Modifier and Type | Method and Description |
---|---|
static Score |
DataAccessUtilities.getScore(ParamGroup params) |
Modifier and Type | Method and Description |
---|---|
Score |
PeptideDataAccess.getPeptideScore(Comparable proteinId,
Comparable peptideId)
Get peptide score generated by search engine.
|
Score |
ProteinDataAccess.getProteinScores(Comparable proteinId)
Get protein identification score
|
Score |
QuantDataAccess.getQuantPeptideScore(Comparable proteinId,
Comparable peptideId)
Get peptide score generated by search engine.
|
Modifier and Type | Method and Description |
---|---|
Score |
CachedDataAccessController.getPeptideScore(Comparable proteinId,
Comparable peptideId)
Get peptide score from search engine
|
Score |
AbstractDataAccessController.getPeptideScore(Comparable proteinId,
Comparable peptideId) |
Score |
AbstractDataAccessController.getProteinScores(Comparable proteinId) |
Score |
AbstractDataAccessController.getQuantPeptideScore(Comparable proteinId,
Comparable peptideId) |
Modifier and Type | Method and Description |
---|---|
Score |
SpectrumIdentification.getScore() |
Score |
Protein.getScore() |
Score |
Peptide.getScore() |
Modifier and Type | Method and Description |
---|---|
void |
SpectrumIdentification.setScore(Score score) |
void |
Protein.setScore(Score score) |
Constructor and Description |
---|
Protein(Comparable id,
String name,
DBSequence dbSequence,
boolean passThreshold,
List<Peptide> peptides,
Score score,
double threshold,
double sequenceCoverage,
Gel gel)
Constructor for Protein Entity Identification
|
Protein(ParamGroup params,
Comparable id,
String name,
DBSequence dbSequence,
boolean passThreshold,
List<Peptide> peptides,
Score score,
double threshold,
double sequenceCoverage,
Gel gel)
Constructor for Protein Entity Identification with CVParams
|
Protein(ParamGroup params,
Comparable id,
String name,
DBSequence dbSequence,
boolean passThreshold,
List<Peptide> peptides,
Score score,
double threshold,
double sequenceCoverage,
Gel gel,
QuantScore quantScore)
Constructor for Protein Entity Identification with CVParams and Quantitation Score based on mzTab model
|
Protein(ParamGroup params,
Comparable id,
String name,
DBSequence dbSequence,
boolean passThreshold,
List<Peptide> peptides,
Score score,
double threshold,
double sequenceCoverage,
Gel gel,
QuantScore quantScore,
List<QuantPeptide> quantPeptides)
Constructor for Protein Entity Identification with CVParams and Quantitation Score based on mzTab model
|
SpectrumIdentification(Comparable id,
String name,
int chargeState,
double experimentalMassToCharge,
double calculatedMassToCharge,
double calculatedPI,
PeptideSequence peptideSequence,
int rank,
boolean passThreshold,
MassTable massTable,
Sample sample,
List<PeptideEvidence> peptideEvidenceList,
List<FragmentIon> fragmentation,
Score score,
Spectrum spectrum,
SpectraData spectraData)
Spectrum Identification Item
|
SpectrumIdentification(ParamGroup params,
Comparable id,
String name,
int chargeState,
double experimentalMassToCharge,
double calculatedMassToCharge,
double calculatedPI,
PeptideSequence peptideSequence,
int rank,
boolean passThreshold,
MassTable massTable,
Sample sample,
List<PeptideEvidence> peptideEvidenceList,
List<FragmentIon> fragmentation,
Score score,
Spectrum spectrum,
SpectraData spectraData)
Spectrum Identification Item
|
Modifier and Type | Method and Description |
---|---|
static List<uk.ac.ebi.pride.jmztab.utils.convert.SearchEngineScoreParam> |
MzTabUtils.getSearchEngineScoreTerm(Score score)
Get the Search Engines Scores for a Proteins or Peptide
|
Copyright © 2015 European Bioinformatics Institute. All Rights Reserved.