Class OnyaseIdfileReader
java.lang.Object
com.compomics.util.experiment.io.identification.idfilereaders.OnyaseIdfileReader
- All Implemented Interfaces:
IdfileReader
,AutoCloseable
public class OnyaseIdfileReader extends Object implements IdfileReader
Id file reader for the scripts in Onyase.
- Author:
- Marc Vaudel
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Field Summary
Fields Modifier and Type Field Description static char
comment
Character to start the comment lines.static String
ENCODING
Encoding for the file, cf the second rule.static String
fastaTag
Tag for the fasta file.static String
paramsTag
Tag for the parameters file path.static char
separator
The columns separator.static String
spectraTag
Tag for the spectrum file.static String
versionTag
Tag for the version. -
Constructor Summary
Constructors Constructor Description OnyaseIdfileReader()
Default constructor instantiation purposes.OnyaseIdfileReader(File resultsFile)
Constructor for an onyase 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.
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Field Details
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separator
public static final char separatorThe columns separator.- See Also:
- Constant Field Values
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comment
public static final char commentCharacter to start the comment lines.- See Also:
- Constant Field Values
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versionTag
Tag for the version.- See Also:
- Constant Field Values
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spectraTag
Tag for the spectrum file.- See Also:
- Constant Field Values
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fastaTag
Tag for the fasta file.- See Also:
- Constant Field Values
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paramsTag
Tag for the parameters file path.- See Also:
- Constant Field Values
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ENCODING
Encoding for the file, cf the second rule.- See Also:
- Constant Field Values
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Constructor Details
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OnyaseIdfileReader
public OnyaseIdfileReader()Default constructor instantiation purposes. -
OnyaseIdfileReader
Constructor for an onyase file reader.- Parameters:
resultsFile
- the Andromeda results file- Throws:
IOException
- if an error occurrs while parsing the file
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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, JAXBExceptionDescription 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 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, JAXBExceptionDescription 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 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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