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chhh / batmass

Mass spectrometry data visualization
https://batmass.org
Apache License 2.0
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pep.xml files #12

Closed glicky1 closed 5 years ago

glicky1 commented 6 years ago

Hi,

When I try to import and open pep.xml files I get this error massage.

umich.ms.batmass.data.core.api.DataLoadingException: Pep xml file had no retention time information. at umich.ms.batmass.filesupport.files.types.pepxml.providers.PepxmlFeaturesDataSource.load(PepxmlFeaturesDataSource.java:56) at umich.ms.batmass.filesupport.files.types.pepxml.providers.PepxmlFeaturesDataSource.load(PepxmlFeaturesDataSource.java:35) at umich.ms.batmass.data.core.api.DataContainer.load(DataContainer.java:101) at umich.ms.batmass.gui.viewers.featuretable.FeatureTableTopComponent$3.run(FeatureTableTopComponent.java:108) at org.netbeans.modules.progress.ui.RunOffEDTImpl$3.run(RunOffEDTImpl.java:275) at org.openide.util.RequestProcessor$Task.run(RequestProcessor.java:1443) at org.netbeans.modules.openide.util.GlobalLookup.execute(GlobalLookup.java:68) at org.openide.util.lookup.Lookups.executeWith(Lookups.java:303) [catch] at org.openide.util.RequestProcessor$Processor.run(RequestProcessor.java:2058)

How can I open to these files?

Thank you

chhh commented 6 years ago

Looks like your pepxml file didn't have retention time (retention_time_sec attribute, that's what it's called there iirc). RT is used to map IDs to the LCMS run as scan numbers are somewhat inconsistent. Where do those pepxml files come from?

chhh commented 5 years ago

No reply