eu.isas.peptideshaker.preferences

Class PeptideShakerPathParameters

java.lang.Object

eu.isas.peptideshaker.preferences.PeptideShakerPathParameters

public class PeptideShakerPathParameters
extends Object

This class sets the path preferences for the files to read/write.

Author:

Marc Vaudel

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	PeptideShakerPathParameters.PeptideShakerPathKey Enum of the paths which can be set in PeptideShaker.

Constructor Summary

Constructors

Constructor and Description
PeptideShakerPathParameters()

Method Summary

Modifier and Type	Method and Description
static ArrayList<com.compomics.software.settings.PathKey>	getErrorKeys() Returns a list containing the keys of the paths where the tool is not able to write.
static String	getPathPreference(PeptideShakerPathParameters.PeptideShakerPathKey peptideShakerPathKey) Sets the path according to the given key and path.
static void	loadPathParametersFromFile(File inputFile) Loads the path preferences from a text file.
static void	loadPathParametersFromLine(String line) Loads a path to be set from a line.
static void	setAllPathsIn(String path) Sets all the paths inside a given folder.
static void	setPathParameters(com.compomics.software.settings.PathKey pathKey, String path) Sets the path according to the given key and path.
static void	setPathPreference(PeptideShakerPathParameters.PeptideShakerPathKey peptideShakerPathKey, String path) Sets the path according to the given key and path.
static void	writeConfigurationToFile(File file) Writes all path configurations to the given file.
static void	writeConfigurationToFile(com.compomics.util.io.flat.SimpleFileWriter writer) Writes the configuration file using the provided buffered writer.
static void	writePathToFile(com.compomics.util.io.flat.SimpleFileWriter writer, PeptideShakerPathParameters.PeptideShakerPathKey pathKey) Writes the path of interest using the provided buffered writer.

Methods inherited from class java.lang.Object

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

Constructor Detail

PeptideShakerPathParameters

public PeptideShakerPathParameters()

Method Detail

loadPathParametersFromFile

public static void loadPathParametersFromFile(File inputFile)
                                       throws FileNotFoundException,
                                              IOException

Loads the path preferences from a text file.

Parameters:

inputFile - the file to load the path preferences from

Throws:

FileNotFoundException - thrown if an FileNotFoundException occurs

IOException - thrown if an IOException occurs

loadPathParametersFromLine

public static void loadPathParametersFromLine(String line)
                                       throws FileNotFoundException,
                                              IOException

Loads a path to be set from a line.

Parameters:

line - the line where to read the path from

Throws:

FileNotFoundException - thrown if an FileNotFoundException occurs

IOException

getPathPreference

public static String getPathPreference(PeptideShakerPathParameters.PeptideShakerPathKey peptideShakerPathKey)
                                throws IOException

Sets the path according to the given key and path.

Parameters:

peptideShakerPathKey - the key of the path

Returns:

returns the path used

Throws:

FileNotFoundException - thrown if an FileNotFoundException occurs

IOException

setPathPreference

public static void setPathPreference(PeptideShakerPathParameters.PeptideShakerPathKey peptideShakerPathKey,
                                     String path)
                              throws IOException

Sets the path according to the given key and path.

Parameters:

peptideShakerPathKey - the key of the path

path - the path to be set

Throws:

FileNotFoundException - thrown if an FileNotFoundException occurs

IOException

setPathParameters

public static void setPathParameters(com.compomics.software.settings.PathKey pathKey,
                                     String path)
                              throws IOException

Sets the path according to the given key and path.

Parameters:

pathKey - the key of the path

path - the path to be set

Throws:

FileNotFoundException - thrown if an FileNotFoundException occurs

IOException

setAllPathsIn

public static void setAllPathsIn(String path)
                          throws FileNotFoundException,
                                 IOException

Sets all the paths inside a given folder.

Parameters:

path - the path of the folder where to redirect all paths.

Throws:

FileNotFoundException - thrown if an FileNotFoundException occurs

IOException

writeConfigurationToFile

public static void writeConfigurationToFile(File file)
                                     throws IOException

Writes all path configurations to the given file.

Parameters:

file - the destination file

Throws:

FileNotFoundException - thrown if an FileNotFoundException occurs

IOException

writeConfigurationToFile

public static void writeConfigurationToFile(com.compomics.util.io.flat.SimpleFileWriter writer)
                                     throws IOException

Writes the configuration file using the provided buffered writer.

Parameters:

writer - the writer to use for writing.

Throws:

FileNotFoundException - thrown if an FileNotFoundException occurs

IOException

writePathToFile

public static void writePathToFile(com.compomics.util.io.flat.SimpleFileWriter writer,
                                   PeptideShakerPathParameters.PeptideShakerPathKey pathKey)
                            throws IOException

Writes the path of interest using the provided buffered writer.

Parameters:

writer - the writer to use for writing

pathKey - the key of the path of interest

Throws:

FileNotFoundException - thrown if an FileNotFoundException occurs

IOException

getErrorKeys

public static ArrayList<com.compomics.software.settings.PathKey> getErrorKeys()
                                                                       throws IOException

Returns a list containing the keys of the paths where the tool is not able to write.

Returns:

a list containing the keys of the paths where the tool is not able to write

Throws:

IOException - exception thrown whenever an error occurred while loading the path configuration