Class MzIdentMLIdfileReader
java.lang.Object
com.compomics.util.experiment.io.identification.idfilereaders.MzIdentMLIdfileReader
- All Implemented Interfaces:
IdfileReader
,AutoCloseable
public class MzIdentMLIdfileReader extends Object implements IdfileReader
This IdfileReader reads identifications from an mzIdentML result file.
- Author:
- Harald Barsnes, Marc Vaudel
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Nested Class Summary
Nested Classes Modifier and Type Class Description static class
MzIdentMLIdfileReader.RawValueConversionType
Enum for the raw value to e-value conversion. -
Constructor Summary
Constructors Constructor Description MzIdentMLIdfileReader()
Default constructor for the purpose of instantiation.MzIdentMLIdfileReader(File mzIdentMLFile)
Constructor for an mzIdentML result file reader.MzIdentMLIdfileReader(File mzIdentMLFile, WaitingHandler waitingHandler)
Constructor for an mzIdentML 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.static void
main(String[] args)
Main method for testing purposes only.
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Constructor Details
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MzIdentMLIdfileReader
public MzIdentMLIdfileReader()Default constructor for the purpose of instantiation. -
MzIdentMLIdfileReader
Constructor for an mzIdentML result file reader.- Parameters:
mzIdentMLFile
- the mzIdentML file- Throws:
FileNotFoundException
- if a FileNotFoundException occursIOException
- if an IOException occurs
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MzIdentMLIdfileReader
Constructor for an mzIdentML result file reader.- Parameters:
mzIdentMLFile
- the mzIdentML filewaitingHandler
- the waiting handler- Throws:
FileNotFoundException
- if a FileNotFoundException occursIOException
- 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, org.xmlpull.v1.XmlPullParserExceptionDescription 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 occursorg.xmlpull.v1.XmlPullParserException
- if an XmlPullParserException 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, org.xmlpull.v1.XmlPullParserExceptionDescription 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 occursorg.xmlpull.v1.XmlPullParserException
- if an XmlPullParserException 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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main
Main method for testing purposes only.- Parameters:
args
- the command line arguments
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