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

java.lang.Object
  fr.orsay.lri.varna.models.rna.ModeleBase
      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)