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 from an Andromeda result file.

Author:
Marc Vaudel
See Also:
Serialized Form

Constructor Summary
AndromedaIdfileReader()
           
AndromedaIdfileReader(java.io.File resFile)
          Constructor for an Andromeda result file reader.
AndromedaIdfileReader(java.io.File resFile, WaitingHandler waitingHandler)
          Constructor for an Andromeda result file reader.
 
Method Summary
 void close()
          Closes the file reader.
 java.util.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.
 java.lang.String getExtension()
          This method should return the extension of the file for which this IdfileReader can be used.
 
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()

AndromedaIdfileReader

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

Parameters:
resFile -
Throws:
java.io.FileNotFoundException
java.io.IOException

AndromedaIdfileReader

public AndromedaIdfileReader(java.io.File resFile,
                             WaitingHandler waitingHandler)
                      throws java.io.FileNotFoundException,
                             java.io.IOException
Constructor for an Andromeda result file reader.

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

getExtension

public java.lang.String getExtension()
Description copied from interface: IdfileReader
This method should return the extension of the file for which this IdfileReader can be used.

Specified by:
getExtension in interface IdfileReader
Returns:
String with the extension (taken to make up the end of the filename) of the file that this IdfileReader can read.

getAllSpectrumMatches

public java.util.HashSet<SpectrumMatch> getAllSpectrumMatches(WaitingHandler waitingHandler)
                                                       throws java.io.IOException,
                                                              java.lang.IllegalArgumentException,
                                                              java.lang.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:
waitingHandler - a waiting handler displaying the progress (can be null). The secondary progress methods will be called.
Returns:
a list of spectrum matches
Throws:
java.io.IOException - exception thrown whenever an error occurred while reading the file
java.lang.IllegalArgumentException - exception thrown whenever an error occurred while parsing the file
java.lang.Exception - exception thrown whenever an error occurred while working with the file

close

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

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


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