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

Class DirecTagIdfileReader

java.lang.Object

com.compomics.util.experiment.personalization.ExperimentObject

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

All Implemented Interfaces:

IdfileReader, Serializable, Cloneable

public class DirecTagIdfileReader
extends ExperimentObject
implements IdfileReader

An identification file reader for Direct tag results.

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.

Constructor Summary

Constructors

Constructor and Description
DirecTagIdfileReader() Default constructor for the purpose of instantiation.
DirecTagIdfileReader(File tagFile) Constructors, parses a file but does not index the results.
DirecTagIdfileReader(File tagFile, boolean indexResults) Constructors, parses a file.

Method Summary

Modifier and Type	Method and Description
void	clearTagsMap() Clears the tags map.
void	close() Closes the file reader.
LinkedList<SpectrumMatch>	getAllSpectrumMatches(WaitingHandler waitingHandler, SearchParameters searchParameters) 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.
LinkedList<SpectrumMatch>	getAllSpectrumMatches(WaitingHandler waitingHandler, SearchParameters searchParameters, SequenceMatchingPreferences sequenceMatchingPreferences, boolean expandAaCombinations) 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	getCopyRight() Returns the copyright.
String	getExtension() Returns the extension of the file for which this IdfileReader can be used.
File	getInputFile() Returns the spectrum file name as found in the parameters section.
String	getLicense() Returns the license information of this file.
Integer	getnProcessingNode() Returns the number of processing nodes 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).
String	getSpectrumComponent(int spectrumId, String componentName) Returns a component in a spectrum line.
Set<String>	getSpectrumComponentNames() Returns all the spectrum components names found in the header.
Set<Integer>	getSpectrumIds() Returns all the spectrum IDs found.
Double	getTaggingTimeSeconds() Returns the tagging time in seconds as listed in the file.
String	getTagParameter(String tagParameterName) Returns the tagging parameter corresponding to a given parameter name.
String	getTagsGenerator() Returns the tags generator used to create the file.
String	getTagsGeneratorVersion() Returns the version of the tags generator used to create the file.
HashMap<String,LinkedList<SpectrumMatch>>	getTagsMap() Returns a map of all simple tags found in this file indexed by the beginning of the amino acid sequence.
Set<String>	getTagsParametersNames() Returns the name of the different parameters names found.
String	getTimeEnd() Returns the ending time of the tagging as given in the file.
String	getTimeStart() Returns the starting time of the tagging as given in the file.
boolean	hasDeNovoTags() Returns a boolean indicating whether the file contains de novo results as tags.

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

cTermCorrection

public final double cTermCorrection

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

See Also:

Constant Field Values

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

DirecTagIdfileReader

public DirecTagIdfileReader()

Default constructor for the purpose of instantiation.

DirecTagIdfileReader

public DirecTagIdfileReader(File tagFile)
                     throws FileNotFoundException,
                            IOException

Constructors, parses a file but does not index the results.

Parameters:

tagFile - the file to parse

Throws:

FileNotFoundException - if a FileNotFoundException occurs

IOException - if an IOException occurs

DirecTagIdfileReader

public DirecTagIdfileReader(File tagFile,
                            boolean indexResults)
                     throws FileNotFoundException,
                            IOException

Constructors, parses a file.

Parameters:

tagFile - the file to parse

indexResults - if true the results section will be indexed

Throws:

FileNotFoundException - if a FileNotFoundException occurs

IOException - if an IOException occurs

Method Detail

getTagsParametersNames

public Set<String> getTagsParametersNames()

Returns the name of the different parameters names found.

Returns:

the name of the different parameters names found

getTagParameter

public String getTagParameter(String tagParameterName)

Returns the tagging parameter corresponding to a given parameter name.

Parameters:

tagParameterName - the name of the parameter of interest

Returns:

the parameter of interest

getSpectrumComponent

public String getSpectrumComponent(int spectrumId,
                                   String componentName)
                            throws IOException

Returns a component in a spectrum line.

Parameters:

spectrumId - the id of the spectrum of interest

componentName - the name of the component of interest according to the header

Returns:

the component

Throws:

IOException - if an IOException occurs

getSpectrumIds

public Set<Integer> getSpectrumIds()

Returns all the spectrum IDs found.

Returns:

the spectrum IDs found in a set

getSpectrumComponentNames

public Set<String> getSpectrumComponentNames()

Returns all the spectrum components names found in the header.

Returns:

all the spectrum components names found in the header

getAllSpectrumMatches

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

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. Using this method secondary maps are not filled.

Specified by:

getAllSpectrumMatches in interface IdfileReader

Parameters:

waitingHandler - a 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

IllegalArgumentException - if an IllegalArgumentException occurs

SQLException - if an SQLException occurs

ClassNotFoundException - if an\ ClassNotFoundException occurs

InterruptedException - if an InterruptedException occurs

JAXBException - if a JAXBException occurs

getAllSpectrumMatches

public LinkedList<SpectrumMatch> getAllSpectrumMatches(WaitingHandler waitingHandler,
                                                       SearchParameters searchParameters,
                                                       SequenceMatchingPreferences sequenceMatchingPreferences,
                                                       boolean expandAaCombinations)
                                                throws IOException,
                                                       IllegalArgumentException,
                                                       SQLException,
                                                       ClassNotFoundException,
                                                       InterruptedException,
                                                       JAXBException

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. 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:

waitingHandler - a 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:

a list of spectrum matches

Throws:

IOException - if an IOException occurs

IllegalArgumentException - if an IllegalArgumentException occurs

SQLException - if an SQLException occurs

ClassNotFoundException - if an\ ClassNotFoundException occurs

InterruptedException - if an InterruptedException occurs

JAXBException - if a JAXBException occurs

getTagsGenerator

public String getTagsGenerator()

Returns the tags generator used to create the file.

Returns:

the tags generator used to create the file

getTagsGeneratorVersion

public String getTagsGeneratorVersion()

Returns the version of the tags generator used to create the file.

Returns:

the version of the tags generator used to create the file

getCopyRight

public String getCopyRight()

Returns the copyright.

Returns:

the copyright

getLicense

public String getLicense()

Returns the license information of this file.

Returns:

the license information of this file

getTimeStart

public String getTimeStart()

Returns the starting time of the tagging as given in the file.

Returns:

the starting time of the tagging

getTimeEnd

public String getTimeEnd()

Returns the ending time of the tagging as given in the file.

Returns:

the ending time of the tagging

getTaggingTimeSeconds

public Double getTaggingTimeSeconds()

Returns the tagging time in seconds as listed in the file.

Returns:

the tagging time in seconds as listed in the file

getnProcessingNode

public Integer getnProcessingNode()

Returns the number of processing nodes used.

Returns:

the number of processing nodes used

getInputFile

public File getInputFile()

Returns the spectrum file name as found in the parameters section.

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 - if an IOException occurs

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

getTagsMap

public HashMap<String,LinkedList<SpectrumMatch>> getTagsMap()

Description copied from interface: IdfileReader

Returns a map of all simple tags found in this file indexed by the beginning of the amino acid sequence. A simple tag is a triplet consisting of a mass gap, an amino acid sequence and a mass gap. The size of the subsequence is the one of the initial size the protein tree in the sequence factory. The subsequence is unique according to the given sequence matching preferences.

Specified by:

getTagsMap in interface IdfileReader

Returns:

a map of all simple tags found in this file indexed by the beginning of the amino acid sequence

clearTagsMap

public void clearTagsMap()

Description copied from interface: IdfileReader

Clears the tags map.

Specified by:

clearTagsMap in interface IdfileReader

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