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

Constructor Summary
OMSSAIdfileReader()
          Constructor for the reader.
OMSSAIdfileReader(File idFile)
          Constructor for the reader.
 
Method Summary
 void close()
          Closes the file reader.
 HashSet<SpectrumMatch> getAllSpectrumMatches(JProgressBar jProgressBar)
          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()
          Get the file name.
 
Methods inherited from class com.compomics.util.experiment.personalization.ExperimentObject
addUrParam, getParameterKey, 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
Method Detail

getFileName

public String getFileName()
Get the file name.

Returns:
the file name

getAllSpectrumMatches

public HashSet<SpectrumMatch> getAllSpectrumMatches(JProgressBar jProgressBar)
                                             throws IOException,
                                                    IllegalArgumentException,
                                                    Exception
Description copied from interface: IdfileReader
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.

Specified by:
getAllSpectrumMatches in interface IdfileReader
Parameters:
jProgressBar - a progress bar displaying the progress (can be null)
Returns:
a list of spectrum matches
Throws:
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 file

close

public void close()
           throws IOException
Description copied from interface: IdfileReader
Closes the file reader.

Specified by:
close in interface IdfileReader
Throws:
IOException


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