kits\Bio\chip_analysis\TreeView-1.1.4r3-win>java -jar -Xmx500m TreeView.jar
created xml config from file
Warning: root is null, creating dummy config node
Warning: root is null, creating dummy config node
Warning: root is null, creating dummy config node
Plugin Jar jar:file:/C:/Kits/Bio/chip_analysis/TreeView-1.1.4r3-win/plugins/Dendrogram.jar!/
Registering Plugin Dendrogram
Registering Plugin Alignment
Registering Plugin KnnDendrogram
Plugin Jar jar:file:/C:/Kits/Bio/chip_analysis/TreeView-1.1.4r3-win/plugins/Karyoscope.jar!/
Registering Plugin Karyoscope
Plugin Jar jar:file:/C:/Kits/Bio/chip_analysis/TreeView-1.1.4r3-win/plugins/Scatterplot.jar!/
Registering Plugin Scatterplot
Plugin Jar jar:file:/C:/Kits/Bio/chip_analysis/TreeView-1.1.4r3-win/plugins/Treeanno.jar!/
Registering Plugin ArrayTreeAnno
Registering Plugin GeneTreeAnno
Warning: root is null, creating dummy config node
Warning: root is null, creating dummy config node
Not printing config to file, config is unchanged.
Warning: root is null, creating dummy config node
Before false
After true
Warning: root is null, creating dummy config node
Warning: root is null, creating dummy config node
Not printing config to file, config is unchanged.
Before true
After false
ViewFrame.dispose
Not printing config to file, config is unchanged.
That error could be caused by having an empty config file. Delete C:\Dokumente und Einstellungen\Alex\jtview.xml and try again. I'll add a check for null config files for the next version, but it's not critical enough for me to push another release right now.
C:\Kits\Bio\chip_analysis\TreeView-1.1.4r3-win>java -jar -Xmx500m TreeView.jar
File not found, will try from URL
Making new configuration file C:\Dokumente und Einstellungen\Alex\jtview.xml
Plugin Jar jar:file:/C:/Kits/Bio/chip_analysis/TreeView-1.1.4r3-win/plugins/Dendrogram.jar!/
Registering Plugin Dendrogram
Registering Plugin Alignment
Registering Plugin KnnDendrogram
Plugin Jar jar:file:/C:/Kits/Bio/chip_analysis/TreeView-1.1.4r3-win/plugins/Karyoscope.jar!/
Registering Plugin Karyoscope
Plugin Jar jar:file:/C:/Kits/Bio/chip_analysis/TreeView-1.1.4r3-win/plugins/Scatterplot.jar!/
Registering Plugin Scatterplot
Plugin Jar jar:file:/C:/Kits/Bio/chip_analysis/TreeView-1.1.4r3-win/plugins/Treeanno.jar!/
Registering Plugin ArrayTreeAnno
Registering Plugin GeneTreeAnno
Successfully stored config file C:\Dokumente und Einstellungen\Alex\jtview.xml
Before false
After true
Successfully stored config file C:\Dokumente und Einstellungen\Alex\jtview.xml
Before true
After false
ViewFrame.dispose
Not printing config to file, config is unchanged.
After quite a few trials, finally solved. Who said "shouldn't be hard to fix"??
Thanks for the patience!
If you consider, you (as programmer) should close the incident. For me, it seems to work, storing also the recent files and remembering the registration status.
Glad to hear it. I generally don't close issues until I'm sure they're resolved. You never know what can go wrong; in this case, we resolved your first issue which had to do with error cases involving invalid urls (at some point I decided it was a good idea to try opening as a url if the file open fails). But that revealed a second issue caused by your empty file, which is that on a null file I expected my XML parsing library to throw an XMLException as valid XML documents must have a root node according to the spec. Instead, it returns null, which I have coincidentally been using to indicate the lack of a place to store global configuration.