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

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

public class AndromedaIdfileReader
extends ExperimentObject
implements IdfileReader

This IdfileReader reads identifications out of an Andromeda result file

Author:
Marc
See Also:
Serialized Form

Constructor Summary
AndromedaIdfileReader(java.io.File resFile, javax.swing.JProgressBar jProgressBar)
          Constructor for an Andromeda result file reader.
 
Method Summary
 void close()
          Method closing the file reader
 java.util.HashSet<SpectrumMatch> getAllSpectrumMatches(javax.swing.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.
 
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

AndromedaIdfileReader

public AndromedaIdfileReader(java.io.File resFile,
                             javax.swing.JProgressBar jProgressBar)
                      throws java.io.FileNotFoundException,
                             java.io.IOException
Constructor for an Andromeda result file reader.

Parameters:
resFile -
jProgressBar -
Throws:
java.io.FileNotFoundException
java.io.IOException
Method Detail

getAllSpectrumMatches

public java.util.HashSet<SpectrumMatch> getAllSpectrumMatches(javax.swing.JProgressBar jProgressBar)
                                                       throws java.io.IOException
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:
java.io.IOException - exception thrown whenever an error occurred while reading the file

close

public void close()
           throws java.io.IOException
Description copied from interface: IdfileReader
Method closing the file reader

Specified by:
close in interface IdfileReader
Throws:
java.io.IOException


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