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Packages that use RNANodeValue2 | |
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fr.orsay.lri.varna.models.templates | |
fr.orsay.lri.varna.models.treealign |
Uses of RNANodeValue2 in fr.orsay.lri.varna.models.templates |
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Methods in fr.orsay.lri.varna.models.templates that return types with arguments of type RNANodeValue2 | |
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static TreeAlignResult<RNANodeValue2,RNANodeValueTemplate> |
RNATemplateAlign.alignRNAWithTemplate(RNA rna,
RNATemplate template)
Align the given RNA with the given RNA template. |
Methods in fr.orsay.lri.varna.models.templates with parameters of type RNANodeValue2 | |
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private static boolean |
RNATemplateAlign.canBePartOfABrokenHelix(RNANodeValue2 leftNodeValue)
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private static boolean |
RNATemplateAlign.canBePartOfAnHelix(RNANodeValue2 leftNodeValue)
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private static boolean |
RNATemplateAlign.canBePartOfASequence(RNANodeValue2 leftNodeValue)
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double |
RNANodeValue2TemplateDistance.delete(RNANodeValue2 v)
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double |
RNANodeValue2TemplateDistance.f(RNANodeValue2 v1,
RNANodeValueTemplate v2)
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Method parameters in fr.orsay.lri.varna.models.templates with type arguments of type RNANodeValue2 | |
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static RNATemplateMapping |
RNATemplateAlign.makeTemplateMapping(TreeAlignResult<RNANodeValue2,RNANodeValueTemplate> alignResult,
RNA rna)
This method takes an alignment between a tree of RNANodeValue2 of RNANodeValue and a tree of RNANodeValue2 of RNANodeValueTemplate, and the original RNA object that was used to create the first tree in the alignment. |
Uses of RNANodeValue2 in fr.orsay.lri.varna.models.treealign |
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Methods in fr.orsay.lri.varna.models.treealign that return types with arguments of type RNANodeValue2 | |
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private static List<Tree<RNANodeValue2>> |
RNATree2.RNAForest2FromRNAForest(List<Tree<RNANodeValue>> originalForest)
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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. |
Methods in fr.orsay.lri.varna.models.treealign with parameters of type RNANodeValue2 | |
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ExampleDistance3.SequenceAlignResult |
ExampleDistance3.alignSequenceNodes(RNANodeValue2 v1,
RNANodeValue2 v2)
Align two sequences contained in nodes. |
double |
ExampleDistance3.f(RNANodeValue2 v1,
RNANodeValue2 v2)
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double |
ExampleDistance2.f(RNANodeValue2 v1,
RNANodeValue2 v2)
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Method parameters in fr.orsay.lri.varna.models.treealign with type arguments of type RNANodeValue2 | |
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Mapping |
RNATree2.ConvertToMapping.convert(Tree<AlignedNode<RNANodeValue2,RNANodeValue2>> tree)
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Mapping |
RNATree2.ConvertToMapping.convert(Tree<AlignedNode<RNANodeValue2,RNANodeValue2>> tree)
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private void |
RNATree2.ConvertToMapping.convertSubTree(Tree<AlignedNode<RNANodeValue2,RNANodeValue2>> tree)
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private void |
RNATree2.ConvertToMapping.convertSubTree(Tree<AlignedNode<RNANodeValue2,RNANodeValue2>> tree)
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static Mapping |
RNATree2.mappingFromAlignment(Tree<AlignedNode<RNANodeValue2,RNANodeValue2>> alignment)
Convert an RNA tree (with RNANodeValue2) alignment into a Mapping. |
static Mapping |
RNATree2.mappingFromAlignment(Tree<AlignedNode<RNANodeValue2,RNANodeValue2>> alignment)
Convert an RNA tree (with RNANodeValue2) alignment into a Mapping. |
private static void |
RNATree2.RNAForest2FromRNAForestCommitNonPaired(List<Tree<RNANodeValue2>> forest,
List<RNANodeValue> consecutiveNonPairedBases)
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