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java.lang.Objectfr.orsay.lri.varna.models.rna.ModeleBase
fr.orsay.lri.varna.models.rna.ModeleBasesComparison
public class ModeleBasesComparison
The RNA base comparison model. In each bases we'll place two characters representing nitrogenous bases of both RNA that have to be compared. So, in each base in the comparison model, we'll have a couple of bases, with the same coordinates on the final drawing.
Field Summary | |
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private int |
_appartenance
This ModeleBasesComparison owning statement. |
private Character |
_base1
The base of the first RNA associated with the base of the second RNA. |
private Character |
_base2
The base of the second RNA associated with the base of the first RNA. |
private int |
_index
This base's offset in the sequence |
static Color |
BOTH_RNA_COLOR
|
static Color |
DEFAULT_RNA_COLOR
|
static Color |
FIRST_RNA_COLOR
|
static Color |
SECOND_RNA_COLOR
|
private static long |
serialVersionUID
|
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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ModeleBasesComparison(char base1,
char base2,
int index)
Creates a new comparison base with the specified nitrogenous bases. |
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ModeleBasesComparison(char base1,
char base2,
int elementStructure,
int index)
Creates a new comparison base with the specified nitrogenous bases. |
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ModeleBasesComparison(char base1,
char base2,
Point2D coords,
int index)
Creates a new comparison base with the specified nitrogenous bases, at the specified coordinates. |
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ModeleBasesComparison(int index)
Creates a new comparison base with the default display style and no nitrogenous bases. |
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ModeleBasesComparison(Point2D coords,
char base1,
char base2,
boolean colorie,
ModeleStyleBase mb,
int elementStructure,
int index)
Creates a new comparison base with the specified nitrogenous bases. |
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ModeleBasesComparison(Point2D coords,
int index)
Creates a new comparison base at the specified coordinates, with the default display style and no nitrogenous bases. |
Method Summary | |
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int |
get_appartenance()
Gets this base's related RNA. |
Character |
get_base1()
Return the base of the first RNA in this comparison base. |
Character |
get_base2()
Return the base of the second RNA in this comparison base. |
Boolean |
get_colored()
Allows to know if this comparison base is colored. |
String |
getBases()
Gets the string representation of the two bases in this ModeleBasesComparison. |
Boolean |
getColorie()
Gets this InterfaceBase color statement. |
String |
getContent()
|
int |
getElementStructure()
Gets this InterfaceBase assiociated structure element. |
int |
getIndex()
The internal index for this Base |
ModeleStyleBase |
getStyleBase()
Return the display style associated to this comparison base. |
void |
set_appartenance(int _appartenance)
Sets this base's related RNA. |
void |
set_base1(Character _base1)
Sets the base of the first RNA in this comparison base. |
void |
set_base2(Character _base2)
Sets the base of the second RNA in this comparison base. |
void |
set_colored(Boolean colored)
Sets the coloration authorization of this comparison base. |
void |
setColorie(Boolean _colorie)
Sets this InterfaceBase color statement. |
void |
setElementStructure(int structure)
Sets this InterfaceBase assiociated structure element. |
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, toString, wait, wait, wait |
Field Detail |
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private static final long serialVersionUID
private Character _base1
private Character _base2
private int _appartenance
private int _index
public static Color FIRST_RNA_COLOR
public static Color SECOND_RNA_COLOR
public static Color BOTH_RNA_COLOR
public static Color DEFAULT_RNA_COLOR
Constructor Detail |
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public ModeleBasesComparison(int index)
public ModeleBasesComparison(Point2D coords, int index)
coords
- - The coordinates in which the comparison base has to be
placed.public ModeleBasesComparison(char base1, char base2, int index)
base1
- - The first RNA' nitrogenous basebase2
- - The second RNA' nitrogenous basepublic ModeleBasesComparison(char base1, char base2, Point2D coords, int index)
base1
- - The first RNA' nitrogenous basebase2
- - The second RNA' nitrogenous basecoords
- - The coordinates in which the comparison base has to be
placed.public ModeleBasesComparison(char base1, char base2, int elementStructure, int index)
base1
- - The first RNA' nitrogenous basebase2
- - The second RNA' nitrogenous basepublic ModeleBasesComparison(Point2D coords, char base1, char base2, boolean colorie, ModeleStyleBase mb, int elementStructure, int index)
coords
- - This base's XY coordinatesbase1
- - The first RNA' nitrogenous basebase2
- - The second RNA' nitrogenous basecolorie
- - Whether or not this base will be drawnmb
- - The drawing style for this baseelementStructure
- - The index of a bp partner in the secondary structureindex
- - Index of this base in its initial sequenceMethod Detail |
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public ModeleStyleBase getStyleBase()
getStyleBase
in class ModeleBase
public Boolean get_colored()
public void set_colored(Boolean colored)
colored
- - TRUE if this comparison base has to be colored, else FALSE.public Character get_base1()
public void set_base1(Character _base1)
_base1
- - The base of the first RNA in this comparison base.public Character get_base2()
public void set_base2(Character _base2)
_base2
- - The base of the second RNA in this comparison base.public String getBases()
public String getContent()
getContent
in class ModeleBase
public int getElementStructure()
getElementStructure
in class ModeleBase
public void setElementStructure(int structure)
structure
- - This new assiociated structure element.public int get_appartenance()
public void set_appartenance(int _appartenance)
_appartenance
- : 0 if this base is common for both RNApublic 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 getIndex()
ModeleBase
getIndex
in class ModeleBase
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