statalign.base
Class Tree

java.lang.Object
  statalign.base.thread.Stoppable
      statalign.base.Tree

All Implemented Interfaces:

DataType

public class Tree
extends Stoppable
implements DataType

This is the current tree in the MCMC run. It extends Stoppable, so the MCMC run can be terminated in graphical interface mode while it calls a function in the Tree class.

Author:

miklos, novak

Field Summary

double	heat The heat parameter for this MCMC chain.
Hmm2	hmm2 When two fragments of two sequences on two neighbor vertices of the tree are realigned, the proposed new alignment is drawn from a forward-backward sampling of this HMM.
HmmSilent	hmm3 When two fragments of two sequences on two sibling vertices are realigned drawing a novel ancestral substring for their parent vertex, the proposed new alignment is drawn from a forward-backward sampling of this HMM.
java.lang.String[]	names The name of the sequences
CNetwork	network
java.lang.String[]	previousFullAlign
Vertex	root The root of the tree
SubstitutionModel	substitutionModel Characters on this tree undergo substitutions according to this model.
java.lang.String	title The name of the tree
Vertex[]	vertex The array of vertices of the tree.

Constructor Summary

Tree()

Method Summary

void	checkPointers()
int	countLeaves()
void	countSilentIndels()
double	getLogLike()
double	getLogPrior()
RawSequences	getSeqs()
State	getState() Returns a State object representing the current state.
java.lang.String	getSummaryAssociatedWith(java.lang.String sequenceName)
int	getTopVertexId(int ind)
void	makeRoot(java.lang.String taxonName) It roots the tree on a taxon
boolean	perSequenceData()
java.lang.String	printedTree() Generates a String contaning the description of the tree in Newick format.
java.lang.String	printedTreeWithNumbers()
void	recomputeCheckLogLike() Recomputes the likelihood from scratch and checks whether everything was correct before.
void	removeDataAssociatedWith(java.lang.String sequenceName)
java.lang.String	rowSequences() It generates the array of row sequences.
void	setSeqs(RawSequences rs)

Methods inherited from class statalign.base.thread.Stoppable

pausable, stoppable

Methods inherited from class java.lang.Object

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

Field Detail

substitutionModel

public SubstitutionModel substitutionModel

Characters on this tree undergo substitutions according to this model.

hmm2

public Hmm2 hmm2

When two fragments of two sequences on two neighbor vertices of the tree are realigned, the proposed new alignment is drawn from a forward-backward sampling of this HMM. It is a simplified version of the TKF92 model.

hmm3

public HmmSilent hmm3

When two fragments of two sequences on two sibling vertices are realigned drawing a novel ancestral substring for their parent vertex, the proposed new alignment is drawn from a forward-backward sampling of this HMM. It is a pair-HMM having states emitting into the non-observable ancestral sequence.

vertex

public Vertex[] vertex

The array of vertices of the tree.

root

public Vertex root

The root of the tree

title

public java.lang.String title

The name of the tree

names

public java.lang.String[] names

The name of the sequences

heat

public double heat

The heat parameter for this MCMC chain.

network

public CNetwork network

previousFullAlign

public java.lang.String[] previousFullAlign

Constructor Detail

Tree

public Tree()

Method Detail

getSeqs

public RawSequences getSeqs()

Specified by:

getSeqs in interface DataType

setSeqs

public void setSeqs(RawSequences rs)

Specified by:

setSeqs in interface DataType

checkPointers

public void checkPointers()

getLogLike

public double getLogLike()

recomputeCheckLogLike

public void recomputeCheckLogLike()

Recomputes the likelihood from scratch and checks whether everything was correct before. Throws error if it finds inconsistency.

countLeaves

public int countLeaves()

countSilentIndels

public void countSilentIndels()

getTopVertexId

public int getTopVertexId(int ind)

getState

public State getState()

Returns a State object representing the current state. Assumes that leaves come first in the vertex array.

printedTree

public java.lang.String printedTree()

Generates a String contaning the description of the tree in Newick format.

Returns:

the string contaning the description of the tree in Newick format.

printedTreeWithNumbers

public java.lang.String printedTreeWithNumbers()

getLogPrior

public double getLogPrior()

rowSequences

public java.lang.String rowSequences()

It generates the array of row sequences. The format is sequence name TAB row sequence.

Returns:

The string array containing the sequence names and sequences.

perSequenceData

public boolean perSequenceData()

Specified by:

perSequenceData in interface DataType

Returns:

true if the DataType contains a List of items, each of which is associated with one of the input sequences, for example protein structure coordinates.

getSummaryAssociatedWith

public java.lang.String getSummaryAssociatedWith(java.lang.String sequenceName)

Specified by:

getSummaryAssociatedWith in interface DataType

removeDataAssociatedWith

public void removeDataAssociatedWith(java.lang.String sequenceName)

Specified by:

removeDataAssociatedWith in interface DataType

makeRoot

public void makeRoot(java.lang.String taxonName)

It roots the tree on a taxon

Parameters:

taxonName - Taxon on which to root tree