Return help message when exception is thrown

[rccc]

java -jar /home/eric/dev/gains/app/bin/MetFrag2.4.5-CL.jar app/MetFrag/1/12-154-parameters.txt

Exception in thread "main" java.lang.IndexOutOfBoundsException: Index -1 out of bounds for length 20
	at java.base/jdk.internal.util.Preconditions.outOfBounds(Preconditions.java:64)
	at java.base/jdk.internal.util.Preconditions.outOfBoundsCheckIndex(Preconditions.java:70)
	at java.base/jdk.internal.util.Preconditions.checkIndex(Preconditions.java:248)
	at java.base/java.util.Objects.checkIndex(Objects.java:372)
	at java.base/java.util.ArrayList.get(ArrayList.java:458)
	at de.ipbhalle.metfraglib.parameter.Constants.getIonisationChargeByNominalMassDifference(Constants.java:302)
	at de.ipbhalle.metfraglib.parameter.SettingsChecker.checkIonModeSettings(SettingsChecker.java:154)
	at de.ipbhalle.metfraglib.parameter.SettingsChecker.check(SettingsChecker.java:15)
	at de.ipbhalle.metfrag.commandline.CommandLineTool.main(CommandLineTool.java:89)

This exception is not clear, cannot guess where the error come from ( csv db file, ms2Peak file, parameters file ?).

I think the PrecursorIonMode parameter may be wrong (value is 191 in this case).

I tried this example on the web version and it return results.

[sneumann]

Hi, can you provide an example including attaching parameter files to this issue So we can reproduce? From the stack trace I would double check ion mode, precursor and neutral mass, but just guessing. Yours Steffen I blame Android for the brevity and typos

[rccc]

@sneumann : Many thanks for response.

Here are two parameters files and their results :

PeakListPath = /home/me/dev/mytool/app/MetFrag/1/22-197-ms2.csv
MetFragDatabaseType = LocalCSV
LocalDatabasePath = /home/me/dev/mytool/app/MetFrag/1/22-db.csv
NeutralPrecursorMass = 266.055165377
FragmentPeakMatchAbsoluteMassDeviation = 0
FragmentPeakMatchRelativeMassDeviation = 2
PrecursorIonMode = 43
IsPositiveIonMode = True
MetFragScoreTypes = FragmenterScore
MetFragScoreWeights = 1.0
MetFragCandidateWriter = ExtendedFragmentsXLS
SampleName = 22-metfrag_result
MaximumTreeDepth = 2
MetFragPreProcessingCandidateFilter = UnconnectedCompoundFilter
MetFragPostProcessingCandidateFilter = InChIKeyFilter
NumberThreads = 8
ResultsPath = /home/me/dev/mytool/app/MetFrag/1/result

Exception trace :

java -jar /home/me/dev/mytool/app/bin/MetFrag2.4.5-CL.jar /home/me/dev/mytool/app/MetFrag/1/22-197-parameters.txt

Exception in thread "main" java.lang.IndexOutOfBoundsException: Index -1 out of bounds for length 20
	at java.base/jdk.internal.util.Preconditions.outOfBounds(Preconditions.java:64)
	at java.base/jdk.internal.util.Preconditions.outOfBoundsCheckIndex(Preconditions.java:70)
	at java.base/jdk.internal.util.Preconditions.checkIndex(Preconditions.java:248)
	at java.base/java.util.Objects.checkIndex(Objects.java:372)
	at java.base/java.util.ArrayList.get(ArrayList.java:458)
	at de.ipbhalle.metfraglib.parameter.Constants.getIonisationChargeByNominalMassDifference(Constants.java:302)
	at de.ipbhalle.metfraglib.parameter.SettingsChecker.checkIonModeSettings(SettingsChecker.java:154)
	at de.ipbhalle.metfraglib.parameter.SettingsChecker.check(SettingsChecker.java:15)
	at de.ipbhalle.metfrag.commandline.CommandLineTool.main(CommandLineTool.java:89)

A second parameter file :

PeakListPath = /home/me/dev/mytool/app/MetFrag/1/78-875-ms2.csv
MetFragDatabaseType = LocalCSV
LocalDatabasePath = /home/me/dev/mytool/app/MetFrag/1/78-db.csv
NeutralPrecursorMass = 324.0835227
FragmentPeakMatchAbsoluteMassDeviation = 0
FragmentPeakMatchRelativeMassDeviation = 2
PrecursorIonMode = 123
IsPositiveIonMode = False
MetFragScoreTypes = FragmenterScore
MetFragScoreWeights = 1.0
MetFragCandidateWriter = ExtendedFragmentsXLS
SampleName = 78-metfrag_result
MaximumTreeDepth = 2
MetFragPreProcessingCandidateFilter = UnconnectedCompoundFilter
MetFragPostProcessingCandidateFilter = InChIKeyFilter
NumberThreads = 8
ResultsPath = /home/me/dev/mytool/app/MetFrag/1/result

The exception trace :

java -jar /home/me/dev/mytool/app/bin/MetFrag2.4.5-CL.jar /home/me/dev/mytool/app/MetFrag/1/78-875-parameters.txt

Exception in thread "main" java.lang.IndexOutOfBoundsException: Index -1 out of bounds for length 20
	at java.base/jdk.internal.util.Preconditions.outOfBounds(Preconditions.java:64)
	at java.base/jdk.internal.util.Preconditions.outOfBoundsCheckIndex(Preconditions.java:70)
	at java.base/jdk.internal.util.Preconditions.checkIndex(Preconditions.java:248)
	at java.base/java.util.Objects.checkIndex(Objects.java:372)
	at java.base/java.util.ArrayList.get(ArrayList.java:458)
	at de.ipbhalle.metfraglib.parameter.Constants.getIonisationChargeByNominalMassDifference(Constants.java:302)
	at de.ipbhalle.metfraglib.parameter.SettingsChecker.checkIonModeSettings(SettingsChecker.java:154)
	at de.ipbhalle.metfraglib.parameter.SettingsChecker.check(SettingsChecker.java:15)
	at de.ipbhalle.metfrag.commandline.CommandLineTool.main(CommandLineTool.java:89)

Regards
Eric