Hello Elkan, It seems that the current release of TPP contains an incomplete version of Qualscore. Please go to this link and click on the 'download' link to get the zip file that contains the software: http://sashimi.svn.sourceforge.net/viewvc/sashimi/trunk/qualscore/qualscore_v1.0_2.zip?view=log
Once you unzip, place the contents (the qualscore.jar file and the entire lib/ directory) under C:\Inetpub\tpp-bin\ . Make sure you copy the entire lib/ directory, and not just its contents. Hope this helps! --Luis On Thu, Mar 1, 2012 at 11:00 PM, Naiheng Dong <[email protected]> wrote: > Hi Eric > > There are two folders in directory C:\Program Files\Java\ (In my opinion, > the lib subdirectory speicfied by you is the lib of Java, and no lib folder > is found in TPP installed directories.), jre1.5.0_03 and jre6. > > Under the subdirectory of lib in jre1.5.0_03, the .jar files are: > deploy.jar, jce.jar, plugin.jar, javaws.jar, jsse.jar, rt.jar, > with subdirectories: > images, javaws, applet, classlist, cmm, ext, management, security, fonts, > tzmappings, i386, zi, im. > > Under the subdirectory of lib in jre 6, .jar files are: > charsets.jar, management-agent.jar, deploy.jar, plugin.jar, javaws.jar, > resources.jar, jce.jar, rt.jar, jsse.jar; > and subfolders are: > applet, audio, management, classlist, cmm, deploy, ext, security, > servicetag, fonts, i386, tzmappings, im, zi, images. > > None of the .jar files mentioned are found under the subdirectories of lib > and the directories under lib. > > Thanks very much. > > > 2012/3/2 Eric Deutsch <[email protected]> >> >> Hi Elkan, can you describe your situation a little more? Is there a lib >> directory? What is in it? Are *some* of the jars there, just not all? Or >> it’s not there at all? >> >> >> >> Thanks, >> >> Eric >> >> >> >> >> >> From: [email protected] >> [mailto:[email protected]] On Behalf Of Naiheng Dong >> Sent: Tuesday, February 28, 2012 7:48 PM >> To: [email protected] >> Subject: Re: [spctools-discuss] Re: Problem in running QualScore in TPP >> v4.5.2 >> >> >> >> Hi Eric >> >> Thanks for your reply. >> >> All of the .jar files listed by you do not appear in the subdirectory >> called lib. >> >> So how can I repair it? >> >> Elkan >> >> 在 2012年2月29日 上午11:26，Eric Deutsch <[email protected]>写道： >> >> Hi Elkan, I think for QualScore to work, all the supplemental jars like >> jfreechart-0.9.15.jar need to be in the subdirectory called lib for things >> to work. So when you execute "java -jar qualscore.jar", it is expecting to >> find all these files: >> >> lib/TableLayout.jar lib/jcommon-0.9.0.jar lib/jfreechart-0.9.15.jar >> lib/jrap.jar lib/jscicore.jar lib/log4j-1.2.8.jar lib/msutils.jar lib/tar. >> jar lib/trove.jar lib/xercesImpl.jar >> >> Are they there? >> >> Eric >> >> >> >> >> > -----Original Message----- >> > From: [email protected] [mailto:spctools- >> > [email protected]] On Behalf Of Jorey Dong >> > Sent: Tuesday, February 28, 2012 5:18 PM >> > To: spctools-discuss >> > Subject: [spctools-discuss] Re: Problem in running QualScore in TPP >> > v4.5.2 >> > >> > Hi Damian >> > >> > Thanks for your kind help. >> > >> > When I type the command "java -jar qualscore.jar" in the Windows >> > command line after moving to directory C:\Inetpub\tpp-bin, error still >> > occurs, as listed below: >> > " >> > Exception in thread "main" java.lang.NoClassDefFoundError: org/jfree/ >> > data/SeriesDataset >> > Caused by: java.lang.ClassNotFoundException: >> > org.jfree.data.SeriesDataset >> > at java.net.URLClassLoader$1.run(Unknown Source) >> > at java.security.AccessController.doPrivileged(Native Method) >> > at java.net.URLClassLoader.findClass(Unknown Source) >> > at java.lang.ClassLoader.loadClass(Unknown Source) >> > at sun.misc.Launcher$AppClassLoader.loadClass(Unknown Source) >> > at java.lang.ClassLoader.loadClass(Unknown Source) >> > Could not find the main class: >> > org.systemsbiology.qualscore.commandline.Main. Program will exit. >> > " >> > >> > Does it mean that the Java Environment I installed is not appropriate? >> > >> > Best Regards. >> > >> > Elkan >> > >> > On 2月29日, 上午12时33分, GATTACA <[email protected]> wrote: >> > > Try executing qualscore from the Windows command line: >> > > cd C:\Inetpub\tpp-bin >> > > java -jar qualscore.jar >> > > >> > > Executing the above commands should give you a usage statement for >> > > Qualscore if everything is okay. >> > > After that, it's just a question of passing it the write parameters. >> > > >> > > Damian >> > > >> > > On Feb 28, 9:00 am, Jorey Dong <[email protected]> wrote: >> > > >> > > >> > > >> > > >> > > >> > > >> > > >> > > > Hi All, >> > > >> > > > When I run QualScore embedded in TPP to assess the quality of >> > tandem >> > > > mass spectra, the error occurs: >> > > > " >> > > > run_in c:/Inetpub/wwwroot/ISB/data; java -jar c:\Inetpub\tpp-bin >> > > > \qualscore.jar -c 1.0 -p 0.1 -a 20060502data06.xml >> > > >> > > > java.lang.NoClassDefFoundError: org/jfree/data/SeriesDataset >> > > > Caused by: java.lang.ClassNotFoundException: >> > > > org.jfree.data.SeriesDataset >> > > > at java.net.URLClassLoader$1.run(Unknown Source) >> > > > at java.security.AccessController.doPrivileged(Native >> > Method) >> > > > at java.net.URLClassLoader.findClass(Unknown Source) >> > > > at java.lang.ClassLoader.loadClass(Unknown Source) >> > > > at sun.misc.Launcher$AppClassLoader.loadClass(Unknown >> > Source) >> > > > at java.lang.ClassLoader.loadClass(Unknown Source) >> > > > Could not find the main class: >> > > > org.systemsbiology.qualscore.commandline.Main. Program will exit. >> > > > Exception in thread "main" >> > > > command "java -jar c:\Inetpub\tpp-bin\qualscore.jar -c 1.0 -p 0.1 - >> > a >> > > > 20060502data06.xml" failed: Operation not permitted >> > > >> > > > Command FAILED >> > > > " >> > > >> > > > Same error occurred when I run the data PeptideProphet output file >> > > > interact-20060502data06.xml. >> > > >> > > > So any one can help me solve this problem? >> > > >> > > > Best Regards. >> > > >> > > > Elkan >> > >> > -- >> > You received this message because you are subscribed to the Google >> > Groups "spctools-discuss" group. >> > To post to this group, send email to [email protected]. >> > To unsubscribe from this group, send email to spctools- >> > [email protected]. >> > For more options, visit this group at >> > http://groups.google.com/group/spctools-discuss?hl=en. >> >> -- >> You received this message because you are subscribed to the Google Groups >> "spctools-discuss" group. >> To post to this group, send email to [email protected]. >> To unsubscribe from this group, send email to >> [email protected]. >> For more options, visit this group at >> http://groups.google.com/group/spctools-discuss?hl=en. >> >> >> >> >> -- >> Naiping Dong (Elkan) >> >> -- >> You received this message because you are subscribed to the Google Groups >> "spctools-discuss" group. >> To post to this group, send email to [email protected]. >> To unsubscribe from this group, send email to >> [email protected]. >> For more options, visit this group at >> http://groups.google.com/group/spctools-discuss?hl=en. >> >> -- >> You received this message because you are subscribed to the Google Groups >> "spctools-discuss" group. >> To post to this group, send email to [email protected]. >> To unsubscribe from this group, send email to >> [email protected]. >> For more options, visit this group at >> http://groups.google.com/group/spctools-discuss?hl=en. > > > > > -- > Naiping Dong (Elkan) > > -- > You received this message because you are subscribed to the Google Groups > "spctools-discuss" group. > To post to this group, send email to [email protected]. > To unsubscribe from this group, send email to > [email protected]. > For more options, visit this group at > http://groups.google.com/group/spctools-discuss?hl=en. -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. 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