Package | Description |
---|---|
com.compomics.util.experiment.identification |
This package contains experiment classes related to identifications.
|
com.compomics.util.experiment.identification.matches |
This package contains experiment classes releated to matches.
|
com.compomics.util.experiment.identification.ptm.ptmscores | |
com.compomics.util.experiment.io.identifications | |
com.compomics.util.experiment.io.identifications.idfilereaders |
This package contains experiment classes related to reading search engine files.
|
Modifier and Type | Method and Description |
---|---|
SpectrumMatch |
Identification.getSpectrumMatch(String spectrumKey)
Returns a spectrum match.
|
SpectrumMatch |
IdentificationDB.getSpectrumMatch(String key,
boolean useDB)
Returns the desired spectrum match.
|
SpectrumMatch |
Identification.getSpectrumMatch(String spectrumKey,
boolean useDB)
Returns a spectrum match.
|
Modifier and Type | Method and Description |
---|---|
void |
IdentificationDB.addSpectrumMatch(SpectrumMatch spectrumMatch)
Adds a spectrum match to the database.
|
void |
Identification.addSpectrumMatch(SpectrumMatch newMatch,
boolean ascendingScore)
Adds a spectrum match to the identification.
|
void |
IdentificationDB.updateSpectrumMatch(SpectrumMatch spectrumMatch)
Updates a spectrum match.
|
void |
Identification.updateSpectrumMatch(SpectrumMatch spectrumMatch)
Updates a spectrum match in the database.
|
Modifier and Type | Method and Description |
---|---|
void |
Identification.addSpectrumMatches(Iterable<SpectrumMatch> spectrumMatches,
boolean ascendingScore)
Add a set of spectrumMatches to the model.
|
Modifier and Type | Method and Description |
---|---|
SpectrumMatch |
SpectrumMatch.getPeptidesFromTags(ProteinTree proteinTree,
SequenceMatchingPreferences sequenceMatchingPreferences,
Double massTolerance,
boolean scoreInAscendingOrder,
ArrayList<String> fixedModifications,
ArrayList<String> variableModifications,
boolean ascendingScore,
boolean reportFixedPtms)
Creates a peptide based spectrum match where peptide assumptions are
deduced from tag assumptions.
|
Modifier and Type | Method and Description |
---|---|
static Double |
MDScore.getMDScore(SpectrumMatch spectrumMatch,
ArrayList<String> ptms,
SequenceMatchingPreferences sequenceMatchingPreferences)
Returns the MD score for the best peptide in a spectrum match (the best
peptide has to be set before).
|
static Double |
MDScore.getMDScore(SpectrumMatch spectrumMatch,
Peptide peptideCandidate,
ArrayList<String> ptms,
SequenceMatchingPreferences sequenceMatchingPreferences)
Returns the MD score for the given peptide in a spectrum match.
|
Modifier and Type | Method and Description |
---|---|
LinkedList<SpectrumMatch> |
IdfileReader.getAllSpectrumMatches(WaitingHandler waitingHandler)
Retrieves all the identifications from an identification file as a list
of spectrum matches It is very important to close the file reader after
creation.
|
LinkedList<SpectrumMatch> |
IdfileReader.getAllSpectrumMatches(WaitingHandler waitingHandler,
SequenceMatchingPreferences sequenceMatchingPreferences)
Retrieves all the identifications from an identification file as a list
of spectrum matches It is very important to close the file reader after
creation.
|
HashMap<String,LinkedList<SpectrumMatch>> |
IdfileReader.getTagsMap()
Returns a map of all simple tags found in this file indexed by the
beginning of the amino acid sequence.
|
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