public class AndromedaIdfileReader extends ExperimentObject implements IdfileReader
Constructor and Description |
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AndromedaIdfileReader()
Default constructor for the purpose of instantiation.
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AndromedaIdfileReader(File resFile)
Constructor for an Andromeda result file reader.
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AndromedaIdfileReader(File resFile,
WaitingHandler waitingHandler)
Constructor for an Andromeda result file reader.
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Modifier and Type | Method and Description |
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void |
close()
Closes the file reader.
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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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String |
getExtension()
This method should return the extension of the file for which this
IdfileReader can be used.
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String |
getSoftwareVersion()
Returns the name and version of the software used to generate the
identification file, e.g., Mascot 2.3.0 or X! Tandem Sledgehammer
(2013.09.01.1).
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addUrParam, getParameterKey, getUrParam
public AndromedaIdfileReader()
public AndromedaIdfileReader(File resFile) throws FileNotFoundException, IOException
resFile
- FileNotFoundException
IOException
public AndromedaIdfileReader(File resFile, WaitingHandler waitingHandler) throws FileNotFoundException, IOException
resFile
- waitingHandler
- FileNotFoundException
IOException
public String getExtension()
IdfileReader
getExtension
in interface IdfileReader
public HashSet<SpectrumMatch> getAllSpectrumMatches(WaitingHandler waitingHandler) throws IOException, IllegalArgumentException, Exception
IdfileReader
getAllSpectrumMatches
in interface IdfileReader
waitingHandler
- a waiting handler displaying the progress (can be
null). The secondary progress methods will be called.IOException
- exception thrown whenever an error occurred while
reading the fileIllegalArgumentException
- exception thrown whenever an error
occurred while parsing the fileException
- exception thrown whenever an error occurred while
working with the filepublic void close() throws IOException
IdfileReader
close
in interface IdfileReader
IOException
public String getSoftwareVersion()
IdfileReader
getSoftwareVersion
in interface IdfileReader
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