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

Packages that use Tree
fr.orsay.lri.varna.models.rna   
fr.orsay.lri.varna.models.templates   
fr.orsay.lri.varna.models.treealign   
 

Uses of Tree in fr.orsay.lri.varna.models.rna
 

Methods in fr.orsay.lri.varna.models.rna with parameters of type Tree
private  void RNA.computeHelixTranslations(Tree<RNANodeValueTemplate> tree, Map<RNATemplate.RNATemplateHelix,Point2D.Double> translateVectors, RNATemplateMapping mapping, Point2D.Double parentDeltaVector)
           
private  Map<RNATemplate.RNATemplateHelix,Point2D.Double> RNA.computeHelixTranslations(Tree<RNANodeValueTemplate> tree, RNATemplateMapping mapping)
           
 

Uses of Tree in fr.orsay.lri.varna.models.templates
 

Methods in fr.orsay.lri.varna.models.templates that return Tree
 Tree<RNANodeValueTemplate> RNATemplate.ConvertToTree.convert()
           
 Tree<RNANodeValueTemplate> RNATemplate.toTree()
          Make a tree of the template.
 

Methods in fr.orsay.lri.varna.models.templates with parameters of type Tree
private  void RNATemplate.ConvertToTree.makeChildren(Tree<RNANodeValueTemplate> father)
           
 

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

Fields in fr.orsay.lri.varna.models.treealign declared as Tree
private  Tree<AlignedNode<ValueType1,ValueType2>> TreeAlignResult.alignment
           
private  Tree<OriginalNodeValueType1> AlignedNode.leftNode
           
 Tree<ValueType>[] TreeAlign.TreeData.nodes
          The trees as an array of its nodes (subtrees rooted at each node in fact), in postorder.
private  Tree<OriginalNodeValueType2> AlignedNode.rightNode
           
 Tree<ValueType> TreeAlign.TreeData.tree
          The tree.
private  Tree<T> Tree.tree
           
 

Fields in fr.orsay.lri.varna.models.treealign with type parameters of type Tree
private  List<Tree<T>> Tree.children
           
private  LinkedList<Tree<T>> Tree.DFSPrefixIterator.remainingNodes
           
 

Methods in fr.orsay.lri.varna.models.treealign that return Tree
 Tree<AlignedNode<ValueType1,ValueType2>> TreeAlign.Aligner.computeAlignment()
           
private  Tree<AlignedNode<ValueType1,ValueType2>> TreeAlign.Aligner.computeTreeAlignment(int i, int j)
           
 Tree<AlignedNode<ValueType1,ValueType2>> TreeAlignResult.getAlignment()
           
 Tree<OriginalNodeValueType1> AlignedNode.getLeftNode()
           
 Tree<OriginalNodeValueType2> AlignedNode.getRightNode()
           
 Tree<T> Tree.DFSPrefixIterator.next()
           
static Tree<RNANodeValue2> RNATree2.RNATree2FromRNA(RNA rna)
          Convert an RNA object into a RNA tree with RNANodeValue2.
static Tree<RNANodeValue2> RNATree2.RNATree2FromRNATree(Tree<RNANodeValue> originalTree)
          Convert from RNANodeValue model to RNANodeValue2 model, ie.
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.
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].
 

Methods in fr.orsay.lri.varna.models.treealign that return types with arguments of type Tree
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].
 List<Tree<T>> Tree.getChildren()
          Returns the list of children.
 Iterator<Tree<T>> Tree.iterator()
           
private static List<Tree<RNANodeValue2>> RNATree2.RNAForest2FromRNAForest(List<Tree<RNANodeValue>> originalForest)
           
 

Methods in fr.orsay.lri.varna.models.treealign with parameters of type Tree
 TreeAlignResult<ValueType1,ValueType2> TreeAlign.align(Tree<ValueType1> T1, Tree<ValueType2> T2)
          Align T1 with T2, computing both the distance and the alignment.
 TreeAlignResult<ValueType1,ValueType2> TreeAlign.align(Tree<ValueType1> T1, Tree<ValueType2> T2)
          Align T1 with T2, computing both the distance and the alignment.
 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)
           
private  void TreeAlign.ConvertTreeToArray.convertTreeToArrayAux(Tree<ValueType> subtree, int[] siblingIndexes, int siblingNumber)
           
 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.
private  String AlignedNode.maybeNodeToGraphvizNodeName(Tree<? extends GraphvizDrawableNodeValue> tree)
           
static Tree<RNANodeValue2> RNATree2.RNATree2FromRNATree(Tree<RNANodeValue> originalTree)
          Convert from RNANodeValue model to RNANodeValue2 model, ie.
 void TreeAlignResult.setAlignment(Tree<AlignedNode<ValueType1,ValueType2>> alignment)
           
 void AlignedNode.setLeftNode(Tree<OriginalNodeValueType1> leftNode)
           
 void AlignedNode.setRightNode(Tree<OriginalNodeValueType2> rightNode)
           
private static String TreeGraphviz.subtreeToGraphviz(Tree<? extends GraphvizDrawableNodeValue> tree)
           
static String TreeGraphviz.treeToGraphviz(Tree<? extends GraphvizDrawableNodeValue> tree, String title)
          Creates a graphviz source from a Tree.
static void TreeGraphviz.treeToGraphvizFile(Tree<? extends GraphvizDrawableNodeValue> tree, String filename)
          Like treeToGraphvizFile(Tree,String,String) but with the title equal to the filename.
static void TreeGraphviz.treeToGraphvizFile(Tree<? extends GraphvizDrawableNodeValue> tree, String filename, String title)
          Creates a graphviz source file from a Tree.
static void TreeGraphviz.treeToGraphvizPostscript(Tree<? extends GraphvizDrawableNodeValue> tree, String filename)
          Like treeToGraphvizPostscript(Tree,String,String) but with the title equal to the filename.
static void TreeGraphviz.treeToGraphvizPostscript(Tree<? extends GraphvizDrawableNodeValue> tree, String filename, String title)
          Generates a PostScript file using graphviz.
 

Method parameters in fr.orsay.lri.varna.models.treealign with type arguments of type Tree
 void Tree.replaceChildrenListBy(List<Tree<T>> children)
          This method replaces the list of children of a tree with the list given as argument.
private static List<Tree<RNANodeValue2>> RNATree2.RNAForest2FromRNAForest(List<Tree<RNANodeValue>> originalForest)
           
private static void RNATree2.RNAForest2FromRNAForestCommitNonPaired(List<Tree<RNANodeValue2>> forest, List<RNANodeValue> consecutiveNonPairedBases)
           
 

Constructors in fr.orsay.lri.varna.models.treealign with parameters of type Tree
TreeAlign.Aligner(Tree<ValueType1> T1, Tree<ValueType2> T2)
           
TreeAlign.Aligner(Tree<ValueType1> T1, Tree<ValueType2> T2)
           
 

Constructor parameters in fr.orsay.lri.varna.models.treealign with type arguments of type Tree
Tree(Iterable<Tree<T>> children)
          Creates a tree, with the given set of children.