Package | Description |
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com.compomics.util.experiment.identification |
Experiment classes related to identifications.
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com.compomics.util.experiment.identification.matches |
Experiment classes related to matches.
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com.compomics.util.experiment.identification.ptm.ptmscores |
PTM scores.
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com.compomics.util.experiment.identification.spectrum_annotation |
Classes used for ms2 spectrum annotation.
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com.compomics.util.experiment.identification.spectrum_assumptions |
Implementations of the SpectrumIdentificationAssumption.
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Modifier and Type | Method and Description |
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HashMap<Integer,HashMap<Double,ArrayList<SpectrumIdentificationAssumption>>> |
Identification.getAssumptions(String spectrumKey)
Returns a the assumptions of a spectrum.
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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.
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HashMap<Integer,HashMap<Double,ArrayList<SpectrumIdentificationAssumption>>> |
Identification.getAssumptions(String spectrumKey,
boolean useDB)
Returns the assumptions of a spectrum.
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HashMap<Integer,HashMap<Double,ArrayList<SpectrumIdentificationAssumption>>> |
Identification.getRawAssumptions(String spectrumKey)
Returns a the raw assumptions of a spectrum.
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HashMap<Integer,HashMap<Double,ArrayList<SpectrumIdentificationAssumption>>> |
IdentificationDB.getRawAssumptions(String key,
boolean useDB)
Returns the raw assumptions of the given spectrum in a map: advocate id →
score → list of assumptions.
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HashMap<Integer,HashMap<Double,ArrayList<SpectrumIdentificationAssumption>>> |
Identification.getRawAssumptions(String spectrumKey,
boolean useDB)
Returns the raw assumptions of a spectrum.
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Modifier and Type | Method and Description |
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void |
IdentificationDB.addAssumptions(String spectrumKey,
HashMap<Integer,HashMap<Double,ArrayList<SpectrumIdentificationAssumption>>> assumptions)
Adds assumptions for a given match to the database.
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void |
Identification.addAssumptions(String spectrumKey,
HashMap<Integer,HashMap<Double,ArrayList<SpectrumIdentificationAssumption>>> newAssumptions,
boolean newSpectrum)
Adds the assumptions corresponding to a spectrum.
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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.
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void |
IdentificationDB.addRawAssumptions(String spectrumKey,
HashMap<Integer,HashMap<Double,ArrayList<SpectrumIdentificationAssumption>>> assumptions)
Adds raw assumptions for a given match to the database.
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void |
Identification.addRawAssumptions(String spectrumKey,
HashMap<Integer,HashMap<Double,ArrayList<SpectrumIdentificationAssumption>>> newAssumptions)
Adds the raw assumptions corresponding to a spectrum to the database.
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void |
IdentificationDB.updateAssumptions(String spectrumKey,
HashMap<Integer,HashMap<Double,ArrayList<SpectrumIdentificationAssumption>>> assumptionsMap)
Updates the map of assumptions for a given spectrum.
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void |
Identification.updateAssumptions(String spectrumKey,
HashMap<Integer,HashMap<Double,ArrayList<SpectrumIdentificationAssumption>>> assumptions)
Updates the assumptions of a spectrum.
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void |
IdentificationDB.updateRawAssumptions(String spectrumKey,
HashMap<Integer,HashMap<Double,ArrayList<SpectrumIdentificationAssumption>>> rawAssumptionsMap)
Updates the map of raw assumptions for a given spectrum.
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void |
Identification.updateRawAssumptions(String spectrumKey,
HashMap<Integer,HashMap<Double,ArrayList<SpectrumIdentificationAssumption>>> assumptions)
Updates the raw assumptions of a spectrum.
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Modifier and Type | Method and Description |
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ArrayList<SpectrumIdentificationAssumption> |
SpectrumMatch.getAllAssumptions()
Return all assumptions for all identification algorithms as a list.
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HashMap<Double,ArrayList<SpectrumIdentificationAssumption>> |
SpectrumMatch.getAllAssumptions(int advocateId)
Return all assumptions for the specified search engine indexed by their
e-value.
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HashMap<Integer,HashMap<Double,ArrayList<SpectrumIdentificationAssumption>>> |
SpectrumMatch.getAssumptionsMap()
Returns the assumptions map: advocate id → score → list of assumptions.
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Modifier and Type | Method and Description |
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void |
SpectrumMatch.addHit(int otherAdvocateId,
SpectrumIdentificationAssumption otherAssumption,
boolean ascendingScore)
Add a first hit.
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void |
SpectrumMatch.removeAssumption(SpectrumIdentificationAssumption assumption)
Removes an assumption from the mapping.
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Constructor and Description |
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SpectrumMatch(String spectrumKey,
SpectrumIdentificationAssumption assumption)
Constructor for the spectrum match.
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Modifier and Type | Method and Description |
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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.
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Modifier and Type | Method and Description |
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SpectrumIdentificationAssumption |
SpecificAnnotationSettings.getSpectrumIdentificationAssumption()
Returns the spectrum identification assumption to annotate with.
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Modifier and Type | Method and Description |
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static NeutralLossesMap |
SpectrumAnnotator.getDefaultLosses(SpectrumIdentificationAssumption spectrumIdentificationAssumption,
SequenceMatchingPreferences sequenceMatchingPreferences,
SequenceMatchingPreferences ptmSequenceMatchingPreferences)
Returns the possible neutral losses expected by default for a given
peptide.
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SpecificAnnotationSettings |
AnnotationSettings.getSpecificAnnotationPreferences(String spectrumKey,
SpectrumIdentificationAssumption spectrumIdentificationAssumption,
SequenceMatchingPreferences sequenceMatchingPreferences,
SequenceMatchingPreferences ptmSequenceMatchingPreferences)
Returns the annotation preferences specific to a spectrum and an
identification assumption.
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Constructor and Description |
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SpecificAnnotationSettings(String spectrumKey,
SpectrumIdentificationAssumption spectrumIdentificationAssumption)
Constructor.
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Modifier and Type | Class and Description |
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class |
PeptideAssumption
This object will models the assumption made by an advocate.
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class |
TagAssumption
This class represent a tag assumption made by an identification algorithm
based on a sequence tag.
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