public class MzIdentMLIdfileReader extends ExperimentObject implements IdfileReader
Constructor and Description |
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MzIdentMLIdfileReader()
Default constructor for the purpose of instantiation.
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MzIdentMLIdfileReader(File mzIdentMLFile)
Constructor for an mzIdentML result file reader.
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MzIdentMLIdfileReader(File mzIdentMLFile,
WaitingHandler waitingHandler)
Constructor for an mzIdentML 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)
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()
Returns the extension of the file for which this IdfileReader can be
used.
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String |
getSoftware()
Returns the name of the software used to generate the identification
file, e.g.
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String |
getSoftwareVersion()
Returns the version of the software used to generate the identification
file, e.g., 2.3.0 or Sledgehammer (2013.09.01.1).
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addUrParam, getParameterKey, getUrParam
public MzIdentMLIdfileReader()
public MzIdentMLIdfileReader(File mzIdentMLFile) throws FileNotFoundException, IOException
mzIdentMLFile
- FileNotFoundException
IOException
public MzIdentMLIdfileReader(File mzIdentMLFile, WaitingHandler waitingHandler) throws FileNotFoundException, IOException
mzIdentMLFile
- 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
public String getSoftware()
IdfileReader
getSoftware
in interface IdfileReader
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