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compomics / peptide-shaker-2.0-issue-tracker

Issue tracker for the beta release of PeptideShaker 2.0
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Protein inference graph results in null pointer #30

Closed hbarsnes closed 5 years ago

hbarsnes commented 5 years ago

The creation of the peptide-level protein inference graph sometimes results in a null pointer.

Example:

1) in the ProteinInferencePeptideLevelDialog constructor the list retainedProteins contains P08238 and Q58FF8 2) but when trying to run identification.getProteinMatch(proteinMatchKey) for the second protein key (of course then provided as a long value) this return null 3) which results in a null pointer when trying to get the corresponding peptides

So it seems like the non-leading retained proteins are not stored in the same way as the leading proteins?

Stacktrace:

Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException
    at com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator.checkEnzymaticPeptides(IdentificationFeaturesGenerator.java:1295)
    at com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator.hasEnzymaticPeptides(IdentificationFeaturesGenerator.java:1270)
    at eu.isas.peptideshaker.gui.protein_inference.ProteinInferencePeptideLevelDialog.<init>(ProteinInferencePeptideLevelDialog.java:147)
    at eu.isas.peptideshaker.gui.tabpanels.OverviewPanel.peptideTableMouseReleased(OverviewPanel.java:2236)
mvaudel commented 5 years ago

I attempted at fixing the issue with https://github.com/compomics/peptide-shaker/commit/f7bb5f6d40b029da0fec22ae8e9d54b630cb2a91. In the new back-end, the method returns the number of termini: 0- non-enzymatic 1- semi-enzymatic 2- enzymatic

So the table model returns an integer and not a boolean, and the gui needs to be updated accordingly.