| Constructor and Description |
|---|
PsmFirstHitRunnable(ConcurrentLinkedQueue<com.compomics.util.experiment.identification.matches.SpectrumMatch> spectrumMatchQueue,
com.compomics.util.parameters.identification.IdentificationParameters identificationParameters,
com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider,
com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider,
InputMap inputMap,
HashMap<String,Integer> proteinCount,
com.compomics.util.waiting.WaitingHandler waitingHandler,
com.compomics.util.exceptions.ExceptionHandler exceptionHandler)
Constructor.
|
| Modifier and Type | Method and Description |
|---|---|
HashSet<Integer> |
getCharges()
Returns the different charges found.
|
double |
getMaxPeptideErrorDa()
Returns the maximal peptide mass error found in Da.
|
double |
getMaxPeptideErrorPpm()
Returns the maximal peptide mass error found in ppm.
|
double |
getMaxTagErrorDa()
Returns the maximal tag mass error found in Da.
|
double |
getMaxTagErrorPpm()
Returns the maximal tag mass error found in ppm.
|
int |
getMissingProteins()
Returns the number of PSMs where a protein was missing.
|
int |
getnRetained()
Returns the number of PSMs retained after filtering.
|
int |
getPeptideIssue()
Returns the number of PSMs which did not pass the import filters due to a
peptide issue.
|
int |
getPrecursorIssue()
Returns the number of PSMs which did not pass the import filters due to a
precursor issue.
|
int |
getProteinIssue()
Returns the number of PSMs which did not pass the import filters due to a
protein issue.
|
int |
getPsmsRejected()
Returns the number of PSMs which did not pass the import filters.
|
void |
run() |
public PsmFirstHitRunnable(ConcurrentLinkedQueue<com.compomics.util.experiment.identification.matches.SpectrumMatch> spectrumMatchQueue, com.compomics.util.parameters.identification.IdentificationParameters identificationParameters, com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, InputMap inputMap, HashMap<String,Integer> proteinCount, com.compomics.util.waiting.WaitingHandler waitingHandler, com.compomics.util.exceptions.ExceptionHandler exceptionHandler)
spectrumMatchQueue - The spectrum matches iterator to use.identificationParameters - The identification parameters.sequenceProvider - The protein sequence provider.spectrumProvider - The spectrum provider.inputMap - The input scores map.proteinCount - The map of protein occurrence.waitingHandler - The waiting handler to display feedback to the
user.exceptionHandler - The handler of exceptions.public HashSet<Integer> getCharges()
public double getMaxPeptideErrorPpm()
public double getMaxPeptideErrorDa()
public double getMaxTagErrorPpm()
public double getMaxTagErrorDa()
public int getPsmsRejected()
public int getProteinIssue()
public int getPeptideIssue()
public int getPrecursorIssue()
public int getMissingProteins()
public int getnRetained()
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