A D G N O P S T

A

AbstractSequence<FamilyType extends StructuralFamily> - Class in de.bioforscher.singa.sequence.model

AbstractSequence(List<FamilyType>) - Constructor for class de.bioforscher.singa.sequence.model.AbstractSequence

addEdgeBetween(int, DynamicProgrammingNode, DynamicProgrammingNode) - Method in class de.bioforscher.singa.sequence.algorithms.alignment.DynamicProgrammingGraph

addEdgeBetween(DynamicProgrammingNode, DynamicProgrammingNode) - Method in class de.bioforscher.singa.sequence.algorithms.alignment.DynamicProgrammingGraph

addEdgeBetween(int, double, DynamicProgrammingNode, DynamicProgrammingNode) - Method in class de.bioforscher.singa.sequence.algorithms.alignment.DynamicProgrammingGraph

addNode(DynamicProgrammingNode, int, int) - Method in class de.bioforscher.singa.sequence.algorithms.alignment.DynamicProgrammingGraph

D

de.bioforscher.singa.sequence.algorithms.alignment - package de.bioforscher.singa.sequence.algorithms.alignment

de.bioforscher.singa.sequence.model - package de.bioforscher.singa.sequence.model

de.bioforscher.singa.sequence.model.interfaces - package de.bioforscher.singa.sequence.model.interfaces

DynamicProgrammingEdge - Class in de.bioforscher.singa.sequence.algorithms.alignment

DynamicProgrammingEdge(int) - Constructor for class de.bioforscher.singa.sequence.algorithms.alignment.DynamicProgrammingEdge

DynamicProgrammingEdge(int, double) - Constructor for class de.bioforscher.singa.sequence.algorithms.alignment.DynamicProgrammingEdge

DynamicProgrammingEdge(int, double, AminoAcidFamily, AminoAcidFamily) - Constructor for class de.bioforscher.singa.sequence.algorithms.alignment.DynamicProgrammingEdge

DynamicProgrammingGraph - Class in de.bioforscher.singa.sequence.algorithms.alignment

DynamicProgrammingGraph(ProteinSequence, ProteinSequence) - Constructor for class de.bioforscher.singa.sequence.algorithms.alignment.DynamicProgrammingGraph

DynamicProgrammingNode - Class in de.bioforscher.singa.sequence.algorithms.alignment

DynamicProgrammingNode(Integer) - Constructor for class de.bioforscher.singa.sequence.algorithms.alignment.DynamicProgrammingNode

G

getAlignedFirstSequence() - Method in class de.bioforscher.singa.sequence.algorithms.alignment.NeedlemanWunschAlignment

getAlignedSecondSequence() - Method in class de.bioforscher.singa.sequence.algorithms.alignment.NeedlemanWunschAlignment

getCopy() - Method in class de.bioforscher.singa.sequence.algorithms.alignment.DynamicProgrammingNode

getFirst() - Method in class de.bioforscher.singa.sequence.algorithms.alignment.DynamicProgrammingEdge

getFirstSequence() - Method in class de.bioforscher.singa.sequence.algorithms.alignment.DynamicProgrammingGraph

getFirstSequenceLength() - Method in class de.bioforscher.singa.sequence.algorithms.alignment.DynamicProgrammingGraph

getGapCost() - Method in class de.bioforscher.singa.sequence.algorithms.alignment.NeedlemanWunschAlignment

getGraph() - Method in class de.bioforscher.singa.sequence.algorithms.alignment.NeedlemanWunschAlignment

getLength() - Method in interface de.bioforscher.singa.sequence.model.interfaces.Sequence

getLetter(int) - Method in interface de.bioforscher.singa.sequence.model.interfaces.Sequence

getNode(int, int) - Method in class de.bioforscher.singa.sequence.algorithms.alignment.DynamicProgrammingGraph

getParing(int, int) - Method in class de.bioforscher.singa.sequence.algorithms.alignment.DynamicProgrammingGraph

getScore() - Method in class de.bioforscher.singa.sequence.algorithms.alignment.DynamicProgrammingNode

getScore() - Method in class de.bioforscher.singa.sequence.algorithms.alignment.NeedlemanWunschAlignment

getSecond() - Method in class de.bioforscher.singa.sequence.algorithms.alignment.DynamicProgrammingEdge

getSecondSequence() - Method in class de.bioforscher.singa.sequence.algorithms.alignment.DynamicProgrammingGraph

getSecondSequenceLength() - Method in class de.bioforscher.singa.sequence.algorithms.alignment.DynamicProgrammingGraph

getSequence() - Method in class de.bioforscher.singa.sequence.model.AbstractSequence

getSequence() - Method in interface de.bioforscher.singa.sequence.model.interfaces.Sequence

getSequenceAsString() - Method in interface de.bioforscher.singa.sequence.model.interfaces.Sequence

N

NeedlemanWunschAlignment - Class in de.bioforscher.singa.sequence.algorithms.alignment

NeedlemanWunschAlignment(SubstitutionMatrix, ProteinSequence, ProteinSequence) - Constructor for class de.bioforscher.singa.sequence.algorithms.alignment.NeedlemanWunschAlignment

NucleotideSequence - Class in de.bioforscher.singa.sequence.model

O

of(List<LeafSubstructure<?>>) - Static method in class de.bioforscher.singa.sequence.model.NucleotideSequence

of(LeafSubstructureContainer) - Static method in class de.bioforscher.singa.sequence.model.NucleotideSequence

of(List<LeafSubstructure<?>>) - Static method in class de.bioforscher.singa.sequence.model.ProteinSequence

of(LeafSubstructureContainer) - Static method in class de.bioforscher.singa.sequence.model.ProteinSequence

of(String) - Static method in class de.bioforscher.singa.sequence.model.ProteinSequence

P

ProteinSequence - Class in de.bioforscher.singa.sequence.model

ProteinSequence(List<AminoAcidFamily>) - Constructor for class de.bioforscher.singa.sequence.model.ProteinSequence

S

Sequence<FamilyType extends StructuralFamily> - Interface in de.bioforscher.singa.sequence.model.interfaces

setFirst(AminoAcidFamily) - Method in class de.bioforscher.singa.sequence.algorithms.alignment.DynamicProgrammingEdge

setGapCost(int) - Method in class de.bioforscher.singa.sequence.algorithms.alignment.NeedlemanWunschAlignment

setScore(double) - Method in class de.bioforscher.singa.sequence.algorithms.alignment.DynamicProgrammingNode

setSecond(AminoAcidFamily) - Method in class de.bioforscher.singa.sequence.algorithms.alignment.DynamicProgrammingEdge

T

toString() - Method in class de.bioforscher.singa.sequence.model.AbstractSequence

A D G N O P S T