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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
Overview
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Index
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