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

Class AndromedaIdfileReader

java.lang.Object

com.compomics.util.experiment.personalization.ExperimentObject

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

Constructors

Constructor and Description
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

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).

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

getSoftwareVersion

public java.lang.String getSoftwareVersion()

Description copied from interface: IdfileReader

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.

Specified by:

getSoftwareVersion in interface IdfileReader

Returns:

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