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java.lang.Objectfr.orsay.lri.varna.models.rna.Motif
public class Motif
Field Summary | |
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private int |
_ajustement
|
private double |
_decalage
|
private ArrayList<ModeleBase> |
_listeBasesM
|
(package private) StructureTemp |
_listStrands
|
private RNA |
_rna
|
private Double |
_spaceBetweenBases
|
Constructor Summary | |
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Motif(RNA rna,
ArrayList<ModeleBase> listeBases)
|
Method Summary | |
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void |
ajusteSpecificStrand(int i)
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void |
ajusteStrand()
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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()
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void |
initChecker(ModeleStrand strand)
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void |
initCheckerAll()
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void |
initInterv()
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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)
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void |
setCenterMotif()
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void |
setDecalage(double a)
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Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
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StructureTemp _listStrands
private Double _spaceBetweenBases
private ArrayList<ModeleBase> _listeBasesM
private int _ajustement
private double _decalage
private RNA _rna
Constructor Detail |
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public Motif(RNA rna, ArrayList<ModeleBase> listeBases)
Method Detail |
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public void listStrand()
public void decalerBase(ModeleStrand strand, double decalage)
public void initChecker(ModeleStrand strand)
public void initCheckerAll()
public void initStrand()
public void initInterv()
public void positionneStrand()
public void positionneSpecificStrand(int i, double d)
i
- the index of the strand in the list of strandsd
- the space which separate two strandspublic void ajusteStrand()
public void ajusteSpecificStrand(int i)
public void reajustement()
public int getCentralStrand()
public void orderStrands(int centralStrand)
public void setCenterMotif()
public void deviationBasePair()
public ArrayList<ModeleBase> listBasePair()
public ModeleBase getBaseAt(int index)
public int getAjustement()
public void setAjustement(int a)
public double getDecalage()
public void setDecalage(double a)
public StructureTemp getListStrand()
public ArrayList<ModeleBase> getListBasesMotif()
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