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

java.lang.Object
  extended by fr.orsay.lri.varna.models.rna.ModeleBase
All Implemented Interfaces:
Serializable, Comparable<ModeleBase>
Direct Known Subclasses:
ExtendedMB, ModeleBaseNucleotide, ModeleBasesComparison

public abstract class ModeleBase
extends Object
implements Serializable, Comparable<ModeleBase>

The abstract rna base model

Author:
darty
See Also:
Serialized Form

Field Summary
private  ModeleBP _BP
           
protected  VARNAPoint _center
          The nearest loop center of this InterfaceBase.
private  boolean _checked
           
protected  Boolean _colorie
          TRUE if this InterfaceBase has to be colored, else FALSE.
protected  VARNAPoint _coords
          The coordinate representation of this InterfaceBase on the final graphic.
protected  int _elementStructure
          The structure information associated with this InterfaceBase.
private  int _numStrand
          Numero du brin auquel la base appartient.
protected  int _realIndex
           
protected  ModeleStyleBase _styleBase
          The base style.
protected  double _value
           
private  boolean intervDroite
           
private  boolean intervGauche
           
 
Constructor Summary
ModeleBase()
           
 
Method Summary
 int compareTo(ModeleBase other)
           
 int getBaseNumber()
           
 Point2D.Double getCenter()
           
 boolean getChecker()
           
 Boolean getColorie()
          Gets this InterfaceBase color statement.
abstract  String getContent()
           
 Point2D.Double getCoords()
           
 int getElementStructure()
          Gets this InterfaceBase associated structure element.
abstract  int getIndex()
          The internal index for this Base
 boolean getIntervDroite()
           
 boolean getIntervGauche()
           
 int getNumStrand()
           
 ModeleStyleBase getStyleBase()
          Gets this InterfaceBase style.
 ModeleBP getStyleBP()
          Gets the base pair type for this element.
 double getValue()
           
 void removeElementStructure()
           
 void setBaseNumber(int bn)
           
 void setCenter(Point2D.Double center)
           
 void setChecker(boolean bool)
           
 void setColorie(Boolean _colorie)
          Sets this InterfaceBase color statement.
 void setCoords(Point2D.Double coords)
           
 void setElementStructure(int structure, ModeleBP type)
          Sets this InterfaceBase associated structure element.
 void setIntervDroite(boolean bool)
           
 void setIntervGauche(boolean bool)
           
 void setNumStrand(int a)
           
 void setStyleBase(ModeleStyleBase base)
          Sets this InterfaceBase style.
 void setStyleBP(ModeleBP type)
          Sets the base pair type for this element.
 void setValue(double d)
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

_BP

private ModeleBP _BP

_checked

private boolean _checked

intervDroite

private boolean intervDroite

intervGauche

private boolean intervGauche

_numStrand

private int _numStrand
Numero du brin auquel la base appartient.


_styleBase

protected ModeleStyleBase _styleBase
The base style.


_colorie

protected Boolean _colorie
TRUE if this InterfaceBase has to be colored, else FALSE.


_coords

protected VARNAPoint _coords
The coordinate representation of this InterfaceBase on the final graphic.


_center

protected VARNAPoint _center
The nearest loop center of this InterfaceBase.


_elementStructure

protected int _elementStructure
The structure information associated with this InterfaceBase. It value is:
-1 if the structure element associated is a point or a dash.
If the structure associated is an opening bracket, it'll be the index of the closing bracket associated with this opening bracket.
If the structure associated is a closing bracket, it'll be the index of the opening bracket associated with this closing bracket.


_value

protected double _value

_realIndex

protected int _realIndex
Constructor Detail

ModeleBase

public ModeleBase()
Method Detail

getIndex

public abstract int getIndex()
The internal index for this Base


getContent

public abstract String getContent()

getStyleBase

public ModeleStyleBase getStyleBase()
Gets this InterfaceBase style.

Returns:
this InterfaceBase style.

getValue

public double getValue()

setValue

public void setValue(double d)

setStyleBase

public void setStyleBase(ModeleStyleBase base)
Sets this InterfaceBase style.

Parameters:
base - - This InterfaceBase new style.

getColorie

public Boolean getColorie()
Gets this InterfaceBase color statement.

Returns:
TRUE if this InterfaceBase has to be colored, else FALSE.

setColorie

public void setColorie(Boolean _colorie)
Sets this InterfaceBase color statement.

Parameters:
_colorie - - TRUE if you want this InterfaceBase to be colored, else FALSE

getElementStructure

public int getElementStructure()
Gets this InterfaceBase associated structure element.

Returns:
this InterfaceBase associated structure element.

setElementStructure

public void setElementStructure(int structure,
                                ModeleBP type)
Sets this InterfaceBase associated structure element.

Parameters:
structure - - This new associated structure element.
type - - The type of this base pair.

removeElementStructure

public void removeElementStructure()

getStyleBP

public ModeleBP getStyleBP()
Gets the base pair type for this element.

Returns:
the base pair type for this element.

setStyleBP

public void setStyleBP(ModeleBP type)
Sets the base pair type for this element.

Parameters:
type - - The new base pair type for this element.

getBaseNumber

public int getBaseNumber()

setBaseNumber

public void setBaseNumber(int bn)

getCoords

public Point2D.Double getCoords()

setCoords

public void setCoords(Point2D.Double coords)

getCenter

public Point2D.Double getCenter()

setCenter

public void setCenter(Point2D.Double center)

getNumStrand

public int getNumStrand()

setNumStrand

public void setNumStrand(int a)

getChecker

public boolean getChecker()

setChecker

public void setChecker(boolean bool)

getIntervGauche

public boolean getIntervGauche()

setIntervGauche

public void setIntervGauche(boolean bool)

getIntervDroite

public boolean getIntervDroite()

setIntervDroite

public void setIntervDroite(boolean bool)

compareTo

public int compareTo(ModeleBase other)
Specified by:
compareTo in interface Comparable<ModeleBase>