Package | Description |
---|---|
com.compomics.util.experiment.biology |
Experiment classes related to biological entities.
|
com.compomics.util.experiment.identification.filtering |
Classes for the filtering of identification objects.
|
com.compomics.util.experiment.identification.matches |
Experiment classes related to matches.
|
com.compomics.util.experiment.identification.protein_sequences |
Protein sequence handling related classes.
|
Modifier and Type | Method and Description |
---|---|
ArrayList<String> |
Peptide.getParentProteins(boolean remap,
SequenceMatchingPreferences sequenceMatchingPreferences,
ProteinTree proteinTree)
Returns the parent proteins and eventually remaps the peptide to the
protein.
|
ArrayList<String> |
Peptide.getParentProteins(SequenceMatchingPreferences sequenceMatchingPreferences,
ProteinTree proteinTree)
Returns the parent proteins and remaps the peptide to the protein if no
protein mapping was set.
|
Modifier and Type | Method and Description |
---|---|
boolean |
PeptideAssumptionFilter.validateProteins(Peptide peptide,
SequenceMatchingPreferences sequenceMatchingPreferences,
ProteinTree proteinTree)
Validates a peptide depending on its protein inference status.
|
Modifier and Type | Method and Description |
---|---|
SpectrumMatch |
SpectrumMatch.getPeptidesFromTags(ProteinTree proteinTree,
TagMatcher tagMatcher,
SequenceMatchingPreferences sequenceMatchingPreferences,
Double massTolerance,
boolean scoreInAscendingOrder,
boolean ascendingScore)
Creates a peptide based spectrum match where peptide assumptions are
deduced from tag assumptions.
|
Modifier and Type | Method and Description |
---|---|
ProteinTree |
SequenceFactory.getDefaultProteinTree()
Returns the default protein tree.
|
ProteinTree |
SequenceFactory.getDefaultProteinTree(int nThreads,
WaitingHandler waitingHandler,
ExceptionHandler exceptionHandler)
Returns the default protein tree corresponding to the database loaded in
factory, creates a new one if none found.
|
ProteinTree |
SequenceFactory.getDefaultProteinTree(int nThreads,
WaitingHandler waitingHandler,
ExceptionHandler exceptionHandler,
boolean displayProgress)
Returns the default protein tree corresponding to the database loaded in
factory, creates a new one if none found.
|
ProteinTree |
SequenceFactory.getDefaultProteinTree(WaitingHandler waitingHandler,
ExceptionHandler exceptionHandler)
Returns the default protein tree corresponding to the database loaded in
factory, creates a new one if none found.
|
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