public class MsAmandaIdfileReader extends ExperimentObject implements IdfileReader
Constructor and Description |
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MsAmandaIdfileReader()
Default constructor for the purpose of instantiation.
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MsAmandaIdfileReader(File msAmandaCsvFile)
Constructor for an MS Amanda csv result file reader.
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MsAmandaIdfileReader(File msAmandaCsvFile,
WaitingHandler waitingHandler)
Constructor for an MS Amanda csv 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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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).
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addUrParam, getParameterKey, getUrParam
public MsAmandaIdfileReader()
public MsAmandaIdfileReader(File msAmandaCsvFile) throws FileNotFoundException, IOException
msAmandaCsvFile
- FileNotFoundException
IOException
public MsAmandaIdfileReader(File msAmandaCsvFile, WaitingHandler waitingHandler) throws FileNotFoundException, IOException
msAmandaCsvFile
- 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 HashMap<String,ArrayList<String>> getSoftwareVersions()
IdfileReader
getSoftwareVersions
in interface IdfileReader
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