Package | Description |
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com.compomics.util.experiment.identification.modification.mapping |
Mapping between search engine and Utilities modifications.
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com.compomics.util.experiment.io.identification |
Experiment identification classes.
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com.compomics.util.experiment.io.identification.idfilereaders |
Experiment classes related to reading search engine files.
|
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 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 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 |
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IdfileReader |
IdfileReaderFactory.getFileReader(File aFile)
This method returns the proper identification file reader depending on
the format of the provided file.
|
Modifier and Type | Class and Description |
---|---|
class |
AndromedaIdfileReader
This IdfileReader reads identifications from an Andromeda result file.
|
class |
CossIdfileReader
This IdfileReader reads identifications from a COSS tsv result file.
|
class |
DirecTagIdfileReader
An identification file reader for Direct tag results.
|
class |
MascotIdfileReader
This IdfileReader reads identifications from a Mascot results file.
|
class |
MsAmandaIdfileReader
This IdfileReader reads identifications from an MS Amanda csv result file.
|
class |
MzIdentMLIdfileReader
This IdfileReader reads identifications from an mzIdentML result file.
|
class |
NovorIdfileReader
This IdfileReader reads identifications from a Novor csv result file.
|
class |
OnyaseIdfileReader
Id file reader for the scripts in Onyase.
|
class |
PepNovoIdfileReader
This class can be used to parse PepNovo identification files.
|
class |
PepxmlIdfileReader
Simple IdfileReader for Pepxml files.
|
class |
PNovoIdfileReader
This class can be used to parse pNovo identification files.
|
class |
TideIdfileReader
This IdfileReader reads identifications from an Tide tsv results file.
|
class |
XTandemIdfileReader
This IdfileReader reads identifications from an X! Tandem xml result file.
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