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

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

public class ModeleBaseNucleotide
extends ModeleBase

The rna base model with the first character of the nitrogenous base and it display

Author:
darty
See Also:
Serialized Form

Nested Class Summary
private static class ModeleBaseNucleotide.STATE_SPECIAL_CHARS_STATES
           
 
Field Summary
private  String _c
           
private static HashMap<String,Character> _commands
           
private  int _index
           
private static HashMap<Character,Character> _subscripts
           
private static HashMap<Character,Character> _superscripts
           
private static long serialVersionUID
           
 
Fields inherited from class fr.orsay.lri.varna.models.rna.ModeleBase
_center, _colorie, _coords, _elementStructure, _realIndex, _styleBase, _value
 
Constructor Summary
ModeleBaseNucleotide(int index)
          Creates a new rna base with the default display style and a space as nitrogenous base
ModeleBaseNucleotide(ModeleBaseNucleotide mb, int index)
          Creates a new rna base from another one with the same attributes
ModeleBaseNucleotide(ModeleStyleBase msb, int index, int baseNumber)
          Creates a new rna base with a display style
ModeleBaseNucleotide(Point2D.Double coord, int index)
          Creates a new rna base with a space as the nitrogenous base and the display style
ModeleBaseNucleotide(Point2D.Double coords, Point2D.Double center, boolean colorie, String label, ModeleStyleBase mb, int elementStruct, int index)
           
ModeleBaseNucleotide(String s, int index)
          Creates a new rna base with the nitrogenous base
ModeleBaseNucleotide(String s, int index, int baseNumber)
          Creates a new rna base with the nitrogenous base
ModeleBaseNucleotide(String s, ModeleStyleBase msb, int index)
          Creates a new rna base with the nitrogenous base and the display style
 
Method Summary
private static String decode(String s)
           
 String get_c()
           
 Boolean getColorie()
          Gets this InterfaceBase color statement.
 String getContent()
           
 int getElementStructure()
          Gets this InterfaceBase associated structure element.
 int getIndex()
          The internal index for this Base
 ModeleStyleBase getStyleBase()
          Gets this InterfaceBase style.
 void set_c(String _s)
           
 void setColorie(Boolean _colorie)
          Sets this InterfaceBase color statement.
 String toString()
           
 
Methods inherited from class fr.orsay.lri.varna.models.rna.ModeleBase
compareTo, getBaseNumber, getCenter, getChecker, getCoords, getIntervDroite, getIntervGauche, getNumStrand, getStyleBP, getValue, removeElementStructure, setBaseNumber, setCenter, setChecker, setCoords, setElementStructure, setIntervDroite, setIntervGauche, setNumStrand, setStyleBase, setStyleBP, setValue
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
 

Field Detail

serialVersionUID

private static final long serialVersionUID
See Also:
Constant Field Values

_c

private String _c

_index

private int _index

_subscripts

private static HashMap<Character,Character> _subscripts

_superscripts

private static HashMap<Character,Character> _superscripts

_commands

private static HashMap<String,Character> _commands
Constructor Detail

ModeleBaseNucleotide

public ModeleBaseNucleotide(int index)
Creates a new rna base with the default display style and a space as nitrogenous base

Parameters:
index - The index of this base

ModeleBaseNucleotide

public ModeleBaseNucleotide(String s,
                            int index)
Creates a new rna base with the nitrogenous base

Parameters:
s - The code of this base
index - The index of this base

ModeleBaseNucleotide

public ModeleBaseNucleotide(String s,
                            int index,
                            int baseNumber)
Creates a new rna base with the nitrogenous base

Parameters:
s - The full label, potentially requiring further decoding
index - The index of this base
baseNumber - The number of this base, which may differ from the index (e.g. discontinuous numbering)

ModeleBaseNucleotide

public ModeleBaseNucleotide(String s,
                            ModeleStyleBase msb,
                            int index)
Creates a new rna base with the nitrogenous base and the display style

Parameters:
s - The full label, potentially requiring further decoding
msb - The display style
index - The index of this base

ModeleBaseNucleotide

public ModeleBaseNucleotide(ModeleStyleBase msb,
                            int index,
                            int baseNumber)
Creates a new rna base with a display style

Parameters:
msb - The display style

ModeleBaseNucleotide

public ModeleBaseNucleotide(Point2D.Double coord,
                            int index)
Creates a new rna base with a space as the nitrogenous base and the display style

Parameters:
coord -
index -

ModeleBaseNucleotide

public ModeleBaseNucleotide(ModeleBaseNucleotide mb,
                            int index)
Creates a new rna base from another one with the same attributes

Parameters:
mb - The base to copy

ModeleBaseNucleotide

public ModeleBaseNucleotide(Point2D.Double coords,
                            Point2D.Double center,
                            boolean colorie,
                            String label,
                            ModeleStyleBase mb,
                            int elementStruct,
                            int index)
Method Detail

getStyleBase

public ModeleStyleBase getStyleBase()
Description copied from class: ModeleBase
Gets this InterfaceBase style.

Overrides:
getStyleBase in class ModeleBase
Returns:
this InterfaceBase style.

get_c

public String get_c()

set_c

public void set_c(String _s)

getColorie

public Boolean getColorie()
Description copied from class: ModeleBase
Gets this InterfaceBase color statement.

Overrides:
getColorie in class ModeleBase
Returns:
TRUE if this InterfaceBase has to be colored, else FALSE.

setColorie

public void setColorie(Boolean _colorie)
Description copied from class: ModeleBase
Sets this InterfaceBase color statement.

Overrides:
setColorie in class ModeleBase
Parameters:
_colorie - - TRUE if you want this InterfaceBase to be colored, else FALSE

getElementStructure

public int getElementStructure()
Description copied from class: ModeleBase
Gets this InterfaceBase associated structure element.

Overrides:
getElementStructure in class ModeleBase
Returns:
this InterfaceBase associated structure element.

getContent

public String getContent()
Specified by:
getContent in class ModeleBase

getIndex

public int getIndex()
Description copied from class: ModeleBase
The internal index for this Base

Specified by:
getIndex in class ModeleBase

toString

public String toString()
Overrides:
toString in class Object

decode

private static String decode(String s)