Modifier and Type | Method and Description |
---|---|
DBSequence |
ProteinDataAccess.getProteinSequence(Comparable proteinId)
Get the sequence of the Identified Protein
|
Modifier and Type | Method and Description |
---|---|
DBSequence |
AbstractDataAccessController.getProteinSequence(Comparable proteinId) |
Modifier and Type | Method and Description |
---|---|
static Peptide |
PrideXmlTransformer.transformPeptide(uk.ac.ebi.pride.jaxb.model.PeptideItem rawPeptide,
DBSequence dbSequence,
Comparable index)
Transform peptide from pride xml to core data model.
|
static Peptide |
MzTabTransformer.transformPeptide(uk.ac.ebi.pride.jmztab.model.PSM rawPeptide,
DBSequence dbSequence,
Comparable index,
uk.ac.ebi.pride.jmztab.model.Metadata metadata)
Transform peptide from pride xml to core data model.
|
static QuantPeptide |
MzTabTransformer.transformQuantPeptide(uk.ac.ebi.pride.jmztab.model.Peptide rawPeptide,
DBSequence dbSequence,
Comparable index,
uk.ac.ebi.pride.jmztab.model.Metadata metadata)
Transform quantitative peptide from pride xml to core data model.
|
Modifier and Type | Method and Description |
---|---|
DBSequence |
Protein.getDbSequence() |
DBSequence |
PeptideEvidence.getDbSequence() |
Modifier and Type | Method and Description |
---|---|
void |
Protein.setDbSequence(DBSequence dbSequence) |
void |
PeptideEvidence.setDbSequence(DBSequence dbSequence) |
Constructor and Description |
---|
PeptideEvidence(ParamGroup params,
String id,
String name,
Integer startPosition,
Integer endPosition,
boolean decoy,
PeptideSequence peptideSequence,
DBSequence dbSequence) |
PeptideEvidence(String id,
String name,
Integer startPosition,
Integer endPosition,
Boolean decoy,
PeptideSequence peptideSequence,
DBSequence dbSequence) |
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
|
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