A B C D E F G H I K L M N O P Q R S T U V W X Y Z _

T

table - Variable in class fr.orsay.lri.varna.views.VueBases
 
table - Variable in class fr.orsay.lri.varna.views.VueBaseValues
 
table - Variable in class fr.orsay.lri.varna.views.VueBPList
 
table - Variable in class fr.orsay.lri.varna.views.VueListeAnnotations
 
tableChanged(TableModelEvent) - Method in class fr.orsay.lri.varna.views.VueBaseValues
 
tableChanged(TableModelEvent) - Method in class fr.orsay.lri.varna.views.VueBPList
 
template - Variable in class fr.orsay.lri.varna.models.templates.RNATemplate
Variable containing "this", used by the internal class to access this object.
testDirectionality(int, int, int) - Method in class fr.orsay.lri.varna.models.rna.RNA
 
testDirectionality(Point2D.Double, Point2D.Double, Point2D.Double) - Static method in class fr.orsay.lri.varna.models.rna.RNA
 
TextAnnotation - Class in fr.orsay.lri.varna.models.annotations
The annotated text model
TextAnnotation(String) - Constructor for class fr.orsay.lri.varna.models.annotations.TextAnnotation
creates an annoted text on a VARNAPanel with the specified text
TextAnnotation(String, double, double) - Constructor for class fr.orsay.lri.varna.models.annotations.TextAnnotation
/** creates an annoted text on a VARNAPanel with the specified text and is static position
TextAnnotation(String, ModeleBase) - Constructor for class fr.orsay.lri.varna.models.annotations.TextAnnotation
creates an annoted text on a VARNAPanel with the specified text fixed to a base
TextAnnotation(String, ArrayList<ModeleBase>, int) - Constructor for class fr.orsay.lri.varna.models.annotations.TextAnnotation
creates an annoted text on a VARNAPanel with the specified text fixed to a helix (if type is HELIX) or to a loop (if type is LOOP)
TextAnnotation(TextAnnotation) - Constructor for class fr.orsay.lri.varna.models.annotations.TextAnnotation
creates an annoted text from another one
textAnnotation - Variable in class fr.orsay.lri.varna.views.VueAnnotation
 
textAnnotationSave - Variable in class fr.orsay.lri.varna.views.VueAnnotation
 
textArea - Variable in class fr.orsay.lri.varna.views.VueAnnotation
 
TextCommand - Class in fr.orsay.lri.varna.models.export
 
TextCommand(Point2D.Double, String) - Constructor for class fr.orsay.lri.varna.models.export.TextCommand
 
TITLE_WIDTH - Static variable in class fr.orsay.lri.varna.views.VueChemProbAnnotation
 
TITLE_WIDTH - Static variable in class fr.orsay.lri.varna.views.VueHighlightRegionEdit
 
titleColorOpt - Static variable in class fr.orsay.lri.varna.models.VARNAConfigLoader
 
titleOpt - Static variable in class fr.orsay.lri.varna.models.VARNAConfigLoader
 
titleSizeOpt - Static variable in class fr.orsay.lri.varna.models.VARNAConfigLoader
 
toggleDrawOutlineBase() - Method in class fr.orsay.lri.varna.VARNAPanel
 
toggleFillBase() - Method in class fr.orsay.lri.varna.VARNAPanel
 
toggleSelection(int) - Method in class fr.orsay.lri.varna.VARNAPanel
 
toggleSelection(Collection<? extends Integer>) - Method in class fr.orsay.lri.varna.VARNAPanel
 
toGraphvizNodeId() - Method in class fr.orsay.lri.varna.models.treealign.Tree
Returns a string unique to this node.
toGraphvizNodeName() - Method in class fr.orsay.lri.varna.models.templates.RNANodeValueTemplate
 
toGraphvizNodeName() - Method in class fr.orsay.lri.varna.models.templates.RNANodeValueTemplateBasePair
 
toGraphvizNodeName() - Method in class fr.orsay.lri.varna.models.templates.RNANodeValueTemplateBrokenBasePair
 
toGraphvizNodeName() - Method in class fr.orsay.lri.varna.models.templates.RNANodeValueTemplateSequence
 
toGraphvizNodeName() - Method in class fr.orsay.lri.varna.models.treealign.AlignedNode
This method will work only if the left and right node already implement GraphvizDrawableNodeValue.
toGraphvizNodeName() - Method in interface fr.orsay.lri.varna.models.treealign.GraphvizDrawableNodeValue
Returns a string that will be displayed on the node by graphviz.
toGraphvizNodeName() - Method in class fr.orsay.lri.varna.models.treealign.RNANodeValue
 
toGraphvizNodeName() - Method in class fr.orsay.lri.varna.models.treealign.RNANodeValue2
 
TOLERANCE - Static variable in class fr.orsay.lri.varna.components.GradientEditorPanel
 
toPoint2D() - Method in class fr.orsay.lri.varna.models.rna.VARNAPoint
 
toRNA() - Method in class fr.orsay.lri.varna.models.templates.RNATemplate
Generate an RNA sequence that exactly matches the template.
toString() - Method in enum fr.orsay.lri.varna.models.annotations.ChemProbAnnotation.ChemProbAnnotationType
 
toString() - Method in class fr.orsay.lri.varna.models.annotations.ChemProbAnnotation
 
toString() - Method in class fr.orsay.lri.varna.models.annotations.HighlightRegionAnnotation
 
toString() - Method in class fr.orsay.lri.varna.models.annotations.TextAnnotation
 
toString() - Method in class fr.orsay.lri.varna.models.FullBackup
 
toString() - Method in class fr.orsay.lri.varna.models.naView.Loop
 
toString() - Method in class fr.orsay.lri.varna.models.rna.Mapping
 
toString() - Method in class fr.orsay.lri.varna.models.rna.ModeleBaseNucleotide
 
toString() - Method in enum fr.orsay.lri.varna.models.rna.ModeleBP.Edge
 
toString() - Method in enum fr.orsay.lri.varna.models.rna.ModeleBP.Stericity
 
toString() - Method in class fr.orsay.lri.varna.models.rna.ModeleBP
 
toString() - Method in enum fr.orsay.lri.varna.models.rna.ModeleColorMap.NamedColorMapTypes
 
toString() - Method in class fr.orsay.lri.varna.models.rna.ModeleColorMap
 
toString() - Method in class fr.orsay.lri.varna.models.rna.RNA
 
toString() - Method in class fr.orsay.lri.varna.models.rna.RNAMLParser.BPTemp
 
toString() - Method in class fr.orsay.lri.varna.models.rna.RNAMLParser.HelixTemp
 
toString() - Method in class fr.orsay.lri.varna.models.rna.VARNAPoint
 
toString() - Method in class fr.orsay.lri.varna.models.rna.VARNASecDraw.HelixEmbedding
 
toString() - Method in class fr.orsay.lri.varna.models.rna.VARNASecDraw.PairedPortion
 
toString() - Method in class fr.orsay.lri.varna.models.rna.VARNASecDraw.RNATree
 
toString() - Method in class fr.orsay.lri.varna.models.rna.VARNASecDraw.UnpairedPortion
 
toString() - Method in class fr.orsay.lri.varna.models.templates.RNANodeValueTemplate
 
toString() - Method in class fr.orsay.lri.varna.models.templates.RNATemplate.RNATemplateElement.EdgeEndPoint
 
toString() - Method in class fr.orsay.lri.varna.models.templates.RNATemplate.RNATemplateHelix
 
toString() - Method in class fr.orsay.lri.varna.models.templates.RNATemplate.RNATemplateUnpairedSequence
 
toString() - Method in class fr.orsay.lri.varna.models.treealign.RNANodeValue
 
toString() - Method in class fr.orsay.lri.varna.models.treealign.RNANodeValue2
 
toString() - Method in enum fr.orsay.lri.varna.models.VARNAConfig.BP_STYLE
 
toString() - Method in enum fr.orsay.lri.varna.views.VueBPList.Actions
 
toTree() - Method in class fr.orsay.lri.varna.models.templates.RNATemplate
Make a tree of the template.
toTreeAux(int) - Method in class fr.orsay.lri.varna.models.treealign.RNATree.ConvertToTree
Starts at the current position i in the sequence and converts the sequence to a tree.
toXMLDocument() - Method in class fr.orsay.lri.varna.models.templates.RNATemplate.ConvertToXml
 
toXMLDocument() - Method in class fr.orsay.lri.varna.models.templates.RNATemplate
 
toXMLFile(File) - Method in class fr.orsay.lri.varna.models.templates.RNATemplate
 
transform(Point2D.Double, double, double, double) - Method in class fr.orsay.lri.varna.models.export.SecStrDrawingProducer
 
transform(double, double, double, double, double) - Method in class fr.orsay.lri.varna.models.export.SecStrDrawingProducer
 
transform(AffineTransform) - Method in class fr.orsay.lri.varna.models.rna.VARNASecDraw.HelixEmbedding
 
transformCoord(Point2D.Double, double, double, double, double, double) - Method in class fr.orsay.lri.varna.VARNAPanel
 
transformCoord(Point2D.Double) - Method in class fr.orsay.lri.varna.VARNAPanel
 
traverse_loop(Loop, Connection) - Method in class fr.orsay.lri.varna.models.naView.NAView
This is the workhorse of the display program.
Tree<T> - Class in fr.orsay.lri.varna.models.treealign
An object of this class is a rooted tree, where children are ordered.
Tree(Iterable<Tree<T>>) - Constructor for class fr.orsay.lri.varna.models.treealign.Tree
Creates a tree, with the given set of children.
Tree() - Constructor for class fr.orsay.lri.varna.models.treealign.Tree
Creates a tree, with an empty list of children.
tree - Variable in class fr.orsay.lri.varna.models.treealign.Tree
 
tree - Variable in class fr.orsay.lri.varna.models.treealign.TreeAlign.TreeData
The tree.
Tree.DFSPrefixIterator - Class in fr.orsay.lri.varna.models.treealign
An iterator that returns the nodes in prefix (fathers before children) DFS (go deep first) order.
Tree.DFSPrefixIterator() - Constructor for class fr.orsay.lri.varna.models.treealign.Tree.DFSPrefixIterator
 
TreeAlign<ValueType1,ValueType2> - Class in fr.orsay.lri.varna.models.treealign
Tree alignment algorithm.
TreeAlign(TreeAlignLabelDistanceAsymmetric<ValueType1, ValueType2>) - Constructor for class fr.orsay.lri.varna.models.treealign.TreeAlign
Create a TreeAlignSymmetric object, which can align trees.
TreeAlign.Aligner - Class in fr.orsay.lri.varna.models.treealign
For arrays that take at least O(|T1|*|T2|) we take care not to use too big data types.
TreeAlign.Aligner(Tree<ValueType1>, Tree<ValueType2>) - Constructor for class fr.orsay.lri.varna.models.treealign.TreeAlign.Aligner
 
TreeAlign.ConvertTreeToArray<ValueType> - Class in fr.orsay.lri.varna.models.treealign
 
TreeAlign.ConvertTreeToArray(TreeAlign<ValueType1, ValueType2>.TreeData<ValueType>) - Constructor for class fr.orsay.lri.varna.models.treealign.TreeAlign.ConvertTreeToArray
 
TreeAlign.TreeData<ValueType> - Class in fr.orsay.lri.varna.models.treealign
 
TreeAlign.TreeData() - Constructor for class fr.orsay.lri.varna.models.treealign.TreeAlign.TreeData
 
TreeAlignException - Exception in fr.orsay.lri.varna.models.treealign
 
TreeAlignException(String) - Constructor for exception fr.orsay.lri.varna.models.treealign.TreeAlignException
 
TreeAlignLabelDistanceAsymmetric<ValueType1,ValueType2> - Interface in fr.orsay.lri.varna.models.treealign
 
TreeAlignLabelDistanceSymmetric<ValueType> - Interface in fr.orsay.lri.varna.models.treealign
Same as TreeAlignLabelDistanceAsymmetric, but elements on both trees are of the same type, and the function is symmetric, ie.
TreeAlignResult<ValueType1,ValueType2> - Class in fr.orsay.lri.varna.models.treealign
The result of aligning a tree T1 with a tree T2.
TreeAlignResult() - Constructor for class fr.orsay.lri.varna.models.treealign.TreeAlignResult
 
treeData - Variable in class fr.orsay.lri.varna.models.treealign.TreeAlign.ConvertTreeToArray
 
treeData1 - Variable in class fr.orsay.lri.varna.models.treealign.TreeAlign.Aligner
The first tree.
treeData2 - Variable in class fr.orsay.lri.varna.models.treealign.TreeAlign.Aligner
The second tree.
treeDeleted(int) - Method in class fr.orsay.lri.varna.models.treealign.TreeAlign.Aligner
Align T1[i] with the empty tree.
TreeGraphviz - Class in fr.orsay.lri.varna.models.treealign
This class translates a Tree to a graphviz file.
TreeGraphviz() - Constructor for class fr.orsay.lri.varna.models.treealign.TreeGraphviz
 
treeInserted(int) - Method in class fr.orsay.lri.varna.models.treealign.TreeAlign.Aligner
Align the empty tree with T2[j].
treeToGraphviz(Tree<? extends GraphvizDrawableNodeValue>, String) - Static method in class fr.orsay.lri.varna.models.treealign.TreeGraphviz
Creates a graphviz source from a Tree.
treeToGraphvizFile(Tree<? extends GraphvizDrawableNodeValue>, String, String) - Static method in class fr.orsay.lri.varna.models.treealign.TreeGraphviz
Creates a graphviz source file from a Tree.
treeToGraphvizFile(Tree<? extends GraphvizDrawableNodeValue>, String) - Static method in class fr.orsay.lri.varna.models.treealign.TreeGraphviz
Like treeToGraphvizFile(Tree,String,String) but with the title equal to the filename.
treeToGraphvizPostscript(Tree<? extends GraphvizDrawableNodeValue>, String, String) - Static method in class fr.orsay.lri.varna.models.treealign.TreeGraphviz
Generates a PostScript file using graphviz.
treeToGraphvizPostscript(Tree<? extends GraphvizDrawableNodeValue>, String) - Static method in class fr.orsay.lri.varna.models.treealign.TreeGraphviz
Like treeToGraphvizPostscript(Tree,String,String) but with the title equal to the filename.
TRIGGERS_SEMI_WIDTH - Static variable in class fr.orsay.lri.varna.components.GradientEditorPanel
 
tseq - Variable in class fr.orsay.lri.varna.views.VueManualInput
 
tstr - Variable in class fr.orsay.lri.varna.views.VueManualInput
 
type - Variable in class fr.orsay.lri.varna.views.VueChemProbAnnotation
 
type - Variable in class fr.orsay.lri.varna.views.VueListeAnnotations
 

A B C D E F G H I K L M N O P Q R S T U V W X Y Z _