fr.orsay.lri.varna.models.treealign
Class RNANodeValue
java.lang.Object
fr.orsay.lri.varna.models.treealign.RNANodeValue
- All Implemented Interfaces:
- GraphvizDrawableNodeValue
public class RNANodeValue
- extends Object
- implements GraphvizDrawableNodeValue
We use the following convention: If the node is marked by a couple (n,m)
these integers are stored in leftBasePosition and rightBasePosition
(ie. we have a pair of bases), if only
one value is present, it is stored in leftBasePosition and rightBasePosition
contains -1 (ie. we have a non-paired base).
The right and left nucleotides follow the same rule, but are optional,
and '_' is used as undefined instead of -1.
Note that it is part of the contract of this class that default
values are -1 and _.
- Author:
- Raphael Champeimont
leftBasePosition
private int leftBasePosition
rightBasePosition
private int rightBasePosition
leftNucleotide
private String leftNucleotide
rightNucleotide
private String rightNucleotide
origin
private RNANodeValue.Origin origin
- Used to store the origin of this base / base pair.
RNANodeValue
public RNANodeValue()
getOrigin
public RNANodeValue.Origin getOrigin()
setOrigin
public void setOrigin(RNANodeValue.Origin comesFromAnHelix)
getLeftNucleotide
public String getLeftNucleotide()
setLeftNucleotide
public void setLeftNucleotide(String leftNucleotide)
getRightNucleotide
public String getRightNucleotide()
setRightNucleotide
public void setRightNucleotide(String rightNucleotide)
getLeftBasePosition
public int getLeftBasePosition()
setLeftBasePosition
public void setLeftBasePosition(int leftBasePosition)
getRightBasePosition
public int getRightBasePosition()
setRightBasePosition
public void setRightBasePosition(int rightBasePosition)
toGraphvizNodeName
public String toGraphvizNodeName()
- Description copied from interface:
GraphvizDrawableNodeValue
- Returns a string that will be displayed on the node by graphviz.
- Specified by:
toGraphvizNodeName
in interface GraphvizDrawableNodeValue
toString
public String toString()
- Overrides:
toString
in class Object