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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.matches | This package contains experiment classes releated to matches. e.g., pepties, proteins, modifications and spectra. |
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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Fields in com.compomics.util.experiment.identification with type parameters of type SpectrumMatch | |
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protected HashMap<String,SpectrumMatch> |
Identification.spectrumIdentification
The identification results as a spectrum match map, indexed by spectrum id: FILE_TITLE |
Methods in com.compomics.util.experiment.identification that return types with arguments of type SpectrumMatch | |
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HashMap<String,SpectrumMatch> |
Identification.getSpectrumIdentification()
Returns the identification results in a spectrum identification map (spectrumMatch id -> spectrumMatch) |
Methods in com.compomics.util.experiment.identification with parameters of type SpectrumMatch | |
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void |
Identification.addSpectrumMatch(SpectrumMatch newMatch)
Add a spectrum match to the model. |
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.matches |
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Methods in com.compomics.util.experiment.identification.matches that return SpectrumMatch | |
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SpectrumMatch |
PeptideMatch.getMainMatch()
method returns the main match |
Methods in com.compomics.util.experiment.identification.matches that return types with arguments of type SpectrumMatch | |
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HashMap<String,SpectrumMatch> |
PeptideMatch.getSpectrumMatches()
returns all spectra matched |
Methods in com.compomics.util.experiment.identification.matches with parameters of type SpectrumMatch | |
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void |
PeptideMatch.addSpectrumMatch(SpectrumMatch spectrumMatch)
add a spectrum match |
void |
PeptideMatch.setMainMatch(SpectrumMatch spectrumMatch)
methods sets the main match |
Method parameters in com.compomics.util.experiment.identification.matches with type arguments of type SpectrumMatch | |
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void |
PeptideMatch.addSpectrumMatches(HashMap<String,SpectrumMatch> newMatches)
add spectrum matches |
Constructors in com.compomics.util.experiment.identification.matches with parameters of type SpectrumMatch | |
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PeptideMatch(Peptide peptide,
SpectrumMatch spectrumMatch)
Constructor for the peptide 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()
This methods retrieves all the identifications from an identification file as a list of spectrum matches |
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> |
XTandemIdfileReader.getAllSpectrumMatches()
method which returns all spectrum matches found in the file |
HashSet<SpectrumMatch> |
OMSSAIdfileReader.getAllSpectrumMatches()
returns all spectrum matches found in the inspected file |
HashSet<SpectrumMatch> |
MascotIdfileReader.getAllSpectrumMatches()
a method to get all the spectrum matches |
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