Package | Description |
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com.compomics.util.experiment.biology.modifications | |
com.compomics.util.experiment.identification.modification.mapping |
Mapping between search engine and Utilities modifications.
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com.compomics.util.experiment.identification.peptide_inference |
Classes related to peptide inference.
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com.compomics.util.experiment.identification.peptide_shaker |
Experiment classes used in PeptideShaker calculations.
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com.compomics.util.experiment.io.identification.writers |
Writer for identification results.
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Modifier and Type | Class and Description |
---|---|
class |
ModificationFactory
This factory will load Modification from an XML file and provide them on
demand as standard class.
|
Modifier and Type | Method and Description |
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static double |
ModificationMassMapper.getMass(String searchEngineModificationName,
IdfileReader idfileReader,
SearchParameters searchParameters,
ModificationProvider modificationProvider)
Returns the mass indicated by the identification algorithm for the given
modification.
|
static double |
ModificationMassMapper.getMassAndromeda(String searchEngineModificationName,
ModificationProvider modificationProvider,
SearchParameters searchParameters)
Returns the mass indicated by the Andromeda for the given modification.
|
static double |
ModificationMassMapper.getMassByName(String searchEngineModificationName,
ModificationProvider modificationProvider)
Returns the mass indicated by the identification algorithm for the given
modification.
|
static double |
ModificationMassMapper.getMassOmssa(String searchEngineModificationName,
ModificationProvider modificationProvider,
SearchParameters searchParameters)
Returns the mass indicated by the OMSSA for the given modification.
|
static HashMap<Integer,HashSet<String>> |
ModificationNameMapper.getPossibleModificationNames(Peptide peptide,
ModificationMatch modificationMatch,
IdfileReader idfileReader,
SearchParameters searchParameters,
SequenceMatchingParameters sequenceMatchingParameters,
SequenceProvider sequenceProvider,
ModificationProvider modificationProvider)
Returns the possible modification names.
|
static HashMap<Integer,HashSet<String>> |
ModificationNameMapper.getPossibleModificationNamesAndromeda(Peptide peptide,
ModificationMatch modificationMatch,
SearchParameters searchParameters,
SequenceMatchingParameters sequenceMatchingParameters,
SequenceProvider sequenceProvider,
ModificationProvider modificationProvider)
Returns the possible Andromeda modification names.
|
static HashMap<Integer,HashSet<String>> |
ModificationNameMapper.getPossibleModificationNamesByMass(Peptide peptide,
ModificationMatch modificationMatch,
SearchParameters searchParameters,
SequenceMatchingParameters sequenceMatchingParameters,
SequenceProvider sequenceProvider,
ModificationProvider modificationProvider)
Returns the possible modifications names by mass.
|
static HashMap<Integer,HashSet<String>> |
ModificationNameMapper.getPossibleModificationNamesByName(Peptide peptide,
ModificationMatch modificationMatch,
SearchParameters searchParameters,
SequenceMatchingParameters sequenceMatchingParameters,
SequenceProvider sequenceProvider,
ModificationProvider modificationProvider)
Returns the possible modifications by name.
|
static HashMap<Integer,HashSet<String>> |
ModificationNameMapper.getPossibleModificationNamesOmssa(Peptide peptide,
ModificationMatch modificationMatch,
SearchParameters searchParameters,
SequenceMatchingParameters sequenceMatchingParameters,
SequenceProvider sequenceProvider,
ModificationProvider modificationProvider)
Returns the possible OMSSA modification names.
|
static void |
ModificationLocalizationMapper.modificationLocalization(Peptide peptide,
HashMap<Integer,ArrayList<String>> expectedNames,
HashMap<ModificationMatch,ArrayList<String>> modNames,
IdentificationParameters identificationParameters,
IdfileReader idfileReader,
ModificationProvider modificationProvider)
Makes an initial modification mapping based on the search engine results
and the compatibility to the searched modifications.
|
Modifier and Type | Method and Description |
---|---|
void |
PeptideInference.peptideInference(Identification identification,
IdentificationParameters identificationParameters,
SequenceProvider sequenceProvider,
ModificationProvider modificationProvider,
WaitingHandler waitingHandler)
Infers the PTM localization and its confidence for the best match of
every spectrum.
|
Modifier and Type | Method and Description |
---|---|
void |
PSModificationScores.changeRepresentativeSite(String modName,
String originalModName,
int originalRepresentativeSite,
int newRepresentativeSite,
int nMod,
ModificationProvider modificationProvider)
Changes the representative site for a given ambiguously localized
modification in all maps.
|
Constructor and Description |
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SimpleMzIdentMLExporter(String softwareName,
String softwareVersion,
String softwareUrl,
File tempFolder,
File destinationFile,
ArrayList<File> spectrumFiles,
File searchEngineFile,
HashMap<String,ArrayList<String>> searchEngines,
File fastaFile,
IdentificationParameters identificationParameters,
SequenceProvider sequenceProvider,
ProteinDetailsProvider proteinDetailsProvider,
SpectrumProvider spectrumProvider,
ModificationProvider modificationProvider,
FastaSummary fastaSummary,
String contactFirstName,
String contactLastName,
String contactAddress,
String contactEmail,
String contactOrganizationName,
String contactOrganizationAddress,
String contactOrganizationEmail,
boolean peptideInference)
Constructor.
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