mesquite.categ.lib
Class DNACharacterHistory

java.lang.Object
  mesquite.lib.characters.CharacterStates
      mesquite.categ.lib.CategoricalStates
          mesquite.categ.lib.CategoricalDistribution
              mesquite.categ.lib.CategoricalAdjustable
                  mesquite.categ.lib.CategoricalHistory
                      mesquite.categ.lib.DNACharacterHistory

All Implemented Interfaces:

AdjustableDistribution, CharacterDistribution, CharacterHistory, CharacterStatesHolder, Listable, Renamable, WithStringDetails

Direct Known Subclasses:

RNACharacterHistory

public class DNACharacterHistory
extends CategoricalHistory

Field Summary

Fields inherited from class mesquite.categ.lib.CategoricalAdjustable

numNodes, states

Fields inherited from class mesquite.categ.lib.CategoricalStates

allStates, enforcedMaxState, extraFrequencies, extraFrequencyColors, extraFrequencyNames, frequencies, maxFound, maxState, minFound, minState

Fields inherited from class mesquite.lib.characters.CharacterStates

characterNumber, data, totalCreated

Constructor Summary

DNACharacterHistory(Taxa taxa)

DNACharacterHistory(Taxa taxa, int num)

Method Summary

CharacterHistory	adjustHistorySize(Tree tree, CharacterHistory charStates) This readjust procedure can be called to readjust the size of storage of states of a character for nodes.
CharacterHistory	clone(CharacterHistory s) clone this; if passed s is not null, place the clone there (so as to avoid creating new object)
long	fullSet() Returns full set of allowed states
long	getAllStates() returns the union of all state sets
java.lang.Class	getCharacterDataClass() returns the corresponding CharacterData subclass
CharacterState	getCharacterState() returns blank CharacterState object
CharacterState	getCharacterState(CharacterState cs, int N) returns CharacterState at node N
MesquiteColorTable	getColorTable(MesquiteColorTable colorTable)
java.lang.String	getDataTypeName() returns the name of the type of data stored
java.awt.Color	getDefaultColor(int maxState, int istate) Places into ColorDistribution the colors at the node, and returns the number of colors.
int	getLegendStates(java.awt.Color[] cs, java.lang.String[] stateNames, java.awt.Point[] tableMappings, MesquiteColorTable stateColors) Get the information about states occurring in this object for a legend.
java.lang.Class	getStateClass() Indicates the type of character stored
CategoricalAdjustable	makeAdjustable(Taxa taxa)
CharacterHistory	makeHistory(Tree tree)
void	prepareColors(Tree tree, int drawnRoot) Must be called before colors for states are used (e.g., before a tree is shaded).
java.lang.String	toString() returns string describing states at nodes.
java.lang.String	toString(int node, java.lang.String lineEnding) returns string describing character states at node

Methods inherited from class mesquite.categ.lib.CategoricalHistory

addInternodeEvent, adjustSize, deassignStates, getColorsAtNode, getColorSequenceAtNode, getColorsOfState, getInternodeEvent, getInternodeHistoryVector, getNumberOfEvents, getObservedStates, getStatesAtTips, polymorphToUncertainties, prepareInternodeHistories, setObservedStates

Methods inherited from class mesquite.categ.lib.CategoricalAdjustable

adjustSize, getNumNodes, getNumTaxa, getState, setCharacterState, setState, setStates, setWatchPoint, tradeStatesBetweenTaxa

Methods inherited from class mesquite.categ.lib.CategoricalDistribution

getAdjustableClone, getMaxState, hasInapplicable, hasInapplicable, hasMissing, hasMissing, hasMultipleStatesInTaxon, hasMultipleStatesInTaxon, isBinary, isBinary, isBinaryCombinable, isBinaryNoMissing, isConstant, isConstant

Methods inherited from class mesquite.categ.lib.CategoricalStates

copyExtraFrequencies, copyFrequencies, disposeExtraFrequencies, disposeFrequencies, extraFrequenciesExist, firstIsGreater, frequenciesExist, getAllStates, getDefaultModel, getExtraFrequencies, getExtraFrequency, getExtraFrequencyColors, getExtraFrequencyNames, getExtraNumFreqCategories, getFrequencies, getFrequency, getNumFreqCategories, getSetFromFrequencies, isInapplicable, isUnassigned, isUncertain, logStates, setExtraFrequencies, setExtraFrequency, setExtraFrequencyColors, setExtraFrequencyNames, setFrequencies, setFrequency, setNumExtraFreqCategories, setNumFreqCategories, statesEqual

Methods inherited from class mesquite.lib.characters.CharacterStates

checkIllegalNode, getName, getParentCharacter, getParentData, getTaxa, makeCharacterState, setName, setParentCharacter, setParentData, setTaxa, toExternal, toInternal, toStringWithDetails

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Methods inherited from interface mesquite.lib.characters.AdjustableDistribution

adjustSize, setCharacterState, setParentCharacter, setParentData, tradeStatesBetweenTaxa

Methods inherited from interface mesquite.lib.characters.CharacterStatesHolder

firstIsGreater, getDefaultModel, getNumNodes, getNumTaxa, getParentCharacter, getParentData, getTaxa, isInapplicable, isUnassigned, isUncertain, logStates, statesEqual, toStringWithDetails

Methods inherited from interface mesquite.lib.Listable

getName

Methods inherited from interface mesquite.lib.Renamable

setName

Constructor Detail

DNACharacterHistory

public DNACharacterHistory(Taxa taxa)

DNACharacterHistory

public DNACharacterHistory(Taxa taxa,
                           int num)

Method Detail

getCharacterState

public CharacterState getCharacterState()

returns blank CharacterState object

Specified by:

getCharacterState in interface CharacterStatesHolder

Overrides:

getCharacterState in class CategoricalStates

getStateClass

public java.lang.Class getStateClass()

Indicates the type of character stored

Specified by:

getStateClass in interface CharacterStatesHolder

Overrides:

getStateClass in class CategoricalStates

getCharacterDataClass

public java.lang.Class getCharacterDataClass()

returns the corresponding CharacterData subclass

Specified by:

getCharacterDataClass in interface CharacterStatesHolder

Overrides:

getCharacterDataClass in class CategoricalStates

fullSet

public long fullSet()

Returns full set of allowed states

Overrides:

fullSet in class CategoricalDistribution

getDataTypeName

public java.lang.String getDataTypeName()

returns the name of the type of data stored

Overrides:

getDataTypeName in class CategoricalStates

getCharacterState

public CharacterState getCharacterState(CharacterState cs,
                                        int N)

returns CharacterState at node N

Specified by:

getCharacterState in interface CharacterStatesHolder

Overrides:

getCharacterState in class CategoricalStates

getAllStates

public long getAllStates()

returns the union of all state sets

Overrides:

getAllStates in class CategoricalStates

clone

public CharacterHistory clone(CharacterHistory s)

clone this; if passed s is not null, place the clone there (so as to avoid creating new object)

Specified by:

clone in interface CharacterHistory

Overrides:

clone in class CategoricalHistory

getDefaultColor

public java.awt.Color getDefaultColor(int maxState,
                                      int istate)

Description copied from class: CategoricalHistory

Places into ColorDistribution the colors at the node, and returns the number of colors. Uses passed stateColors as color key. If null is passed, uses color system of parent data (using maxState of this StsOfCharcter) or, if there is not parent data object, the default colors. * public int getColorsAtNode(int node, ColorDistribution colors,MesquiteColorTable stateColors, boolean showWeights) { return getColorsAtNode(node, colors, stateColors, showWeights, MesquiteColorTable.DEFAULT); }

Overrides:

getDefaultColor in class CategoricalHistory

prepareColors

public void prepareColors(Tree tree,
                          int drawnRoot)

Must be called before colors for states are used (e.g., before a tree is shaded). Goes through all nodes to find states present, to set minima and maxima and record all states present. This allows the color range to be known before colors for particular states are requested by a tree shade, for example.

Specified by:

prepareColors in interface CharacterHistory

Overrides:

prepareColors in class CategoricalHistory

getColorTable

public MesquiteColorTable getColorTable(MesquiteColorTable colorTable)

Specified by:

getColorTable in interface CharacterHistory

Overrides:

getColorTable in class CategoricalHistory

getLegendStates

public int getLegendStates(java.awt.Color[] cs,
                           java.lang.String[] stateNames,
                           java.awt.Point[] tableMappings,
                           MesquiteColorTable stateColors)

Description copied from class: CategoricalHistory

Get the information about states occurring in this object for a legend. Colors and state names of states are place in the passed array. The colors for states are taken from the passed MesquiteColorTable.

Specified by:

getLegendStates in interface CharacterHistory

Overrides:

getLegendStates in class CategoricalHistory

toString

public java.lang.String toString(int node,
                                 java.lang.String lineEnding)

returns string describing character states at node

Specified by:

toString in interface CharacterStatesHolder

Overrides:

toString in class CategoricalHistory

toString

public java.lang.String toString()

returns string describing states at nodes.

Overrides:

toString in class CategoricalStates

adjustHistorySize

public CharacterHistory adjustHistorySize(Tree tree,
                                          CharacterHistory charStates)

This readjust procedure can be called to readjust the size of storage of states of a character for nodes.

Specified by:

adjustHistorySize in interface CharacterDistribution

Overrides:

adjustHistorySize in class CategoricalDistribution

makeHistory

public CharacterHistory makeHistory(Tree tree)

Overrides:

makeHistory in class CategoricalHistory

makeAdjustable

public CategoricalAdjustable makeAdjustable(Taxa taxa)

Overrides:

makeAdjustable in class CategoricalDistribution