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Packages that use SpectrumMatch | |
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com.compomics.util.experiment.identification | This package contains experiment classes related to identifications. |
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. |
Uses of SpectrumMatch in com.compomics.util.experiment.identification |
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Methods in com.compomics.util.experiment.identification that return SpectrumMatch | |
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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. |
Methods in com.compomics.util.experiment.identification with parameters of type SpectrumMatch | |
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void |
IdentificationDB.addSpectrumMatch(SpectrumMatch spectrumMatch)
Adds a spectrum match to the database. |
void |
Identification.addSpectrumMatch(SpectrumMatch newMatch)
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. |
Method parameters in com.compomics.util.experiment.identification with type arguments of type SpectrumMatch | |
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void |
Identification.addSpectrumMatch(Set<SpectrumMatch> spectrumMatches)
Add a set of spectrumMatches to the model. |
Uses of SpectrumMatch in com.compomics.util.experiment.identification.ptm.ptmscores |
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Methods in com.compomics.util.experiment.identification.ptm.ptmscores with parameters of type SpectrumMatch | |
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static Double |
MDScore.getMDScore(SpectrumMatch spectrumMatch,
ArrayList<String> ptms)
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)
Returns the MD score for the given peptide in a spectrum match. |
Uses of SpectrumMatch in com.compomics.util.experiment.io.identifications |
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Methods in com.compomics.util.experiment.io.identifications that return types with arguments of type SpectrumMatch | |
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HashSet<SpectrumMatch> |
IdfileReader.getAllSpectrumMatches(WaitingHandler waitingHandler)
This methods 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. |
Uses of SpectrumMatch in com.compomics.util.experiment.io.identifications.idfilereaders |
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Methods in com.compomics.util.experiment.io.identifications.idfilereaders that return types with arguments of type SpectrumMatch | |
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HashSet<SpectrumMatch> |
AndromedaIdfileReader.getAllSpectrumMatches(WaitingHandler waitingHandler)
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