public class PepNovoIdfileReader extends ExperimentObject implements IdfileReader
Modifier and Type | Field and Description |
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static java.lang.String |
tableHeader
The standard format.
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Constructor and Description |
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PepNovoIdfileReader()
Default constructor for the purpose of instantiation.
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PepNovoIdfileReader(java.io.File identificationFile)
Constructor, initiate the parser.
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PepNovoIdfileReader(java.io.File identificationFile,
WaitingHandler waitingHandler)
Constructor, initiate the parser.
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Modifier and Type | Method and Description |
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void |
close()
Closes the file reader.
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java.util.HashSet<SpectrumMatch> |
getAllSpectrumMatches(WaitingHandler waitingHandler)
This methods retrieves all the identifications from an identification
file as a list of spectrum matches It is very important to close the file
reader after creation.
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java.lang.String |
getExtension()
This method should return the extension of the file for which this IdfileReader can be used.
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java.lang.String |
getMgfFileName()
Returns the spectrum file name.
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addUrParam, getParameterKey, getUrParam
public static final java.lang.String tableHeader
public PepNovoIdfileReader()
public PepNovoIdfileReader(java.io.File identificationFile) throws java.io.FileNotFoundException, java.io.IOException
identificationFile
- the identification file to parsejava.io.FileNotFoundException
- exception thrown whenever the provided file
was not foundjava.io.IOException
- exception thrown whenever an error occurred while
reading the filepublic PepNovoIdfileReader(java.io.File identificationFile, WaitingHandler waitingHandler) throws java.io.FileNotFoundException, java.io.IOException
identificationFile
- the identification file to parsewaitingHandler
- a waiting handler providing progress feedback to
the userjava.io.FileNotFoundException
- exception thrown whenever the provided file
was not foundjava.io.IOException
- exception thrown whenever an error occurred while
reading the filepublic java.util.HashSet<SpectrumMatch> getAllSpectrumMatches(WaitingHandler waitingHandler) throws java.io.IOException, java.lang.IllegalArgumentException, java.lang.Exception
IdfileReader
getAllSpectrumMatches
in interface IdfileReader
waitingHandler
- a waiting handler displaying the progress (can be null). The secondary progress methods will be called.java.io.IOException
- exception thrown whenever an error occurred while
reading the filejava.lang.IllegalArgumentException
- exception thrown whenever an error occurred while
parsing the filejava.lang.Exception
- exception thrown whenever an error occurred while
working with the filepublic java.lang.String getMgfFileName()
public java.lang.String getExtension()
IdfileReader
getExtension
in interface IdfileReader
public void close() throws java.io.IOException
IdfileReader
close
in interface IdfileReader
java.io.IOException
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