com.hfg.bio.seq.alignment.muscle

Class MuscleSettings

java.lang.Object

com.hfg.setting.Settings

com.hfg.bio.seq.alignment.muscle.MuscleSettings

All Implemented Interfaces:

Cloneable

public class MuscleSettings
extends Settings
implements Cloneable

Settings used for Muscle multiple sequence alignment execution.

Field Summary

Fields

Modifier and Type	Field and Description
static String	COMMAND_LINE_PARAMS
static String	EXECUTABLE
static String	EXECUTABLE_DIR
static String	INPUT_FILENAME
static String	OUTPUT_FILENAME
static String	OUTPUT_FORMAT

Constructor Summary

Constructors

Constructor and Description
MuscleSettings()
MuscleSettings(XMLTag inXMLTag)

Method Summary

Modifier and Type	Method and Description
String	getCommandLineParams()
static String	getDefaultExecutable()
static File	getDefaultExecutableDir()
String	getExecutable()
File	getExecutableDir()
File	getInputFile()
File	getOutputFile()
MuscleOutputFormat	getOutputFormat()
protected void	init() For subclasses to override.
MuscleSettings	setCommandLineParams(String inValue) Additional (optional) command line parameters for the end of the Muscle command
static void	setDefaultExecutable(String inValue)
static void	setDefaultExecutableDir(File inValue)
MuscleSettings	setExecutable(String inValue)
MuscleSettings	setExecutableDir(File inValue)
MuscleSettings	setInputFile(File inValue)
MuscleSettings	setOutputFile(File inValue)
MuscleSettings	setOutputFormat(MuscleOutputFormat inValue)

Methods inherited from class com.hfg.setting.Settings

add, clone, get, name, setName, setTagName, size, toXMLTag

Methods inherited from class java.lang.Object

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

Field Detail

EXECUTABLE_DIR

public static final String EXECUTABLE_DIR

See Also:

Constant Field Values

EXECUTABLE

public static final String EXECUTABLE

See Also:

Constant Field Values

INPUT_FILENAME

public static final String INPUT_FILENAME

See Also:

Constant Field Values

OUTPUT_FILENAME

public static final String OUTPUT_FILENAME

See Also:

Constant Field Values

OUTPUT_FORMAT

public static final String OUTPUT_FORMAT

See Also:

Constant Field Values

COMMAND_LINE_PARAMS

public static final String COMMAND_LINE_PARAMS

See Also:

Constant Field Values

Constructor Detail

MuscleSettings

public MuscleSettings()

MuscleSettings

public MuscleSettings(XMLTag inXMLTag)

Method Detail

init

protected void init()

Description copied from class: Settings

For subclasses to override.

Overrides:

init in class Settings

setDefaultExecutableDir

public static void setDefaultExecutableDir(File inValue)

getDefaultExecutableDir

public static File getDefaultExecutableDir()

setDefaultExecutable

public static void setDefaultExecutable(String inValue)

getDefaultExecutable

public static String getDefaultExecutable()

getExecutableDir

public File getExecutableDir()

setExecutableDir

public MuscleSettings setExecutableDir(File inValue)

getExecutable

public String getExecutable()

setExecutable

public MuscleSettings setExecutable(String inValue)

getInputFile

public File getInputFile()

setInputFile

public MuscleSettings setInputFile(File inValue)

getOutputFile

public File getOutputFile()

setOutputFile

public MuscleSettings setOutputFile(File inValue)

getOutputFormat

public MuscleOutputFormat getOutputFormat()

setOutputFormat

public MuscleSettings setOutputFormat(MuscleOutputFormat inValue)

getCommandLineParams

public String getCommandLineParams()

setCommandLineParams

public MuscleSettings setCommandLineParams(String inValue)

Additional (optional) command line parameters for the end of the Muscle command

Parameters:

inValue - the additional command line parameters to be appended to the end of the command

Returns:

this Settings object to enable chaining