public class DirecTagIdfileReader extends Object 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.
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double |
nTermCorrection
The mass to add to the N-terminal gap so that is corresponds to a peptide
fragment.
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Constructor and Description |
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DirecTagIdfileReader()
Default constructor for the purpose of instantiation.
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DirecTagIdfileReader(File tagFile)
Constructors, parses a file.
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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 |
getCopyRight()
Returns the copyright.
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String |
getExtension()
Returns the extension of the file for which this IdfileReader can be
used.
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File |
getInputFile()
Returns the spectrum file name as found in the parameters section.
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String |
getLicense()
Returns the license information of this file.
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Integer |
getnProcessingNode()
Returns the number of processing nodes 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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Double |
getTaggingTimeSeconds()
Returns the tagging time in seconds as listed in the file.
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String |
getTagParameter(String tagParameterName)
Returns the tagging parameter corresponding to a given parameter name.
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String |
getTagsGenerator()
Returns the tags generator used to create the file.
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String |
getTagsGeneratorVersion()
Returns the version of the tags generator used to create the file.
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Set<String> |
getTagsParametersNames()
Returns the name of the different parameters names found.
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String |
getTimeEnd()
Returns the ending time of the tagging as given in the file.
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String |
getTimeStart()
Returns the starting time of the tagging as given in the file.
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boolean |
hasDeNovoTags()
Returns a boolean indicating whether the file contains de novo results as
tags.
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public final double cTermCorrection
public final double nTermCorrection
public DirecTagIdfileReader()
public DirecTagIdfileReader(File tagFile)
tagFile
- the file to parsepublic Set<String> getTagsParametersNames()
public String getTagParameter(String tagParameterName)
tagParameterName
- the name of the parameter of interestpublic 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, IllegalArgumentException, 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 occursIllegalArgumentException
public String getTagsGenerator()
public String getTagsGeneratorVersion()
public String getCopyRight()
public String getLicense()
public String getTimeStart()
public String getTimeEnd()
public Double getTaggingTimeSeconds()
public Integer getnProcessingNode()
public File getInputFile()
public String getExtension()
IdfileReader
getExtension
in interface IdfileReader
public 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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