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Packages that use pal.misc | |
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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 | |
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Identifier
An identifier for some sampled data. |
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IdGroup
An indexed group of identifiers. |
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LabelMapping
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Report
interface for classes that can print out a human readable report of itself |
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TableReport
interface for classes with data that can be presented in tables |
Classes in pal.misc used by pal.coalescent | |
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IdGroup
An indexed group of identifiers. |
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Parameterized
interface for class with (optimizable) parameters |
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Report
interface for classes that can print out a human readable report of itself |
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Summarizable
interface for classes that can provide summaries |
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TimeOrderCharacterData
Character data that expresses an order through time. |
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Units
interface holding unit constants |
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UnitsProvider
interface for classes that can provide the related Units used, (as |
Classes in pal.misc used by pal.distance | |
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Identifier
An identifier for some sampled data. |
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IdGroup
An indexed group of identifiers. |
Classes in pal.misc used by pal.eval | |
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NeoParameterized
interface for class with (optimizable) parameters. |
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PalObjectEvent
An event used by PalObjectListeners |
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PalObjectListener
Defines objects that monitor certain PalObjects for changes |
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Parameterized
interface for class with (optimizable) parameters |
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TimeOrderCharacterData
Character data that expresses an order through time. |
Classes in pal.misc used by pal.gui | |
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Identifier
An identifier for some sampled data. |
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LabelMapping
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TimeOrderCharacterData
Character data that expresses an order through time. |
Classes in pal.misc used by pal.mep | |
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PalObjectListener
Defines objects that monitor certain PalObjects for changes |
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Parameterized
interface for class with (optimizable) parameters |
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Report
interface for classes that can print out a human readable report of itself |
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SampleInformation
Title: SampleInformation |
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Summarizable
interface for classes that can provide summaries |
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TimeOrderCharacterData
Character data that expresses an order through time. |
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Units
interface holding unit constants |
Classes in pal.misc used by pal.misc | |
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BranchLimits
limits for branch lengths |
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ExternalParameterListener
Defines objects that listen to exteneral ParameterEvents |
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Identifier
An identifier for some sampled data. |
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IdGroup
An indexed group of identifiers. |
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IndividualParameterHandler
Title: |
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IndividualParameterHandler.Listener
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LabelMapping
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LabelMapping.Relabeller
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MultiParameterized.ParameterAccessWatcher
An interface for classes that wish to find out about particular parameter access |
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MutableDouble
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Nameable
interface for classes that can be named. |
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NeoParameterized
interface for class with (optimizable) parameters. |
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PalObjectEvent
An event used by PalObjectListeners |
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PalObjectListener
Defines objects that monitor certain PalObjects for changes |
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PalObjectListener.EventGenerator
A base class for classes that fire PalObject events |
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ParameterEvent
An event used by ExternalParameterListeners |
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Parameterized
interface for class with (optimizable) parameters |
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SampleInformation
Title: SampleInformation |
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Summarizable
interface for classes that can provide summaries |
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TimeOrderCharacterData
Character data that expresses an order through time. |
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Units
interface holding unit constants |
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UnitsProvider
interface for classes that can provide the related Units used, (as |
Classes in pal.misc used by pal.popgen | |
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TableReport
interface for classes with data that can be presented in tables |
Classes in pal.misc used by pal.statistics | |
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Report
interface for classes that can print out a human readable report of itself |
Classes in pal.misc used by pal.substmodel | |
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ExternalParameterListener
Defines objects that listen to exteneral ParameterEvents |
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MutableDouble
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NamedParameterized
interface for class with (optimizable) named parameters |
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NeoParameterized
interface for class with (optimizable) parameters. |
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PalObjectEvent
An event used by PalObjectListeners |
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PalObjectListener
Defines objects that monitor certain PalObjects for changes |
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PalObjectListener.EventGenerator
A base class for classes that fire PalObject events |
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ParameterEvent
An event used by ExternalParameterListeners |
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Parameterized
interface for class with (optimizable) parameters |
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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) |
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Report
interface for classes that can print out a human readable report of itself |
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TimeOrderCharacterData
Character data that expresses an order through time. |
Classes in pal.misc used by pal.supgma | |
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IdGroup
An indexed group of identifiers. |
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Report
interface for classes that can print out a human readable report of itself |
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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 | |
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Identifier
An identifier for some sampled data. |
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IdGroup
An indexed group of identifiers. |
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LabelMapping
|
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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 | |
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NeoParameterized
interface for class with (optimizable) parameters. |
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SampleInformation
Title: SampleInformation |
Classes in pal.misc used by pal.xml | |
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Attribute
An immutable attribute has a name and value. |
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Identifier
An identifier for some sampled data. |
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TimeOrderCharacterData
Character data that expresses an order through time. |
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