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NAMESPACE
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NAMESPACE
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exportPattern("^[^\\.]");
import(grid)
import(R.oo)
import(ape)
import(ggplot2)
import(R.methodsS3)
S3method('!=',Alphabet)
S3method('!=',Process)
S3method('==',Alphabet)
S3method('==',Process)
S3method(areSynonymous,CodonAlphabet)
S3method(as.character,Alphabet)
S3method(as.character,Event)
S3method(as.character,GeneralSubstitution)
S3method(as.character,PhyloSim)
S3method(as.character,Process)
S3method(as.character,QMatrix)
S3method(as.character,Sequence)
S3method(as.character,Site)
S3method(as.character,ToleranceSubstitution)
S3method(attachHookToNode,PhyloSim)
S3method(attachProcess,Sequence)
S3method(attachProcess,Site)
S3method(attachSeqToNode,PhyloSim)
S3method(BrownianPath,BrownianInsertor)
S3method(buildFromPAML,AminoAcidSubst)
S3method(buildFromPAML,CodonSubst)
S3method(checkConsistency,Alphabet)
S3method(checkConsistency,AminoAcidSubst)
S3method(checkConsistency,BinarySubst)
S3method(checkConsistency,BrownianInsertor)
S3method(checkConsistency,CodonAlphabet)
S3method(checkConsistency,CodonSequence)
S3method(checkConsistency,CodonSubst)
S3method(checkConsistency,CodonUNREST)
S3method(checkConsistency,ContinuousDeletor)
S3method(checkConsistency,ContinuousInsertor)
S3method(checkConsistency,DiscreteDeletor)
S3method(checkConsistency,DiscreteInsertor)
S3method(checkConsistency,Event)
S3method(checkConsistency,F81)
S3method(checkConsistency,F84)
S3method(checkConsistency,FastFieldDeletor)
S3method(checkConsistency,GeneralDeletor)
S3method(checkConsistency,GeneralInDel)
S3method(checkConsistency,GeneralInsertor)
S3method(checkConsistency,GeneralSubstitution)
S3method(checkConsistency,GTR)
S3method(checkConsistency,GY94)
S3method(checkConsistency,HKY)
S3method(checkConsistency,JC69)
S3method(checkConsistency,K80)
S3method(checkConsistency,K81)
S3method(checkConsistency,PhyloSim)
S3method(checkConsistency,Process)
S3method(checkConsistency,PSRoot)
S3method(checkConsistency,PSRootSummary)
S3method(checkConsistency,QMatrix)
S3method(checkConsistency,Sequence)
S3method(checkConsistency,Site)
S3method(checkConsistency,T92)
S3method(checkConsistency,TN93)
S3method(checkConsistency,ToleranceSubstitution)
S3method(checkConsistency,UNREST)
S3method(clearStates,Sequence)
S3method(clone,GeneralSubstitution)
S3method(clone,Process)
S3method(clone,Sequence)
S3method(clone,ToleranceSubstitution)
S3method(copySubSequence,Sequence)
S3method(Debug,PhyloSim)
S3method(deleteSubSequence,Sequence)
S3method(detachHookFromNode,PhyloSim)
S3method(detachProcess,Sequence)
S3method(detachProcess,Site)
S3method(detachSeqFromNode,PhyloSim)
S3method(enableVirtual,PSRoot)
S3method(exportStatTree,PhyloSim)
S3method(flagTotalRate,Site)
S3method(generateInsert,GeneralInsertor)
S3method(getAcceptBy,GeneralInDel)
S3method(getAcceptWin,GeneralInsertor)
S3method(getAlignment,PhyloSim)
S3method(getAlignmentLength,PhyloSim)
S3method(getAlphabet,GeneralSubstitution)
S3method(getAlphabet,Process)
S3method(getAlphabet,QMatrix)
S3method(getAlphabet,Site)
S3method(getAlphabet,ToleranceSubstitution)
S3method(getAlphabets,Sequence)
S3method(getAncestral,Sequence)
S3method(getAncestral,Site)
S3method(getBaseFreqs,F81)
S3method(getBaseFreqs,F84)
S3method(getBaseFreqs,GTR)
S3method(getBaseFreqs,HKY)
S3method(getBaseFreqs,K80)
S3method(getBaseFreqs,K81)
S3method(getBaseFreqs,TN93)
S3method(getBigRate,Sequence)
S3method(getBranchEvents,PhyloSim)
S3method(getCodonFreqs,GY94)
S3method(getComments,PSRoot)
S3method(getCumulativeRates,Sequence)
S3method(getCumulativeRatesFromRange,Sequence)
S3method(getDeletionTolerance,Sequence)
S3method(getDist,ContinuousDeletor)
S3method(getDist,ContinuousInsertor)
S3method(getEdge,PhyloSim)
S3method(getEdges,PhyloSim)
S3method(getEquDist,GeneralSubstitution)
S3method(getEquDist,ToleranceSubstitution)
S3method(getEventRate,GeneralSubstitution)
S3method(getEventRate,QMatrix)
S3method(getEventRate,ToleranceSubstitution)
S3method(getEventRateAtSite,GeneralSubstitution)
S3method(getEventRateAtSite,ToleranceSubstitution)
S3method(getEvents,Sequence)
S3method(getEvents,Site)
S3method(getEventsAtSite,FastFieldDeletor)
S3method(getEventsAtSite,GeneralDeletor)
S3method(getEventsAtSite,GeneralInsertor)
S3method(getEventsAtSite,GeneralSubstitution)
S3method(getEventsAtSite,GY94)
S3method(getEventsAtSite,Process)
S3method(getEventsAtSite,ToleranceSubstitution)
S3method(getGenerateBy,GeneralInsertor)
S3method(getHandler,Event)
S3method(getId,PhyloSim)
S3method(getId,Process)
S3method(getId,QMatrix)
S3method(getId,Sequence)
S3method(getInsertHook,GeneralInsertor)
S3method(getInsertionTolerance,Sequence)
S3method(getKappa,F84)
S3method(getKappa,GY94)
S3method(getLength,Sequence)
S3method(getLengthParam1,FastFieldDeletor)
S3method(getLengthParam2,FastFieldDeletor)
S3method(getLogFile,PhyloSim)
S3method(getLogLevel,PhyloSim)
S3method(getMatrix,QMatrix)
S3method(getMaxLength,ContinuousDeletor)
S3method(getMaxLength,ContinuousInsertor)
S3method(getMethodsList,PSRoot)
S3method(getName,Event)
S3method(getName,PhyloSim)
S3method(getName,Process)
S3method(getName,QMatrix)
S3method(getName,Sequence)
S3method(getNedges,PhyloSim)
S3method(getNodes,PhyloSim)
S3method(getNtips,PhyloSim)
S3method(getOmegas,CodonSequence)
S3method(getOmegas,Sequence)
S3method(getOmegaScalingFactor,GY94)
S3method(getParameterAtSite,Process)
S3method(getParameterAtSites,Sequence)
S3method(getPhylo,PhyloSim)
S3method(getPosition,Event)
S3method(getProbs,DiscreteDeletor)
S3method(getProbs,DiscreteInsertor)
S3method(getProcess,Event)
S3method(getProcess,QMatrix)
S3method(getProcesses,Sequence)
S3method(getProcesses,Site)
S3method(getProposeBy,GeneralInDel)
S3method(getQMatrix,GeneralSubstitution)
S3method(getQMatrix,ToleranceSubstitution)
S3method(getRate,Event)
S3method(getRate,GeneralInDel)
S3method(getRate,GeneralSubstitution)
S3method(getRate,QMatrix)
S3method(getRate,ToleranceSubstitution)
S3method(getRateList,GeneralSubstitution)
S3method(getRateList,QMatrix)
S3method(getRateList,ToleranceSubstitution)
S3method(getRateMultipliers,Sequence)
S3method(getRateParam,F81)
S3method(getRateParam,F84)
S3method(getRateParam,GTR)
S3method(getRateParam,HKY)
S3method(getRateParam,K80)
S3method(getRateParam,K81)
S3method(getRateParam,T92)
S3method(getRateParam,TN93)
S3method(getRateParamList,F81)
S3method(getRateParamList,F84)
S3method(getRateParamList,GTR)
S3method(getRateParamList,HKY)
S3method(getRateParamList,K80)
S3method(getRateParamList,K81)
S3method(getRateParamList,T92)
S3method(getRateParamList,TN93)
S3method(getRootNode,PhyloSim)
S3method(getRootSeq,PhyloSim)
S3method(getScale,BrownianInsertor)
S3method(getScaledMatrix,QMatrix)
S3method(getSeqFromNode,PhyloSim)
S3method(getSequence,Site)
S3method(getSequences,PhyloSim)
S3method(getSite,Event)
S3method(getSites,Sequence)
S3method(getSiteSpecificParamIds,Process)
S3method(getSiteSpecificParamList,Process)
S3method(getSize,Alphabet)
S3method(getSizes,DiscreteDeletor)
S3method(getSizes,DiscreteInsertor)
S3method(getState,Site)
S3method(getStates,Sequence)
S3method(getString,Sequence)
S3method(getSymbolFreqs,Sequence)
S3method(getSymbolLength,Alphabet)
S3method(getSymbols,Alphabet)
S3method(getTableId,CodonAlphabet)
S3method(getTemplateSeq,GeneralInsertor)
S3method(getTheta,T92)
S3method(getTipLabels,PhyloSim)
S3method(getTips,PhyloSim)
S3method(getToleranceMargin,FastFieldDeletor)
S3method(getTotalRate,Site)
S3method(getTotalRates,Sequence)
S3method(getTotalRatesFromRange,Sequence)
S3method(getTransTable,CodonAlphabet)
S3method(getTreeLength,PhyloSim)
S3method(getType,Alphabet)
S3method(getType,BrownianInsertor)
S3method(getType,FastFieldDeletor)
S3method(getUniqueAlphabets,Sequence)
S3method(getUniqueProcesses,Sequence)
S3method(getWriteProtected,Alphabet)
S3method(getWriteProtected,Event)
S3method(getWriteProtected,Process)
S3method(getWriteProtected,QMatrix)
S3method(getWriteProtected,Sequence)
S3method(globalConsistencyCheck,PSRoot)
S3method(hasSiteSpecificParameter,Process)
S3method(hasSymbols,Alphabet)
S3method(hasUndefinedRate,GeneralInDel)
S3method(hasUndefinedRate,GeneralSubstitution)
S3method(hasUndefinedRate,Process)
S3method(hasUndefinedRate,ToleranceSubstitution)
S3method(insertSequence,Sequence)
S3method(intersect,list)
S3method(intersect.list,PSRoot)
S3method(is,Alphabet)
S3method(is.Alphabet,default)
S3method(is,CodonAlphabet)
S3method(is.CodonAlphabet,default)
S3method(is,CodonUNREST)
S3method(is.CodonUNREST,default)
S3method(is,Event)
S3method(is.Event,default)
S3method(is,GeneralDeletor)
S3method(is.GeneralDeletor,default)
S3method(is,GeneralInDel)
S3method(is.GeneralInDel,default)
S3method(is,GeneralInsertor)
S3method(is.GeneralInsertor,default)
S3method(is,GeneralSubstitution)
S3method(is.GeneralSubstitution,default)
S3method(is,GY94)
S3method(is.GY94,default)
S3method(is.na,PSRoot)
S3method(is,phylo)
S3method(is.phylo,default)
S3method(is,Process)
S3method(is.Process,default)
S3method(is,PSRoot)
S3method(is.PSRoot,default)
S3method(is,QMatrix)
S3method(is.QMatrix,default)
S3method(is,Sequence)
S3method(is.Sequence,default)
S3method(is,Site)
S3method(is.Site,default)
S3method(is,tip)
S3method(is.tip,PhyloSim)
S3method(is,ToleranceSubstitution)
S3method(is.ToleranceSubstitution,default)
S3method(isAttached,Site)
S3method(isEmpty,Alphabet)
S3method(isStartCodon,CodonAlphabet)
S3method(isStopCodon,CodonAlphabet)
S3method(JTT,dcmut)
S3method(ll,PSRoot)
S3method(Log,PhyloSim)
S3method(my.all.equal,PSRoot)
S3method(newAAMatrix,AminoAcidSubst)
S3method(newMatrix,CodonSubst)
S3method(omegaHist,CodonSequence)
S3method(omegaVarM0,CodonSequence)
S3method(omegaVarM1,CodonSequence)
S3method(omegaVarM2,CodonSequence)
S3method(omegaVarM3,CodonSequence)
S3method(omegaVarM4,CodonSequence)
S3method(PAM,dcmut)
S3method(Perform,Event)
S3method(plot,ContinuousDeletor)
S3method(plot,ContinuousInsertor)
S3method(plot,DiscreteDeletor)
S3method(plot,DiscreteInsertor)
S3method(plot,GeneralSubstitution)
S3method(plot,PhyloSim)
S3method(plot,PSRoot)
S3method(plot,Sequence)
S3method(plot,ToleranceSubstitution)
S3method(plotParametersAtSites,Sequence)
S3method(plusGamma,Sequence)
S3method(plusInvGamma,Sequence)
S3method(print,PSRootSummary)
S3method(print,QMatrix)
S3method(proposeLength,GeneralInDel)
S3method(readAlignment,PhyloSim)
S3method(readTree,PhyloSim)
S3method(rescaleQMatrix,GeneralSubstitution)
S3method(rescaleQMatrix,ToleranceSubstitution)
S3method(revComp,NucleotideSequence)
S3method(sampleState,GeneralSubstitution)
S3method(sampleState,ToleranceSubstitution)
S3method(sampleStates,Sequence)
S3method(saveAlignment,PhyloSim)
S3method(Scale,QMatrix)
S3method(scaleTree,PhyloSim)
S3method(setAcceptBy,GeneralInDel)
S3method(setAcceptWin,GeneralInsertor)
S3method(setAlignment,PhyloSim)
S3method(setAlphabet,GeneralSubstitution)
S3method(setAlphabet,Process)
S3method(setAlphabet,QMatrix)
S3method(setAlphabet,Site)
S3method(setAlphabet,ToleranceSubstitution)
S3method(setAlphabets,Sequence)
S3method(setAncestral,Sequence)
S3method(setAncestral,Site)
S3method(setBaseFreqs,F81)
S3method(setBaseFreqs,F84)
S3method(setBaseFreqs,GTR)
S3method(setBaseFreqs,HKY)
S3method(setBaseFreqs,K80)
S3method(setBaseFreqs,K81)
S3method(setBaseFreqs,TN93)
S3method(setBigRate,Sequence)
S3method(setBranchEvents,PhyloSim)
S3method(setCodonFreqs,GY94)
S3method(setComments,PSRoot)
S3method(setCumulativeRates,Sequence)
S3method(setDeletionTolerance,Sequence)
S3method(setDist,ContinuousDeletor)
S3method(setDist,ContinuousInsertor)
S3method(setEdges,PhyloSim)
S3method(setEquDist,AminoAcidSubst)
S3method(setEquDist,CodonSubst)
S3method(setEquDist,GeneralSubstitution)
S3method(setEquDist,ToleranceSubstitution)
S3method(setEvents,Site)
S3method(setGenerateBy,GeneralInsertor)
S3method(setHandler,Event)
S3method(setId,PhyloSim)
S3method(setId,Process)
S3method(setId,QMatrix)
S3method(setId,Sequence)
S3method(setInsertHook,GeneralInsertor)
S3method(setInsertionTolerance,Sequence)
S3method(setKappa,F84)
S3method(setKappa,GY94)
S3method(setLength,Sequence)
S3method(setLengthParam1,FastFieldDeletor)
S3method(setLengthParam2,FastFieldDeletor)
S3method(setLogFile,PhyloSim)
S3method(setLogLevel,PhyloSim)
S3method(setMatrix,QMatrix)
S3method(setMaxLength,ContinuousDeletor)
S3method(setMaxLength,ContinuousInsertor)
S3method(setMethodsList,PSRoot)
S3method(setName,Event)
S3method(setName,PhyloSim)
S3method(setName,Process)
S3method(setName,QMatrix)
S3method(setName,Sequence)
S3method(setNedges,PhyloSim)
S3method(setNodes,PhyloSim)
S3method(setNtips,PhyloSim)
S3method(setOmegas,CodonSequence)
S3method(setOmegas,Sequence)
S3method(setParameterAtSite,FastFieldDeletor)
S3method(setParameterAtSite,Process)
S3method(setParameterAtSites,Sequence)
S3method(setPhylo,PhyloSim)
S3method(setPosition,Event)
S3method(setProbs,DiscreteDeletor)
S3method(setProbs,DiscreteInsertor)
S3method(setProcess,Event)
S3method(setProcess,QMatrix)
S3method(setProcesses,Sequence)
S3method(setProcesses,Site)
S3method(setProposeBy,GeneralInDel)
S3method(setQMatrix,GeneralSubstitution)
S3method(setQMatrix,ToleranceSubstitution)
S3method(setRate,Event)
S3method(setRate,GeneralInDel)
S3method(setRate,GeneralSubstitution)
S3method(setRate,GY94)
S3method(setRate,QMatrix)
S3method(setRate,ToleranceSubstitution)
S3method(setRateList,GeneralSubstitution)
S3method(setRateList,QMatrix)
S3method(setRateList,ToleranceSubstitution)
S3method(setRateMultipliers,Sequence)
S3method(setRateParam,F81)
S3method(setRateParam,F84)
S3method(setRateParam,GTR)
S3method(setRateParam,HKY)
S3method(setRateParam,K80)
S3method(setRateParam,K81)
S3method(setRateParam,T92)
S3method(setRateParam,TN93)
S3method(setRateParamList,F81)
S3method(setRateParamList,F84)
S3method(setRateParamList,GTR)
S3method(setRateParamList,HKY)
S3method(setRateParamList,K80)
S3method(setRateParamList,K81)
S3method(setRateParamList,T92)
S3method(setRateParamList,TN93)
S3method(setRootNode,PhyloSim)
S3method(setRootSeq,PhyloSim)
S3method(setScale,BrownianInsertor)
S3method(setScaledMatrix,QMatrix)
S3method(setSequence,Site)
S3method(setSequences,PhyloSim)
S3method(setSite,Event)
S3method(setSiteSpecificParamIds,Process)
S3method(setSiteSpecificParamList,Process)
S3method(setSize,Alphabet)
S3method(setSizes,DiscreteDeletor)
S3method(setSizes,DiscreteInsertor)
S3method(setState,Site)
S3method(setStates,Sequence)
S3method(setString,Sequence)
S3method(setSymbolLength,Alphabet)
S3method(setSymbols,Alphabet)
S3method(setTableId,CodonAlphabet)
S3method(setTemplateSeq,GeneralInsertor)
S3method(setTheta,T92)
S3method(setTipLabels,PhyloSim)
S3method(setTips,PhyloSim)
S3method(setToleranceMargin,FastFieldDeletor)
S3method(setTotalRate,Site)
S3method(setTotalRates,Sequence)
S3method(setTransTable,CodonAlphabet)
S3method(setTreeLength,PhyloSim)
S3method(setType,Alphabet)
S3method(setType,BrownianInsertor)
S3method(setType,FastFieldDeletor)
S3method(setUniqueAlphabets,Sequence)
S3method(setUniqueProcesses,Sequence)
S3method(setWriteProtected,Alphabet)
S3method(setWriteProtected,Event)
S3method(setWriteProtected,Process)
S3method(setWriteProtected,QMatrix)
S3method(setWriteProtected,Sequence)
S3method(Simulate,PhyloSim)
S3method(stringLength,default)
S3method(stringLengthVector,default)
S3method(summary,Alphabet)
S3method(summary,AminoAcidSubst)
S3method(summary,BinarySubst)
S3method(summary,BrownianInsertor)
S3method(summary,CodonAlphabet)
S3method(summary,CodonSubst)
S3method(summary,ContinuousDeletor)
S3method(summary,ContinuousInsertor)
S3method(summary,DiscreteDeletor)
S3method(summary,DiscreteInsertor)
S3method(summary,Event)
S3method(summary,F81)
S3method(summary,F84)
S3method(summary,FastFieldDeletor)
S3method(summary,GeneralDeletor)
S3method(summary,GeneralInDel)
S3method(summary,GeneralInsertor)
S3method(summary,GeneralSubstitution)
S3method(summary,GTR)
S3method(summary,GY94)
S3method(summary,HKY)
S3method(summary,JC69)
S3method(summary,K80)
S3method(summary,K81)
S3method(summary,PhyloSim)
S3method(summary,Process)
S3method(summary,PSRoot)
S3method(summary,QMatrix)
S3method(summary,Sequence)
S3method(summary,Site)
S3method(summary,T92)
S3method(summary,TN93)
S3method(summary,ToleranceSubstitution)
S3method(summary,UNREST)
S3method(Translate,CodonSequence)
S3method(translateCodon,CodonAlphabet)
S3method(Undocumented,PhyloSim)
S3method(virtualAssignmentForbidden,PSRoot)