Uses of Package
pal.misc

Packages that use pal.misc

Package	Description
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

Class and Description
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

Class and Description
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

Class and Description
Identifier An identifier for some sampled data.
IdGroup An indexed group of identifiers.

Classes in pal.misc used by pal.eval

Class and Description
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

Class and Description
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

Class and Description
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

Class and Description
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

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

Classes in pal.misc used by pal.statistics

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

Classes in pal.misc used by pal.substmodel

Class and Description
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

Class and Description
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

Class and Description
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

Class and Description
NeoParameterized interface for class with (optimizable) parameters.
SampleInformation Title: SampleInformation

Classes in pal.misc used by pal.xml

Class and Description
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.