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

Methods

Modifier and Type	Method and Description
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.
java.lang.String	getSoftwareVersion() Returns the name and version of the software used to generate the identification file, e.g., Mascot 2.3.0 or X! Tandem Sledgehammer (2013.09.01.1).

Method Detail

getAllSpectrumMatches

java.util.HashSet<SpectrumMatch> getAllSpectrumMatches(WaitingHandler waitingHandler)
                                                       throws java.io.IOException,
                                                              java.lang.IllegalArgumentException,
                                                              java.lang.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:

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

getExtension

java.lang.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 java.io.IOException

Closes the file reader.

Throws:

java.io.IOException

getSoftwareVersion

java.lang.String getSoftwareVersion()

Returns the name and version of the software used to generate the identification file, e.g., Mascot 2.3.0 or X! Tandem Sledgehammer (2013.09.01.1). Null if not known.

Returns:

the version of the software used to generate the identification file, null if not known