Package | Description |
---|---|
com.compomics.util.experiment.identification.filtering |
Classes for the filtering of identification objects.
|
com.compomics.util.experiment.identification.matches |
Experiment classes related to matches.
|
com.compomics.util.experiment.identification.modification |
Modification mapping and localization.
|
com.compomics.util.experiment.io.identification.writers |
Writer for identification results.
|
Modifier and Type | Method and Description |
---|---|
boolean |
AssumptionFilter.isValidated(long spectrumMatchKey,
String spectrumFile,
String spectrumTitle,
PeptideAssumption peptideAssumption,
Identification identification,
SequenceProvider sequenceProvider,
SpectrumProvider spectrumProvider,
IdentificationFeaturesGenerator identificationFeaturesGenerator,
IdentificationParameters identificationParameters)
Tests whether a match is validated by this filter.
|
boolean |
AssumptionFilter.isValidated(String itemName,
FilterItemComparator filterItemComparator,
Object value,
long spectrumMatchKey,
String spectrumFile,
String spectrumTitle,
PeptideAssumption peptideAssumption,
Identification identification,
SequenceProvider sequenceProvider,
SpectrumProvider spectrumProvider,
IdentificationFeaturesGenerator identificationFeaturesGenerator,
IdentificationParameters identificationParameters)
Indicates whether the match designated by the match key validates the
given item using the given comparator and value threshold.
|
boolean |
PeptideAssumptionFilter.validatePrecursor(PeptideAssumption assumption,
String spectrumFile,
String spectrumTitle,
SpectrumProvider spectrumProvider,
SearchParameters searchParameters)
Validates the mass deviation of a peptide assumption.
|
Modifier and Type | Method and Description |
---|---|
PeptideAssumption |
SpectrumMatch.getBestPeptideAssumption()
Getter for the best peptide assumption.
|
Modifier and Type | Method and Description |
---|---|
java.util.stream.Stream<PeptideAssumption> |
SpectrumMatch.getAllPeptideAssumptions()
Returns a stream of all peptide assumptions
|
TreeMap<Double,ArrayList<PeptideAssumption>> |
SpectrumMatch.getAllPeptideAssumptions(int advocateId)
Returns all peptide assumptions for the specified search engine indexed
by their score.
|
HashMap<Integer,TreeMap<Double,ArrayList<PeptideAssumption>>> |
SpectrumMatch.getPeptideAssumptionsMap()
Returns the peptide assumptions map: advocate id > score > list of
assumptions.
|
Modifier and Type | Method and Description |
---|---|
void |
SpectrumMatch.addPeptideAssumption(int advocateId,
PeptideAssumption peptideAssumption)
Add a hit.
|
void |
SpectrumMatch.removePeptideAssumption(PeptideAssumption peptideAssumption)
Removes an assumption from the mapping.
|
void |
SpectrumMatch.setBestPeptideAssumption(PeptideAssumption bestPeptideAssumption)
Setter for the best peptide assumption.
|
Modifier and Type | Method and Description |
---|---|
void |
SpectrumMatch.setPeptideAssumptionMap(HashMap<Integer,TreeMap<Double,ArrayList<PeptideAssumption>>> peptideAssumptionsMap)
Sets the peptide assumption map.
|
Modifier and Type | Method and Description |
---|---|
static ModificationtableContent |
ModificationtableContent.getModificationTableContent(PeptideAssumption peptideAssumption,
Modification modification,
int nMod,
String spectrumFile,
String spectrumTitle,
Spectrum spectrum,
AnnotationParameters annotationParameters,
ModificationParameters modificationParameters,
SequenceProvider sequenceProvider,
SequenceMatchingParameters modificationSequenceMatchingParameters)
Get the table content.
|
Modifier and Type | Method and Description |
---|---|
void |
SimpleMzIdentMLExporter.addSpectrum(String spectrumFile,
String spectrumTitle,
ArrayList<PeptideAssumption> peptideAssumptions,
ArrayList<TreeMap<Double,HashMap<Integer,Double>>> modificationLocalizationScores,
PeptideSpectrumAnnotator peptideSpectrumAnnotator)
Adds a peptide-spectrum match to the file.
|
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