public class OnyaseIdfileReader extends Object implements IdfileReader
Modifier and Type | Field and Description |
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static char |
comment
Character to start the comment lines.
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static String |
ENCODING
Encoding for the file, cf the second rule.
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static String |
fastaTag
Tag for the fasta file.
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static String |
paramsTag
Tag for the parameters file path.
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static char |
separator
The columns separator.
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static String |
spectraTag
Tag for the spectrum file.
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static String |
versionTag
Tag for the version.
|
Constructor and Description |
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OnyaseIdfileReader()
Default constructor instantiation purposes.
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OnyaseIdfileReader(File resultsFile)
Constructor for an onyase file reader.
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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.
|
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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public static final char separator
public static final char comment
public static final String versionTag
public static final String spectraTag
public static final String fastaTag
public static final String paramsTag
public static final String ENCODING
public OnyaseIdfileReader()
public OnyaseIdfileReader(File resultsFile) throws IOException
resultsFile
- the Andromeda results fileIOException
- if an error occurrs while parsing the filepublic String getExtension()
IdfileReader
getExtension
in interface IdfileReader
public 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 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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