ImmutableDag

java.lang.Object
- dag.ImmutableDag

All Implemented Interfaces:

Dag
```
public final class ImmutableDag
extends java.lang.Object
implements Dag
```
Class ImmutableDag represents a leveled Directed Acyclic Graph (DAG).

Instances of class ImmutableDag are immutable.

Constructor Summary

Constructors
Constructor and Description

ImmutableDag(Markers markers, DagLevel[] levels)
Constructs a new ImmutableDag instance from the specified data.

Constructors
Constructor and Description
`ImmutableDag(Markers markers, DagLevel[] levels)` Constructs a new `ImmutableDag` instance from the specified data.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`int`	`childNode(int level, int edge)` Returns the index of the specified child node in the DAG.
`float`	`condEdgeProb(int level, int edge)` Returns the ratio of the sum of the weights of the sequences that pass through the specified edge of the DAG and the sum of the weights of the sequences that pass through the parent node of the specified edge of the DAG.
`float`	`edgeProb(int level, int edge)` Returns the ratio of the sum of the weights of the sequences that pass through the specified edge of the DAG and the sum of the weights of all sequences.
`float`	`edgeWeight(int level, int edge)` Returns the sum of the weights of the sequences that pass through the specified edge of the DAG.
`int`	`inEdge(int level, int childNode, int inEdge)` Returns the index of the specified edge in the DAG.
`boolean`	`isChildOf(int parentLevel, int parentEdge, int childEdge)` Returns `true` if the child node of the specified parent edge equals the parent node of the specified child edge and returns `false` otherwise.
`Markers`	`markers()` Returns the markers represented by this DAG.
`int`	`maxEdges()` Returns the maximum number of edges at any level of the DAG.
`int`	`maxNodes()` Returns the maximum number of parent nodes at any level of the DAG.
`int`	`nChildNodes(int level)` Returns the number of child nodes at the specified level of the DAG.
`long`	`nEdges()` Returns the number of edges in the DAG.
`int`	`nEdges(int level)` Returns the number of edges at the specified level of the DAG.
`int`	`nInEdges(int level, int childNode)` Returns the number of ingoing edges for the specified node of the DAG.
`int`	`nLevels()` Returns the number of markers.
`long`	`nNodes()` Returns the number of nodes in the DAG.
`int`	`nOutEdges(int level, int parentNode)` Returns the number of outgoing edges for the specified node of the DAG.
`int`	`nParentNodes(int level)` Returns the number of parent nodes at the specified level of the DAG.
`int`	`outEdge(int level, int parentNode, int outEdge)` Returns the index of the specified edge in the DAG.
`int`	`outEdgeBySymbol(int level, int parentNode, int symbol)` Returns the index of the specified edge at the specified level of the DAG or `-1` if no such edge exists.
`int`	`parentNode(int level, int edge)` Returns the index of the specified parent node in the DAG.
`float`	`parentProb(int level, int node)` Returns the ratio of the sum of the weights of the sequences that pass through the specified parent node of the DAG and the sum of the weights of all sequences.
`float`	`parentWeight(int level, int parentNode)` Returns the sum of the weights of the sequences that pass through the specified node of the DAG.
`double[]`	`posArray()` Returns an array of length `this.nMarkers()` whose `j`-th element is the distance from the root node to the child node at level `j` of the DAG.
`int`	`symbol(int level, int edge)` Returns the symbol labeling the specified edge of the DAG.
`java.lang.String`	`toString()` Returns a string representation of `this`.
`java.lang.String`	`toString(int startLevel, int endLevel)` Returns a description of the specified levels of the DAG.

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

- Constructor Detail
  - ImmutableDag
```
public ImmutableDag(Markers markers,
                    DagLevel[] levels)
```
    Constructs a new ImmutableDag instance from the specified data.
    
    Parameters:
    
    markers - the markers
    
    levels - the levels of the leveled DAG
    
    Throws:
    
    java.lang.IllegalArgumentException - if levels.length == 0
    
    java.lang.IllegalArgumentException - if levels[0].nParentNodes() != 1
    
    java.lang.IllegalArgumentException - if levels[j-1].nChildNodes() != levels[j].nParentNodes() for any j satisfying 0 < j && j < levels.length
    
    java.lang.NullPointerException - if (markers == null || levels==null), or if levels[j] == null for any j satisfying 0 <= j && j < levels.length
- Method Detail
  - nEdges
```
public int nEdges(int level)
```
    Description copied from interface: Dag
    
    Returns the number of edges at the specified level of the DAG.
    
    Specified by:
    
    nEdges in interface Dag
    
    Parameters:
    
    level - a level of the DAG
    
    Returns:
    
    the number of edges at the specified level of the DAG.
  - nParentNodes
```
public int nParentNodes(int level)
```
    Description copied from interface: Dag
    
    Returns the number of parent nodes at the specified level of the DAG.
    
    Specified by:
    
    nParentNodes in interface Dag
    
    Parameters:
    
    level - a level of the DAG
    
    Returns:
    
    the number of parent nodes at the specified level of the DAG
  - nChildNodes
```
public int nChildNodes(int level)
```
    Description copied from interface: Dag
    
    Returns the number of child nodes at the specified level of the DAG.
    
    Specified by:
    
    nChildNodes in interface Dag
    
    Parameters:
    
    level - a level of the DAG
    
    Returns:
    
    the number of child nodes at the specified level of the DAG
  - parentNode
```
public int parentNode(int level,
                      int edge)
```
    Description copied from interface: Dag
    
    Returns the index of the specified parent node in the DAG.
    
    Specified by:
    
    parentNode in interface Dag
    
    Parameters:
    
    level - a level of the DAG.
    
    edge - the index of an edge at the specified level of the DAG
    
    Returns:
    
    the index of the specified parent node in the DAG
  - childNode
```
public int childNode(int level,
                     int edge)
```
    Description copied from interface: Dag
    
    Returns the index of the specified child node in the DAG.
    
    Specified by:
    
    childNode in interface Dag
    
    Parameters:
    
    level - a level of the DAG
    
    edge - the index of an edge at the specified level of the DAG
    
    Returns:
    
    the index of the specified child node in the DAG
  - symbol
```
public int symbol(int level,
                  int edge)
```
    Description copied from interface: Dag
    
    Returns the symbol labeling the specified edge of the DAG.
    
    Specified by:
    
    symbol in interface Dag
    
    Parameters:
    
    level - a level of the DAG
    
    edge - the index of an edge at the specified level of the DAG
    
    Returns:
    
    the symbol labeling the specified edge of the DAG
  - edgeWeight
```
public float edgeWeight(int level,
                        int edge)
```
    Description copied from interface: Dag
    
    Returns the sum of the weights of the sequences that pass through the specified edge of the DAG.
    
    Specified by:
    
    edgeWeight in interface Dag
    
    Parameters:
    
    level - a level of the DAG
    
    edge - the index of an edge at the specified level of the DAG
    
    Returns:
    
    the sum of the weights of the sequences that pass through the specified edge of the DAG
  - parentWeight
```
public float parentWeight(int level,
                          int parentNode)
```
    Description copied from interface: Dag
    
    Returns the sum of the weights of the sequences that pass through the specified node of the DAG.
    
    Specified by:
    
    parentWeight in interface Dag
    
    Parameters:
    
    level - a level of the DAG
    
    parentNode - the index of a parent node at the specified level of the DAG
    
    Returns:
    
    the sum of the weights of the sequences that pass through the specified node of the DAG
  - condEdgeProb
```
public float condEdgeProb(int level,
                          int edge)
```
    Description copied from interface: Dag
    
    Returns the ratio of the sum of the weights of the sequences that pass through the specified edge of the DAG and the sum of the weights of the sequences that pass through the parent node of the specified edge of the DAG.
    
    Specified by:
    
    condEdgeProb in interface Dag
    
    Parameters:
    
    level - a level of the DAG
    
    edge - the index of an edge at the specified level of the DAG
    
    Returns:
    
    the ratio of the sum of the weights of the sequences that pass through the specified edge of the DAG and the sum of the weights of the sequences that pass through the parent node of the specified edge of the DAG
  - edgeProb
```
public float edgeProb(int level,
                      int edge)
```
    Description copied from interface: Dag
    
    Returns the ratio of the sum of the weights of the sequences that pass through the specified edge of the DAG and the sum of the weights of all sequences.
    
    Specified by:
    
    edgeProb in interface Dag
    
    Parameters:
    
    level - a level of the DAG
    
    edge - the index of an edge at the specified level of the DAG
    
    Returns:
    
    the ratio of the sum of the weights of the sequences that pass through the specified edge of the DAG and the sum of the weights of all sequences
  - parentProb
```
public float parentProb(int level,
                        int node)
```
    Description copied from interface: Dag
    
    Returns the ratio of the sum of the weights of the sequences that pass through the specified parent node of the DAG and the sum of the weights of all sequences.
    
    Specified by:
    
    parentProb in interface Dag
    
    Parameters:
    
    level - a level of the DAG
    
    node - the index of a parent node at the specified level of the DAG
    
    Returns:
    
    the ratio of the sum of the weights of the sequences that pass through the specified parent node of the DAG and the sum of the weights of all sequences
  - nLevels
```
public int nLevels()
```
    Description copied from interface: Dag
    
    Returns the number of markers.
    
    Specified by:
    
    nLevels in interface Dag
    
    Returns:
    
    the number of markers
  - markers
```
public Markers markers()
```
    Description copied from interface: Dag
    
    Returns the markers represented by this DAG.
    
    Specified by:
    
    markers in interface Dag
    
    Returns:
    
    the markers represented by this DAG
  - nNodes
```
public long nNodes()
```
    Description copied from interface: Dag
    
    Returns the number of nodes in the DAG.
    
    Specified by:
    
    nNodes in interface Dag
    
    Returns:
    
    the number of node in the DAG
  - nEdges
```
public long nEdges()
```
    Description copied from interface: Dag
    
    Returns the number of edges in the DAG.
    
    Specified by:
    
    nEdges in interface Dag
    
    Returns:
    
    the number of edges in the DAG
  - maxNodes
```
public int maxNodes()
```
    Description copied from interface: Dag
    
    Returns the maximum number of parent nodes at any level of the DAG.
    
    Specified by:
    
    maxNodes in interface Dag
    
    Returns:
    
    the maximum number of parent nodes at any level of the DAG
  - maxEdges
```
public int maxEdges()
```
    Description copied from interface: Dag
    
    Returns the maximum number of edges at any level of the DAG.
    
    Specified by:
    
    maxEdges in interface Dag
    
    Returns:
    
    the maximum number of edges at any level of the DAG
  - nOutEdges
```
public int nOutEdges(int level,
                     int parentNode)
```
    Description copied from interface: Dag
    
    Returns the number of outgoing edges for the specified node of the DAG.
    
    Specified by:
    
    nOutEdges in interface Dag
    
    Parameters:
    
    level - a level of the DAG
    
    parentNode - the index of a parent node at the specified level of the DAG
    
    Returns:
    
    the number of outgoing edges for the specified node of the DAG
  - outEdge
```
public int outEdge(int level,
                   int parentNode,
                   int outEdge)
```
    Description copied from interface: Dag
    
    Returns the index of the specified edge in the DAG.
    
    Specified by:
    
    outEdge in interface Dag
    
    Parameters:
    
    level - a level of the DAG
    
    parentNode - the index of a parent node at the specified level of the DAG
    
    outEdge - the index of an outgoing edge of the specified parent node
    
    Returns:
    
    the index of the specified edge in the DAG
  - outEdgeBySymbol
```
public int outEdgeBySymbol(int level,
                           int parentNode,
                           int symbol)
```
    Description copied from interface: Dag
    
    Returns the index of the specified edge at the specified level of the DAG or -1 if no such edge exists.
    
    Specified by:
    
    outEdgeBySymbol in interface Dag
    
    Parameters:
    
    level - a level of the DAG
    
    parentNode - the index of a parent node at the specified level of the DAG
    
    symbol - a symbol labeling an outgoing edge of the specified parent node of the DAG
    
    Returns:
    
    the index of the specified edge at the specified level of the DAG or -1 if no such edge exists
  - nInEdges
```
public int nInEdges(int level,
                    int childNode)
```
    Description copied from interface: Dag
    
    Returns the number of ingoing edges for the specified node of the DAG.
    
    Specified by:
    
    nInEdges in interface Dag
    
    Parameters:
    
    level - a level of the DAG
    
    childNode - the index of a child node at the specified level of the DAG
    
    Returns:
    
    the number of ingoing edges for the specified node of the DAG
  - inEdge
```
public int inEdge(int level,
                  int childNode,
                  int inEdge)
```
    Description copied from interface: Dag
    
    Returns the index of the specified edge in the DAG.
    
    Specified by:
    
    inEdge in interface Dag
    
    Parameters:
    
    level - a level of the DAG
    
    childNode - the index of a child node at the specified level of the DAG
    
    inEdge - the index of an ingoing edge of the specified child node in the DAG
    
    Returns:
    
    the index of the specified edge in the DAG
  - isChildOf
```
public boolean isChildOf(int parentLevel,
                         int parentEdge,
                         int childEdge)
```
    Description copied from interface: Dag
    
    Returns true if the child node of the specified parent edge equals the parent node of the specified child edge and returns false otherwise.
    
    Specified by:
    
    isChildOf in interface Dag
    
    Parameters:
    
    parentLevel - a level of the DAG
    
    parentEdge - the index of an edge at the specified level of the DAG
    
    childEdge - the index of an edge at level (parentLevel + 1) of the DAG
    
    Returns:
    
    true if the child node of the specified parent edge equals the parent node of the specified child edge
  - posArray
```
public double[] posArray()
```
    Description copied from interface: Dag
    
    Returns an array of length this.nMarkers() whose j-th element is the distance from the root node to the child node at level j of the DAG. The distance from parent node to child node at level lev equals -Math.log10(P) where P is the weighted conditional edge probability at level lev, when each edge e is weighted by this.counts(lev, e).
    
    Specified by:
    
    posArray in interface Dag
    
    Returns:
    
    an array of length this.nMarkers() whose j-th element is the distance from the root node to the child node at level j of the DAG
  - toString
```
public java.lang.String toString(int startLevel,
                                 int endLevel)
```
    Description copied from interface: Dag
    
    Returns a description of the specified levels of the DAG. The exact details of the description are unspecified and subject to change.
    
    Specified by:
    
    toString in interface Dag
    
    Parameters:
    
    startLevel - the first level (inclusive)
    
    endLevel - the last level (exclusive)
    
    Returns:
    
    a description of the specified levels of the DAG
  - toString
```
public java.lang.String toString()
```
    Description copied from interface: Dag
    
    Returns a string representation of this. The exact details of the representation are unspecifed and subject to change.
    
    Specified by:
    
    toString in interface Dag
    
    Overrides:
    
    toString in class java.lang.Object
    
    Returns:
    
    a string representation of this

Class ImmutableDag

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

ImmutableDag

Method Detail

nEdges

nParentNodes

nChildNodes

parentNode

childNode

symbol

edgeWeight

parentWeight

condEdgeProb

edgeProb

parentProb

nLevels

markers

nNodes

nEdges

maxNodes

maxEdges

nOutEdges

outEdge

outEdgeBySymbol

nInEdges

inEdge

isChildOf

posArray

toString

toString