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

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.
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

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 -

Throws:

FileNotFoundException

IOException

MsAmandaIdfileReader

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

Constructor for an MS Amanda csv result file reader.

Parameters:

msAmandaCsvFile -

waitingHandler -

Throws:

FileNotFoundException

IOException

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 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

close

public void close()
           throws IOException

Description copied from interface: IdfileReader

Closes the file reader.

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