public class AndromedaIdfileReader extends ExperimentObject implements IdfileReader
Constructor and Description |
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AndromedaIdfileReader() |
AndromedaIdfileReader(java.io.File resFile)
Constructor for an Andromeda result file reader.
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AndromedaIdfileReader(java.io.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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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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addUrParam, getParameterKey, getUrParam
public AndromedaIdfileReader()
public AndromedaIdfileReader(java.io.File resFile) throws java.io.FileNotFoundException, java.io.IOException
resFile
- java.io.FileNotFoundException
java.io.IOException
public AndromedaIdfileReader(java.io.File resFile, WaitingHandler waitingHandler) throws java.io.FileNotFoundException, java.io.IOException
resFile
- waitingHandler
- java.io.FileNotFoundException
java.io.IOException
public java.lang.String getExtension()
IdfileReader
getExtension
in interface IdfileReader
public 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 void close() throws java.io.IOException
IdfileReader
close
in interface IdfileReader
java.io.IOException
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