com.compomics.util.experiment.identification.parameters_cli

Class IdentificationParametersInputBean

java.lang.Object

com.compomics.util.experiment.identification.parameters_cli.IdentificationParametersInputBean

public class IdentificationParametersInputBean
extends Object

This class contains the parses parameters from a command line and stores them in a SearchParameters object.

Author:

Marc Vaudel, Harald Barsnes

Constructor Summary

Constructors

Constructor and Description
IdentificationParametersInputBean(org.apache.commons.cli.CommandLine aLine) Takes all the arguments from a command line.

Method Summary

Modifier and Type	Method and Description
File	getDestinationFile() Returns the file where to save the identification parameters.
IdentificationParameters	getIdentificationParameters() Returns the identification parameters.
File	getInputFile() Returns the input parameters file.
static boolean	inDoubleRange(String argType, String arg, double minValue, double maxValue) Returns true if the input is a double value inside the given range.
static boolean	inIntegerRange(String argType, String arg, int minValue, int maxValue) Returns true if the input is an integer value inside the given range.
static boolean	isBooleanInput(String argType, String arg) Returns true of the input is 0 or 1.
static boolean	isDouble(String argType, String arg) Returns true if the argument can be parsed as a double value.
static boolean	isInList(String argType, String arg, List<String> supportedInput) Returns true of the input is in the provided list.
static boolean	isInteger(String argType, String arg) Returns true if the argument can be parsed as an integer value.
Boolean	isListMods() Indicates whether the modifications should be printed on the screen.
static boolean	isPositiveDouble(String argType, String arg, boolean allowZero) Returns true if the argument can be parsed as a positive double value.
static boolean	isPositiveInteger(String argType, String arg, boolean allowZero) Returns true if the argument can be parsed as a positive integer value.
static boolean	isSequenceMatchingType(String argType, String arg) Returns true of the input is in the provided list.
static boolean	isValidModifications(org.apache.commons.cli.CommandLine aLine) Verifies that modifications are correctly recognized.
static boolean	isValidStartup(org.apache.commons.cli.CommandLine aLine, boolean checkMandatoryParameters) Verifies the command line start parameters.
void	setIdentificationParameters(IdentificationParameters identificationParameters) Sets the identification parameters.
void	updateIdentificationParameters() Updates the identification parameters according to the command line.

Methods inherited from class java.lang.Object

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

Constructor Detail

IdentificationParametersInputBean

public IdentificationParametersInputBean(org.apache.commons.cli.CommandLine aLine)
                                  throws FileNotFoundException,
                                         IOException,
                                         ClassNotFoundException

Takes all the arguments from a command line.

Parameters:

aLine - the command line

Throws:

FileNotFoundException - if a FileNotFoundException occurs

IOException - if an IOException occurs

ClassNotFoundException - if aClassNotFoundException ClassNotFoundException occurs

Method Detail

updateIdentificationParameters

public void updateIdentificationParameters()
                                    throws FileNotFoundException,
                                           IOException,
                                           ClassNotFoundException

Updates the identification parameters according to the command line.

Throws:

FileNotFoundException - if a FileNotFoundException occurs

IOException - if an IOException occurs

ClassNotFoundException - if aClassNotFoundException ClassNotFoundException occurs

setIdentificationParameters

public void setIdentificationParameters(IdentificationParameters identificationParameters)

Sets the identification parameters.

Parameters:

identificationParameters - the identification parameters

getIdentificationParameters

public IdentificationParameters getIdentificationParameters()

Returns the identification parameters.

Returns:

the identification parameters

getInputFile

public File getInputFile()

Returns the input parameters file.

Returns:

the input parameters file

getDestinationFile

public File getDestinationFile()

Returns the file where to save the identification parameters.

Returns:

the file where to save the identification parameters

isListMods

public Boolean isListMods()

Indicates whether the modifications should be printed on the screen.

Returns:

true if the modifications should be printed on the screen

isValidModifications

public static boolean isValidModifications(org.apache.commons.cli.CommandLine aLine)
                                    throws IOException

Verifies that modifications are correctly recognized.

Parameters:

aLine - the command line to validate

Returns:

true if the startup was valid

Throws:

IOException - if an IOException occurs

isValidStartup

public static boolean isValidStartup(org.apache.commons.cli.CommandLine aLine,
                                     boolean checkMandatoryParameters)
                              throws IOException

Verifies the command line start parameters.

Parameters:

aLine - the command line to validate

checkMandatoryParameters - if true, check if mandatory parameters are included

Returns:

true if the startup was valid

Throws:

IOException - if an IOException occurs

isPositiveDouble

public static boolean isPositiveDouble(String argType,
                                       String arg,
                                       boolean allowZero)

Returns true if the argument can be parsed as a positive double value.

Parameters:

argType - the name of the argument

arg - the content of the argument

allowZero - if true, zero values are allowed

Returns:

true if the argument can be parsed as a positive double value

isPositiveInteger

public static boolean isPositiveInteger(String argType,
                                        String arg,
                                        boolean allowZero)

Returns true if the argument can be parsed as a positive integer value.

Parameters:

argType - the name of the argument

arg - the content of the argument

allowZero - if true, zero values are allowed

Returns:

true if the argument can be parsed as a positive integer value

isInteger

public static boolean isInteger(String argType,
                                String arg)

Returns true if the argument can be parsed as an integer value.

Parameters:

argType - the name of the argument

arg - the content of the argument

Returns:

true if the argument can be parsed as an integer value

isDouble

public static boolean isDouble(String argType,
                               String arg)

Returns true if the argument can be parsed as a double value.

Parameters:

argType - the name of the argument

arg - the content of the argument

Returns:

true if the argument can be parsed as a double value

isBooleanInput

public static boolean isBooleanInput(String argType,
                                     String arg)

Returns true of the input is 0 or 1.

Parameters:

argType - the name of the argument

arg - the content of the argument

Returns:

true of the input is 0 or 1

isInList

public static boolean isInList(String argType,
                               String arg,
                               List<String> supportedInput)

Returns true of the input is in the provided list.

Parameters:

argType - the name of the argument

arg - the content of the argument

supportedInput - the list of supported input

Returns:

true of the input is in the list

isSequenceMatchingType

public static boolean isSequenceMatchingType(String argType,
                                             String arg)

Returns true of the input is in the provided list.

Parameters:

argType - the name of the argument

arg - the content of the argument

Returns:

true of the input is in the list

inIntegerRange

public static boolean inIntegerRange(String argType,
                                     String arg,
                                     int minValue,
                                     int maxValue)

Returns true if the input is an integer value inside the given range.

Parameters:

argType - the name of the argument

arg - the content of the argument

minValue - the minimum value allowed

maxValue - the maximum value allowed

Returns:

true if the input is an integer value inside the given range

inDoubleRange

public static boolean inDoubleRange(String argType,
                                    String arg,
                                    double minValue,
                                    double maxValue)

Returns true if the input is a double value inside the given range.

Parameters:

argType - the name of the argument

arg - the content of the argument

minValue - the minimum value allowed

maxValue - the maximum value allowed

Returns:

true if the input is a double value inside the given range