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java.lang.Objectfr.orsay.lri.varna.models.templates.RNATemplate.RNATemplateElement
fr.orsay.lri.varna.models.templates.RNATemplate.RNATemplateHelix
public class RNATemplate.RNATemplateHelix
An helix 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 String |
caption
A string displayed on the helix. |
private Point2D.Double |
endPosition
Position of the helix end point, ie. |
private boolean |
flipped
Tells whether the helix is flipped. |
private RNATemplate.RNATemplateElement.EdgeEndPoint |
in1
If we go through all bases of the RNA from first to last, we will pass twice through this helix. |
private RNATemplate.In1Is |
in1Is
For an helix, tells us whether IN1/OUT1 is the 5' strand (the first strand we meet if we follow the RNA sequence) or the 3' strand (the second we meet if we follow the RNA sequence). |
private RNATemplate.RNATemplateElement.EdgeEndPoint |
in2
If we go through all bases of the RNA from first to last, we will pass twice through this helix. |
private int |
length
Number of base pairs in the helix. |
private RNATemplate.RNATemplateElement.EdgeEndPoint |
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 |
out2
If we go through all bases of the RNA from first to last, we will pass twice through this helix. |
private Point2D.Double |
startPosition
Position of the helix start point, ie. |
Fields inherited from class fr.orsay.lri.varna.models.templates.RNATemplate.RNATemplateElement |
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_id |
Constructor Summary | |
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RNATemplate.RNATemplateHelix(String name)
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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 Point2D.Double startPosition
private Point2D.Double endPosition
private boolean flipped
private RNATemplate.In1Is in1Is
private String caption
private final RNATemplate.RNATemplateElement.EdgeEndPoint in1
private final RNATemplate.RNATemplateElement.EdgeEndPoint out1
private final RNATemplate.RNATemplateElement.EdgeEndPoint in2
private final RNATemplate.RNATemplateElement.EdgeEndPoint out2
private String _name
Constructor Detail |
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public RNATemplate.RNATemplateHelix(String name)
Method Detail |
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public boolean isFlipped()
public void setFlipped(boolean flipped)
public RNATemplate.In1Is getIn1Is()
public void setIn1Is(RNATemplate.In1Is in1Is)
public String getCaption()
public void setCaption(String caption)
public boolean hasCaption()
public String toString()
toString
in class Object
public String getName()
getName
in class RNATemplate.RNATemplateElement
public int getLength()
public void setLength(int length)
public Point2D.Double getStartPosition()
public void setStartPosition(Point2D.Double startPosition)
public Point2D.Double getEndPosition()
public void setEndPosition(Point2D.Double endPosition)
public RNATemplate.RNATemplateElement.EdgeEndPoint getIn1()
public RNATemplate.RNATemplateElement.EdgeEndPoint getOut1()
public RNATemplate.RNATemplateElement.EdgeEndPoint getIn2()
public RNATemplate.RNATemplateElement.EdgeEndPoint getOut2()
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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