fr.orsay.lri.varna.models.treealign
Class RNATree

java.lang.Object
  extended by fr.orsay.lri.varna.models.treealign.RNATree

public class RNATree
extends Object

This class contains all functions that are specific to trees (class Tree) of RNA.

Author:
Raphael Champeimont

Nested Class Summary
private static class RNATree.ConvertToMapping
           
private static class RNATree.ConvertToTree
           
 
Constructor Summary
RNATree()
           
 
Method Summary
static Mapping mappingFromAlignment(Tree<AlignedNode<RNANodeValue,RNANodeValue>> alignment)
          Convert an RNA tree alignment into a Mapping.
static Tree<RNANodeValue> RNATreeFromRNA(RNA rna)
          Convert an RNA object into a RNA tree.
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

RNATree

public RNATree()
Method Detail

RNATreeFromRNA

public static Tree<RNANodeValue> RNATreeFromRNA(RNA rna)
Convert an RNA object into a RNA tree. The root node will have a null value because it is a fake node added to have a tree (otherwise we would have a forest).


mappingFromAlignment

public static Mapping mappingFromAlignment(Tree<AlignedNode<RNANodeValue,RNANodeValue>> alignment)
                                    throws fr.orsay.lri.varna.exceptions.MappingException
Convert an RNA tree alignment into a Mapping.

Throws:
fr.orsay.lri.varna.exceptions.MappingException