Package | Description |
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com.compomics.util.experiment |
Gene factory classes.
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com.compomics.util.experiment.identification.identifications |
Experiment classes related to MS//MS identifications.
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com.compomics.util.experiment.identification.matches_iterators |
Identification match iterators.
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Modifier and Type | Method and Description |
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Identification |
ProteomicAnalysis.getIdentification(int identificationMethod)
Returns identification results obtained with an identification method.
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Modifier and Type | Method and Description |
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void |
ProteomicAnalysis.addIdentificationResults(int identificationMethod,
Identification identificationResults)
Adds identification results obtained with an identification method.
|
Modifier and Type | Class and Description |
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class |
Ms2Identification
This class models an MS2 Identification.
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Constructor and Description |
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PeptideMatchesIterator(ArrayList<String> peptideKeys,
Identification identification,
ArrayList<UrParameter> peptideParameters,
boolean loadPsms,
ArrayList<UrParameter> psmParameters,
WaitingHandler waitingHandler)
Constructor.
|
PeptideMatchesIterator(ArrayList<String> peptideKeys,
Identification identification,
ArrayList<UrParameter> peptideParameters,
WaitingHandler waitingHandler)
Constructor.
|
PeptideMatchesIterator(Identification identification,
ArrayList<UrParameter> peptideParameters,
boolean loadPsms,
ArrayList<UrParameter> psmParameters,
WaitingHandler waitingHandler)
Constructor.
|
ProteinMatchesIterator(ArrayList<String> proteinKeys,
Identification identification,
ArrayList<UrParameter> proteinParameters,
boolean loadPeptides,
ArrayList<UrParameter> peptideParameters,
boolean loadPsms,
ArrayList<UrParameter> psmParameters,
WaitingHandler waitingHandler)
Constructor.
|
ProteinMatchesIterator(Identification identification,
ArrayList<UrParameter> proteinParameters,
boolean loadPeptides,
ArrayList<UrParameter> peptideParameters,
boolean loadPsms,
ArrayList<UrParameter> psmParameters,
WaitingHandler waitingHandler)
Constructor for an iterator iterating all protein keys.
|
PsmIterator(ArrayList<String> spectrumKeys,
Identification identification,
ArrayList<UrParameter> psmParameters,
boolean loadAssumptions,
WaitingHandler waitingHandler)
Constructor.
|
PsmIterator(ArrayList<String> spectrumKeys,
Identification identification,
boolean loadAssumptions,
WaitingHandler waitingHandler)
Constructor.
|
PsmIterator(Identification identification,
ArrayList<UrParameter> psmParameters,
boolean loadAssumptions,
WaitingHandler waitingHandler)
Constructor.
|
PsmIterator(Identification identification,
boolean loadAssumptions,
WaitingHandler waitingHandler)
Constructor.
|
PsmIterator(String spectrumFile,
ArrayList<String> spectrumKeys,
Identification identification,
ArrayList<UrParameter> psmParameters,
boolean loadAssumptions,
WaitingHandler waitingHandler)
Constructor.
|
PsmIterator(String spectrumFile,
ArrayList<String> spectrumKeys,
Identification identification,
boolean loadAssumptions,
WaitingHandler waitingHandler)
Constructor.
|
PsmIterator(String spectrumFile,
Identification identification,
ArrayList<UrParameter> psmParameters,
boolean loadAssumptions,
WaitingHandler waitingHandler)
Constructor.
|
PsmIterator(String spectrumFile,
Identification identification,
boolean loadAssumptions,
ArrayList<UrParameter> psmParameters,
WaitingHandler waitingHandler)
Constructor.
|
PsmIterator(String spectrumFile,
Identification identification,
boolean loadAssumptions,
WaitingHandler waitingHandler)
Constructor.
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