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java.lang.Objectfr.orsay.lri.varna.models.templates.RNATemplate.RNATemplateElement
fr.orsay.lri.varna.models.templates.RNATemplate.RNATemplateUnpairedSequence
public class RNATemplate.RNATemplateUnpairedSequence
A sequence of non-paired bases in an RNA template.
Nested Class Summary |
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Nested classes/interfaces inherited from class fr.orsay.lri.varna.models.templates.RNATemplate.RNATemplateElement |
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RNATemplate.RNATemplateElement.EdgeEndPoint |
Field Summary | |
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private String |
_name
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private static double |
defaultTangentVectorAngle
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private static double |
defaultTangentVectorLength
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private RNATemplate.RNATemplateElement.EdgeEndPoint |
in
The helixes connected on both sides. |
private double |
inTangentVectorAngle
The sequence is drawn along a cubic Bezier curve. |
private double |
inTangentVectorLength
The sequence is drawn along a cubic Bezier curve. |
private int |
length
Number of (non-paired) bases. |
private RNATemplate.RNATemplateElement.EdgeEndPoint |
out
The helixes connected on both sides. |
private double |
outTangentVectorAngle
The sequence is drawn along a cubic Bezier curve. |
private double |
outTangentVectorLength
The sequence is drawn along a cubic Bezier curve. |
private Point2D.Double |
vertex3
Position of the end (at the "out" endpoint) of the line. |
private Point2D.Double |
vertex5
Position of the begginning (at the "in" endpoint) of the line. |
Fields inherited from class fr.orsay.lri.varna.models.templates.RNATemplate.RNATemplateElement |
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_id |
Constructor Summary | |
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RNATemplate.RNATemplateUnpairedSequence(String name)
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Method Summary | |
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void |
disconnectFromAny()
Disconnect this endpoint from any other elements it may be connected to. |
RNATemplate.RNATemplateElement.EdgeEndPoint |
getEndPointFromPosition(RNATemplate.EdgeEndPointPosition position)
Get the EdgeEndPoint object corresponding to the the given position on this endpoint. |
RNATemplate.RNATemplateElement.EdgeEndPoint |
getIn()
|
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. |
double |
getInTangentVectorAngle()
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double |
getInTangentVectorLength()
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int |
getLength()
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String |
getName()
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protected 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.RNATemplateElement.EdgeEndPoint |
getOut()
|
double |
getOutTangentVectorAngle()
|
double |
getOutTangentVectorLength()
|
RNATemplate.EdgeEndPointPosition |
getPositionFromEndPoint(RNATemplate.RNATemplateElement.EdgeEndPoint endPoint)
The inverse of getEndPointFromPosition. |
protected 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. |
Point2D.Double |
getVertex3()
|
Point2D.Double |
getVertex5()
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void |
setInTangentVectorAngle(double inTangentVectorAngle)
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void |
setInTangentVectorLength(double inTangentVectorLength)
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void |
setLength(int length)
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void |
setOutTangentVectorAngle(double outTangentVectorAngle)
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void |
setOutTangentVectorLength(double outTangentVectorLength)
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void |
setVertex3(Point2D.Double vertex3)
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void |
setVertex5(Point2D.Double vertex5)
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String |
toString()
|
Methods inherited from class fr.orsay.lri.varna.models.templates.RNATemplate.RNATemplateElement |
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connectTo, connectTo, getParentTemplate |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Field Detail |
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private int length
private static final double defaultTangentVectorAngle
private static final double defaultTangentVectorLength
private double inTangentVectorAngle
private double inTangentVectorLength
private double outTangentVectorAngle
private double outTangentVectorLength
private Point2D.Double vertex5
private Point2D.Double vertex3
private final RNATemplate.RNATemplateElement.EdgeEndPoint in
private final RNATemplate.RNATemplateElement.EdgeEndPoint out
private String _name
Constructor Detail |
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public RNATemplate.RNATemplateUnpairedSequence(String name)
Method Detail |
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public Point2D.Double getVertex5()
public void setVertex5(Point2D.Double vertex5)
public Point2D.Double getVertex3()
public void setVertex3(Point2D.Double vertex3)
public String toString()
toString
in class Object
public String getName()
getName
in class RNATemplate.RNATemplateElement
public int getLength()
public void setLength(int length)
public double getInTangentVectorAngle()
public void setInTangentVectorAngle(double inTangentVectorAngle)
public double getInTangentVectorLength()
public void setInTangentVectorLength(double inTangentVectorLength)
public double getOutTangentVectorAngle()
public void setOutTangentVectorAngle(double outTangentVectorAngle)
public double getOutTangentVectorLength()
public void setOutTangentVectorLength(double outTangentVectorLength)
public RNATemplate.RNATemplateElement.EdgeEndPoint getIn()
public RNATemplate.RNATemplateElement.EdgeEndPoint getOut()
public void disconnectFromAny()
RNATemplate.RNATemplateElement
disconnectFromAny
in class RNATemplate.RNATemplateElement
protected RNATemplate.RNATemplateElement.EdgeEndPoint getNextEndPoint(RNATemplate.RNATemplateElement.EdgeEndPoint endpoint)
RNATemplate.RNATemplateElement
getNextEndPoint
in class RNATemplate.RNATemplateElement
protected RNATemplate.RNATemplateElement.EdgeEndPoint getPreviousEndPoint(RNATemplate.RNATemplateElement.EdgeEndPoint endpoint)
RNATemplate.RNATemplateElement
getPreviousEndPoint
in class RNATemplate.RNATemplateElement
public RNATemplate.RNATemplateElement.EdgeEndPoint getIn1EndPoint()
RNATemplate.RNATemplateElement
getIn1EndPoint
in class RNATemplate.RNATemplateElement
public RNATemplate.RNATemplateElement.EdgeEndPoint getEndPointFromPosition(RNATemplate.EdgeEndPointPosition position)
RNATemplate.RNATemplateElement
getEndPointFromPosition
in class RNATemplate.RNATemplateElement
public RNATemplate.EdgeEndPointPosition getPositionFromEndPoint(RNATemplate.RNATemplateElement.EdgeEndPoint endPoint)
RNATemplate.RNATemplateElement
getPositionFromEndPoint
in class RNATemplate.RNATemplateElement
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