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Packages that use RNATemplate.RNATemplateElement.EdgeEndPoint | |
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fr.orsay.lri.varna.models.rna | |
fr.orsay.lri.varna.models.templates |
Uses of RNATemplate.RNATemplateElement.EdgeEndPoint in fr.orsay.lri.varna.models.rna |
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Methods in fr.orsay.lri.varna.models.rna with parameters of type RNATemplate.RNATemplateElement.EdgeEndPoint | |
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private void |
RNA.computeBezierTangentVectorTarget(RNATemplate.RNATemplateElement.EdgeEndPoint endPoint,
Point2D.Double curveEndPoint,
Point2D.Double curveVectorOtherPoint)
A cubic Bezier curve can be defined by 4 points, see http://en.wikipedia.org/wiki/Bezier_curve#Cubic_B.C3.A9zier_curves For each of the curve end points, there is the last/first point of the curve and a point which gives the direction and length of the tangent vector on that side. |
private void |
RNA.computeHelixEndPointDirections(RNATemplate.RNATemplateElement.EdgeEndPoint helixEndPoint,
Point2D.Double i,
Point2D.Double j)
IN: Argument helixEndPoint is an IN argument (will be read), and must contain an helix edge endpoint. |
Uses of RNATemplate.RNATemplateElement.EdgeEndPoint in fr.orsay.lri.varna.models.templates |
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Fields in fr.orsay.lri.varna.models.templates declared as RNATemplate.RNATemplateElement.EdgeEndPoint | |
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private RNATemplate.RNATemplateElement.EdgeEndPoint |
RNATemplate.VertexIterator.endpoint
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private RNATemplate.RNATemplateElement.EdgeEndPoint |
RNATemplate.RNATemplateUnpairedSequence.in
The helixes connected on both sides. |
private RNATemplate.RNATemplateElement.EdgeEndPoint |
RNATemplate.RNATemplateHelix.in1
If we go through all bases of the RNA from first to last, we will pass twice through this helix. |
private RNATemplate.RNATemplateElement.EdgeEndPoint |
RNATemplate.RNATemplateHelix.in2
If we go through all bases of the RNA from first to last, we will pass twice through this helix. |
private RNATemplate.RNATemplateElement.EdgeEndPoint |
RNATemplate.RNATemplateElement.EdgeEndPoint.otherEndPoint
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private RNATemplate.RNATemplateElement.EdgeEndPoint |
RNATemplate.RNATemplateUnpairedSequence.out
The helixes connected on both sides. |
private RNATemplate.RNATemplateElement.EdgeEndPoint |
RNATemplate.RNATemplateHelix.out1
If we go through all bases of the RNA from first to last, we will pass twice through this helix. |
private RNATemplate.RNATemplateElement.EdgeEndPoint |
RNATemplate.RNATemplateHelix.out2
If we go through all bases of the RNA from first to last, we will pass twice through this helix. |
Fields in fr.orsay.lri.varna.models.templates with type parameters of type RNATemplate.RNATemplateElement.EdgeEndPoint | |
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private Iterator<RNATemplate.RNATemplateElement.EdgeEndPoint> |
RNATemplate.RNAIterator.iter
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(package private) List<RNATemplate.RNATemplateElement.EdgeEndPoint> |
RNATemplate.MakeEdgeList.list
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Methods in fr.orsay.lri.varna.models.templates that return RNATemplate.RNATemplateElement.EdgeEndPoint | |
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private RNATemplate.RNATemplateElement.EdgeEndPoint |
RNATemplate.LoadFromXml.endPointFromXml(Element xmlEdgeEndPoint)
Takes an element of the form: |
RNATemplate.RNATemplateElement.EdgeEndPoint |
RNATemplate.getAnyEndPoint()
Return an arbitrary endpoint of the template, null if empty. |
abstract RNATemplate.RNATemplateElement.EdgeEndPoint |
RNATemplate.RNATemplateElement.getEndPointFromPosition(RNATemplate.EdgeEndPointPosition position)
Get the EdgeEndPoint object corresponding to the the given position on this endpoint. |
RNATemplate.RNATemplateElement.EdgeEndPoint |
RNATemplate.RNATemplateHelix.getEndPointFromPosition(RNATemplate.EdgeEndPointPosition position)
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RNATemplate.RNATemplateElement.EdgeEndPoint |
RNATemplate.RNATemplateUnpairedSequence.getEndPointFromPosition(RNATemplate.EdgeEndPointPosition position)
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RNATemplate.RNATemplateElement.EdgeEndPoint |
RNATemplate.getFirstEndPoint()
The first endpoint edge endpoint (in sequence order) of the template. |
RNATemplate.RNATemplateElement.EdgeEndPoint |
RNATemplate.RNATemplateUnpairedSequence.getIn()
|
RNATemplate.RNATemplateElement.EdgeEndPoint |
RNATemplate.RNATemplateHelix.getIn1()
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abstract RNATemplate.RNATemplateElement.EdgeEndPoint |
RNATemplate.RNATemplateElement.getIn1EndPoint()
Get the the IN endpoint in the case of a sequence and the IN1 endpoint in the case of an helix. |
RNATemplate.RNATemplateElement.EdgeEndPoint |
RNATemplate.RNATemplateHelix.getIn1EndPoint()
|
RNATemplate.RNATemplateElement.EdgeEndPoint |
RNATemplate.RNATemplateUnpairedSequence.getIn1EndPoint()
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RNATemplate.RNATemplateElement.EdgeEndPoint |
RNATemplate.RNATemplateHelix.getIn2()
|
RNATemplate.RNATemplateElement.EdgeEndPoint |
RNATemplate.RNATemplateElement.EdgeEndPoint.getNextEndPoint()
Get the next endpoint. |
protected abstract RNATemplate.RNATemplateElement.EdgeEndPoint |
RNATemplate.RNATemplateElement.getNextEndPoint(RNATemplate.RNATemplateElement.EdgeEndPoint endpoint)
Provided endpoint is an endpoint of this endpoint, get the next endpoint, either on this same endpoint, or or the connected endpoint. |
protected RNATemplate.RNATemplateElement.EdgeEndPoint |
RNATemplate.RNATemplateHelix.getNextEndPoint(RNATemplate.RNATemplateElement.EdgeEndPoint endpoint)
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protected RNATemplate.RNATemplateElement.EdgeEndPoint |
RNATemplate.RNATemplateUnpairedSequence.getNextEndPoint(RNATemplate.RNATemplateElement.EdgeEndPoint endpoint)
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RNATemplate.RNATemplateElement.EdgeEndPoint |
RNATemplate.RNATemplateElement.EdgeEndPoint.getOtherEndPoint()
Returns the other endpoint of the edge. |
RNATemplate.RNATemplateElement.EdgeEndPoint |
RNATemplate.RNATemplateUnpairedSequence.getOut()
|
RNATemplate.RNATemplateElement.EdgeEndPoint |
RNATemplate.RNATemplateHelix.getOut1()
|
RNATemplate.RNATemplateElement.EdgeEndPoint |
RNATemplate.RNATemplateHelix.getOut2()
|
RNATemplate.RNATemplateElement.EdgeEndPoint |
RNATemplate.RNATemplateElement.EdgeEndPoint.getPreviousEndPoint()
Same as getNextEndPoint(), but with the previous endpoint. |
protected abstract RNATemplate.RNATemplateElement.EdgeEndPoint |
RNATemplate.RNATemplateElement.getPreviousEndPoint(RNATemplate.RNATemplateElement.EdgeEndPoint endpoint)
Provided endpoint is an endpoint of this endpoint, get the previous endpoint, either on this same endpoint, or or the connected endpoint. |
protected RNATemplate.RNATemplateElement.EdgeEndPoint |
RNATemplate.RNATemplateHelix.getPreviousEndPoint(RNATemplate.RNATemplateElement.EdgeEndPoint endpoint)
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protected RNATemplate.RNATemplateElement.EdgeEndPoint |
RNATemplate.RNATemplateUnpairedSequence.getPreviousEndPoint(RNATemplate.RNATemplateElement.EdgeEndPoint endpoint)
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RNATemplate.RNATemplateElement.EdgeEndPoint |
RNATemplate.VertexIterator.next()
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Methods in fr.orsay.lri.varna.models.templates that return types with arguments of type RNATemplate.RNATemplateElement.EdgeEndPoint | |
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List<RNATemplate.RNATemplateElement.EdgeEndPoint> |
RNATemplate.MakeEdgeList.make()
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List<RNATemplate.RNATemplateElement.EdgeEndPoint> |
RNATemplate.makeEdgeList()
Return over all edges in an arbitrary order. |
Iterator<RNATemplate.RNATemplateElement.EdgeEndPoint> |
RNATemplate.vertexIterator()
Iterates over the elements edge endpoints of the template, in the sequence order. |
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