compomics/spectrum_similarity

Scoring functions to compare MS/MS spectra

spectrum_similarity's Issues

There may be an error when calculating the number of peaks matched

Because the existence of fragment tolerance, a peak may match two or more peaks. Like the picture show, p3 will match p1 and p2. However, in your code(/src/main/java/cal/cumulativeBinomialProbability/spectra/CompareAndScore.java line from 150 to 215), you did not use a array to store all possible matching peaks but only use a variable to store one possible matching peak. Is it a problem？
Thanks

the program spectrum_similarity_pairwise_GUI-0.1.jar exception

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!