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

All Known Implementing Classes:
AndromedaIdfileReader

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(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.
 String getExtension()
          This method should return the extension of the file for which this IdfileReader can be used.
 

Method Detail

getAllSpectrumMatches

HashSet<SpectrumMatch> getAllSpectrumMatches(WaitingHandler waitingHandler)
                                             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:
waitingHandler - a waiting handler displaying the progress (can be null). The secondary progress methods will be called.
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

getExtension

String getExtension()
This method should return the extension of the file for which this IdfileReader can be used.

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

close

void close()
           throws IOException
Closes the file reader.

Throws:
IOException


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