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

Class PepNovoIdfileReader

java.lang.Object

com.compomics.util.experiment.personalization.ExperimentObject

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

All Implemented Interfaces:

IdfileReader, Serializable, Cloneable

public class PepNovoIdfileReader
extends ExperimentObject
implements IdfileReader

This class can be used to parse PepNovo identification files.

Author:

Marc Vaudel

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
double	cTermCorrection The mass to add to the C-terminal gap so that is corresponds to a peptide fragment.
double	nTermCorrection The mass to add to the N-terminal gap so that is corresponds to a peptide fragment.
static String	tableHeader The standard format.

Constructor Summary

Constructors

Constructor and Description
PepNovoIdfileReader() Default constructor for the purpose of instantiation.
PepNovoIdfileReader(File identificationFile) Constructor, initiate the parser.
PepNovoIdfileReader(File identificationFile, WaitingHandler waitingHandler) Constructor, initiate the parser.

Method Summary

Methods

Modifier and Type	Method and Description
void	close() Closes the file reader.
HashSet<SpectrumMatch>	getAllSpectrumMatches(WaitingHandler waitingHandler) 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() Returns the extension of the file for which this IdfileReader can be used.
String	getMgfFileName() Returns the spectrum file name.
static String	getPTM(PepnovoParameters pepnovoParameters, String pepNovoModification) Get a PTM.
HashMap<String,ArrayList<String>>	getSoftwareVersions() Returns the names and versions of the software used to generate the identification file in a map, e.g., Mascot -> (2.2 and 2.3) and 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

Field Detail

tableHeader

public static final String tableHeader

The standard format.

See Also:

Constant Field Values

cTermCorrection

public final double cTermCorrection

The mass to add to the C-terminal gap so that is corresponds to a peptide fragment.

nTermCorrection

public final double nTermCorrection

The mass to add to the N-terminal gap so that is corresponds to a peptide fragment.

See Also:

Constant Field Values

Constructor Detail

PepNovoIdfileReader

public PepNovoIdfileReader()

Default constructor for the purpose of instantiation.

PepNovoIdfileReader

public PepNovoIdfileReader(File identificationFile)
                    throws FileNotFoundException,
                           IOException

Constructor, initiate the parser. Displays the progress using the waiting handler. The close() method shall be used when the file reader is no longer used.

Parameters:

identificationFile - the identification file to parse

Throws:

FileNotFoundException - exception thrown whenever the provided file was not found

IOException - exception thrown whenever an error occurred while reading the file

PepNovoIdfileReader

public PepNovoIdfileReader(File identificationFile,
                   WaitingHandler waitingHandler)
                    throws FileNotFoundException,
                           IOException

Constructor, initiate the parser. Displays the progress using the waiting handler. The close() method shall be used when the file reader is no longer used.

Parameters:

identificationFile - the identification file to parse

waitingHandler - a waiting handler providing progress feedback to the user

Throws:

FileNotFoundException - exception thrown whenever the provided file was not found

IOException - exception thrown whenever an error occurred while reading the file

Method Detail

getAllSpectrumMatches

public HashSet<SpectrumMatch> getAllSpectrumMatches(WaitingHandler waitingHandler)
                                             throws IOException,
                                                    IllegalArgumentException,
                                                    Exception

Description copied from interface: IdfileReader

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:

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

getMgfFileName

public String getMgfFileName()

Returns the spectrum file name. This method assumes that the PepNovo output file is the mgf file name + ".out"

Returns:

the spectrum file name

getExtension

public String getExtension()

Description copied from interface: IdfileReader

Returns 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.

close

public void close()
           throws IOException

Description copied from interface: IdfileReader

Closes the file reader.

Specified by:

close in interface IdfileReader

Throws:

IOException

getPTM

public static String getPTM(PepnovoParameters pepnovoParameters,
            String pepNovoModification)

Get a PTM.

Parameters:

pepnovoParameters - the PepNovo parameters

pepNovoModification - the PepNovo modification

Returns:

the PTM as a string

getSoftwareVersions

public HashMap<String,ArrayList<String>> getSoftwareVersions()

Description copied from interface: IdfileReader

Returns the names and versions of the software used to generate the identification file in a map, e.g., Mascot -> (2.2 and 2.3) and X!Tandem -> Sledgehammer (2013.09.01.1). Null if not known.

Specified by:

getSoftwareVersions in interface IdfileReader

Returns:

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