dag

Class MergeableDag

java.lang.Object

dag.MergeableDag

public final class MergeableDag
extends java.lang.Object

Class MergeableDag contains a static, thread-safe factory method that constructs a Directed Acyclic Graph (DAG) from sequence data.

References:
Ron D, Singer Y, and Tishby N (1998) On the Learnability and usage of acyclic probabilistic finite automata. Journal of Computer and SystemSciences 56:133-152.
Browning S (2006) Multi-locus association mapping using variable length Markov chains. Am J Hum Genet. 78:903-913.

Method Summary

Modifier and Type	Method and Description
Dag	dag() Returns the constructed DAG.
static Dag	dag(HapPairs hapPairs, float[] weights, float scale, int nInitLevels) Constructs and returns a new Dag instance from the specified data.
java.lang.String	toString() Returns a string description of this.

Methods inherited from class java.lang.Object

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

Method Detail

dag

public static Dag dag(HapPairs hapPairs,
                      float[] weights,
                      float scale,
                      int nInitLevels)

Constructs and returns a new Dag instance from the specified data.

Parameters:

hapPairs - the sequence data

weights - an array whose j-th element is the weight for the j-th haplotype

scale - a parameter that multiplicatively scales the node similarity threshold

nInitLevels - the number of initial levels to read

Returns:

a new Dag instance

Throws:

java.lang.IllegalArgumentException - if hapPairs.nMarkers() == 0

java.lang.IllegalArgumentException - if (weights[j] <= 0 || Float.isFinite(weights[j]) == false) for any j satisfying (0 <= j && j < weights.length)

java.lang.IllegalArgumentException - if Double.isFinite(scale) == false || scale <= 0

java.lang.IllegalArgumentException - if nInitLevels < 1

java.lang.NullPointerException - if hapPairs == null || weights == null

dag

public Dag dag()

Returns the constructed DAG.

Returns:

the constructed DAG

toString

public java.lang.String toString()

Returns a string description of this. The exact details of the representation are unspecified and subject to change.

Overrides:

toString in class java.lang.Object

Returns:

a string description of this