mesquite.cont.lib
Class ContinuousState

java.lang.Object
  mesquite.lib.characters.CharacterState
      mesquite.cont.lib.ContinuousState

All Implemented Interfaces:

ItemContainer

Direct Known Subclasses:

GeographicState

public class ContinuousState
extends CharacterState
implements ItemContainer

This class provides some basic utilities for Continuous characters. It represents the entry for one character and one taxon. Thus, it can contain more than one item (min, max, mean, variance, etc.).

Field Summary

static double	impossible The state (MesquiteDouble.impossible) that corresponds to an impossible value.
static double	inapplicable The state (MesquiteDouble.inapplicable) that corresponds to a gap (inapplicable data).
static double	infinite The state (MesquiteDouble.infinite) that corresponds to infinite.
static int	MAXITEMS The maximum allowed number of items
static double	unassigned The state (MesquiteDouble.unassigned) that corresponds to missing data.

Constructor Summary

ContinuousState()

ContinuousState(double value)

Method Summary

static double	absolute(double d)
boolean	equals(CharacterState s) returns true iff state sets are same
boolean	equals(CharacterState s, boolean allowMissing) returns true iff state sets are same
boolean	equals(CharacterState s, boolean allowMissing, boolean allowNearExact) returns true iff state sets are same
java.lang.Class	getCharacterDataClass() returns the subclass of CharacterData that is equivalent to this character type (i.e., in which sort of matrix would this character state reside?
java.lang.Class	getCharacterDistributionClass() returns the subclass of CharacterDistribution that is equivalent to this character type (i.e., in which sort of Distribution would this character state reside?.
java.lang.Class	getCharacterHistoryClass() returns the subclass of CharacterHistory that is equivalent to this character type (i.e., in which sort of Distribution would this character state reside?
java.lang.String	getDataTypeName() returns the name of the type of data stored
java.lang.String	getItemName(int n) gets name of item n
int	getItemNumber(NameReference nr) returns which item number has NameReference nr nr
NameReference	getItemReference(int n) gets NameReferece of item n
NameReference	getItemReference(java.lang.String name) gets NameReferece of item n
java.lang.Class	getMCharactersDistributionClass() returns the subclass of MCharactersDistribution that is equivalent to this character type (i.e., in which sort of matrix would this character state reside?
int	getNumItems() returns the number of items (min, max, mean, variance, etc.) in this state
double	getValue(int n) gets the value of item # n
double	getValue(NameReference nr) gets the name value of item with NameReference NR
boolean	isCombinable() returns true if at least one item is combinable (i.e.
static boolean	isCombinable(double d) returns whether value is combinable (i.e.
boolean	isImpossible() returns true if at least one item is invalid
static boolean	isImpossible(double s) returns true if value is invalid
boolean	isInapplicable() returns true if all items are inapplicable
static boolean	isInapplicable(double s) returns true if inapplicable
boolean	isUnassigned() returns true if all items have missing data (unassigned)
static boolean	isUnassigned(double s) returns true if missing data (unassigned)
AdjustableDistribution	makeAdjustableDistribution(Taxa taxa, int numNodes) returns a AdjustableDistribution that is equivalent to this character type (i.e., in which sort of matrix would this character state reside?
CharacterHistory	makeCharacterHistory(Taxa taxa, int numNodes) returns a CharacterHistory that is equivalent to this character type (i.e., in which sort of matrix would this character state reside?
static double	maximum(double d1, double d2)
static double	minimum(double d1, double d2)
void	setItemReference(int n, NameReference nr) sets NameReference of item n
void	setItemsAs(ItemContainer iCont)
void	setNumItems(int n) sets the number of items in this state
void	setToInapplicable() sets the value to inapplicable
void	setToUnassigned() sets the value to unassigned
void	setValue(CharacterState cs) sets its value to the value in CharacterState passed to it
void	setValue(int n, double d) sets value of item n
void	setValue(java.lang.String st, CharacterData parentData) sets its value to the value given by the String passed to it
void	setValue(java.lang.String st, MesquiteInteger pos) sets its value to the value given by the String passed to it starting at position pos
java.lang.String	toDisplayString() Returns string as would be displayed to user (not necessarily internal shorthand).
java.lang.String	toString() returns string representation of the character state

Methods inherited from class mesquite.lib.characters.CharacterState

equals, makeMCharactersDistribution

Methods inherited from class java.lang.Object

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

Field Detail

unassigned

public static final double unassigned

The state (MesquiteDouble.unassigned) that corresponds to missing data.

See Also:

Constant Field Values

inapplicable

public static final double inapplicable

The state (MesquiteDouble.inapplicable) that corresponds to a gap (inapplicable data).

See Also:

Constant Field Values

infinite

public static final double infinite

The state (MesquiteDouble.infinite) that corresponds to infinite.

See Also:

Constant Field Values

impossible

public static final double impossible

The state (MesquiteDouble.impossible) that corresponds to an impossible value. This is returned when a value is invalid, e.g. a string is parsed for a number but no valid number is found.

See Also:

Constant Field Values

MAXITEMS

public static final int MAXITEMS

The maximum allowed number of items

See Also:

Constant Field Values

Constructor Detail

ContinuousState

public ContinuousState()

ContinuousState

public ContinuousState(double value)

Method Detail

getDataTypeName

public java.lang.String getDataTypeName()

returns the name of the type of data stored

Specified by:

getDataTypeName in class CharacterState

getNumItems

public int getNumItems()

returns the number of items (min, max, mean, variance, etc.) in this state

Specified by:

getNumItems in interface ItemContainer

setNumItems

public void setNumItems(int n)

sets the number of items in this state

getItemName

public java.lang.String getItemName(int n)

gets name of item n

Specified by:

getItemName in interface ItemContainer

getItemReference

public NameReference getItemReference(java.lang.String name)

gets NameReferece of item n

Specified by:

getItemReference in interface ItemContainer

getItemReference

public NameReference getItemReference(int n)

gets NameReferece of item n

Specified by:

getItemReference in interface ItemContainer

setItemReference

public void setItemReference(int n,
                             NameReference nr)

sets NameReference of item n

getItemNumber

public int getItemNumber(NameReference nr)

returns which item number has NameReference nr nr

Specified by:

getItemNumber in interface ItemContainer

setItemsAs

public void setItemsAs(ItemContainer iCont)

getCharacterDataClass

public java.lang.Class getCharacterDataClass()

Description copied from class: CharacterState

returns the subclass of CharacterData that is equivalent to this character type (i.e., in which sort of matrix would this character state reside?

Specified by:

getCharacterDataClass in class CharacterState

getMCharactersDistributionClass

public java.lang.Class getMCharactersDistributionClass()

Description copied from class: CharacterState

returns the subclass of MCharactersDistribution that is equivalent to this character type (i.e., in which sort of matrix would this character state reside?

Specified by:

getMCharactersDistributionClass in class CharacterState

getCharacterDistributionClass

public java.lang.Class getCharacterDistributionClass()

Description copied from class: CharacterState

returns the subclass of CharacterDistribution that is equivalent to this character type (i.e., in which sort of Distribution would this character state reside?. Should return an MAdjustableDistribution

Specified by:

getCharacterDistributionClass in class CharacterState

getCharacterHistoryClass

public java.lang.Class getCharacterHistoryClass()

Description copied from class: CharacterState

returns the subclass of CharacterHistory that is equivalent to this character type (i.e., in which sort of Distribution would this character state reside?

Specified by:

getCharacterHistoryClass in class CharacterState

makeAdjustableDistribution

public AdjustableDistribution makeAdjustableDistribution(Taxa taxa,
                                                         int numNodes)

Description copied from class: CharacterState

returns a AdjustableDistribution that is equivalent to this character type (i.e., in which sort of matrix would this character state reside?

Specified by:

makeAdjustableDistribution in class CharacterState

makeCharacterHistory

public CharacterHistory makeCharacterHistory(Taxa taxa,
                                             int numNodes)

Description copied from class: CharacterState

returns a CharacterHistory that is equivalent to this character type (i.e., in which sort of matrix would this character state reside?

Specified by:

makeCharacterHistory in class CharacterState

isUnassigned

public static boolean isUnassigned(double s)

returns true if missing data (unassigned)

isUnassigned

public boolean isUnassigned()

returns true if all items have missing data (unassigned)

Specified by:

isUnassigned in class CharacterState

isInapplicable

public static boolean isInapplicable(double s)

returns true if inapplicable

isInapplicable

public boolean isInapplicable()

returns true if all items are inapplicable

Specified by:

isInapplicable in class CharacterState

isImpossible

public static boolean isImpossible(double s)

returns true if value is invalid

isImpossible

public boolean isImpossible()

returns true if at least one item is invalid

Specified by:

isImpossible in class CharacterState

isCombinable

public boolean isCombinable()

returns true if at least one item is combinable (i.e. a valid assigned state).

Specified by:

isCombinable in class CharacterState

isCombinable

public static boolean isCombinable(double d)

returns whether value is combinable (i.e. a valid assigned state) or not.

equals

public boolean equals(CharacterState s)

returns true iff state sets are same

Specified by:

equals in class CharacterState

equals

public boolean equals(CharacterState s,
                      boolean allowMissing)

returns true iff state sets are same

Specified by:

equals in class CharacterState

equals

public boolean equals(CharacterState s,
                      boolean allowMissing,
                      boolean allowNearExact)

returns true iff state sets are same

Specified by:

equals in class CharacterState

absolute

public static double absolute(double d)

maximum

public static double maximum(double d1,
                             double d2)

minimum

public static double minimum(double d1,
                             double d2)

setToInapplicable

public void setToInapplicable()

sets the value to inapplicable

Specified by:

setToInapplicable in class CharacterState

setToUnassigned

public void setToUnassigned()

sets the value to unassigned

Specified by:

setToUnassigned in class CharacterState

setValue

public void setValue(int n,
                     double d)

sets value of item n

setValue

public void setValue(CharacterState cs)

Description copied from class: CharacterState

sets its value to the value in CharacterState passed to it

Specified by:

setValue in class CharacterState

setValue

public void setValue(java.lang.String st,
                     CharacterData parentData)

Description copied from class: CharacterState

sets its value to the value given by the String passed to it

Specified by:

setValue in class CharacterState

getValue

public double getValue(int n)

gets the value of item # n

getValue

public double getValue(NameReference nr)

gets the name value of item with NameReference NR

setValue

public void setValue(java.lang.String st,
                     MesquiteInteger pos)

Description copied from class: CharacterState

sets its value to the value given by the String passed to it starting at position pos

Specified by:

setValue in class CharacterState

toString

public java.lang.String toString()

Description copied from class: CharacterState

returns string representation of the character state

Specified by:

toString in class CharacterState

toDisplayString

public java.lang.String toDisplayString()

Returns string as would be displayed to user (not necessarily internal shorthand).

Specified by:

toDisplayString in class CharacterState