fr.orsay.lri.varna.models.treealign
Class RNANodeValue

java.lang.Object
  extended by 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

Nested Class Summary
static class RNANodeValue.Origin
           
 
Field Summary
private  int leftBasePosition
           
private  String leftNucleotide
           
private  RNANodeValue.Origin origin
          Used to store the origin of this base / base pair.
private  int rightBasePosition
           
private  String rightNucleotide
           
 
Constructor Summary
RNANodeValue()
           
 
Method Summary
 int getLeftBasePosition()
           
 String getLeftNucleotide()
           
 RNANodeValue.Origin getOrigin()
           
 int getRightBasePosition()
           
 String getRightNucleotide()
           
 void setLeftBasePosition(int leftBasePosition)
           
 void setLeftNucleotide(String leftNucleotide)
           
 void setOrigin(RNANodeValue.Origin comesFromAnHelix)
           
 void setRightBasePosition(int rightBasePosition)
           
 void setRightNucleotide(String rightNucleotide)
           
 String toGraphvizNodeName()
          Returns a string that will be displayed on the node by graphviz.
 String toString()
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
 

Field Detail

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.

Constructor Detail

RNANodeValue

public RNANodeValue()
Method Detail

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