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Packages that use ModeleBase | |
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fr.orsay.lri.varna | |
fr.orsay.lri.varna.interfaces | |
fr.orsay.lri.varna.models | |
fr.orsay.lri.varna.models.annotations | |
fr.orsay.lri.varna.models.rna | |
fr.orsay.lri.varna.views |
Uses of ModeleBase in fr.orsay.lri.varna |
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Fields in fr.orsay.lri.varna declared as ModeleBase | |
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ModeleBase |
VARNAPanel._hoveredBase
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Fields in fr.orsay.lri.varna with type parameters of type ModeleBase | |
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private ArrayList<ModeleBase> |
VARNAPanel._backupSelection
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Methods in fr.orsay.lri.varna that return ModeleBase | |
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ModeleBase |
VARNAPanel.getBaseAt(Point2D.Double po)
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Methods in fr.orsay.lri.varna with parameters of type ModeleBase | |
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(package private) Point2D.Double |
VARNAPanel.buildCaptionPosition(ModeleBase mb,
double scaleFactor,
double heightEstimate)
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void |
VARNAPanel.fireHoverChanged(ModeleBase mold,
ModeleBase mnew)
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void |
VARNAPanel.highlightSelectedBase(ModeleBase m)
Starts highlighting the selected base. |
void |
VARNAPanel.highlightSelectedStem(ModeleBase m)
Starts highlighting the selected base. |
void |
VARNAPanel.setHoverBase(ModeleBase m)
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Method parameters in fr.orsay.lri.varna with type arguments of type ModeleBase | |
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void |
VARNAPanel.setSelection(Collection<? extends ModeleBase> mbs)
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Uses of ModeleBase in fr.orsay.lri.varna.interfaces |
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Methods in fr.orsay.lri.varna.interfaces with parameters of type ModeleBase | |
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void |
InterfaceVARNASelectionListener.onHoverChanged(ModeleBase oldbase,
ModeleBase newBase)
Specifies an action that should be performed upon changing the hovered base. |
Uses of ModeleBase in fr.orsay.lri.varna.models |
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Fields in fr.orsay.lri.varna.models with type parameters of type ModeleBase | |
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private HashSet<ModeleBase> |
BaseList._bases
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Methods in fr.orsay.lri.varna.models that return types with arguments of type ModeleBase | |
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ArrayList<ModeleBase> |
BaseList.getBases()
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Methods in fr.orsay.lri.varna.models with parameters of type ModeleBase | |
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void |
BaseList.addBase(ModeleBase b)
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boolean |
BaseList.contains(ModeleBase mb)
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void |
BaseList.removeBase(ModeleBase b)
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Method parameters in fr.orsay.lri.varna.models with type arguments of type ModeleBase | |
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void |
BaseList.addBases(Collection<? extends ModeleBase> mbs)
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Constructors in fr.orsay.lri.varna.models with parameters of type ModeleBase | |
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BaseList(String caption,
ModeleBase mb)
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Uses of ModeleBase in fr.orsay.lri.varna.models.annotations |
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Fields in fr.orsay.lri.varna.models.annotations declared as ModeleBase | |
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private ModeleBase |
ChemProbAnnotation._mbfst
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private ModeleBase |
ChemProbAnnotation._mbsnd
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Fields in fr.orsay.lri.varna.models.annotations with type parameters of type ModeleBase | |
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private ArrayList<ModeleBase> |
HighlightRegionAnnotation._bases
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Methods in fr.orsay.lri.varna.models.annotations that return types with arguments of type ModeleBase | |
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private ArrayList<ModeleBase> |
TextAnnotation.extractedArrayListModeleBaseFromAncrage()
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ArrayList<ModeleBase> |
HighlightRegionAnnotation.getBases()
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Methods in fr.orsay.lri.varna.models.annotations with parameters of type ModeleBase | |
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void |
TextAnnotation.setAncrage(ModeleBase mb)
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Method parameters in fr.orsay.lri.varna.models.annotations with type arguments of type ModeleBase | |
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void |
TextAnnotation.setAncrage(ArrayList<ModeleBase> list,
int type)
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void |
HighlightRegionAnnotation.setBases(ArrayList<ModeleBase> b)
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Constructors in fr.orsay.lri.varna.models.annotations with parameters of type ModeleBase | |
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ChemProbAnnotation(ModeleBase mbfst,
ModeleBase mbsnd)
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ChemProbAnnotation(ModeleBase mbfst,
ModeleBase mbsnd,
ChemProbAnnotation.ChemProbAnnotationType type)
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ChemProbAnnotation(ModeleBase mbfst,
ModeleBase mbsnd,
ChemProbAnnotation.ChemProbAnnotationType type,
double intensity)
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ChemProbAnnotation(ModeleBase mbfst,
ModeleBase mbsnd,
double intensity)
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ChemProbAnnotation(ModeleBase mbfst,
ModeleBase mbsnd,
String styleDesc)
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TextAnnotation(String texte,
ModeleBase mb)
creates an annoted text on a VARNAPanel with the specified text fixed to a base |
Constructor parameters in fr.orsay.lri.varna.models.annotations with type arguments of type ModeleBase | |
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HighlightRegionAnnotation(ArrayList<ModeleBase> b)
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HighlightRegionAnnotation(ArrayList<ModeleBase> b,
Color fill,
Color outline,
double radius)
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TextAnnotation(String texte,
ArrayList<ModeleBase> listeBase,
int type)
creates an annoted text on a VARNAPanel with the specified text fixed to a helix (if type is HELIX) or to a loop (if type is LOOP) |
Uses of ModeleBase in fr.orsay.lri.varna.models.rna |
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Subclasses of ModeleBase in fr.orsay.lri.varna.models.rna | |
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class |
ExtendedMB
|
class |
ModeleBaseNucleotide
The rna base model with the first character of the nitrogenous base and it display |
class |
ModeleBasesComparison
The RNA base comparison model. |
Fields in fr.orsay.lri.varna.models.rna declared as ModeleBase | |
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private ModeleBase |
ModeleBP._partner3
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private ModeleBase |
ModeleBP._partner5
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Fields in fr.orsay.lri.varna.models.rna with type parameters of type ModeleBase | |
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protected ArrayList<ModeleBase> |
RNA._listeBases
the base list |
private ArrayList<ModeleBase> |
Motif._listeBasesM
|
private ArrayList<ModeleBase> |
ModeleStrand._strand
|
Methods in fr.orsay.lri.varna.models.rna that return ModeleBase | |
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ModeleBase |
RNA.getBaseAt(int index)
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ModeleBase |
Motif.getBaseAt(int index)
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ModeleBase |
ModeleStrand.getMB(int a)
|
ModeleBase |
ModeleBP.getPartner(ModeleBase mb)
|
ModeleBase |
ModeleBP.getPartner3()
|
ModeleBase |
ModeleBP.getPartner5()
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Methods in fr.orsay.lri.varna.models.rna that return types with arguments of type ModeleBase | |
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ArrayList<ModeleBase> |
RNA.get_listeBases()
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ArrayList<ModeleBase> |
RNA.getAllPartners(int indice)
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ArrayList<ModeleBase> |
ModeleStrand.getArrayListMB()
|
ArrayList<ModeleBase> |
RNA.getBasesAt(Collection<? extends Integer> indices)
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ArrayList<ModeleBase> |
RNA.getBasesBetween(int from,
int to)
|
ArrayList<ModeleBase> |
Motif.getListBasesMotif()
|
ArrayList<ModeleBase> |
Motif.listBasePair()
Create an arrayList which contain all bases which are involved in a base pair. |
Methods in fr.orsay.lri.varna.models.rna with parameters of type ModeleBase | |
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void |
ModeleStrand.addBase(int index,
ModeleBase mb)
|
void |
ModeleStrand.addBase(ModeleBase mb)
|
(package private) Point2D.Double |
RNA.buildCaptionPosition(ModeleBase mb,
double heightEstimate,
VARNAConfig conf)
|
int |
ModeleBase.compareTo(ModeleBase other)
|
ModeleBP |
RNAMLParser.BPTemp.createBPStyle(ModeleBase mb5,
ModeleBase mb3)
|
TextAnnotation |
RNA.getAnnotation(int type,
ModeleBase base)
|
ModeleBase |
ModeleBP.getPartner(ModeleBase mb)
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boolean |
RNA.isNumberDrawn(ModeleBase mb,
int numPeriod)
|
void |
ModeleBP.setPartner3(ModeleBase mb)
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void |
ModeleBP.setPartner5(ModeleBase mb)
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Method parameters in fr.orsay.lri.varna.models.rna with type arguments of type ModeleBase | |
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private void |
VARNASecDraw.HelixEmbedding.placeTerminalLoop(ArrayList<ModeleBase> mbl,
RNA r)
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void |
RNA.set_listeBases(ArrayList<ModeleBase> _liste)
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Constructors in fr.orsay.lri.varna.models.rna with parameters of type ModeleBase | |
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ModeleBP(ModeleBase part5,
ModeleBase part3)
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ModeleBP(ModeleBase part5,
ModeleBase part3,
ModeleBP.Edge edge5,
ModeleBP.Edge edge3,
ModeleBP.Stericity ster)
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Constructor parameters in fr.orsay.lri.varna.models.rna with type arguments of type ModeleBase | |
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Motif(RNA rna,
ArrayList<ModeleBase> listeBases)
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Uses of ModeleBase in fr.orsay.lri.varna.views |
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Fields in fr.orsay.lri.varna.views with type parameters of type ModeleBase | |
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private ArrayList<ModeleBase> |
VueBaseValues.data
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Methods in fr.orsay.lri.varna.views that return types with arguments of type ModeleBase | |
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private ArrayList<ModeleBase> |
VueUI.extractMaxContiguousPortion(ArrayList<ModeleBase> m)
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Method parameters in fr.orsay.lri.varna.views with type arguments of type ModeleBase | |
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private ArrayList<ModeleBase> |
VueUI.extractMaxContiguousPortion(ArrayList<ModeleBase> m)
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