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java.lang.Objectfr.orsay.lri.varna.models.rna.ModeleBase
fr.orsay.lri.varna.models.rna.ModeleBaseNucleotide
public class ModeleBaseNucleotide
The rna base model with the first character of the nitrogenous base and it display
Nested Class Summary | |
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private static class |
ModeleBaseNucleotide.STATE_SPECIAL_CHARS_STATES
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Field Summary | |
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private String |
_c
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private static HashMap<String,Character> |
_commands
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private int |
_index
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private static HashMap<Character,Character> |
_subscripts
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private static HashMap<Character,Character> |
_superscripts
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private static long |
serialVersionUID
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Fields inherited from class fr.orsay.lri.varna.models.rna.ModeleBase |
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_center, _colorie, _coords, _elementStructure, _realIndex, _styleBase, _value |
Constructor Summary | |
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ModeleBaseNucleotide(int index)
Creates a new rna base with the default display style and a space as nitrogenous base |
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ModeleBaseNucleotide(ModeleBaseNucleotide mb,
int index)
Creates a new rna base from another one with the same attributes |
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ModeleBaseNucleotide(ModeleStyleBase msb,
int index,
int baseNumber)
Creates a new rna base with a display style |
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ModeleBaseNucleotide(Point2D.Double coord,
int index)
Creates a new rna base with a space as the nitrogenous base and the display style |
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ModeleBaseNucleotide(Point2D.Double coords,
Point2D.Double center,
boolean colorie,
String label,
ModeleStyleBase mb,
int elementStruct,
int index)
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ModeleBaseNucleotide(String s,
int index)
Creates a new rna base with the nitrogenous base |
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ModeleBaseNucleotide(String s,
int index,
int baseNumber)
Creates a new rna base with the nitrogenous base |
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ModeleBaseNucleotide(String s,
ModeleStyleBase msb,
int index)
Creates a new rna base with the nitrogenous base and the display style |
Method Summary | |
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private static String |
decode(String s)
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String |
get_c()
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Boolean |
getColorie()
Gets this InterfaceBase color statement. |
String |
getContent()
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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)
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void |
setColorie(Boolean _colorie)
Sets this InterfaceBase color statement. |
String |
toString()
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Methods inherited from class fr.orsay.lri.varna.models.rna.ModeleBase |
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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 |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Field Detail |
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private static final long serialVersionUID
private String _c
private int _index
private static HashMap<Character,Character> _subscripts
private static HashMap<Character,Character> _superscripts
private static HashMap<String,Character> _commands
Constructor Detail |
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public ModeleBaseNucleotide(int index)
index
- The index of this basepublic ModeleBaseNucleotide(String s, int index)
s
- The code of this baseindex
- The index of this basepublic ModeleBaseNucleotide(String s, int index, int baseNumber)
s
- The full label, potentially requiring further decodingindex
- The index of this basebaseNumber
- The number of this base, which may differ from the index (e.g. discontinuous numbering)public ModeleBaseNucleotide(String s, ModeleStyleBase msb, int index)
s
- The full label, potentially requiring further decodingmsb
- The display styleindex
- The index of this basepublic ModeleBaseNucleotide(ModeleStyleBase msb, int index, int baseNumber)
msb
- The display stylepublic ModeleBaseNucleotide(Point2D.Double coord, int index)
coord
- index
- public ModeleBaseNucleotide(ModeleBaseNucleotide mb, int index)
mb
- The base to copypublic ModeleBaseNucleotide(Point2D.Double coords, Point2D.Double center, boolean colorie, String label, ModeleStyleBase mb, int elementStruct, int index)
Method Detail |
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public ModeleStyleBase getStyleBase()
ModeleBase
getStyleBase
in class ModeleBase
public String get_c()
public void set_c(String _s)
public Boolean getColorie()
ModeleBase
getColorie
in class ModeleBase
public void setColorie(Boolean _colorie)
ModeleBase
setColorie
in class ModeleBase
_colorie
- - TRUE if you want this InterfaceBase to be colored, else
FALSEpublic int getElementStructure()
ModeleBase
getElementStructure
in class ModeleBase
public String getContent()
getContent
in class ModeleBase
public int getIndex()
ModeleBase
getIndex
in class ModeleBase
public String toString()
toString
in class Object
private static String decode(String s)
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