Uses of Package
pal.misc

Packages that use pal.misc

pal.alignment	Classes dealing with sequence alignments, including methods for reading and printing in several possible formats, as well as rearranging and concatenating.
pal.coalescent	Classes to model population genetic processes using the coalescent.
pal.distance	Classes for reading and generating distance matrices, including computation of pairwise distances for sequence data (maximum-likelihood and observed distances).
pal.eval	Classes for evaluating evolutionary hypothesis (chi-square and likelihood criteria) and estimating model parameters.
pal.gui	GUI components for some special objects (e.g., trees).
pal.mep	Classes for the analysis of "measurably evolving populations" (mep).
pal.misc	Classes that don't fit elsewhere ;^)
pal.popgen	Classes for providing 'classical' population genetics analyses.
pal.statistics	Classes with useful for statistics (normal distribution, Gamma distribution, chi-square distribution, exponential distribution, likelihood-ratio test, chi-square test, descriptive statistics, bootstrap estimators etc.)
pal.substmodel	Classes describing substitution models, i.e.
pal.supgma
pal.tree	Classes for providing the data structure of trees, for constructing and modifying trees, and for parameterizing trees (e.g., clock constraint).
pal.treesearch
pal.xml	Utility classes for converting PAL objects to and from XML documents.

Classes in pal.misc used by pal.alignment

Identifier
An identifier for some sampled data.

IdGroup
An indexed group of identifiers.

LabelMapping

Report
interface for classes that can print out a human readable report of itself

TableReport
interface for classes with data that can be presented in tables

Classes in pal.misc used by pal.coalescent

IdGroup
An indexed group of identifiers.

Parameterized
interface for class with (optimizable) parameters

Report
interface for classes that can print out a human readable report of itself

Summarizable
interface for classes that can provide summaries

TimeOrderCharacterData
Character data that expresses an order through time.

Units
interface holding unit constants

UnitsProvider
interface for classes that can provide the related Units used, (as

Classes in pal.misc used by pal.distance

Identifier
An identifier for some sampled data.

IdGroup
An indexed group of identifiers.

Classes in pal.misc used by pal.eval

NeoParameterized
interface for class with (optimizable) parameters.

PalObjectEvent
An event used by PalObjectListeners

PalObjectListener
Defines objects that monitor certain PalObjects for changes

Parameterized
interface for class with (optimizable) parameters

TimeOrderCharacterData
Character data that expresses an order through time.

Classes in pal.misc used by pal.gui

Identifier
An identifier for some sampled data.

LabelMapping

TimeOrderCharacterData
Character data that expresses an order through time.

Classes in pal.misc used by pal.mep

PalObjectListener
Defines objects that monitor certain PalObjects for changes

Parameterized
interface for class with (optimizable) parameters

Report
interface for classes that can print out a human readable report of itself

SampleInformation
Title: SampleInformation

Summarizable
interface for classes that can provide summaries

TimeOrderCharacterData
Character data that expresses an order through time.

Units
interface holding unit constants

Classes in pal.misc used by pal.misc

BranchLimits
limits for branch lengths

ExternalParameterListener
Defines objects that listen to exteneral ParameterEvents

Identifier
An identifier for some sampled data.

IdGroup
An indexed group of identifiers.

IndividualParameterHandler
Title:

IndividualParameterHandler.Listener

LabelMapping

LabelMapping.Relabeller

MultiParameterized.ParameterAccessWatcher
An interface for classes that wish to find out about particular parameter access

MutableDouble

Nameable
interface for classes that can be named.

NeoParameterized
interface for class with (optimizable) parameters.

PalObjectEvent
An event used by PalObjectListeners

PalObjectListener
Defines objects that monitor certain PalObjects for changes

PalObjectListener.EventGenerator
A base class for classes that fire PalObject events

ParameterEvent
An event used by ExternalParameterListeners

Parameterized
interface for class with (optimizable) parameters

SampleInformation
Title: SampleInformation

Summarizable
interface for classes that can provide summaries

TimeOrderCharacterData
Character data that expresses an order through time.

Units
interface holding unit constants

UnitsProvider
interface for classes that can provide the related Units used, (as

Classes in pal.misc used by pal.popgen

TableReport
interface for classes with data that can be presented in tables

Classes in pal.misc used by pal.statistics

Report
interface for classes that can print out a human readable report of itself

Classes in pal.misc used by pal.substmodel

ExternalParameterListener
Defines objects that listen to exteneral ParameterEvents

MutableDouble

NamedParameterized
interface for class with (optimizable) named parameters

NeoParameterized
interface for class with (optimizable) parameters.

PalObjectEvent
An event used by PalObjectListeners

PalObjectListener
Defines objects that monitor certain PalObjects for changes

PalObjectListener.EventGenerator
A base class for classes that fire PalObject events

ParameterEvent
An event used by ExternalParameterListeners

Parameterized
interface for class with (optimizable) parameters

Parameterized.ParameterizedUser
A Utility class for using as the superclass to subclasses which work by adding functionality to a general Parameterized object (the base Parameterized object)

Report
interface for classes that can print out a human readable report of itself

TimeOrderCharacterData
Character data that expresses an order through time.

Classes in pal.misc used by pal.supgma

IdGroup
An indexed group of identifiers.

Report
interface for classes that can print out a human readable report of itself

TimeOrderCharacterData
Character data that expresses an order through time.

Units
interface holding unit constants

UnitsProvider
interface for classes that can provide the related Units used, (as

Classes in pal.misc used by pal.tree

Identifier
An identifier for some sampled data.

IdGroup
An indexed group of identifiers.

LabelMapping

Parameterized
interface for class with (optimizable) parameters

Report
interface for classes that can print out a human readable report of itself

TimeOrderCharacterData
Character data that expresses an order through time.

Units
interface holding unit constants

UnitsProvider
interface for classes that can provide the related Units used, (as

Classes in pal.misc used by pal.treesearch

NeoParameterized
interface for class with (optimizable) parameters.

SampleInformation
Title: SampleInformation

Classes in pal.misc used by pal.xml

Attribute
An immutable attribute has a name and value.

Identifier
An identifier for some sampled data.

TimeOrderCharacterData
Character data that expresses an order through time.