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

Class MsAmandaIdfileReader

java.lang.Object

com.compomics.util.experiment.personalization.ExperimentObject

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

All Implemented Interfaces:

IdfileReader, Serializable, Cloneable

public class MsAmandaIdfileReader
extends ExperimentObject
implements IdfileReader

This IdfileReader reads identifications from an MS Amanda csv result file.

Author:

Harald Barsnes

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor and Description
MsAmandaIdfileReader() Default constructor for the purpose of instantiation.
MsAmandaIdfileReader(File msAmandaCsvFile) Constructor for an MS Amanda csv result file reader.
MsAmandaIdfileReader(File msAmandaCsvFile, WaitingHandler waitingHandler) Constructor for an MS Amanda csv result file reader.

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	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).
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.
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

Constructor Detail

MsAmandaIdfileReader

public MsAmandaIdfileReader()

Default constructor for the purpose of instantiation.

MsAmandaIdfileReader

public MsAmandaIdfileReader(File msAmandaCsvFile)
                     throws FileNotFoundException,
                            IOException

Constructor for an MS Amanda csv result file reader.

Parameters:

msAmandaCsvFile - the MS Amanda csv file

Throws:

FileNotFoundException - if a FileNotFoundException occurs

IOException - if an IOException occurs

MsAmandaIdfileReader

public MsAmandaIdfileReader(File msAmandaCsvFile,
                            WaitingHandler waitingHandler)
                     throws FileNotFoundException,
                            IOException

Constructor for an MS Amanda csv result file reader.

Parameters:

msAmandaCsvFile - the MS Amanda csv file

waitingHandler - the waiting handler

Throws:

FileNotFoundException - if a FileNotFoundException occurs

IOException - if an IOException occurs

Method Detail

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 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

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