the program spectrum_similarity_pairwise_GUI-0.1.jar exception

[Jia Huang]

1. run a probabilistic based scoring function to compare two given spectra data sets

• my mgf file(two mgf file with the same content)
  
• my setting
  
• program output

java -cp .\scoring_pipeline-1.3.jar main.ScorePipelineStarter
2018-03-12 17:15:19 INFO  MainController:474 - starting spectrum similarity score pipeline
2018-03-12 17:15:20 INFO  ScorePipeline:677 - Successfully sent analytics event.
2018-03-12 17:15:20 INFO  ScorePipeline:677 - Successfully sent analytics event.
2018-03-12 17:15:20 INFO  MainController:179 - The version of score.pipeline :1.3
2018-03-12 17:15:20 INFO  MainController:190 - Run is ready to start with NF_None_TR_None_PPR_None_CHR_None_PRECTOL_0_MSRobin.txt for msrobin
2018-03-12 17:15:20 INFO  MainController:191 - Only calculate +/-2 slices up and down: false
2018-03-12 17:15:20 INFO  MainController:256 - a name of an mgf from the spectra.folder=data1.mgf
2018-03-12 17:15:20 INFO  MainController:257 - a name of an mgf from the spectra.to.compare.folder=data2.mgf
10%10%2018-03-12 17:15:20 INFO  MainController:280 - Size of MSnSpectra at spectra.folder=1
2018-03-12 17:15:20 INFO  MainController:281 - Size of MSnSpectra at spectra.to.compare.folder=1
2018-03-12 17:15:20 INFO  MainController:484 - finished spectrum similarity score pipeline

2. when I was ready to run the program spectrum_similarity_pairwise_GUI-0.1.jar to see the result I came the exception ArrayIndexOutOfBoundsException, what can I do to solve the problem?

java  -jar
 .\spectrum_similarity_pairwise_GUI-0.1.jar
Exception in thread "AWT-EventQueue-0" java.lang.ArrayIndexOutOfBoundsException: 2
        at gui_spectral_match_visualization.MainGUI.prepareTable(MainGUI.java:177)
        at gui_spectral_match_visualization.MainGUI.<init>(MainGUI.java:89)
        at gui_spectral_match_visualization.MainGUI$20.run(MainGUI.java:1060)
        at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311)
        at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:756)
        at java.awt.EventQueue.access$500(EventQueue.java:97)
        at java.awt.EventQueue$3.run(EventQueue.java:709)
        at java.awt.EventQueue$3.run(EventQueue.java:703)
        at java.security.AccessController.doPrivileged(Native Method)
        at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80)
        at java.awt.EventQueue.dispatchEvent(EventQueue.java:726)
        at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201)
        at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
        at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)
        at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
        at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)
        at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)

Thanks!

[Genet-Abay]

can you send me the files, please?

[Jia Huang]

Yes, you can download the files in https://drive.google.com/open?id=1bc1pjeYdZKqgUZuWY6IyHUqY2jBAp1aB
the contents of two files are the same!
thanks！

[Genet-Abay]

it runs fine and here is the output:

The version of Score.Pipeline is 1.3
Spectrum Title Charge PrecursorMZ Spectrum_Title_Comparison_Dataset ScoringFunction_Pipeline_NF_0_TR_0_PPR_None_CHR_false_PRECTOL_0.0
Locus:1.1.1.1763.2 2+ 400.18626002909855 Locus:1.1.1.1763.2 228.43181179205064
Locus:1.1.1.2555.2 2+ 400.2300200290985 Locus:1.1.1.2555.2 279.58800173440756
Locus:1.1.1.2178.2 4+ 401.2031400145492 Locus:1.1.1.2178.2 182.74544943364052

[Genet-Abay]

One more thing, which version are you using? you can try the newest version by cloning from the github itself, not from the link.