phylosort.util
Class Config

java.lang.Object
  phylosort.util.Config

public final class Config
extends java.lang.Object

A singleton PhyloSort set of configurations

Version:

$Revision: 1.12 $

Author:

Ahmed Moustafa

Field Summary

static float	DEFAULT_MAXIMUM_AVERAGE_NUMBER_OF_COPIES Default maximum average number of copies
static int	DEFAULT_MAXIMUM_NUMBER_OF_TAXA Default maximum number of taxa
static float	DEFAULT_MINIMUM_BOOTSTRAP_SUPPORT Default minimum bootstrap support
static int	DEFAULT_MINIMUM_NUMBER_OF_TAXA Default minimum number of taxa
static java.lang.String	DEFAULT_MODE Default mode of operation
static java.lang.String	DEFAULT_ON_MATCH_ACTION Default on match action
static java.lang.String	DEFAULT_PHYLOSORT_FILE_NAME Default PhyloSort config file name
static java.lang.String	DEFAULT_REGEXP Default pattern for taxa extraction
static java.lang.String	DEFAULT_ROOT Default tree rerooting (midpoint)
static java.lang.String	PROPERTY_MAXIMUM_AVERAGE_NUMBER_OF_COPIES Property maximum average number of copies
static java.lang.String	PROPERTY_MAXIMUM_NUMBER_OF_TAXA Property maximum number of taxa
static java.lang.String	PROPERTY_MINIMUM_BOOTSTRAP_SUPPORT Property minimum bootstrap support
static java.lang.String	PROPERTY_MINIMUM_NUMBER_OF_TAXA Property minimum number of taxa
static java.lang.String	PROPERTY_MODE System property mode of operation
static java.lang.String	PROPERTY_MODE_EXCLUSIVE Exclusive mode of searching
static java.lang.String	PROPERTY_MODE_INCLUSIVE Inclusive mode of searching
static java.lang.String	PROPERTY_ON_MATCH_ACTION Property on match action
static java.lang.String	PROPERTY_ON_MATCH_ACTION_COPY On match action copy
static java.lang.String	PROPERTY_ON_MATCH_ACTION_COUNT On match action count
static java.lang.String	PROPERTY_ON_MATCH_ACTION_MOVE On match action copy
static java.lang.String	PROPERTY_REGEXP Property pattern for taxa extraction
static java.lang.String	PROPERTY_ROOT System property tree rooting
static java.lang.String	PROPERTY_ROOT_OUTGROUP_NO Tree rooting using an outgroup NO
static java.lang.String	PROPERTY_ROOT_OUTGROUP_YES Tree rooting using an outgroup YES
static java.lang.String	SYSTEM_PROPERTY_PHYLOSORT_CONFIG PhyloSort config system property

Method Summary

static Config	getInstance() Returns an instance of Config
float	getMaximumAverageNumberOfCopies() Returns the maximum average number of copies
int	getMaximumNumberOfTaxa() Returns the maximum number of taxa
float	getMinimumBootstrapSupport() Returns the minimum bootstrap support
int	getMinimumNumberOfTaxa() Returns the minimum number of taxa
java.lang.String	getMode() Returns mode
java.lang.String	getOnMatchAction() Returns on match action
java.util.regex.Pattern	getRegexp() Returns the taxa extraction regular expression
java.lang.String	getRoot() Returns rooting method
boolean	isExclusive() Returns true if the mode is set to "exclusive"
boolean	isMaximumAverageNumberOfCopiesOn() Returns true if the maximum number of copies is negative, otherwise false
boolean	isMaximumNumberOfTaxaOn() Returns true if the maximum bootstrap support is negative, otherwise false
boolean	isMinimumBootstrapSupportOn() Returns true if the minimum bootstrap support is negative, otherwise false
boolean	isMinimumNumberOfTaxaOn() Returns true if the minimum number of taxa is negative, otherwise false
boolean	isOutgroup() Returns the root boolean flag
static Config	load(java.lang.String filename) Loads configuration settings from a file
static void	save(java.io.File file)
void	setMaximumAverageNumberOfCopies(float maximumAverageNumberOfCopies) Sets the maximum average number of copies
void	setMaximumNumberOfTaxa(int maximumNumberOfTaxa) Sets the maximum number of taxa
void	setMinimumBootstrapSupport(float minimumBootstrapSupport) Sets the minimum bootstrap support
void	setMinimumNumberOfTaxa(int minimumNumberOfTaxa) Sets the minimum number of taxa
void	setMode(java.lang.String mode) Sets the mode
void	setOnMatchAction(java.lang.String onMatchAction) Sets the on match action
void	setOutgroup(boolean outgroup) Sets the rooting boolean flag
void	setRegexp(java.lang.String regexp) Sets the taxa extraction regular expression

Methods inherited from class java.lang.Object

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

Field Detail

SYSTEM_PROPERTY_PHYLOSORT_CONFIG

public static final java.lang.String SYSTEM_PROPERTY_PHYLOSORT_CONFIG

PhyloSort config system property

See Also:

Constant Field Values

DEFAULT_PHYLOSORT_FILE_NAME

public static final java.lang.String DEFAULT_PHYLOSORT_FILE_NAME

Default PhyloSort config file name

See Also:

Constant Field Values

PROPERTY_REGEXP

public static final java.lang.String PROPERTY_REGEXP

Property pattern for taxa extraction

See Also:

Constant Field Values

DEFAULT_REGEXP

public static final java.lang.String DEFAULT_REGEXP

Default pattern for taxa extraction

See Also:

Constant Field Values

PROPERTY_ROOT

public static final java.lang.String PROPERTY_ROOT

System property tree rooting

See Also:

Constant Field Values

PROPERTY_ROOT_OUTGROUP_NO

public static final java.lang.String PROPERTY_ROOT_OUTGROUP_NO

Tree rooting using an outgroup NO

See Also:

Constant Field Values

PROPERTY_ROOT_OUTGROUP_YES

public static final java.lang.String PROPERTY_ROOT_OUTGROUP_YES

Tree rooting using an outgroup YES

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Constant Field Values

DEFAULT_ROOT

public static final java.lang.String DEFAULT_ROOT

Default tree rerooting (midpoint)

See Also:

Constant Field Values

PROPERTY_MODE

public static final java.lang.String PROPERTY_MODE

System property mode of operation

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Constant Field Values

PROPERTY_MODE_EXCLUSIVE

public static final java.lang.String PROPERTY_MODE_EXCLUSIVE

Exclusive mode of searching

See Also:

Constant Field Values

PROPERTY_MODE_INCLUSIVE

public static final java.lang.String PROPERTY_MODE_INCLUSIVE

Inclusive mode of searching

See Also:

Constant Field Values

DEFAULT_MODE

public static final java.lang.String DEFAULT_MODE

Default mode of operation

See Also:

Constant Field Values

PROPERTY_MINIMUM_NUMBER_OF_TAXA

public static final java.lang.String PROPERTY_MINIMUM_NUMBER_OF_TAXA

Property minimum number of taxa

See Also:

Constant Field Values

DEFAULT_MINIMUM_NUMBER_OF_TAXA

public static final int DEFAULT_MINIMUM_NUMBER_OF_TAXA

Default minimum number of taxa

See Also:

Constant Field Values

PROPERTY_MAXIMUM_NUMBER_OF_TAXA

public static final java.lang.String PROPERTY_MAXIMUM_NUMBER_OF_TAXA

Property maximum number of taxa

See Also:

Constant Field Values

DEFAULT_MAXIMUM_NUMBER_OF_TAXA

public static final int DEFAULT_MAXIMUM_NUMBER_OF_TAXA

Default maximum number of taxa

See Also:

Constant Field Values

PROPERTY_MINIMUM_BOOTSTRAP_SUPPORT

public static final java.lang.String PROPERTY_MINIMUM_BOOTSTRAP_SUPPORT

Property minimum bootstrap support

See Also:

Constant Field Values

DEFAULT_MINIMUM_BOOTSTRAP_SUPPORT

public static final float DEFAULT_MINIMUM_BOOTSTRAP_SUPPORT

Default minimum bootstrap support

See Also:

Constant Field Values

PROPERTY_MAXIMUM_AVERAGE_NUMBER_OF_COPIES

public static final java.lang.String PROPERTY_MAXIMUM_AVERAGE_NUMBER_OF_COPIES

Property maximum average number of copies

See Also:

Constant Field Values

DEFAULT_MAXIMUM_AVERAGE_NUMBER_OF_COPIES

public static final float DEFAULT_MAXIMUM_AVERAGE_NUMBER_OF_COPIES

Default maximum average number of copies

See Also:

Constant Field Values

PROPERTY_ON_MATCH_ACTION

public static final java.lang.String PROPERTY_ON_MATCH_ACTION

Property on match action

See Also:

Constant Field Values

PROPERTY_ON_MATCH_ACTION_COPY

public static final java.lang.String PROPERTY_ON_MATCH_ACTION_COPY

On match action copy

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Constant Field Values

PROPERTY_ON_MATCH_ACTION_MOVE

public static final java.lang.String PROPERTY_ON_MATCH_ACTION_MOVE

On match action copy

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Constant Field Values

PROPERTY_ON_MATCH_ACTION_COUNT

public static final java.lang.String PROPERTY_ON_MATCH_ACTION_COUNT

On match action count

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Constant Field Values

DEFAULT_ON_MATCH_ACTION

public static final java.lang.String DEFAULT_ON_MATCH_ACTION

Default on match action

See Also:

Constant Field Values

Method Detail

getInstance

public static Config getInstance()

Returns an instance of Config

Returns:

Config

getRoot

public java.lang.String getRoot()

Returns rooting method

Returns:

Rooting method

getMode

public java.lang.String getMode()

Returns mode

Returns:

Mode

isExclusive

public boolean isExclusive()

Returns true if the mode is set to "exclusive"

Returns:

True if the mode is set to "exclusive"

getMaximumNumberOfTaxa

public int getMaximumNumberOfTaxa()

Returns the maximum number of taxa

Returns:

The maximum number of taxa

setMaximumNumberOfTaxa

public void setMaximumNumberOfTaxa(int maximumNumberOfTaxa)

Sets the maximum number of taxa

Parameters:

maximumNumberOfTaxa - The maximum number of taxa to set

isMaximumNumberOfTaxaOn

public boolean isMaximumNumberOfTaxaOn()

Returns true if the maximum bootstrap support is negative, otherwise false

Returns:

True if the maximum bootstrap support is negative, otherwise false

getMinimumBootstrapSupport

public float getMinimumBootstrapSupport()

Returns the minimum bootstrap support

Returns:

The minimum bootstrap support

setMinimumBootstrapSupport

public void setMinimumBootstrapSupport(float minimumBootstrapSupport)

Sets the minimum bootstrap support

Parameters:

minimumBootstrapSupport - The minimum bootstrap support to set

isMinimumBootstrapSupportOn

public boolean isMinimumBootstrapSupportOn()

Returns true if the minimum bootstrap support is negative, otherwise false

Returns:

True if the minimum bootstrap support is negative, otherwise false

getMinimumNumberOfTaxa

public int getMinimumNumberOfTaxa()

Returns the minimum number of taxa

Returns:

The minimum number of taxa

setMinimumNumberOfTaxa

public void setMinimumNumberOfTaxa(int minimumNumberOfTaxa)

Sets the minimum number of taxa

Parameters:

minimumNumberOfTaxa - The minimum number of taxa to set

isMinimumNumberOfTaxaOn

public boolean isMinimumNumberOfTaxaOn()

Returns true if the minimum number of taxa is negative, otherwise false

Returns:

True if the minimum number of taxa is negative, otherwise false

setMode

public void setMode(java.lang.String mode)
             throws java.lang.Exception

Sets the mode

Parameters:

mode - The mode to set

Throws:

java.lang.Exception

setOnMatchAction

public void setOnMatchAction(java.lang.String onMatchAction)
                      throws java.lang.Exception

Sets the on match action

Parameters:

onMatchAction - The on match action to set

Throws:

java.lang.Exception

getRegexp

public java.util.regex.Pattern getRegexp()

Returns the taxa extraction regular expression

Returns:

The taxa extraction regular expression

setRegexp

public void setRegexp(java.lang.String regexp)

Sets the taxa extraction regular expression

Parameters:

regexp - Regular expression

load

public static Config load(java.lang.String filename)
                   throws java.lang.Exception

Loads configuration settings from a file

Parameters:

filename - File name

Returns:

Instance of Config loaded from a file

Throws:

java.lang.Exception

save

public static void save(java.io.File file)
                 throws java.lang.Exception

Throws:

java.lang.Exception

isOutgroup

public boolean isOutgroup()

Returns the root boolean flag

Returns:

True if the current rooting option is yes and false if it is no

setOutgroup

public void setOutgroup(boolean outgroup)

Sets the rooting boolean flag

Parameters:

outgroup - True (=> root by an outgroup) or false (=> do not root)

getMaximumAverageNumberOfCopies

public float getMaximumAverageNumberOfCopies()

Returns the maximum average number of copies

Returns:

The maximum average number of copies

setMaximumAverageNumberOfCopies

public void setMaximumAverageNumberOfCopies(float maximumAverageNumberOfCopies)

Sets the maximum average number of copies

Parameters:

maximumAverageNumberOfCopies - the maximum average number of copies to set

isMaximumAverageNumberOfCopiesOn

public boolean isMaximumAverageNumberOfCopiesOn()

Returns true if the maximum number of copies is negative, otherwise false

Returns:

True if the maximum number of copies is negative, otherwise false

getOnMatchAction

public java.lang.String getOnMatchAction()

Returns on match action

Returns:

On match action