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)