com.compomics.util.experiment.io.identifications.idfilereaders
Class OMSSAIdfileReader

java.lang.Object
  extended by com.compomics.util.experiment.personalization.ExperimentObject
      extended by com.compomics.util.experiment.io.identifications.idfilereaders.OMSSAIdfileReader
All Implemented Interfaces:
IdfileReader, Serializable, Cloneable

public class OMSSAIdfileReader
extends ExperimentObject
implements IdfileReader

This reader will import identifications from an OMSSA omx file. Created by IntelliJ IDEA. User: Marc Date: Jun 23, 2010 Time: 9:45:45 AM

See Also:
Serialized Form

Field Summary
 
Fields inherited from interface com.compomics.util.experiment.io.identifications.IdfileReader
DECOY_FLAG
 
Constructor Summary
OMSSAIdfileReader()
          constructor for the reader
OMSSAIdfileReader(File idFile)
          Constructor for the reader
OMSSAIdfileReader(File idFile, SpectrumCollection spectrumCollection)
          Constructor for the reader with a spectrum collection where to put spectrum information in.
 
Method Summary
 HashSet<SpectrumMatch> getAllSpectrumMatches()
          returns all spectrum matches found in the inspected file
 String getFileName()
          get the file name
 
Methods inherited from class com.compomics.util.experiment.personalization.ExperimentObject
addUrParam, getUrParam
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

OMSSAIdfileReader

public OMSSAIdfileReader()
constructor for the reader


OMSSAIdfileReader

public OMSSAIdfileReader(File idFile)
Constructor for the reader

Parameters:
idFile - the inspected file

OMSSAIdfileReader

public OMSSAIdfileReader(File idFile,
                         SpectrumCollection spectrumCollection)
Constructor for the reader with a spectrum collection where to put spectrum information in.

Parameters:
idFile - the inspected file
spectrumCollection - the spectrum collection used
Method Detail

getFileName

public String getFileName()
get the file name

Returns:
the file name

getAllSpectrumMatches

public HashSet<SpectrumMatch> getAllSpectrumMatches()
returns all spectrum matches found in the inspected file

Specified by:
getAllSpectrumMatches in interface IdfileReader
Returns:
a set of all spectrum matches


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