PhyloSort

phylosort.util
Class Config

java.lang.Object
  extended by 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

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Constant Field Values

DEFAULT_REGEXP

public static final java.lang.String DEFAULT_REGEXP
Default pattern for taxa extraction

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Constant Field Values

PROPERTY_ROOT

public static final java.lang.String PROPERTY_ROOT
System property tree rooting

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Constant Field Values

PROPERTY_ROOT_OUTGROUP_NO

public static final java.lang.String PROPERTY_ROOT_OUTGROUP_NO
Tree rooting using an outgroup NO

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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)

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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

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Constant Field Values

PROPERTY_MODE_INCLUSIVE

public static final java.lang.String PROPERTY_MODE_INCLUSIVE
Inclusive mode of searching

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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

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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

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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

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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

PhyloSort

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