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 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 itselfTableReport interface for classes with data that can be presented in tables -
Classes in pal.misc used by pal.coalescent Class Description IdGroup An indexed group of identifiers.Parameterized interface for class with (optimizable) parametersReport interface for classes that can print out a human readable report of itselfSummarizable interface for classes that can provide summariesTimeOrderCharacterData Character data that expresses an order through time.Units interface holding unit constantsUnitsProvider interface for classes that can provide the related Units used, (as -
Classes in pal.misc used by pal.distance Class Description Identifier An identifier for some sampled data.IdGroup An indexed group of identifiers. -
Classes in pal.misc used by pal.eval Class Description NeoParameterized interface for class with (optimizable) parameters.PalObjectEvent An event used by PalObjectListenersPalObjectListener Defines objects that monitor certain PalObjects for changesParameterized interface for class with (optimizable) parametersTimeOrderCharacterData Character data that expresses an order through time. -
Classes in pal.misc used by pal.gui Class 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 Description PalObjectListener Defines objects that monitor certain PalObjects for changesParameterized interface for class with (optimizable) parametersReport interface for classes that can print out a human readable report of itselfSampleInformation Title: SampleInformationSummarizable interface for classes that can provide summariesTimeOrderCharacterData Character data that expresses an order through time.Units interface holding unit constants -
Classes in pal.misc used by pal.misc Class Description BranchLimits limits for branch lengthsExternalParameterListener Defines objects that listen to exteneral ParameterEventsIdentifier 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 accessMutableDouble Nameable interface for classes that can be named.NeoParameterized interface for class with (optimizable) parameters.PalObjectEvent An event used by PalObjectListenersPalObjectListener Defines objects that monitor certain PalObjects for changesPalObjectListener.EventGenerator A base class for classes that fire PalObject eventsParameterEvent An event used by ExternalParameterListenersParameterized interface for class with (optimizable) parametersSampleInformation Title: SampleInformationSummarizable interface for classes that can provide summariesTimeOrderCharacterData Character data that expresses an order through time.Units interface holding unit constantsUnitsProvider interface for classes that can provide the related Units used, (as -
Classes in pal.misc used by pal.popgen Class Description TableReport interface for classes with data that can be presented in tables -
Classes in pal.misc used by pal.statistics Class Description Report interface for classes that can print out a human readable report of itself -
Classes in pal.misc used by pal.substmodel Class Description ExternalParameterListener Defines objects that listen to exteneral ParameterEventsMutableDouble NamedParameterized interface for class with (optimizable) named parametersNeoParameterized interface for class with (optimizable) parameters.PalObjectEvent An event used by PalObjectListenersPalObjectListener Defines objects that monitor certain PalObjects for changesPalObjectListener.EventGenerator A base class for classes that fire PalObject eventsParameterEvent An event used by ExternalParameterListenersParameterized interface for class with (optimizable) parametersParameterized.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 itselfTimeOrderCharacterData Character data that expresses an order through time. -
Classes in pal.misc used by pal.supgma Class Description IdGroup An indexed group of identifiers.Report interface for classes that can print out a human readable report of itselfTimeOrderCharacterData Character data that expresses an order through time.Units interface holding unit constantsUnitsProvider interface for classes that can provide the related Units used, (as -
Classes in pal.misc used by pal.tree Class Description Identifier An identifier for some sampled data.IdGroup An indexed group of identifiers.LabelMapping Parameterized interface for class with (optimizable) parametersReport interface for classes that can print out a human readable report of itselfTimeOrderCharacterData Character data that expresses an order through time.Units interface holding unit constantsUnitsProvider interface for classes that can provide the related Units used, (as -
Classes in pal.misc used by pal.treesearch Class Description NeoParameterized interface for class with (optimizable) parameters.SampleInformation Title: SampleInformation -
Classes in pal.misc used by pal.xml Class 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.