pal.treesearch
public class GeneralConstructionTool extends java.lang.Object
Constructor and Description |
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GeneralConstructionTool(ConstraintModel constraints,
Alignment alignment)
The constructor
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public GeneralConstructionTool(ConstraintModel constraints, Alignment alignment)
alignment
- the base alignmentnumberOfStates
- the number of statesnumberOfCategories
- the number of model classesfreeCalculatorGenerator
- The generator for free calculation (may be null if no free components)constrainedCalcGenerator
- The generator for constrained calculation (assuming a Molecular Clock, and may be null if no constrained components)public FreeNode createFreeNode(Node peer, FreeBranch parent, GeneralConstraintGroupManager.Store store)
peer
- The normal PAL node peerparent
- The parent branchpublic RootAccess createRootAccess(Node baseTree, GeneralConstraintGroupManager.Store store)
public ConstrainedNode createConstrainedNode(Node peer, ParentableConstrainedNode parent, GeneralConstraintGroupManager.Store store, GeneralConstraintGroupManager groupManager)
peer
- The normal PAL node peerparent
- The parent nodepublic PatternInfo constructFreshPatternInfo(boolean binaryPattern)
public final ConditionalProbabilityStore obtainTempConditionalProbabilityStore()
public final ConditionalProbabilityStore newConditionalProbabilityStore(boolean isForLeaf)
public final int allocateNextConnectionIndex()
public UnconstrainedLikelihoodModel.Internal allocateNewFreeInternalCalculator()
public UnconstrainedLikelihoodModel.External obtainFreeExternalCalculator()
public UnconstrainedLikelihoodModel.Leaf createNewFreeLeafCalculator(int[] patternStateMatchup, int numberOfPatterns)
public int build(PatternInfo beingBuilt, PatternInfo left, PatternInfo right)
public DataType getDataType()
public final int getNumberOfSites()
public int getNumberOfStates()
public int[] getSequence(java.lang.String name)
name
- The name of the OTUjava.lang.IllegalArgumentException
- if no such OTU with given namepublic java.lang.String[] getLeafLabelSet(Node peer)
peer
- the root of the sub treepublic void getLeafLabelSet(Node peer, java.util.ArrayList al)