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

Packages that use AlignedNode

fr.orsay.lri.varna.models.treealign

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

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

private Tree<AlignedNode<ValueType1,ValueType2>>

TreeAlignResult.alignment

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

Tree<AlignedNode<ValueType1,ValueType2>>	TreeAlign.Aligner.computeAlignment()
private List<Tree<AlignedNode<ValueType1,ValueType2>>>	TreeAlign.Aligner.computeForestAlignment(int i, int s, int p, int j, int t, int q) Align F1[i_s,i_p] with F2[j_t,j_q].
private Tree<AlignedNode<ValueType1,ValueType2>>	TreeAlign.Aligner.computeTreeAlignment(int i, int j)
Tree<AlignedNode<ValueType1,ValueType2>>	TreeAlignResult.getAlignment()
private Tree<AlignedNode<ValueType1,ValueType2>>	TreeAlign.Aligner.treeDeleted(int i) Align T1[i] with the empty tree.
private Tree<AlignedNode<ValueType1,ValueType2>>	TreeAlign.Aligner.treeInserted(int j) Align the empty tree with T2[j].

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

Mapping	RNATree2.ConvertToMapping.convert(Tree<AlignedNode<RNANodeValue2,RNANodeValue2>> tree)
Mapping	RNATree.ConvertToMapping.convert(Tree<AlignedNode<RNANodeValue,RNANodeValue>> tree)
private void	RNATree2.ConvertToMapping.convertSubTree(Tree<AlignedNode<RNANodeValue2,RNANodeValue2>> tree)
private void	RNATree.ConvertToMapping.convertSubTree(Tree<AlignedNode<RNANodeValue,RNANodeValue>> tree)
float	TreeAlign.distanceFromAlignment(Tree<AlignedNode<ValueType1,ValueType2>> alignment) Takes a alignment, and compute the distance between the two original trees.
static Mapping	RNATree2.mappingFromAlignment(Tree<AlignedNode<RNANodeValue2,RNANodeValue2>> alignment) Convert an RNA tree (with RNANodeValue2) alignment into a Mapping.
static Mapping	RNATree.mappingFromAlignment(Tree<AlignedNode<RNANodeValue,RNANodeValue>> alignment) Convert an RNA tree alignment into a Mapping.
void	TreeAlignResult.setAlignment(Tree<AlignedNode<ValueType1,ValueType2>> alignment)