Package fr.orsay.lri.varna.models.treealign

Interface Summary
GraphvizDrawableNodeValue A tree can be displayed using graphviz (using class TreeGraphviz) if the node values in the tree implement this interface.
TreeAlignLabelDistanceAsymmetric<ValueType1,ValueType2>  
TreeAlignLabelDistanceSymmetric<ValueType> Same as TreeAlignLabelDistanceAsymmetric, but elements on both trees are of the same type, and the function is symmetric, ie.
 

Class Summary
AlignedNode<OriginalNodeValueType1,OriginalNodeValueType2> The type of node values in an alignment.
ExampleDistance2 This distance is such that a substitution costs nothing.
ExampleDistance3  
RNANodeValue We use the following convention: If the node is marked by a couple (n,m) these integers are stored in leftBasePosition and rightBasePosition (ie.
RNANodeValue2 In this model, nodes are either: 1.
RNATree This class contains all functions that are specific to trees (class Tree) of RNA.
RNATree.ConvertToMapping  
RNATree.ConvertToTree  
RNATree2 This class contains all functions that are specific to trees (class Tree) of RNA, with RNANodeValue2.
RNATree2.ConvertToMapping  
Tree<T> An object of this class is a rooted tree, where children are ordered.
TreeAlign<ValueType1,ValueType2> Tree alignment algorithm.
TreeAlignResult<ValueType1,ValueType2> The result of aligning a tree T1 with a tree T2.
TreeGraphviz This class translates a Tree to a graphviz file.
 

Enum Summary
RNANodeValue.Origin  
 

Exception Summary
RNANodeValue2WrongTypeException  
RNATree2Exception  
TreeAlignException