pal.treesearch

Class GeneralConstructionTool

java.lang.Object

pal.treesearch.GeneralConstructionTool

public class GeneralConstructionTool
extends java.lang.Object

Constructor Summary

Constructors

Constructor and Description
GeneralConstructionTool(ConstraintModel constraints, Alignment alignment) The constructor

Method Summary

Methods

Modifier and Type	Method and Description
UnconstrainedLikelihoodModel.Internal	allocateNewFreeInternalCalculator()
int	allocateNextConnectionIndex()
int	build(PatternInfo beingBuilt, PatternInfo left, PatternInfo right)
PatternInfo	constructFreshPatternInfo(boolean binaryPattern)
ConstrainedNode	createConstrainedNode(Node peer, ParentableConstrainedNode parent, GeneralConstraintGroupManager.Store store, GeneralConstraintGroupManager groupManager) Create an appropriate constrained node given a peer, and it's parent node
FreeNode	createFreeNode(Node peer, FreeBranch parent, GeneralConstraintGroupManager.Store store) Create an appropriate free node given a peer, and it's parent branch
UnconstrainedLikelihoodModel.Leaf	createNewFreeLeafCalculator(int[] patternStateMatchup, int numberOfPatterns)
RootAccess	createRootAccess(Node baseTree, GeneralConstraintGroupManager.Store store)
DataType	getDataType()
java.lang.String[]	getLeafLabelSet(Node peer) A horibly inefficient way of doing things.
void	getLeafLabelSet(Node peer, java.util.ArrayList al)
int	getNumberOfSites()
int	getNumberOfStates()
int[]	getSequence(java.lang.String name) Get the sequence data for a particular OTU
ConditionalProbabilityStore	newConditionalProbabilityStore(boolean isForLeaf)
UnconstrainedLikelihoodModel.External	obtainFreeExternalCalculator()
ConditionalProbabilityStore	obtainTempConditionalProbabilityStore()

Methods inherited from class java.lang.Object

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

Constructor Detail

GeneralConstructionTool

public GeneralConstructionTool(ConstraintModel constraints,
                       Alignment alignment)

The constructor

Parameters:

alignment - the base alignment

numberOfStates - the number of states

numberOfCategories - the number of model classes

freeCalculatorGenerator - 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)

Method Detail

createFreeNode

public FreeNode createFreeNode(Node peer,
                      FreeBranch parent,
                      GeneralConstraintGroupManager.Store store)

Create an appropriate free node given a peer, and it's parent branch

Parameters:

peer - The normal PAL node peer

parent - The parent branch

Returns:

A FreeNode

createRootAccess

public RootAccess createRootAccess(Node baseTree,
                          GeneralConstraintGroupManager.Store store)

createConstrainedNode

public ConstrainedNode createConstrainedNode(Node peer,
                                    ParentableConstrainedNode parent,
                                    GeneralConstraintGroupManager.Store store,
                                    GeneralConstraintGroupManager groupManager)

Create an appropriate constrained node given a peer, and it's parent node

Parameters:

peer - The normal PAL node peer

parent - The parent node

Returns:

A ConstrainedNode

constructFreshPatternInfo

public PatternInfo constructFreshPatternInfo(boolean binaryPattern)

obtainTempConditionalProbabilityStore

public final ConditionalProbabilityStore obtainTempConditionalProbabilityStore()

newConditionalProbabilityStore

public final ConditionalProbabilityStore newConditionalProbabilityStore(boolean isForLeaf)

allocateNextConnectionIndex

public final int allocateNextConnectionIndex()

allocateNewFreeInternalCalculator

public UnconstrainedLikelihoodModel.Internal allocateNewFreeInternalCalculator()

obtainFreeExternalCalculator

public UnconstrainedLikelihoodModel.External obtainFreeExternalCalculator()

createNewFreeLeafCalculator

public UnconstrainedLikelihoodModel.Leaf createNewFreeLeafCalculator(int[] patternStateMatchup,
                                                            int numberOfPatterns)

build

public int build(PatternInfo beingBuilt,
        PatternInfo left,
        PatternInfo right)

getDataType

public DataType getDataType()

getNumberOfSites

public final int getNumberOfSites()

getNumberOfStates

public int getNumberOfStates()

getSequence

public int[] getSequence(java.lang.String name)

Get the sequence data for a particular OTU

Parameters:

name - The name of the OTU

Returns:

the sequence data stored as integer values

Throws:

java.lang.IllegalArgumentException - if no such OTU with given name

getLeafLabelSet

public java.lang.String[] getLeafLabelSet(Node peer)

A horibly inefficient way of doing things. Finds the leaf index for all leaves from the tree defined by the PAL node. Returns -1 if more than one index.

Parameters:

peer - the root of the sub tree

Returns:

the common leaf index, of -1 if no common leaf index

getLeafLabelSet

public void getLeafLabelSet(Node peer,
                   java.util.ArrayList al)