public class XTandemIdfileReader extends ExperimentObject implements IdfileReader
NO_KEY
Constructor and Description |
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XTandemIdfileReader()
Default constructor for the purpose of instantiation.
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XTandemIdfileReader(File inputFile)
Constructor for an X!Tandem xml result file reader.
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XTandemIdfileReader(File inputFile,
WaitingHandler waitingHandler)
Constructor for an X!Tandem xml result file reader.
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Modifier and Type | Method and Description |
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void |
close() |
ArrayList<SpectrumMatch> |
getAllSpectrumMatches(SpectrumProvider spectrumProvider,
WaitingHandler waitingHandler,
SearchParameters searchParameters)
Retrieves all the spectrum matches from an identification file as a list
of spectrum matches, one spectrum match per spectrum.
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ArrayList<SpectrumMatch> |
getAllSpectrumMatches(SpectrumProvider spectrumProvider,
WaitingHandler waitingHandler,
SearchParameters searchParameters,
SequenceMatchingParameters sequenceMatchingPreferences,
boolean expandAaCombinations)
Retrieves all the spectrum matches from an identification file as a list
of spectrum matches, one spectrum match per spectrum.It is very important
to close the file reader after creation.
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String |
getExtension()
Returns the extension of the file for which this IdfileReader can be
used.
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HashMap<String,ArrayList<String>> |
getSoftwareVersions()
Returns the names and versions of the software used to generate the
identification file in a map, e.g., Mascot > (2.2 and 2.3) and
X!Tandem > Sledgehammer (2013.09.01.1).
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boolean |
hasDeNovoTags()
Returns a boolean indicating whether the file contains de novo results as
tags.
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addUrParam, asLong, clearParametersMap, getId, getUrParam, getUrParams, removeUrParam, setId, setUrParams
public XTandemIdfileReader()
public XTandemIdfileReader(File inputFile) throws IOException
inputFile
- the Mascot dat fileIOException
- if an IOException occurspublic XTandemIdfileReader(File inputFile, WaitingHandler waitingHandler) throws IOException
inputFile
- the Mascot dat filewaitingHandler
- the waiting handlerIOException
- if an IOException occurspublic String getExtension()
IdfileReader
getExtension
in interface IdfileReader
public ArrayList<SpectrumMatch> getAllSpectrumMatches(SpectrumProvider spectrumProvider, WaitingHandler waitingHandler, SearchParameters searchParameters) throws IOException, SQLException, ClassNotFoundException, InterruptedException, JAXBException, XMLStreamException
IdfileReader
getAllSpectrumMatches
in interface IdfileReader
spectrumProvider
- A spectrum provider with the spectra of the file loaded.waitingHandler
- The waiting handler displaying the progress (can be
null). The secondary progress methods will be called.searchParameters
- The search parameters.IOException
- if an IOException occursSQLException
- if an SQLException occursClassNotFoundException
- if an\ ClassNotFoundException occursInterruptedException
- if an InterruptedException occursJAXBException
- if a JAXBException occursXMLStreamException
- if an XMLStreamException occurspublic ArrayList<SpectrumMatch> getAllSpectrumMatches(SpectrumProvider spectrumProvider, WaitingHandler waitingHandler, SearchParameters searchParameters, SequenceMatchingParameters sequenceMatchingPreferences, boolean expandAaCombinations) throws IOException, SQLException, ClassNotFoundException, InterruptedException, JAXBException, XMLStreamException
IdfileReader
getAllSpectrumMatches
in interface IdfileReader
spectrumProvider
- A spectrum provider with the spectra of the file loaded.waitingHandler
- The waiting handler displaying the progress (can be
null). The secondary progress methods will be called.searchParameters
- The search parameters.sequenceMatchingPreferences
- The sequence matching preferences to
use for the creation of the secondary maps.expandAaCombinations
- If true, a peptide assumption (not
implemented for tag assumptions) will be created for all possible amino
acid combination for peptide sequences containing an ambiguity like an X.IOException
- if an IOException occursSQLException
- if an SQLException occursClassNotFoundException
- if an\ ClassNotFoundException occursInterruptedException
- if an InterruptedException occursJAXBException
- if a JAXBException occursXMLStreamException
- if an XMLStreamException occurspublic void close() throws IOException
close
in interface IdfileReader
close
in interface AutoCloseable
IOException
public HashMap<String,ArrayList<String>> getSoftwareVersions()
IdfileReader
getSoftwareVersions
in interface IdfileReader
public boolean hasDeNovoTags()
IdfileReader
hasDeNovoTags
in interface IdfileReader
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