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java.lang.Objectcom.compomics.util.experiment.personalization.ExperimentObject
com.compomics.util.experiment.io.identifications.idfilereaders.MascotIdfileReader
public class MascotIdfileReader
This reader will import identifications from a Mascot dat file.
Constructor Summary | |
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MascotIdfileReader(File aFile)
Constructor for the MascotIdfilereader. |
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MascotIdfileReader(File aFile,
boolean index)
Constructor for the MascotIdilereader. |
Method Summary | |
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void |
close()
Closes the file reader. |
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. |
String |
getFileName()
Getter for the file name. |
String |
getMgfFileName()
Get the spectrum file name. |
Methods inherited from class com.compomics.util.experiment.personalization.ExperimentObject |
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addUrParam, getParameterKey, getUrParam |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
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public MascotIdfileReader(File aFile)
aFile
- a file to readpublic MascotIdfileReader(File aFile, boolean index)
aFile
- a file to readindex
- indicating whether the parsing shall be indexed or in memoryMethod Detail |
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public String getMgfFileName()
public String getFileName()
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 file
IllegalArgumentException
- exception thrown whenever an error occurred while
parsing the file
Exception
- exception thrown whenever an error occurred while
working with the filepublic void close() throws IOException
IdfileReader
close
in interface IdfileReader
IOException
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