Class XTandemIdfileReader
java.lang.Object
com.compomics.util.experiment.personalization.ExperimentObject
com.compomics.util.experiment.io.identification.idfilereaders.XTandemIdfileReader
- All Implemented Interfaces:
IdfileReader
,Serializable
,AutoCloseable
public class XTandemIdfileReader extends ExperimentObject implements IdfileReader
This IdfileReader reads identifications from an X! Tandem xml result file.
- Author:
- Dominik Kopczynski, Harald Barsnes
- See Also:
- Serialized Form
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Field Summary
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Constructor Summary
Constructors Constructor Description XTandemIdfileReader()
Default constructor for the purpose of instantiation.XTandemIdfileReader(File inputFile)
Constructor for an X!Tandem xml result file reader.XTandemIdfileReader(File inputFile, WaitingHandler waitingHandler)
Constructor for an X!Tandem xml result file reader. -
Method Summary
Modifier and Type Method Description 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.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.Methods inherited from class com.compomics.util.experiment.personalization.ExperimentObject
addUrParam, asLong, clearParametersMap, getId, getUrParam, getUrParams, removeUrParam, setId, setUrParams
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Constructor Details
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XTandemIdfileReader
public XTandemIdfileReader()Default constructor for the purpose of instantiation. -
XTandemIdfileReader
Constructor for an X!Tandem xml result file reader.- Parameters:
inputFile
- the Mascot dat file- Throws:
IOException
- if an IOException occurs
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XTandemIdfileReader
Constructor for an X!Tandem xml result file reader.- Parameters:
inputFile
- the Mascot dat filewaitingHandler
- the waiting handler- Throws:
IOException
- if an IOException occurs
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Method Details
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getExtension
Description copied from interface:IdfileReader
Returns the extension of the file for which this IdfileReader can be used.- Specified by:
getExtension
in interfaceIdfileReader
- Returns:
- String with the extension (taken to make up the end of the filename) of the file that this IdfileReader can read.
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getAllSpectrumMatches
public ArrayList<SpectrumMatch> getAllSpectrumMatches(SpectrumProvider spectrumProvider, WaitingHandler waitingHandler, SearchParameters searchParameters) throws IOException, SQLException, ClassNotFoundException, InterruptedException, JAXBException, XMLStreamExceptionDescription copied from interface:IdfileReader
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. Using this method secondary maps are not filled.- Specified by:
getAllSpectrumMatches
in interfaceIdfileReader
- Parameters:
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.- Returns:
- a list of spectrum matches
- Throws:
IOException
- if an IOException occursSQLException
- if an SQLException occursClassNotFoundException
- if an\ ClassNotFoundException occursInterruptedException
- if an InterruptedException occursJAXBException
- if a JAXBException occursXMLStreamException
- if an XMLStreamException occurs
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getAllSpectrumMatches
public ArrayList<SpectrumMatch> getAllSpectrumMatches(SpectrumProvider spectrumProvider, WaitingHandler waitingHandler, SearchParameters searchParameters, SequenceMatchingParameters sequenceMatchingPreferences, boolean expandAaCombinations) throws IOException, SQLException, ClassNotFoundException, InterruptedException, JAXBException, XMLStreamExceptionDescription copied from interface:IdfileReader
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. Secondary peptide and tag maps are filled according to the file content and the sequence matching preferences. If the sequence matching preferences are null, the maps are not filled.- Specified by:
getAllSpectrumMatches
in interfaceIdfileReader
- Parameters:
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.- Returns:
- the spectrum matches
- Throws:
IOException
- if an IOException occursSQLException
- if an SQLException occursClassNotFoundException
- if an\ ClassNotFoundException occursInterruptedException
- if an InterruptedException occursJAXBException
- if a JAXBException occursXMLStreamException
- if an XMLStreamException occurs
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close
- Specified by:
close
in interfaceAutoCloseable
- Specified by:
close
in interfaceIdfileReader
- Throws:
IOException
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getSoftwareVersions
Description copied from interface:IdfileReader
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). Null if not known.- Specified by:
getSoftwareVersions
in interfaceIdfileReader
- Returns:
- the version of the software used to generate the identification file, null if not known
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hasDeNovoTags
public boolean hasDeNovoTags()Description copied from interface:IdfileReader
Returns a boolean indicating whether the file contains de novo results as tags.- Specified by:
hasDeNovoTags
in interfaceIdfileReader
- Returns:
- a boolean indicating whether the file contains de novo results as tags
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