com.compomics.software

Class CommandLineUtils

java.lang.Object

com.compomics.software.CommandLineUtils

public class CommandLineUtils
extends Object

This class groups some convenience methods for the use of compomics tools in command line.

Author:

Marc Vaudel

Field Summary

Fields

Modifier and Type	Field and Description
static String	SEPARATOR The command line argument separator.

Constructor Summary

Constructors

Constructor and Description
CommandLineUtils()

Method Summary

Modifier and Type	Method and Description
static String	concatenate(ArrayList<String> args) Returns the list of arguments as space separated string for the command line.
static String	concatenate(String[] args) Returns the list of arguments as space separated string for the command line.
static String	getCommandLineArgument(ArrayList<File> files) Returns the list of file as argument for the command line.
static String	getCommandLineArgument(File file) Returns the file as argument for the command line.
static ArrayList<Double>	getDoubleListFromString(String aString, String separator) Parses a list of doubles from a command line option.
static ArrayList<File>	getFiles(String optionInput, ArrayList<String> fileExtentions) Returns a list of files as imported from the command line option.
static ArrayList<Integer>	getIntegerListFromString(String aString, String separator) Parses a list of integers from a command line option.
static String	getQuoteType() Returns the quote type to use.
static ArrayList<String>	splitInput(String cliInput) Splits the input of comma separated command line input and returns the results as an arraylist.

Methods inherited from class java.lang.Object

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

Field Detail

SEPARATOR

public static final String SEPARATOR

The command line argument separator.

See Also:

Constant Field Values

Constructor Detail

CommandLineUtils

public CommandLineUtils()

Method Detail

getCommandLineArgument

public static String getCommandLineArgument(ArrayList<File> files)

Returns the list of file as argument for the command line.

Parameters:

files - the files

Returns:

the list of file as string for command line argument

concatenate

public static String concatenate(ArrayList<String> args)

Returns the list of arguments as space separated string for the command line.

Parameters:

args - the arguments

Returns:

a comma separated string

concatenate

public static String concatenate(String[] args)

Returns the list of arguments as space separated string for the command line. Adds quotes where they seem to be needed.

Parameters:

args - the arguments

Returns:

a comma separated string

getQuoteType

public static String getQuoteType()

Returns the quote type to use. For example around file paths with spaces.

Returns:

the quote type to use

getCommandLineArgument

public static String getCommandLineArgument(File file)

Returns the file as argument for the command line.

Parameters:

file - the file

Returns:

the list of file as string for command line argument

splitInput

public static ArrayList<String> splitInput(String cliInput)

Splits the input of comma separated command line input and returns the results as an arraylist.

Parameters:

cliInput - the CLI input

Returns:

an arraylist containing the results, empty list if empty string

getFiles

public static ArrayList<File> getFiles(String optionInput,
                                       ArrayList<String> fileExtentions)
                                throws FileNotFoundException

Returns a list of files as imported from the command line option.

Parameters:

optionInput - the command line option

fileExtentions - the file extensions to be considered

Returns:

a list of file candidates

Throws:

FileNotFoundException - exception thrown whenever a file is not found

getIntegerListFromString

public static ArrayList<Integer> getIntegerListFromString(String aString,
                                                          String separator)

Parses a list of integers from a command line option.

Parameters:

aString - the command line option

separator - the separator used to separate the string

Returns:

the list if integers

getDoubleListFromString

public static ArrayList<Double> getDoubleListFromString(String aString,
                                                        String separator)

Parses a list of doubles from a command line option.

Parameters:

aString - the command line option

separator - the separator used to separate the string

Returns:

the list if doubles