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

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

public class XTandemIdfileReader
extends ExperimentObject
implements IdfileReader

This reader will import identifications from an X!Tandem xml result file.

Created by IntelliJ IDEA. User: Marc Date: Jun 23, 2010 Time: 9:45:54 AM

See Also:
Serialized Form

Constructor Summary
XTandemIdfileReader()
          Constructor for the reader
XTandemIdfileReader(java.io.File aFile)
          constructor for the 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.
 java.lang.String getFileName()
          getter for 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

XTandemIdfileReader

public XTandemIdfileReader()
Constructor for the reader


XTandemIdfileReader

public XTandemIdfileReader(java.io.File aFile)
                    throws org.xml.sax.SAXException
constructor for the reader

Parameters:
aFile - the inspected file
Throws:
org.xml.sax.SAXException
Method Detail

getFileName

public java.lang.String getFileName()
getter for the file name

Returns:
the file name

getAllSpectrumMatches

public java.util.HashSet<SpectrumMatch> getAllSpectrumMatches(javax.swing.JProgressBar jProgressBar)
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

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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