Package | Description |
---|---|
com.compomics.util.experiment.identification |
Experiment classes related to identifications.
|
com.compomics.util.experiment.identification.matches |
Experiment classes related to matches.
|
com.compomics.util.experiment.identification.ptm.ptmscores |
PTM scores.
|
com.compomics.util.preferences |
Utilities preferences classes.
|
Modifier and Type | Class and Description |
---|---|
class |
PeptideAssumption
This object will models the assumption made by an advocate.
|
class |
TagAssumption
This class represent a tag assumption made by an identification algorithm
based on a sequence tag.
|
Modifier and Type | Method and Description |
---|---|
HashMap<Integer,HashMap<Double,ArrayList<SpectrumIdentificationAssumption>>> |
Identification.getAssumptions(String spectrumKey)
Returns a the assumptions of a spectrum.
|
HashMap<Integer,HashMap<Double,ArrayList<SpectrumIdentificationAssumption>>> |
IdentificationDB.getAssumptions(String key,
boolean useDB)
Returns the assumptions of the given spectrum in a map: advocate id →
score → list of assumptions.
|
HashMap<Integer,HashMap<Double,ArrayList<SpectrumIdentificationAssumption>>> |
Identification.getAssumptions(String spectrumKey,
boolean useDB)
Returns the assumptions of a spectrum.
|
HashMap<Integer,HashMap<Double,ArrayList<SpectrumIdentificationAssumption>>> |
Identification.getAssumptions(String spectrumKey,
boolean useDB,
boolean backwardCompatibility)
Returns the assumptions of a spectrum.
|
Modifier and Type | Method and Description |
---|---|
static NeutralLossesMap |
SpectrumAnnotator.getDefaultLosses(SpectrumIdentificationAssumption spectrumIdentificationAssumption,
SequenceMatchingPreferences sequenceMatchingPreferences)
Returns the possible neutral losses expected by default for a given
peptide.
|
Modifier and Type | Method and Description |
---|---|
void |
IdentificationDB.addAssumptions(String spectrumKey,
HashMap<Integer,HashMap<Double,ArrayList<SpectrumIdentificationAssumption>>> assumptions)
Adds assumptions for a given match to the database.
|
void |
Identification.addAssumptions(String spectrumKey,
HashMap<Integer,HashMap<Double,ArrayList<SpectrumIdentificationAssumption>>> newAssumptions,
boolean newSpectrum)
Adds the assumptions corresponding to a spectrum.
|
void |
Identification.addAssumptions(String spectrumKey,
HashMap<Integer,HashMap<Double,ArrayList<SpectrumIdentificationAssumption>>> newAssumptions,
boolean overwriteExisting,
boolean newSpectrum)
Adds the assumptions corresponding to a spectrum to the database.
|
void |
IdentificationDB.updateAssumptions(String spectrumKey,
HashMap<Integer,HashMap<Double,ArrayList<SpectrumIdentificationAssumption>>> assumptionsMap)
Updates the map of assumptions for a given spectrum.
|
void |
Identification.updateAssumptions(String spectrumKey,
HashMap<Integer,HashMap<Double,ArrayList<SpectrumIdentificationAssumption>>> assumptions)
Updates the assumptions of a spectrum.
|
Modifier and Type | Method and Description |
---|---|
ArrayList<SpectrumIdentificationAssumption> |
SpectrumMatch.getAllAssumptions()
Return all assumptions for all identification algorithms as a list.
|
HashMap<Double,ArrayList<SpectrumIdentificationAssumption>> |
SpectrumMatch.getAllAssumptions(int advocateId)
Return all assumptions for the specified search engine indexed by their
e-value.
|
HashMap<Integer,HashMap<Double,ArrayList<SpectrumIdentificationAssumption>>> |
SpectrumMatch.getAssumptionsMap()
Returns the assumptions map: advocate id → score → list of assumptions.
|
Modifier and Type | Method and Description |
---|---|
void |
SpectrumMatch.addHit(int otherAdvocateId,
SpectrumIdentificationAssumption otherAssumption,
boolean ascendingScore)
Add a first hit.
|
void |
SpectrumMatch.removeAssumption(SpectrumIdentificationAssumption assumption)
Removes an assumption from the mapping.
|
Constructor and Description |
---|
SpectrumMatch(String spectrumKey,
SpectrumIdentificationAssumption assumption)
Constructor for the spectrum match.
|
Modifier and Type | Method and Description |
---|---|
static Double |
MDScore.getMDScore(ArrayList<SpectrumIdentificationAssumption> mascotAssumptions,
Peptide peptideCandidate,
ArrayList<String> ptms,
SequenceMatchingPreferences sequenceMatchingPreferences,
Integer rounding)
Returns the MD score for the given peptide in a spectrum match.
|
Modifier and Type | Method and Description |
---|---|
void |
AnnotationPreferences.setCurrentSettings(SpectrumIdentificationAssumption spectrumIdentificationAssumption,
boolean newSpectrum,
SequenceMatchingPreferences sequenceMatchingPreferences)
Sets the annotation settings for the current peptide and precursor
charge.
|
Copyright © 2015. All rights reserved.