broad.core.siphy.PiHMM Class Reference

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Classes
class	ConstrainedModel
class	PiStateModel

Public Member Functions
	PiHMM (EvolutionaryModel neutral, int stateNumber)
	PiHMM (EvolutionaryModel neutral, double minExpectedElementLength, double expectedCoverage)
void	addConservedPi (Matrix pi, String name)
short[]	viterbiMostLikelyEstimation (MultipleAlignment alignment) throws BadModelException
double	computePathLogLikelihood (MultipleAlignment alignment, short[] path, int initialStateIdx, int endStateIdx)
ForwardResult< Map< String, Matrix > >	runForwardAlgorithm (MultipleAlignment alignment) throws BadModelException
BackwardResult< Map< String, Matrix > >	runBackwardAlgorithm (MultipleAlignment alignment, ForwardResult< Map< String, Matrix >> forwardData) throws BadModelException

Static Public Member Functions
static void	main (String[] args) throws Exception
static PiHMM	createDefaultTwoStateChain (double l, double gamma, EvolutionaryModel model)
static PiHMM	createTwoStateChain (double l, double gamma, EvolutionaryModel model, Matrix otherPi)

Static Public Attributes
static final String	USAGE

Protected Member Functions
MultipleAlignment	generateAlignment (List< Integer > emittedPath, String format)

Constructor & Destructor Documentation

broad.core.siphy.PiHMM.PiHMM	(	EvolutionaryModel	neutral,
		int	stateNumber
	)

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broad.core.siphy.PiHMM.PiHMM	(	EvolutionaryModel	neutral,
		double	minExpectedElementLength,
		double	expectedCoverage
	)

Member Function Documentation

void broad.core.siphy.PiHMM.addConservedPi	(	Matrix	pi,
		String	name
	)

double broad.core.siphy.PiHMM.computePathLogLikelihood	(	MultipleAlignment	alignment,
		short[]	path,
		int	initialStateIdx,
		int	endStateIdx
	)

static PiHMM broad.core.siphy.PiHMM.createDefaultTwoStateChain ( double  l, double  gamma, EvolutionaryModel  model  )

static

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static PiHMM broad.core.siphy.PiHMM.createTwoStateChain ( double  l, double  gamma, EvolutionaryModel  model, Matrix  otherPi  )

static

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MultipleAlignment broad.core.siphy.PiHMM.generateAlignment ( List< Integer >  emittedPath, String  format  )

protected

static void broad.core.siphy.PiHMM.main ( String[]  args ) throws Exception

static

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BackwardResult<Map<String, Matrix> > broad.core.siphy.PiHMM.runBackwardAlgorithm	(	MultipleAlignment	alignment,
		ForwardResult< Map< String, Matrix >>	forwardData
	)		throws BadModelException

ForwardResult<Map<String, Matrix> > broad.core.siphy.PiHMM.runForwardAlgorithm

(

MultipleAlignment

alignment

)

throws BadModelException

short [] broad.core.siphy.PiHMM.viterbiMostLikelyEstimation

(

MultipleAlignment

alignment

)

throws BadModelException

Member Data Documentation

final String broad.core.siphy.PiHMM.USAGE

static

Initial value:

= "Usage: PiHMM TASK=<task_num> <task_args>\n" +
    "\tTasks:\n" +
    "\t\t1. Segment genome into pi-conserved and noncoserved.  -in <multiple alignment file>  -mod <Neutral Evolutionary model consisting of aminoacid background distribution, mutation matrix and neutral phylogenetic tree>" +
    "\n\t\t -l <The smoothness parameter, and should be the expected average conserved element length> and -gamma <The expected coverage parameter, how much of the genome is expected to be conserved>" +
    "\n\t\t -format <Alignment format default is FASTA is default> -ignore <comma separated species to ignore> -ref <reference sequence id, necessary if the alignment is not in MAF format>" +
    "\n\t\t  [-start <If MAF file, you may specify the reference start coordinate> -end <If MAF file, you may specify the reference end coordinate>]" +
    "\n\t\t2. Compute posterior probabilities of each site of being pi-conserved.  -in <multiple alignment file>  -mod <Neutral Evolutionary model consisting of aminoacid background distribution, mutation matrix and neutral phylogenetic tree>" +
    "\n\t\t -l <The smoothness parameter, and should be the expected minimum conserved element length> and -gamma <The expected coverage parameter, how much of the genome is expected to be conserved>" +
    "\n\t\t -format <Alignment format default is FASTA is default> -ignore <comma separated species to ignore> -ref <reference sequence id, necessary if the alignment is not in MAF format>" +
    "\n\t\t  [-start <If MAF file, you may specify the reference start coordinate> -end <If MAF file, you may specify the reference end coordinate>]" +
    "\n\t\t3. Compute log odds score for annotations in file. Scores reflect the log ratio of the probability of the path through each element being fully conserved or non conserved.  -in <Annotation file default format is assumed to be BED>  -mod <Neutral Evolutionary model consisting of aminoacid background distribution, mutation matrix and neutral phylogenetic tree>" +
    "\n\t\t -l <The smoothness parameter, and should be the expected minimum conserved element length> and -gamma <The expected coverage parameter, how much of the genome is expected to be conserved>" +
    "\n\t\t -format <Alignment format default is FASTA is default> -ignore <comma separated species to ignore> -ref <reference sequence id, necessary if the alignment is not in MAF format>" +
    "\n\t\t  [-start <If MAF file, you may specify the reference start coordinate> -end <If MAF file, you may specify the reference end coordinate>]" +
    "\n\t\t4. Simulate an alignment with for given HMM parameters. \n\t\tParameters:\n\t\t-mod <Base m,odel to use> \n\t\t-ignore <optional -- comma separated species to ignore in the given model tree> \n\t\t-colNum <Number of columns to sample> -\n\t\t-otherPI <Conserved or alternative PI distribution, as a comma separated list of the A,C,G,T frequencies, add as many -otherPI as different PI states are desired. > " +
    "\n\t\t -l <The smoothness parameter, how long in average should be the stretches of the generated alignment should be from the alternative PI model> and -gamma <The coverage parameter, how much of the sampled alignmnet should be made of the alternative PI model> \n\t\t-out <Generated alignment output file>" +
    "\n"

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The documentation for this class was generated from the following file:

• java/broad/core/siphy/PiHMM.java