com.compomics.util.experiment.io.identifications
Interface IdfileReader

All Known Implementing Classes:
AndromedaIdfileReader, MascotIdfileReader, OMSSAIdfileReader, XTandemIdfileReader

public interface IdfileReader

This interface will retrieve spectrum matches from any identification file.

Author:
Marc Vaudel

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.
 

Method Detail

getAllSpectrumMatches

HashSet<SpectrumMatch> getAllSpectrumMatches(JProgressBar jProgressBar)
                                             throws IOException,
                                                    IllegalArgumentException,
                                                    Exception
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.

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

void close()
           throws IOException
Closes the file reader.

Throws:
IOException


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