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java.lang.Objectfr.orsay.lri.varna.models.templates.RNATemplate.RNATemplateElement
public abstract class RNATemplate.RNATemplateElement
An endpoint of an RNA template, it can be an helix or a sequence of non-paired bases. You cannot create an object of this class directly, use RNATemplateHelix or RNATemplateUnpairedSequence instead.
Nested Class Summary | |
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class |
RNATemplate.RNATemplateElement.EdgeEndPoint
An edge endpoint is where an edge can connect. |
Field Summary | |
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int |
_id
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private RNATemplate.RNATemplateElement |
element
This variable is just there so that "this" can be accessed by a name from the internal class EdgeEndPoint. |
Constructor Summary | |
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RNATemplate.RNATemplateElement()
When the endpoint is created, it is added to the list of elements in this template. |
Method Summary | |
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void |
connectTo(RNATemplate.EdgeEndPointPosition positionHere,
RNATemplate.RNATemplateElement.EdgeEndPoint otherEndPoint)
Connect the endpoint at position positionHere of this endpoint to the otherEndPoint. |
void |
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. |
abstract void |
disconnectFromAny()
Disconnect this endpoint from any other elements it may be connected to. |
abstract RNATemplate.RNATemplateElement.EdgeEndPoint |
getEndPointFromPosition(RNATemplate.EdgeEndPointPosition position)
Get the EdgeEndPoint object corresponding to the the given position on this endpoint. |
abstract RNATemplate.RNATemplateElement.EdgeEndPoint |
getIn1EndPoint()
Get the the IN endpoint in the case of a sequence and the IN1 endpoint in the case of an helix. |
String |
getName()
|
protected abstract RNATemplate.RNATemplateElement.EdgeEndPoint |
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. |
RNATemplate |
getParentTemplate()
Returns the template to which this endpoint belongs. |
abstract RNATemplate.EdgeEndPointPosition |
getPositionFromEndPoint(RNATemplate.RNATemplateElement.EdgeEndPoint endPoint)
The inverse of getEndPointFromPosition. |
protected abstract RNATemplate.RNATemplateElement.EdgeEndPoint |
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. |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
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public int _id
private final RNATemplate.RNATemplateElement element
Constructor Detail |
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public RNATemplate.RNATemplateElement()
Method Detail |
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public String getName()
public abstract void disconnectFromAny()
public abstract RNATemplate.RNATemplateElement.EdgeEndPoint getIn1EndPoint()
public RNATemplate getParentTemplate()
protected abstract RNATemplate.RNATemplateElement.EdgeEndPoint getNextEndPoint(RNATemplate.RNATemplateElement.EdgeEndPoint endpoint)
protected abstract RNATemplate.RNATemplateElement.EdgeEndPoint getPreviousEndPoint(RNATemplate.RNATemplateElement.EdgeEndPoint endpoint)
public abstract RNATemplate.RNATemplateElement.EdgeEndPoint getEndPointFromPosition(RNATemplate.EdgeEndPointPosition position)
public abstract RNATemplate.EdgeEndPointPosition getPositionFromEndPoint(RNATemplate.RNATemplateElement.EdgeEndPoint endPoint)
public void connectTo(RNATemplate.EdgeEndPointPosition positionHere, RNATemplate.RNATemplateElement.EdgeEndPoint otherEndPoint) throws fr.orsay.lri.varna.exceptions.ExceptionEdgeEndpointAlreadyConnected, fr.orsay.lri.varna.exceptions.ExceptionInvalidRNATemplate
fr.orsay.lri.varna.exceptions.ExceptionEdgeEndpointAlreadyConnected
fr.orsay.lri.varna.exceptions.ExceptionInvalidRNATemplate
public void connectTo(RNATemplate.EdgeEndPointPosition positionHere, RNATemplate.RNATemplateElement otherElement, RNATemplate.EdgeEndPointPosition positionOnOtherElement) throws fr.orsay.lri.varna.exceptions.ExceptionEdgeEndpointAlreadyConnected, fr.orsay.lri.varna.exceptions.ExceptionEdgeEndpointAlreadyConnected, fr.orsay.lri.varna.exceptions.ExceptionInvalidRNATemplate
fr.orsay.lri.varna.exceptions.ExceptionInvalidRNATemplate
ExceptionEdgeEndpointAlreadyConnected,
- ExceptionEdgeEndpointAlreadyConnected
fr.orsay.lri.varna.exceptions.ExceptionEdgeEndpointAlreadyConnected
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