statalign.model.ext.plugins
Class StructAlign

java.lang.Object
  statalign.mcmc.McmcModule
      statalign.model.ext.ModelExtension
          statalign.model.ext.plugins.StructAlign

All Implemented Interfaces:

java.awt.event.ActionListener, java.util.EventListener

public class StructAlign
extends ModelExtension
implements java.awt.event.ActionListener

Field Summary

double	angleP Starting value for rotation proposal tuning parameter.
double[]	angles Rotation angle for each protein along the rotation axis
double[][]	axes Axis of rotation for each sequence
double[][]	bFactors Crystallographic temperature factors, for weighting epsilon.
double[][][]	coords Alpha-C atomic coordinate for each sequence and each residue
java.lang.String[]	curAlign Current alignment between all leaf sequences
double[][]	distanceMatrix Pairwise distances implied by current tree topology
double	epsilon
PriorDistribution<java.lang.Double>	epsilonPrior
boolean	fixedEpsilon
double	fixedEpsilonValue Value to fix epsilon at if we're not estimating it.
boolean	fixedSigma2
double	fixedSigma2Value Value to fix sigma at if we're not estimating it.
double[][]	fullCovar Covariance matrix implied by current tree topology
boolean	globalSigma
boolean	globalSigmaSpike If globalSigma = false then this switches on a spike prior at sigma2Hier.
java.lang.String	linkType
boolean	localEpsilon
double	MIN_EPSILON Minimum value for epsilon, to prevent numerical errors.
java.util.HashMap<java.lang.Integer,MultiNormCholesky>	multiNorms
java.util.HashMap<statalign.model.ext.plugins.StructAlign.Column,MultiNormCholesky>	multiNormsLocal
double	nu
GammaPrior	nuPrior
java.lang.String[]	oldAlign
double[][]	oldCovar
double[][]	oldDist
double	oldLogLi
java.util.HashMap<statalign.model.ext.plugins.StructAlign.Column,MultiNormCholesky>	oldMultiNormsLocal
double[][][]	rotCoords Alpha-C atomic coordinates under the current set of rotations/translations
RotationProposal	rotProp independence rotation proposal distribution
double[]	sigma2 Parameters of structural drift
double	sigma2Hier
GammaPrior	sigma2HPrior
PriorDistribution<java.lang.Double>	sigma2Prior
double	tau
InverseGammaPrior	tauPrior
boolean	useLibrary
double	xlatP Starting value for translation proposal tuning parameter.
double[][]	xlats Translation vector for each protein

Fields inherited from class statalign.mcmc.McmcModule

curLogLike, printExtraInfo

Constructor Summary

StructAlign()

Method Summary

void	actionPerformed(java.awt.event.ActionEvent e)
void	addEdgeLength(double[][] distMat, int[] subTree, double edgeLength)
void	afterAlignChange(Tree tree, Vertex selectRoot, boolean accepted) Called after an alignment change proposal (accepted or rejected).
void	afterContinuousParamChange(Tree tree, boolean accepted)
void	afterEdgeLenChange(Tree tree, Vertex vertex, boolean accepted) Called after a proposed edge length change (accepted or rejected).
void	afterFirstHalfBurnin()
void	afterTreeChange(Tree tree, Vertex nephew, boolean accepted) Called after a proposed topology change (accepted or rejected).
void	beforeAlignChange(Tree tree, Vertex selectRoot) Called before an alignment change is proposed, but after the affected subtree has been selected.
void	beforeContinuousParamChange(Tree tree)
void	beforeEdgeLenChange(Tree tree, Vertex vertex) Called before an edge length change is proposed, but after the affected edge is selected.
void	beforeSampling(Tree tree) Called before the start of MCMC sampling, but after the initial tree, alignment etc. have been generated.
void	beforeTreeChange(Tree tree, Vertex nephew) Called before a topology change is proposed, but after the affected branches are selected.
double	calcAllColumnContrib()
int[]	calcDistanceMatrix(Vertex vertex, double[][] distMat)
int[]	calcDistanceMatrix(Vertex vertex, double[][] distMat, boolean unweighted) recursive algorithm to traverse tree and calculate distance matrix between leaves
double[][]	calcFullCovar(Tree tree) return the full covariance matrix for the tree topology and branch lengths
double	calcLogEm(int[] aligned)
void	calcRotation(int ind)
int[]	calcUnweightedDistanceMatrix(Vertex vertex, double[][] distMat)
double	columnContrib(int[] col) Calculates the structural likelihood contribution of a single alignment column
double	computeLogLikeFactor(Tree tree)
void	connectRmsdTrace(RmsdTrace _rmsdTrace)
void	connectStructTrace(StructTrace structTrace)
void	dataAdded(java.io.File file, DataType data)
int	getParamChangeWeight() Returns the weight for choosing a parameter change for this model extension in the MCMC kernel.
java.lang.String	getPluginID()
java.util.List<javax.swing.JComponent>	getToolBarItems() Override this to return the list of toolbar items to be added.
java.lang.String	getUsageInfo() Prints the usage information for this plugin.
void	init() Called during StatAlign startup, after all ModelExtension plugins have been loaded and command line arguments have been processed (if present).
void	initRun(InputData inputData) Called during the initialisation of a run if plugin is active.
double	logLikeAlignChange(Tree tree, Vertex selectRoot)
double	logLikeContinuousParamChange(Tree tree)
double	logLikeEdgeLenChange(Tree tree, Vertex vertex)
double	logLikeFactor(Tree tree) This should return the log of the model's contribution to the likelihood, it will be added on to the log-likelihood of the current point in the MCMC state space.
double	logLikeIndelParamChange(Tree tree, Hmm hmm, McmcMove m)
double	logLikeModExtParamChange(Tree tree, ModelExtension ext) Computes the change in likelihood to this ModelExtension, after a change to ext.
double	logLikeSubstParamChange(Tree tree, SubstitutionModel model, int ind)
double	logLikeTreeChange(Tree tree, Vertex nephew)
void	printTree(Vertex v, java.lang.String vname)
void	setActive(boolean active) Enables or disables this plugin.
void	setParam(java.lang.String paramName, boolean paramValue)
void	setParam(java.lang.String paramName, java.lang.Number paramValue)
void	setParam(java.lang.String paramName, java.lang.String paramValue) This function is called when command line arguments are specified for a plugin.
boolean	useInAlignmentProposals() If true, then this plugin is able to compute a column-wise contribution to the likelihood, and can be used to influence the alignment proposals that are carried out by functions inside statalign.base.Vertex By default this is false.

Methods inherited from class statalign.model.ext.ModelExtension

addToFilenameExtension, afterIndelParamChange, afterModExtParamChange, afterSubstParamChange, beforeIndelParamChange, beforeModExtParamChange, beforeSubstParamChange, getFilenameExtension, getPluginList, isActive, isParamChangeAccepted, isSelectable, setManager

Methods inherited from class statalign.mcmc.McmcModule

addMcmcMove, addMcmcMove, afterSampling, getLogLike, getMcmcInfo, getMcmcMove, getMcmcMoves, incrementWeights, isFirstHalfBurnin, logPrior, modifyProposalWidths, proposeParamChange, setAllMovesNotProposed, setLogLike, setMcmc, setWeight, zeroAllMoveCounts

Methods inherited from class java.lang.Object

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

Field Detail

globalSigma

public boolean globalSigma

useLibrary

public boolean useLibrary

fixedEpsilon

public boolean fixedEpsilon

fixedSigma2

public boolean fixedSigma2

globalSigmaSpike

public boolean globalSigmaSpike

If globalSigma = false then this switches on a spike prior at sigma2Hier.

localEpsilon

public boolean localEpsilon

coords

public double[][][] coords

Alpha-C atomic coordinate for each sequence and each residue

bFactors

public double[][] bFactors

Crystallographic temperature factors, for weighting epsilon.

rotCoords

public double[][][] rotCoords

Alpha-C atomic coordinates under the current set of rotations/translations

axes

public double[][] axes

Axis of rotation for each sequence

angles

public double[] angles

Rotation angle for each protein along the rotation axis

xlats

public double[][] xlats

Translation vector for each protein

sigma2

public double[] sigma2

Parameters of structural drift

sigma2Hier

public double sigma2Hier

nu

public double nu

tau

public double tau

epsilon

public double epsilon

distanceMatrix

public double[][] distanceMatrix

Pairwise distances implied by current tree topology

fullCovar

public double[][] fullCovar

Covariance matrix implied by current tree topology

curAlign

public java.lang.String[] curAlign

Current alignment between all leaf sequences

rotProp

public RotationProposal rotProp

independence rotation proposal distribution

oldCovar

public double[][] oldCovar

oldDist

public double[][] oldDist

oldAlign

public java.lang.String[] oldAlign

oldLogLi

public double oldLogLi

linkType

public java.lang.String linkType

sigma2Prior

public PriorDistribution<java.lang.Double> sigma2Prior

epsilonPrior

public PriorDistribution<java.lang.Double> epsilonPrior

tauPrior

public InverseGammaPrior tauPrior

sigma2HPrior

public GammaPrior sigma2HPrior

nuPrior

public GammaPrior nuPrior

angleP

public final double angleP

Starting value for rotation proposal tuning parameter.

See Also:

Constant Field Values

xlatP

public final double xlatP

Starting value for translation proposal tuning parameter.

See Also:

Constant Field Values

fixedSigma2Value

public double fixedSigma2Value

Value to fix sigma at if we're not estimating it.

MIN_EPSILON

public double MIN_EPSILON

Minimum value for epsilon, to prevent numerical errors.

fixedEpsilonValue

public double fixedEpsilonValue

Value to fix epsilon at if we're not estimating it.

multiNorms

public java.util.HashMap<java.lang.Integer,MultiNormCholesky> multiNorms

multiNormsLocal

public java.util.HashMap<statalign.model.ext.plugins.StructAlign.Column,MultiNormCholesky> multiNormsLocal

oldMultiNormsLocal

public java.util.HashMap<statalign.model.ext.plugins.StructAlign.Column,MultiNormCholesky> oldMultiNormsLocal

Constructor Detail

StructAlign

public StructAlign()

Method Detail

getPluginID

public java.lang.String getPluginID()

Overrides:

getPluginID in class ModelExtension

Returns:

The command line identifier string for the plugin.

useInAlignmentProposals

public boolean useInAlignmentProposals()

Description copied from class: ModelExtension

If true, then this plugin is able to compute a column-wise contribution to the likelihood, and can be used to influence the alignment proposals that are carried out by functions inside statalign.base.Vertex By default this is false.

Overrides:

useInAlignmentProposals in class ModelExtension

getToolBarItems

public java.util.List<javax.swing.JComponent> getToolBarItems()

Description copied from class: ModelExtension

Override this to return the list of toolbar items to be added. By default returns null.

Overrides:

getToolBarItems in class ModelExtension

actionPerformed

public void actionPerformed(java.awt.event.ActionEvent e)

Specified by:

actionPerformed in interface java.awt.event.ActionListener

getUsageInfo

public java.lang.String getUsageInfo()

Description copied from class: ModelExtension

Prints the usage information for this plugin.

Overrides:

getUsageInfo in class ModelExtension

setActive

public void setActive(boolean active)

Description copied from class: ModelExtension

Enables or disables this plugin.

Overrides:

setActive in class ModelExtension

Parameters:

active - true if plugin should be enabled

setParam

public void setParam(java.lang.String paramName,
                     java.lang.String paramValue)

Description copied from class: ModelExtension

This function is called when command line arguments are specified for a plugin. If the specific ModelExtension does not override these methods then it cannot handle any command line arguments, and so the default error is returned. The overriding method should call super.setParam(paramName,paramValue) in the case that paramName is unrecognised. An overriding method can also include a call such as addToFilenameExtension(paramName+"_"+paramValue); which will result in an informative string being appended to the names of any output files generated by the Postprocess plugins.

Overrides:

setParam in class ModelExtension

Parameters:

paramName - The name of a parameter that is to be set.

paramValue - The value to which it will be set.

setParam

public void setParam(java.lang.String paramName,
                     java.lang.Number paramValue)

Overrides:

setParam in class ModelExtension

setParam

public void setParam(java.lang.String paramName,
                     boolean paramValue)

Overrides:

setParam in class ModelExtension

init

public void init()

Description copied from class: ModelExtension

Called during StatAlign startup, after all ModelExtension plugins have been loaded and command line arguments have been processed (if present).

Overrides:

init in class ModelExtension

initRun

public void initRun(InputData inputData)
             throws java.lang.IllegalArgumentException

Description copied from class: ModelExtension

Called during the initialisation of a run if plugin is active. Override to process input data.

Overrides:

initRun in class ModelExtension

Throws:

java.lang.IllegalArgumentException - if the run should be terminated as input data is illegal

beforeSampling

public void beforeSampling(Tree tree)

Description copied from class: McmcModule

Called before the start of MCMC sampling, but after the initial tree, alignment etc. have been generated. Override to initialise data structures etc.

Overrides:

beforeSampling in class McmcModule

Parameters:

tree - the starting tree

afterFirstHalfBurnin

public void afterFirstHalfBurnin()

Overrides:

afterFirstHalfBurnin in class McmcModule

computeLogLikeFactor

public double computeLogLikeFactor(Tree tree)

logLikeFactor

public double logLikeFactor(Tree tree)

Description copied from class: McmcModule

This should return the log of the model's contribution to the likelihood, it will be added on to the log-likelihood of the current point in the MCMC state space. Normally it will be called once at the initialisation of the MCMC process and from then on once in each MCMC step, when proposing any change. In debug mode, will be called more often (including after proposed changes) to ensure consistency.

Specified by:

logLikeFactor in class McmcModule

Parameters:

tree - current tree

Returns:

log of model extension likelihood, conditional on current tree, alignment and params

calcAllColumnContrib

public double calcAllColumnContrib()

columnContrib

public double columnContrib(int[] col)

Calculates the structural likelihood contribution of a single alignment column

Parameters:

col - the column, id of the residue for each sequence (or -1 if gapped in column)

Returns:

the likelihood contribution

calcRotation

public void calcRotation(int ind)

calcFullCovar

public double[][] calcFullCovar(Tree tree)

return the full covariance matrix for the tree topology and branch lengths

printTree

public void printTree(Vertex v,
                      java.lang.String vname)

calcUnweightedDistanceMatrix

public int[] calcUnweightedDistanceMatrix(Vertex vertex,
                                          double[][] distMat)

calcDistanceMatrix

public int[] calcDistanceMatrix(Vertex vertex,
                                double[][] distMat)

calcDistanceMatrix

public int[] calcDistanceMatrix(Vertex vertex,
                                double[][] distMat,
                                boolean unweighted)

recursive algorithm to traverse tree and calculate distance matrix between leaves

addEdgeLength

public void addEdgeLength(double[][] distMat,
                          int[] subTree,
                          double edgeLength)

getParamChangeWeight

public int getParamChangeWeight()

Description copied from class: ModelExtension

Returns the weight for choosing a parameter change for this model extension in the MCMC kernel. By default, returns 0, preventing McmcModule.proposeParamChange(Tree) from ever being called.

Overrides:

getParamChangeWeight in class ModelExtension

logLikeModExtParamChange

public double logLikeModExtParamChange(Tree tree,
                                       ModelExtension ext)

Description copied from class: ModelExtension

Computes the change in likelihood to this ModelExtension, after a change to ext.

Overrides:

logLikeModExtParamChange in class ModelExtension

ext - The ModelExtension that just changed.

Returns:

beforeAlignChange

public void beforeAlignChange(Tree tree,
                              Vertex selectRoot)

Description copied from class: ModelExtension

Called before an alignment change is proposed, but after the affected subtree has been selected. May change later to be called after subalignment (window) has also been selected.

Overrides:

beforeAlignChange in class ModelExtension

Parameters:

tree - the current tree

selectRoot - root of the selected subtree

logLikeAlignChange

public double logLikeAlignChange(Tree tree,
                                 Vertex selectRoot)

Overrides:

logLikeAlignChange in class ModelExtension

Returns:

afterAlignChange

public void afterAlignChange(Tree tree,
                             Vertex selectRoot,
                             boolean accepted)

Description copied from class: ModelExtension

Called after an alignment change proposal (accepted or rejected).

Overrides:

afterAlignChange in class ModelExtension

Parameters:

tree - the current tree

selectRoot - root of the selected subtree

accepted - true if the change was accepted

beforeTreeChange

public void beforeTreeChange(Tree tree,
                             Vertex nephew)

Description copied from class: ModelExtension

Called before a topology change is proposed, but after the affected branches are selected.

Overrides:

beforeTreeChange in class ModelExtension

Parameters:

tree - the current tree

nephew - node that is proposed to be swapped with its "uncle"

logLikeTreeChange

public double logLikeTreeChange(Tree tree,
                                Vertex nephew)

Overrides:

logLikeTreeChange in class ModelExtension

afterTreeChange

public void afterTreeChange(Tree tree,
                            Vertex nephew,
                            boolean accepted)

Description copied from class: ModelExtension

Called after a proposed topology change (accepted or rejected).

Overrides:

afterTreeChange in class ModelExtension

Parameters:

tree - the tree after the change

nephew - the new nephew (this is the deepest lying node that was affected by the change if there was one)

accepted - true if the change was accepted

beforeContinuousParamChange

public void beforeContinuousParamChange(Tree tree)

logLikeContinuousParamChange

public double logLikeContinuousParamChange(Tree tree)

afterContinuousParamChange

public void afterContinuousParamChange(Tree tree,
                                       boolean accepted)

logLikeEdgeLenChange

public double logLikeEdgeLenChange(Tree tree,
                                   Vertex vertex)

Overrides:

logLikeEdgeLenChange in class ModelExtension

beforeEdgeLenChange

public void beforeEdgeLenChange(Tree tree,
                                Vertex vertex)

Description copied from class: ModelExtension

Called before an edge length change is proposed, but after the affected edge is selected.

Overrides:

beforeEdgeLenChange in class ModelExtension

Parameters:

tree - the current tree

vertex - the node whose edge to its parent is selected to be changed

afterEdgeLenChange

public void afterEdgeLenChange(Tree tree,
                               Vertex vertex,
                               boolean accepted)

Description copied from class: ModelExtension

Called after a proposed edge length change (accepted or rejected).

Overrides:

afterEdgeLenChange in class ModelExtension

Parameters:

tree - the current tree

vertex - the node whose edge to its parent was selected

accepted - true if the change was accepted

logLikeIndelParamChange

public double logLikeIndelParamChange(Tree tree,
                                      Hmm hmm,
                                      McmcMove m)

Overrides:

logLikeIndelParamChange in class ModelExtension

logLikeSubstParamChange

public double logLikeSubstParamChange(Tree tree,
                                      SubstitutionModel model,
                                      int ind)

Overrides:

logLikeSubstParamChange in class ModelExtension

calcLogEm

public double calcLogEm(int[] aligned)

Overrides:

calcLogEm in class ModelExtension

Parameters:

aligned - Vector indicating which characters are aligned to the current column in the subtrees below.

Returns:

Logarithm of emission probability for subtrees

connectStructTrace

public void connectStructTrace(StructTrace structTrace)

connectRmsdTrace

public void connectRmsdTrace(RmsdTrace _rmsdTrace)

dataAdded

public void dataAdded(java.io.File file,
                      DataType data)

Overrides:

dataAdded in class ModelExtension