| Constructor and Description |
|---|
StirRunnable(ConcurrentLinkedQueue<com.compomics.util.experiment.identification.matches.SpectrumMatch> spectrumMatches,
com.compomics.util.experiment.io.identification.IdfileReader idfileReader,
com.compomics.util.experiment.io.identification.writers.SimpleMzIdentMLExporter writer,
com.compomics.util.parameters.identification.IdentificationParameters identificationParameters,
com.compomics.util.experiment.identification.protein_inference.FastaMapper fastaMapper,
com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider,
com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider,
com.compomics.software.log.CliLogger cliLogger)
Constructor.
|
| Modifier and Type | Method and Description |
|---|---|
int |
getnModificationIssues()
Returns the number of peptides where the modification could not be
parsed.
|
int |
getnPeptides()
Returns the total number of peptides processed.
|
void |
run() |
public StirRunnable(ConcurrentLinkedQueue<com.compomics.util.experiment.identification.matches.SpectrumMatch> spectrumMatches, com.compomics.util.experiment.io.identification.IdfileReader idfileReader, com.compomics.util.experiment.io.identification.writers.SimpleMzIdentMLExporter writer, com.compomics.util.parameters.identification.IdentificationParameters identificationParameters, com.compomics.util.experiment.identification.protein_inference.FastaMapper fastaMapper, com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, com.compomics.software.log.CliLogger cliLogger)
spectrumMatches - The spectrum matches to process.idfileReader - The id file reader.writer - The mzIdentML writer.identificationParameters - The identification parameters.fastaMapper - The sequence mapper.sequenceProvider - The sequence provider.spectrumProvider - The spectrum provider.cliLogger - The logger for CLI feedback.public int getnModificationIssues()
public int getnPeptides()
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