Issue with importing MGF files in Sirius #127
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mfleisch
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Resolve "Remove window size from wavelet filter" Closes #127 See merge request bright-giant/sirius/sirius-libs!95
mfleisch
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…mono-repo' into 'master' Resolve "Merge sirius-libs into sirius-frontend to create a mono repo." Closes #300, #132, #126, #123, #128, #125, #127, #124, #122, #121, #120, #109, #115, #106, #99, #112, #111, #61, #110, #103, #108, #107, #104, #221, #102, #98, #198, #92, #94, #93, #85, #84, #87, #76, #56, #73, #32, #70, #65, #43, #63, #33, #53, #58, #59, #57, #54, #52, #41, #47, #50, #49, #48, #39, #46, #37, #38, #27, #34, #22, #31, #28, #18, #23, #21, #19, #9, #240, #280, #254, #242, #246, #238, #156, #25, #155, #189, #172, #154, #11, #6, #16, and #4 See merge request bright-giant/sirius/sirius-frontend!106
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Dear Sirius team,
I am using Sirius version 5.5.7, and I have encountered an issue while trying to import two MGF files, f1.mgf and f11.mgf, which have identical content. Surprisingly, the import process works fine for f1.mgf, but I receive an error when attempting to import f11.mgf. The error message I receive is as follows:
For input string: "MS2" at java.base/java.lang.NumberFormatException.forInputString(Unknown Source) at java.base/java.lang.Integer.parseInt(Unknown Source) at java.base/java.lang.Integer.parseInt(Unknown Source) at de.unijena.bioinf.babelms.mgf.MgfParser$MgfParserInstance.handleKeyword(MgfParser.java:202) at de.unijena.bioinf.babelms.mgf.MgfParser$MgfParserInstance.readNext(MgfParser.java:245) at de.unijena.bioinf.babelms.mgf.MgfParser$MgfParserInstance.addNextEntry(MgfParser.java:114) at de.unijena.bioinf.babelms.mgf.MgfParser$MgfParserInstance.hasNext(MgfParser.java:98) at de.unijena.bioinf.babelms.mgf.MgfParser.parse(MgfParser.java:329) at de.unijena.bioinf.babelms.mgf.MgfParser.parse(MgfParser.java:42) at de.unijena.bioinf.babelms.GenericParser.parse(GenericParser.java:177) at de.unijena.bioinf.babelms.GenericParser$1.<init>(GenericParser.java:84) at de.unijena.bioinf.babelms.GenericParser.parseIterator(GenericParser.java:76) at de.unijena.bioinf.babelms.GenericParser.parseIterator(GenericParser.java:72) at de.unijena.bioinf.projectspace.MS2ExpInputIterator.fetchNext(MS2ExpInputIterator.java:101) at de.unijena.bioinf.projectspace.MS2ExpInputIterator.<init>(MS2ExpInputIterator.java:71) at de.unijena.bioinf.projectspace.InstanceImporter$ImportInstancesJJob.importMsParserInput(InstanceImporter.java:149) at de.unijena.bioinf.projectspace.InstanceImporter$ImportInstancesJJob.importMultipleSources(InstanceImporter.java:118) at de.unijena.bioinf.projectspace.InstanceImporter$ImportInstancesJJob.compute(InstanceImporter.java:107) at de.unijena.bioinf.projectspace.InstanceImporter$ImportInstancesJJob.compute(InstanceImporter.java:94) at de.unijena.bioinf.jjobs.BasicJJob.call(BasicJJob.java:117) at java.base/java.util.concurrent.FutureTask.run(Unknown Source) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source) at java.base/java.lang.Thread.run(Unknown Source)I am wondering what could be the reason behind this issue and how can I resolve it? It seems that there is a problem parsing the MGF file, specifically with the "MS2" string. Both files have similar content, so I expected them to behave the same way during the import process. Any insights or suggestions on how to overcome this issue would be greatly appreciated.
Thank you in advance for your help!
f1.zip
f11.zip
yh sheng
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