Uses of Class
fr.orsay.lri.varna.models.rna.ModeleBase

Packages that use ModeleBase
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
 

Fields in fr.orsay.lri.varna declared as ModeleBase
 ModeleBase VARNAPanel._hoveredBase
           
 

Fields in fr.orsay.lri.varna with type parameters of type ModeleBase
private  ArrayList<ModeleBase> VARNAPanel._backupSelection
           
 

Methods in fr.orsay.lri.varna that return ModeleBase
 ModeleBase VARNAPanel.getBaseAt(Point2D.Double po)
           
 

Methods in fr.orsay.lri.varna with parameters of type ModeleBase
(package private)  Point2D.Double VARNAPanel.buildCaptionPosition(ModeleBase mb, double scaleFactor, double heightEstimate)
           
 void VARNAPanel.fireHoverChanged(ModeleBase mold, ModeleBase mnew)
           
 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)
           
 

Method parameters in fr.orsay.lri.varna with type arguments of type ModeleBase
 void VARNAPanel.setSelection(Collection<? extends ModeleBase> mbs)
           
 

Uses of ModeleBase in fr.orsay.lri.varna.interfaces
 

Methods in fr.orsay.lri.varna.interfaces with parameters of type ModeleBase
 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
 

Fields in fr.orsay.lri.varna.models with type parameters of type ModeleBase
private  HashSet<ModeleBase> BaseList._bases
           
 

Methods in fr.orsay.lri.varna.models that return types with arguments of type ModeleBase
 ArrayList<ModeleBase> BaseList.getBases()
           
 

Methods in fr.orsay.lri.varna.models with parameters of type ModeleBase
 void BaseList.addBase(ModeleBase b)
           
 boolean BaseList.contains(ModeleBase mb)
           
 void BaseList.removeBase(ModeleBase b)
           
 

Method parameters in fr.orsay.lri.varna.models with type arguments of type ModeleBase
 void BaseList.addBases(Collection<? extends ModeleBase> mbs)
           
 

Constructors in fr.orsay.lri.varna.models with parameters of type ModeleBase
BaseList(String caption, ModeleBase mb)
           
 

Uses of ModeleBase in fr.orsay.lri.varna.models.annotations
 

Fields in fr.orsay.lri.varna.models.annotations declared as ModeleBase
private  ModeleBase ChemProbAnnotation._mbfst
           
private  ModeleBase ChemProbAnnotation._mbsnd
           
 

Fields in fr.orsay.lri.varna.models.annotations with type parameters of type ModeleBase
private  ArrayList<ModeleBase> HighlightRegionAnnotation._bases
           
 

Methods in fr.orsay.lri.varna.models.annotations that return types with arguments of type ModeleBase
private  ArrayList<ModeleBase> TextAnnotation.extractedArrayListModeleBaseFromAncrage()
           
 ArrayList<ModeleBase> HighlightRegionAnnotation.getBases()
           
 

Methods in fr.orsay.lri.varna.models.annotations with parameters of type ModeleBase
 void TextAnnotation.setAncrage(ModeleBase mb)
           
 

Method parameters in fr.orsay.lri.varna.models.annotations with type arguments of type ModeleBase
 void TextAnnotation.setAncrage(ArrayList<ModeleBase> list, int type)
           
 void HighlightRegionAnnotation.setBases(ArrayList<ModeleBase> b)
           
 

Constructors in fr.orsay.lri.varna.models.annotations with parameters of type ModeleBase
ChemProbAnnotation(ModeleBase mbfst, ModeleBase mbsnd)
           
ChemProbAnnotation(ModeleBase mbfst, ModeleBase mbsnd, ChemProbAnnotation.ChemProbAnnotationType type)
           
ChemProbAnnotation(ModeleBase mbfst, ModeleBase mbsnd, ChemProbAnnotation.ChemProbAnnotationType type, double intensity)
           
ChemProbAnnotation(ModeleBase mbfst, ModeleBase mbsnd, double intensity)
           
ChemProbAnnotation(ModeleBase mbfst, ModeleBase mbsnd, String styleDesc)
           
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
HighlightRegionAnnotation(ArrayList<ModeleBase> b)
           
HighlightRegionAnnotation(ArrayList<ModeleBase> b, Color fill, Color outline, double radius)
           
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
 

Subclasses of ModeleBase in fr.orsay.lri.varna.models.rna
 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
private  ModeleBase ModeleBP._partner3
           
private  ModeleBase ModeleBP._partner5
           
 

Fields in fr.orsay.lri.varna.models.rna with type parameters of type ModeleBase
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
 ModeleBase RNA.getBaseAt(int index)
           
 ModeleBase Motif.getBaseAt(int index)
           
 ModeleBase ModeleStrand.getMB(int a)
           
 ModeleBase ModeleBP.getPartner(ModeleBase mb)
           
 ModeleBase ModeleBP.getPartner3()
           
 ModeleBase ModeleBP.getPartner5()
           
 

Methods in fr.orsay.lri.varna.models.rna that return types with arguments of type ModeleBase
 ArrayList<ModeleBase> RNA.get_listeBases()
           
 ArrayList<ModeleBase> RNA.getAllPartners(int indice)
           
 ArrayList<ModeleBase> ModeleStrand.getArrayListMB()
           
 ArrayList<ModeleBase> RNA.getBasesAt(Collection<? extends Integer> indices)
           
 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
 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)
           
 boolean RNA.isNumberDrawn(ModeleBase mb, int numPeriod)
           
 void ModeleBP.setPartner3(ModeleBase mb)
           
 void ModeleBP.setPartner5(ModeleBase mb)
           
 

Method parameters in fr.orsay.lri.varna.models.rna with type arguments of type ModeleBase
private  void VARNASecDraw.HelixEmbedding.placeTerminalLoop(ArrayList<ModeleBase> mbl, RNA r)
           
 void RNA.set_listeBases(ArrayList<ModeleBase> _liste)
           
 

Constructors in fr.orsay.lri.varna.models.rna with parameters of type ModeleBase
ModeleBP(ModeleBase part5, ModeleBase part3)
           
ModeleBP(ModeleBase part5, ModeleBase part3, ModeleBP.Edge edge5, ModeleBP.Edge edge3, ModeleBP.Stericity ster)
           
 

Constructor parameters in fr.orsay.lri.varna.models.rna with type arguments of type ModeleBase
Motif(RNA rna, ArrayList<ModeleBase> listeBases)
           
 

Uses of ModeleBase in fr.orsay.lri.varna.views
 

Fields in fr.orsay.lri.varna.views with type parameters of type ModeleBase
private  ArrayList<ModeleBase> VueBaseValues.data
           
 

Methods in fr.orsay.lri.varna.views that return types with arguments of type ModeleBase
private  ArrayList<ModeleBase> VueUI.extractMaxContiguousPortion(ArrayList<ModeleBase> m)
           
 

Method parameters in fr.orsay.lri.varna.views with type arguments of type ModeleBase
private  ArrayList<ModeleBase> VueUI.extractMaxContiguousPortion(ArrayList<ModeleBase> m)