Uses of Class
fr.orsay.lri.varna.models.templates.RNATemplate.RNATemplateElement.EdgeEndPoint

Packages that use RNATemplate.RNATemplateElement.EdgeEndPoint
fr.orsay.lri.varna.models.rna   
fr.orsay.lri.varna.models.templates   
 

Uses of RNATemplate.RNATemplateElement.EdgeEndPoint in fr.orsay.lri.varna.models.rna
 

Methods in fr.orsay.lri.varna.models.rna with parameters of type RNATemplate.RNATemplateElement.EdgeEndPoint
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
 

Fields in fr.orsay.lri.varna.models.templates declared as RNATemplate.RNATemplateElement.EdgeEndPoint
private  RNATemplate.RNATemplateElement.EdgeEndPoint RNATemplate.VertexIterator.endpoint
           
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
           
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
private  Iterator<RNATemplate.RNATemplateElement.EdgeEndPoint> RNATemplate.RNAIterator.iter
           
(package private)  List<RNATemplate.RNATemplateElement.EdgeEndPoint> RNATemplate.MakeEdgeList.list
           
 

Methods in fr.orsay.lri.varna.models.templates that return RNATemplate.RNATemplateElement.EdgeEndPoint
private  RNATemplate.RNATemplateElement.EdgeEndPoint RNATemplate.LoadFromXml.endPointFromXml(Element xmlEdgeEndPoint)
          Takes an element of the form: and returns the corresponding EdgeEndPoint object.
 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)
           
 RNATemplate.RNATemplateElement.EdgeEndPoint RNATemplate.RNATemplateUnpairedSequence.getEndPointFromPosition(RNATemplate.EdgeEndPointPosition position)
           
 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()
           
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()
           
 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)
           
protected  RNATemplate.RNATemplateElement.EdgeEndPoint RNATemplate.RNATemplateUnpairedSequence.getNextEndPoint(RNATemplate.RNATemplateElement.EdgeEndPoint endpoint)
           
 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)
           
protected  RNATemplate.RNATemplateElement.EdgeEndPoint RNATemplate.RNATemplateUnpairedSequence.getPreviousEndPoint(RNATemplate.RNATemplateElement.EdgeEndPoint endpoint)
           
 RNATemplate.RNATemplateElement.EdgeEndPoint RNATemplate.VertexIterator.next()
           
 

Methods in fr.orsay.lri.varna.models.templates that return types with arguments of type RNATemplate.RNATemplateElement.EdgeEndPoint
 List<RNATemplate.RNATemplateElement.EdgeEndPoint> RNATemplate.MakeEdgeList.make()
           
 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.
 

Methods in fr.orsay.lri.varna.models.templates with parameters of type RNATemplate.RNATemplateElement.EdgeEndPoint
private  void RNATemplate.ConvertToXml.addConnectionIfNecessary(RNATemplate.RNATemplateElement.EdgeEndPoint endPoint)
           
private  void RNATemplate.MakeEdgeList.addEdgeIfNecessary(RNATemplate.RNATemplateElement.EdgeEndPoint endPoint)
           
private  void RNATemplate.LoadFromXml.connect(RNATemplate.RNATemplateElement.EdgeEndPoint v1, RNATemplate.RNATemplateElement.EdgeEndPoint v2)
           
 boolean RNATemplate.connectedComponentIsCyclic(RNATemplate.RNATemplateElement.EdgeEndPoint endPoint)
          Tells whether the connected component to which endPoint belongs to is cyclic.
private  String RNATemplate.LoadFromXml.connectErrMsg(RNATemplate.RNATemplateElement.EdgeEndPoint v1, RNATemplate.RNATemplateElement.EdgeEndPoint v2, String reason)
           
 void RNATemplate.RNATemplateElement.connectTo(RNATemplate.EdgeEndPointPosition positionHere, RNATemplate.RNATemplateElement.EdgeEndPoint otherEndPoint)
          Connect the endpoint at position positionHere of this endpoint to the otherEndPoint.
 void RNATemplate.RNATemplateElement.EdgeEndPoint.connectTo(RNATemplate.RNATemplateElement.EdgeEndPoint otherEndPoint)
          Create an edge between two edge endpoints.
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)
           
protected  RNATemplate.RNATemplateElement.EdgeEndPoint RNATemplate.RNATemplateUnpairedSequence.getNextEndPoint(RNATemplate.RNATemplateElement.EdgeEndPoint endpoint)
           
abstract  RNATemplate.EdgeEndPointPosition RNATemplate.RNATemplateElement.getPositionFromEndPoint(RNATemplate.RNATemplateElement.EdgeEndPoint endPoint)
          The inverse of getEndPointFromPosition.
 RNATemplate.EdgeEndPointPosition RNATemplate.RNATemplateHelix.getPositionFromEndPoint(RNATemplate.RNATemplateElement.EdgeEndPoint endPoint)
           
 RNATemplate.EdgeEndPointPosition RNATemplate.RNATemplateUnpairedSequence.getPositionFromEndPoint(RNATemplate.RNATemplateElement.EdgeEndPoint 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)
           
protected  RNATemplate.RNATemplateElement.EdgeEndPoint RNATemplate.RNATemplateUnpairedSequence.getPreviousEndPoint(RNATemplate.RNATemplateElement.EdgeEndPoint endpoint)