Deprecated API

Deprecated Classes

pal.tree.UPGMATree
Use ClusterTree

Deprecated Methods

pal.misc.Utils.argmax(double[])

pal.misc.Utils.argmax(int[])

pal.tree.TreeUtils.getBootstrapSupportByCladeTree(String, Tree, Tree[])
Use getReplicateCladeSupport instead

pal.distance.DistanceMatrix.getIdGroup()
distance matrix now implements IdGroup

pal.misc.TimeOrderCharacterData.getIdGroup()
TimeOrderCharacterData now implements IdGroup

pal.substmodel.RateMatrix.getRelativeRates()
try not to use.

pal.misc.TimeOrderCharacterData.getSampleCount()
Use getOrdinalCount()

pal.datatype.DataType.Utils.isGap(DataType, char)
use DataType.isGapChar()

pal.tree.TreeUtils.scale(Tree, double, int)
use getScaled()

pal.tree.TreeUtils.scale(Tree, MutationRateModel)
use getScaled()

pal.tree.TreeUtils.scale(Tree, MutationRateModel, int)
use getScaled()