Package eu.isas.searchgui.processbuilders

Class AndromedaProcessBuilder

java.lang.Object

eu.isas.searchgui.processbuilders.SearchGUIProcessBuilder

eu.isas.searchgui.processbuilders.AndromedaProcessBuilder

All Implemented Interfaces:

Runnable

public class AndromedaProcessBuilder
extends SearchGUIProcessBuilder

ProcessBuilder for the Andromeda search engine.

Author:

Marc Vaudel, Harald Barsnes

Field Summary

Fields

Modifier and Type	Field	Description
static final String	EXECUTABLE_FILE_NAME	The name of the Andromeda executable.

Fields inherited from class eu.isas.searchgui.processbuilders.SearchGUIProcessBuilder

exceptionHandler, waitingHandler

Constructor Summary

Constructors

Constructor	Description
AndromedaProcessBuilder(File andromedaFolder, File andromedaTempFolder, com.compomics.util.parameters.identification.search.SearchParameters searchParameters, File searchParametersFile, File spectrumFile, File fastaFile, com.compomics.util.waiting.WaitingHandler waitingHandler, com.compomics.util.exceptions.ExceptionHandler exceptionHandler, int nThreads)	Constructor.

Method Summary

Modifier and Type	Method	Description
static void	createDatabaseFile(File andromedaFolder, File andromedaTempFolder, File fastaFile)	Creates the database configuration file.
static void	createEnzymesFile(File andromedaFolder)	Creates the enzyme configuration file.
static File	createGenericFastaFile(File andromedaTempFolder, File originalFastaFile, com.compomics.util.waiting.WaitingHandler waitingHandler)	Create the FASTA file.
static void	createPtmFile(File andromedaFolder, com.compomics.util.parameters.identification.IdentificationParameters identificationParameters, File identificationParametersFile)	Creates the Andromeda PTM file and saves the PTM indexes in the search parameters.
String	getCurrentlyProcessedFileName()	Returns the file name of the currently processed file.
String	getType()	Returns the type of the process.

Methods inherited from class eu.isas.searchgui.processbuilders.SearchGUIProcessBuilder

endProcess, run, startProcess

Methods inherited from class java.lang.Object

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

Field Details

EXECUTABLE_FILE_NAME

public static final String EXECUTABLE_FILE_NAME

The name of the Andromeda executable.

See Also:

• Constant Field Values

Constructor Details

AndromedaProcessBuilder

public AndromedaProcessBuilder(File andromedaFolder,
 File andromedaTempFolder,
 com.compomics.util.parameters.identification.search.SearchParameters searchParameters,
 File searchParametersFile,
 File spectrumFile,
 File fastaFile,
 com.compomics.util.waiting.WaitingHandler waitingHandler,
 com.compomics.util.exceptions.ExceptionHandler exceptionHandler,
 int nThreads)
                        throws IOException

Constructor.

Parameters:

andromedaFolder - the Andromeda folder

andromedaTempFolder - the temp folder for Andromeda

searchParameters - the search parameters

searchParametersFile - the file where to save the search parameters

spectrumFile - the spectrum file

fastaFile - the FASTA file

waitingHandler - the waiting handler

exceptionHandler - the handler of exceptions

nThreads - the number of threads

Throws:

IOException - thrown whenever an error occurred while reading or writing a file.

Method Details

createGenericFastaFile

public static File createGenericFastaFile(File andromedaTempFolder,
 File originalFastaFile,
 com.compomics.util.waiting.WaitingHandler waitingHandler)
                                   throws IOException

Create the FASTA file.

Parameters:

andromedaTempFolder - the Andromeda temp folder

originalFastaFile - the original FASTA file

waitingHandler - the waiting handler

Returns:

the parameters file

Throws:

IOException - exception thrown whenever an error occurred while reading or writing a file

createDatabaseFile

public static void createDatabaseFile(File andromedaFolder,
 File andromedaTempFolder,
 File fastaFile)
                               throws IOException

Creates the database configuration file.

Parameters:

andromedaFolder - the Andromeda installation folder

andromedaTempFolder - the Andromeda temp folder

fastaFile - the FASTA file

Throws:

IOException - exception thrown whenever an error occurred while writing the database configuration file.

createEnzymesFile

public static void createEnzymesFile(File andromedaFolder)
                              throws IOException

Creates the enzyme configuration file.

Parameters:

andromedaFolder - the Andromeda installation folder

Throws:

IOException - exception thrown whenever an error occurred while writing the file.

createPtmFile

public static void createPtmFile(File andromedaFolder,
 com.compomics.util.parameters.identification.IdentificationParameters identificationParameters,
 File identificationParametersFile)
                          throws IOException,
ClassNotFoundException

Creates the Andromeda PTM file and saves the PTM indexes in the search parameters.

Parameters:

andromedaFolder - the Andromeda installation folder

identificationParameters - the identification parameters

identificationParametersFile - the file where to save the search parameters

Throws:

IOException - exception thrown whenever an error occurs while writing to the file.

ClassNotFoundException - exception thrown whenever an error occurred while saving the search parameters

getType

public String getType()

Description copied from class: SearchGUIProcessBuilder

Returns the type of the process.

Specified by:

getType in class SearchGUIProcessBuilder

Returns:

the type of the process

getCurrentlyProcessedFileName

public String getCurrentlyProcessedFileName()

Description copied from class: SearchGUIProcessBuilder

Returns the file name of the currently processed file.

Specified by:

getCurrentlyProcessedFileName in class SearchGUIProcessBuilder

Returns:

the file name of the currently processed file