fr.orsay.lri.varna.models.rna
Class Motif

java.lang.Object
  extended by fr.orsay.lri.varna.models.rna.Motif
All Implemented Interfaces:
Serializable

public class Motif
extends Object
implements Serializable

See Also:
Serialized Form

Field Summary
private  int _ajustement
           
private  double _decalage
           
private  ArrayList<ModeleBase> _listeBasesM
           
(package private)  StructureTemp _listStrands
           
private  RNA _rna
           
private  Double _spaceBetweenBases
           
 
Constructor Summary
Motif(RNA rna, ArrayList<ModeleBase> listeBases)
           
 
Method Summary
 void ajusteSpecificStrand(int i)
           
 void ajusteStrand()
           
 void decalerBase(ModeleStrand strand, double decalage)
           
 void deviationBasePair()
           
 int getAjustement()
           
 ModeleBase getBaseAt(int index)
           
 int getCentralStrand()
          Find the central strand in a RNA star pattern
 double getDecalage()
           
 ArrayList<ModeleBase> getListBasesMotif()
           
 StructureTemp getListStrand()
           
 void initChecker(ModeleStrand strand)
           
 void initCheckerAll()
           
 void initInterv()
           
 void initStrand()
           
 ArrayList<ModeleBase> listBasePair()
          Create an arrayList which contain all bases which are involved in a base pair.
 void listStrand()
          Find all the strands and store them in an arrayList.
 void orderStrands(int centralStrand)
           
 void positionneSpecificStrand(int i, double d)
          Set the coordinates of all bases for one strand in particular
 void positionneStrand()
          Set the coordinates of all bases for all strands in the list of strands
 void reajustement()
           
 void setAjustement(int a)
           
 void setCenterMotif()
           
 void setDecalage(double a)
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

_listStrands

StructureTemp _listStrands

_spaceBetweenBases

private Double _spaceBetweenBases

_listeBasesM

private ArrayList<ModeleBase> _listeBasesM

_ajustement

private int _ajustement

_decalage

private double _decalage

_rna

private RNA _rna
Constructor Detail

Motif

public Motif(RNA rna,
             ArrayList<ModeleBase> listeBases)
Method Detail

listStrand

public void listStrand()
Find all the strands and store them in an arrayList.


decalerBase

public void decalerBase(ModeleStrand strand,
                        double decalage)

initChecker

public void initChecker(ModeleStrand strand)

initCheckerAll

public void initCheckerAll()

initStrand

public void initStrand()

initInterv

public void initInterv()

positionneStrand

public void positionneStrand()
Set the coordinates of all bases for all strands in the list of strands


positionneSpecificStrand

public void positionneSpecificStrand(int i,
                                     double d)
Set the coordinates of all bases for one strand in particular

Parameters:
i - the index of the strand in the list of strands
d - the space which separate two strands

ajusteStrand

public void ajusteStrand()

ajusteSpecificStrand

public void ajusteSpecificStrand(int i)

reajustement

public void reajustement()

getCentralStrand

public int getCentralStrand()
Find the central strand in a RNA star pattern

Returns:
the index of the strand which is the central strand in a star pattern, or -1 if there is no central strand.

orderStrands

public void orderStrands(int centralStrand)

setCenterMotif

public void setCenterMotif()

deviationBasePair

public void deviationBasePair()

listBasePair

public ArrayList<ModeleBase> listBasePair()
Create an arrayList which contain all bases which are involved in a base pair.


getBaseAt

public ModeleBase getBaseAt(int index)

getAjustement

public int getAjustement()

setAjustement

public void setAjustement(int a)

getDecalage

public double getDecalage()

setDecalage

public void setDecalage(double a)

getListStrand

public StructureTemp getListStrand()

getListBasesMotif

public ArrayList<ModeleBase> getListBasesMotif()