Package com.compomics.util.experiment.io.identification.idfilereaders

Class SageIdfileReader

java.lang.Object

com.compomics.util.experiment.io.identification.idfilereaders.SageIdfileReader

All Implemented Interfaces:

IdfileReader, AutoCloseable

public class SageIdfileReader
extends Object
implements IdfileReader

This IdfileReader reads identifications from a Sage tsv file.

Author:

Harald Barsnes

Field Summary

Fields

Modifier and Type	Field	Description
static final double	MOD_MASS_TOLERANCE	The mass tolerance to be used to match modifications from search engines and expected modifications.

Constructor Summary

Constructors

Constructor	Description
SageIdfileReader()	Default constructor for the purpose of instantiation.
SageIdfileReader(File sageTsvFile)	Constructor for a Sage tsv file reader.
SageIdfileReader(File sageTsvFile, WaitingHandler waitingHandler)	Constructor for a Sage tsv file reader.

Method Summary

Modifier and Type	Method	Description
void	close()
ArrayList<SpectrumMatch>	getAllSpectrumMatches(SpectrumProvider spectrumProvider, WaitingHandler waitingHandler, SearchParameters searchParameters)	Retrieves all the spectrum matches from an identification file as a list of spectrum matches, one spectrum match per spectrum.
ArrayList<SpectrumMatch>	getAllSpectrumMatches(SpectrumProvider spectrumProvider, WaitingHandler waitingHandler, SearchParameters searchParameters, SequenceMatchingParameters sequenceMatchingPreferences, boolean expandAaCombinations)	Retrieves all the spectrum matches from an identification file as a list of spectrum matches, one spectrum match per spectrum.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.
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).
boolean	hasDeNovoTags()	Returns a boolean indicating whether the file contains de novo results as tags.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Details

MOD_MASS_TOLERANCE

public static final double MOD_MASS_TOLERANCE

The mass tolerance to be used to match modifications from search engines and expected modifications. 0.01 by default, the mass resolution in X !Tandem result files.

See Also:

• Constant Field Values

Constructor Details

SageIdfileReader

public SageIdfileReader()

Default constructor for the purpose of instantiation.

SageIdfileReader

public SageIdfileReader(File sageTsvFile)
                 throws IOException

Constructor for a Sage tsv file reader.

Parameters:

sageTsvFile - the Sage tsv file

Throws:

FileNotFoundException - if a FileNotFoundException occurs

IOException - if an IOException occurs

SageIdfileReader

public SageIdfileReader(File sageTsvFile,
 WaitingHandler waitingHandler)
                 throws IOException

Constructor for a Sage tsv file reader.

Parameters:

sageTsvFile - the Sage tsv file

waitingHandler - the waiting handler

Throws:

FileNotFoundException - if a FileNotFoundException occurs

IOException - if an IOException occurs

Method Details

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.

getAllSpectrumMatches

public ArrayList<SpectrumMatch> getAllSpectrumMatches(SpectrumProvider spectrumProvider,
 WaitingHandler waitingHandler,
 SearchParameters searchParameters)
                                               throws IOException,
IllegalArgumentException,
SQLException,
ClassNotFoundException,
InterruptedException,
JAXBException

Description copied from interface: IdfileReader

Retrieves all the spectrum matches from an identification file as a list of spectrum matches, one spectrum match per spectrum. It is very important to close the file reader after creation. Using this method secondary maps are not filled.

Specified by:

getAllSpectrumMatches in interface IdfileReader

Parameters:

spectrumProvider - A spectrum provider with the spectra of the file loaded.

waitingHandler - The waiting handler displaying the progress (can be null). The secondary progress methods will be called.

searchParameters - The search parameters.

Returns:

a list of spectrum matches

Throws:

IOException - if an IOException occurs

SQLException - if an SQLException occurs

ClassNotFoundException - if an\ ClassNotFoundException occurs

InterruptedException - if an InterruptedException occurs

JAXBException - if a JAXBException occurs

IllegalArgumentException

getAllSpectrumMatches

public ArrayList<SpectrumMatch> getAllSpectrumMatches(SpectrumProvider spectrumProvider,
 WaitingHandler waitingHandler,
 SearchParameters searchParameters,
 SequenceMatchingParameters sequenceMatchingPreferences,
 boolean expandAaCombinations)
                                               throws IOException,
IllegalArgumentException,
SQLException,
ClassNotFoundException,
InterruptedException,
JAXBException

Description copied from interface: IdfileReader

Retrieves all the spectrum matches from an identification file as a list of spectrum matches, one spectrum match per spectrum.It is very important to close the file reader after creation. Secondary peptide and tag maps are filled according to the file content and the sequence matching preferences. If the sequence matching preferences are null, the maps are not filled.

Specified by:

getAllSpectrumMatches in interface IdfileReader

Parameters:

spectrumProvider - A spectrum provider with the spectra of the file loaded.

waitingHandler - The waiting handler displaying the progress (can be null). The secondary progress methods will be called.

searchParameters - The search parameters.

sequenceMatchingPreferences - The sequence matching preferences to use for the creation of the secondary maps.

expandAaCombinations - If true, a peptide assumption (not implemented for tag assumptions) will be created for all possible amino acid combination for peptide sequences containing an ambiguity like an X.

Returns:

the spectrum matches

Throws:

IOException - if an IOException occurs

SQLException - if an SQLException occurs

ClassNotFoundException - if an\ ClassNotFoundException occurs

InterruptedException - if an InterruptedException occurs

JAXBException - if a JAXBException occurs

IllegalArgumentException

close

public void close()
           throws IOException

Specified by:

close in interface AutoCloseable

Specified by:

close in interface IdfileReader

Throws:

IOException

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

hasDeNovoTags

public boolean hasDeNovoTags()

Description copied from interface: IdfileReader

Returns a boolean indicating whether the file contains de novo results as tags.

Specified by:

hasDeNovoTags in interface IdfileReader

Returns:

a boolean indicating whether the file contains de novo results as tags