Package pal.treesearch
Class GeneralConstructionTool
java.lang.Object
pal.treesearch.GeneralConstructionTool
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Constructor Summary
ConstructorsConstructorDescriptionGeneralConstructionTool
(ConstraintModel constraints, Alignment alignment) The constructor -
Method Summary
Modifier and TypeMethodDescriptionfinal int
int
build
(PatternInfo beingBuilt, PatternInfo left, PatternInfo right) constructFreshPatternInfo
(boolean binaryPattern) createConstrainedNode
(Node peer, ParentableConstrainedNode parent, GeneralConstraintGroupManager.Store store, GeneralConstraintGroupManager groupManager) Create an appropriate constrained node given a peer, and it's parent nodecreateFreeNode
(Node peer, FreeBranch parent, GeneralConstraintGroupManager.Store store) Create an appropriate free node given a peer, and it's parent branchcreateNewFreeLeafCalculator
(int[] patternStateMatchup, int numberOfPatterns) createRootAccess
(Node baseTree, GeneralConstraintGroupManager.Store store) String[]
getLeafLabelSet
(Node peer) A horibly inefficient way of doing things.void
getLeafLabelSet
(Node peer, ArrayList al) final int
int
int[]
getSequence
(String name) Get the sequence data for a particular OTUnewConditionalProbabilityStore
(boolean isForLeaf)
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Constructor Details
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GeneralConstructionTool
The constructor- Parameters:
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)
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Method Details
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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 peerparent
- The parent branch- Returns:
- A FreeNode
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createRootAccess
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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 peerparent
- The parent node- Returns:
- A ConstrainedNode
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constructFreshPatternInfo
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obtainTempConditionalProbabilityStore
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newConditionalProbabilityStore
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allocateNextConnectionIndex
public final int allocateNextConnectionIndex() -
allocateNewFreeInternalCalculator
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obtainFreeExternalCalculator
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createNewFreeLeafCalculator
public UnconstrainedLikelihoodModel.Leaf createNewFreeLeafCalculator(int[] patternStateMatchup, int numberOfPatterns) -
build
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getDataType
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getNumberOfSites
public final int getNumberOfSites() -
getNumberOfStates
public int getNumberOfStates() -
getSequence
Get the sequence data for a particular OTU- Parameters:
name
- The name of the OTU- Returns:
- the sequence data stored as integer values
- Throws:
IllegalArgumentException
- if no such OTU with given name
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getLeafLabelSet
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
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getLeafLabelSet
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