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Packages that use Tree | |
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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 |
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Methods in fr.orsay.lri.varna.models.rna with parameters of type Tree | |
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private void |
RNA.computeHelixTranslations(Tree<RNANodeValueTemplate> tree,
Map<RNATemplate.RNATemplateHelix,Point2D.Double> translateVectors,
RNATemplateMapping mapping,
Point2D.Double parentDeltaVector)
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private Map<RNATemplate.RNATemplateHelix,Point2D.Double> |
RNA.computeHelixTranslations(Tree<RNANodeValueTemplate> tree,
RNATemplateMapping mapping)
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Uses of Tree in fr.orsay.lri.varna.models.templates |
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Methods in fr.orsay.lri.varna.models.templates that return Tree | |
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Tree<RNANodeValueTemplate> |
RNATemplate.ConvertToTree.convert()
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Tree<RNANodeValueTemplate> |
RNATemplate.toTree()
Make a tree of the template. |
Methods in fr.orsay.lri.varna.models.templates with parameters of type Tree | |
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private void |
RNATemplate.ConvertToTree.makeChildren(Tree<RNANodeValueTemplate> father)
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Uses of Tree in fr.orsay.lri.varna.models.treealign |
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Fields in fr.orsay.lri.varna.models.treealign declared as Tree | |
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private Tree<AlignedNode<ValueType1,ValueType2>> |
TreeAlignResult.alignment
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private Tree<OriginalNodeValueType1> |
AlignedNode.leftNode
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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
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Tree<ValueType> |
TreeAlign.TreeData.tree
The tree. |
private Tree<T> |
Tree.tree
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Fields in fr.orsay.lri.varna.models.treealign with type parameters of type Tree | |
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private List<Tree<T>> |
Tree.children
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private LinkedList<Tree<T>> |
Tree.DFSPrefixIterator.remainingNodes
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Methods in fr.orsay.lri.varna.models.treealign that return Tree | |
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Tree<AlignedNode<ValueType1,ValueType2>> |
TreeAlign.Aligner.computeAlignment()
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private Tree<AlignedNode<ValueType1,ValueType2>> |
TreeAlign.Aligner.computeTreeAlignment(int i,
int j)
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Tree<AlignedNode<ValueType1,ValueType2>> |
TreeAlignResult.getAlignment()
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Tree<OriginalNodeValueType1> |
AlignedNode.getLeftNode()
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Tree<OriginalNodeValueType2> |
AlignedNode.getRightNode()
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Tree<T> |
Tree.DFSPrefixIterator.next()
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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 | |
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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()
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private static List<Tree<RNANodeValue2>> |
RNATree2.RNAForest2FromRNAForest(List<Tree<RNANodeValue>> originalForest)
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Methods in fr.orsay.lri.varna.models.treealign with parameters of type Tree | |
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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)
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Mapping |
RNATree.ConvertToMapping.convert(Tree<AlignedNode<RNANodeValue,RNANodeValue>> tree)
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private void |
RNATree2.ConvertToMapping.convertSubTree(Tree<AlignedNode<RNANodeValue2,RNANodeValue2>> tree)
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private void |
RNATree.ConvertToMapping.convertSubTree(Tree<AlignedNode<RNANodeValue,RNANodeValue>> tree)
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private void |
TreeAlign.ConvertTreeToArray.convertTreeToArrayAux(Tree<ValueType> subtree,
int[] siblingIndexes,
int siblingNumber)
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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)
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static Tree<RNANodeValue2> |
RNATree2.RNATree2FromRNATree(Tree<RNANodeValue> originalTree)
Convert from RNANodeValue model to RNANodeValue2 model, ie. |
void |
TreeAlignResult.setAlignment(Tree<AlignedNode<ValueType1,ValueType2>> alignment)
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void |
AlignedNode.setLeftNode(Tree<OriginalNodeValueType1> leftNode)
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void |
AlignedNode.setRightNode(Tree<OriginalNodeValueType2> rightNode)
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private static String |
TreeGraphviz.subtreeToGraphviz(Tree<? extends GraphvizDrawableNodeValue> tree)
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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 | |
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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)
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private static void |
RNATree2.RNAForest2FromRNAForestCommitNonPaired(List<Tree<RNANodeValue2>> forest,
List<RNANodeValue> consecutiveNonPairedBases)
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Constructors in fr.orsay.lri.varna.models.treealign with parameters of type Tree | |
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TreeAlign.Aligner(Tree<ValueType1> T1,
Tree<ValueType2> T2)
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TreeAlign.Aligner(Tree<ValueType1> T1,
Tree<ValueType2> T2)
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Constructor parameters in fr.orsay.lri.varna.models.treealign with type arguments of type Tree | |
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Tree(Iterable<Tree<T>> children)
Creates a tree, with the given set of children. |
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