Uses of Class
fr.orsay.lri.varna.models.treealign.RNANodeValue

Packages that use RNANodeValue

fr.orsay.lri.varna.models.treealign

Uses of RNANodeValue in fr.orsay.lri.varna.models.treealign

Fields in fr.orsay.lri.varna.models.treealign declared as RNANodeValue

private RNANodeValue

RNANodeValue2.node Defined if singleNode is true.

Fields in fr.orsay.lri.varna.models.treealign with type parameters of type RNANodeValue

private List<RNANodeValue>

RNANodeValue2.nodes Defined if singleNode is false;

Methods in fr.orsay.lri.varna.models.treealign that return RNANodeValue

RNANodeValue

RNANodeValue2.getNode() In case of a single node, return it.

Methods in fr.orsay.lri.varna.models.treealign that return types with arguments of type RNANodeValue

List<RNANodeValue>	RNANodeValue2.getNodes() In case of multiple nodes, return them.
static Tree<RNANodeValue>	RNATree.RNATreeFromRNA(RNA rna) Convert an RNA object into a RNA tree.
Tree<RNANodeValue>	RNATree.ConvertToTree.toTreeAux(int depth) Starts at the current position i in the sequence and converts the sequence to a tree.

Methods in fr.orsay.lri.varna.models.treealign with parameters of type RNANodeValue

void	RNANodeValue2.setNode(RNANodeValue node)

Method parameters in fr.orsay.lri.varna.models.treealign with type arguments of type RNANodeValue

Mapping	RNATree.ConvertToMapping.convert(Tree<AlignedNode<RNANodeValue,RNANodeValue>> tree)
Mapping	RNATree.ConvertToMapping.convert(Tree<AlignedNode<RNANodeValue,RNANodeValue>> tree)
private void	RNATree.ConvertToMapping.convertSubTree(Tree<AlignedNode<RNANodeValue,RNANodeValue>> tree)
private void	RNATree.ConvertToMapping.convertSubTree(Tree<AlignedNode<RNANodeValue,RNANodeValue>> tree)
static Mapping	RNATree.mappingFromAlignment(Tree<AlignedNode<RNANodeValue,RNANodeValue>> alignment) Convert an RNA tree alignment into a Mapping.
static Mapping	RNATree.mappingFromAlignment(Tree<AlignedNode<RNANodeValue,RNANodeValue>> alignment) Convert an RNA tree alignment into a Mapping.
private static List<Tree<RNANodeValue2>>	RNATree2.RNAForest2FromRNAForest(List<Tree<RNANodeValue>> originalForest)
private static void	RNATree2.RNAForest2FromRNAForestCommitNonPaired(List<Tree<RNANodeValue2>> forest, List<RNANodeValue> consecutiveNonPairedBases)
static Tree<RNANodeValue2>	RNATree2.RNATree2FromRNATree(Tree<RNANodeValue> originalTree) Convert from RNANodeValue model to RNANodeValue2 model, ie.
void	RNANodeValue2.setNodes(List<RNANodeValue> nodes)