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Packages that use RNATemplate.RNATemplateElement | |
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fr.orsay.lri.varna.models.templates |
Uses of RNATemplate.RNATemplateElement in fr.orsay.lri.varna.models.templates |
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Subclasses of RNATemplate.RNATemplateElement in fr.orsay.lri.varna.models.templates | |
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class |
RNATemplate.RNATemplateHelix
An helix in an RNA template. |
class |
RNATemplate.RNATemplateUnpairedSequence
A sequence of non-paired bases in an RNA template. |
Fields in fr.orsay.lri.varna.models.templates declared as RNATemplate.RNATemplateElement | |
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private RNATemplate.RNATemplateElement |
RNATemplate.RNATemplateElement.element
This variable is just there so that "this" can be accessed by a name from the internal class EdgeEndPoint. |
Fields in fr.orsay.lri.varna.models.templates with type parameters of type RNATemplate.RNATemplateElement | |
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private Map<RNATemplate.RNATemplateElement,String> |
RNATemplate.ConvertToXml.elementNames
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private Map<String,RNATemplate.RNATemplateElement> |
RNATemplate.LoadFromXml.elementNames
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private Collection<RNATemplate.RNATemplateElement> |
RNATemplate.elements
The list of template elements. |
private Map<RNATemplate.RNATemplateElement,ArrayList<Integer>> |
RNATemplateMapping.invmap
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private Iterator<RNATemplate.RNATemplateElement> |
RNATemplate.ConvertToTree.iter
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private Map<Integer,RNATemplate.RNATemplateElement> |
RNATemplateMapping.map
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Methods in fr.orsay.lri.varna.models.templates that return RNATemplate.RNATemplateElement | |
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RNATemplate.RNATemplateElement |
RNATemplate.getAny()
Return an arbitrary element of the template, null if empty. |
RNATemplate.RNATemplateElement |
RNATemplate.RNATemplateElement.EdgeEndPoint.getElement()
Returns the endpoint on which this edge endpoint is. |
RNATemplate.RNATemplateElement |
RNATemplate.getFirst()
The first endpoint (in sequence order) of the template. |
RNATemplate.RNATemplateElement |
RNATemplate.RNATemplateElement.EdgeEndPoint.getOtherElement()
Returns the endpoint at the other endpoint of the edge. |
RNATemplate.RNATemplateElement |
RNATemplateMapping.getPartner(int baseIndex)
If the given base index is in the mapping, return the corresponding template element, otherwise return null. |
RNATemplate.RNATemplateElement |
RNATemplate.RNAIterator.next()
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Methods in fr.orsay.lri.varna.models.templates that return types with arguments of type RNATemplate.RNATemplateElement | |
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Iterator<RNATemplate.RNATemplateElement> |
RNATemplate.classicIterator()
Iterates over all elements (each endpoint is given only once) in an arbitrary order. |
Set<RNATemplate.RNATemplateElement> |
RNATemplateMapping.getTargetElemsAsSet()
Return a set containing all the template elements in the mapping. |
Iterator<RNATemplate.RNATemplateElement> |
RNATemplate.rnaIterator()
Iterates over the elements of the template, in the sequence order. |
Methods in fr.orsay.lri.varna.models.templates with parameters of type RNATemplate.RNATemplateElement | |
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void |
RNATemplateMapping.addCouple(int baseIndex,
RNATemplate.RNATemplateElement templateElement)
Tell this mapping object that this base index and this element are mapped with each other. |
void |
RNATemplate.RNATemplateElement.connectTo(RNATemplate.EdgeEndPointPosition positionHere,
RNATemplate.RNATemplateElement otherElement,
RNATemplate.EdgeEndPointPosition positionOnOtherElement)
Connect the endpoint at position positionHere of this endpoint to the endpoint of otherElement at position positionOnOtherElement. |
ArrayList<Integer> |
RNATemplateMapping.getAncestor(RNATemplate.RNATemplateElement templateElement)
If the given template element is in the mapping, return an ArrayList containing the corresponding base indexes, otherwise return null. |
boolean |
RNATemplate.removeElement(RNATemplate.RNATemplateElement element)
Remove the element from the template. |
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