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.