de.bioforscher.singa.sequence.algorithms.alignment

Class DynamicProgrammingGraph

java.lang.Object

de.bioforscher.singa.mathematics.graphs.model.AbstractMapGraph<NodeType,EdgeType,de.bioforscher.singa.mathematics.vectors.Vector2D,Integer>

de.bioforscher.singa.mathematics.graphs.model.DirectedWeightedGraph<DynamicProgrammingNode,DynamicProgrammingEdge>

de.bioforscher.singa.sequence.algorithms.alignment.DynamicProgrammingGraph

All Implemented Interfaces:

de.bioforscher.singa.mathematics.graphs.model.Graph<DynamicProgrammingNode,DynamicProgrammingEdge,Integer>

public class DynamicProgrammingGraph
extends de.bioforscher.singa.mathematics.graphs.model.DirectedWeightedGraph<DynamicProgrammingNode,DynamicProgrammingEdge>

Author:

cl

Constructor Summary

Constructors

Constructor and Description
DynamicProgrammingGraph(ProteinSequence firstSequence, ProteinSequence secondSequence)

Method Summary

Modifier and Type	Method and Description
int	addEdgeBetween(DynamicProgrammingNode source, DynamicProgrammingNode target)
int	addEdgeBetween(int identifier, double weight, DynamicProgrammingNode source, DynamicProgrammingNode target)
int	addEdgeBetween(int identifier, DynamicProgrammingNode source, DynamicProgrammingNode target)
Integer	addNode(DynamicProgrammingNode node, int firstIndex, int secondIndex)
ProteinSequence	getFirstSequence()
int	getFirstSequenceLength()
DynamicProgrammingNode	getNode(int firstIndex, int secondIndex)
de.bioforscher.singa.core.utility.Pair<AminoAcidFamily>	getParing(int firstIndex, int secondIndex)
ProteinSequence	getSecondSequence()
int	getSecondSequenceLength()

Methods inherited from class de.bioforscher.singa.mathematics.graphs.model.DirectedWeightedGraph

nextNodeIdentifier

Methods inherited from class de.bioforscher.singa.mathematics.graphs.model.AbstractMapGraph

addEdgeBetween, addNode, containsEdge, containsNode, getEdge, getEdges, getMaximumDegree, getNode, getNodes, nextEdgeIdentifier, removeNode, removeNode, toString

Methods inherited from class java.lang.Object

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

Methods inherited from interface de.bioforscher.singa.mathematics.graphs.model.Graph

getEdgeBetween

Constructor Detail

DynamicProgrammingGraph

public DynamicProgrammingGraph(ProteinSequence firstSequence,
                               ProteinSequence secondSequence)

Method Detail

addNode

public Integer addNode(DynamicProgrammingNode node,
                       int firstIndex,
                       int secondIndex)

getNode

public DynamicProgrammingNode getNode(int firstIndex,
                                      int secondIndex)

getParing

public de.bioforscher.singa.core.utility.Pair<AminoAcidFamily> getParing(int firstIndex,
                                                                         int secondIndex)

getFirstSequence

public ProteinSequence getFirstSequence()

getFirstSequenceLength

public int getFirstSequenceLength()

getSecondSequence

public ProteinSequence getSecondSequence()

getSecondSequenceLength

public int getSecondSequenceLength()

addEdgeBetween

public int addEdgeBetween(int identifier,
                          DynamicProgrammingNode source,
                          DynamicProgrammingNode target)

Specified by:

addEdgeBetween in interface de.bioforscher.singa.mathematics.graphs.model.Graph<DynamicProgrammingNode,DynamicProgrammingEdge,Integer>

Specified by:

addEdgeBetween in class de.bioforscher.singa.mathematics.graphs.model.AbstractMapGraph<DynamicProgrammingNode,DynamicProgrammingEdge,de.bioforscher.singa.mathematics.vectors.Vector2D,Integer>

addEdgeBetween

public int addEdgeBetween(DynamicProgrammingNode source,
                          DynamicProgrammingNode target)

Specified by:

addEdgeBetween in interface de.bioforscher.singa.mathematics.graphs.model.Graph<DynamicProgrammingNode,DynamicProgrammingEdge,Integer>

Specified by:

addEdgeBetween in class de.bioforscher.singa.mathematics.graphs.model.AbstractMapGraph<DynamicProgrammingNode,DynamicProgrammingEdge,de.bioforscher.singa.mathematics.vectors.Vector2D,Integer>

addEdgeBetween

public int addEdgeBetween(int identifier,
                          double weight,
                          DynamicProgrammingNode source,
                          DynamicProgrammingNode target)