public class PepNovoIdfileReader extends ExperimentObject implements IdfileReader
Modifier and Type | Field and Description |
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double |
cTermCorrection
The mass to add to the C-terminal gap so that is corresponds to a peptide
fragment.
|
static String |
DEFAULT_HEADER
The standard format.
|
double |
nTermCorrection
The mass to add to the N-terminal gap so that is corresponds to a peptide
fragment.
|
NO_KEY
Constructor and Description |
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PepNovoIdfileReader()
Default constructor for the purpose of instantiation.
|
PepNovoIdfileReader(File identificationFile)
Constructor, initiate the parser.
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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.
|
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.
|
String |
getExtension()
Returns the extension of the file for which this IdfileReader can be
used.
|
static String |
getMgfFileName(String fileName)
Returns the spectrum file name.This method assumes that the PepNovo
output file is the mgf file name + ".out"
|
static String |
getPTM(PepnovoParameters pepnovoParameters,
String pepNovoModification)
Get a PTM.
|
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).
|
boolean |
hasDeNovoTags()
Returns a boolean indicating whether the file contains de novo results as
tags.
|
addUrParam, asLong, clearParametersMap, getId, getUrParam, getUrParams, removeUrParam, setId, setUrParams
public static final String DEFAULT_HEADER
public final double cTermCorrection
public final double nTermCorrection
public PepNovoIdfileReader()
public PepNovoIdfileReader(File identificationFile)
identificationFile
- the identification file to parsepublic ArrayList<SpectrumMatch> getAllSpectrumMatches(SpectrumProvider spectrumProvider, WaitingHandler waitingHandler, SearchParameters searchParameters) throws IOException, SQLException, ClassNotFoundException, InterruptedException, JAXBException
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 occurspublic ArrayList<SpectrumMatch> getAllSpectrumMatches(SpectrumProvider spectrumProvider, WaitingHandler waitingHandler, SearchParameters searchParameters, SequenceMatchingParameters sequenceMatchingPreferences, boolean expandAaCombinations) throws IOException, SQLException, ClassNotFoundException, InterruptedException, JAXBException
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 occurspublic static String getMgfFileName(String fileName)
fileName
- the name of the results filepublic String getExtension()
IdfileReader
getExtension
in interface IdfileReader
public void close() throws IOException
close
in interface IdfileReader
close
in interface AutoCloseable
IOException
public static String getPTM(PepnovoParameters pepnovoParameters, String pepNovoModification)
pepnovoParameters
- the PepNovo parameterspepNovoModification
- the PepNovo modificationpublic HashMap<String,ArrayList<String>> getSoftwareVersions()
IdfileReader
getSoftwareVersions
in interface IdfileReader
public boolean hasDeNovoTags()
IdfileReader
hasDeNovoTags
in interface IdfileReader
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