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

Packages that use ModeleBP
fr.orsay.lri.varna   
fr.orsay.lri.varna.interfaces   
fr.orsay.lri.varna.models   
fr.orsay.lri.varna.models.rna   
fr.orsay.lri.varna.views   
 

Uses of ModeleBP in fr.orsay.lri.varna
 

Methods in fr.orsay.lri.varna with parameters of type ModeleBP
private  void VARNAPanel.drawBasePair(VueVARNAGraphics g2D, Point2D.Double orig, Point2D.Double dest, ModeleBP style, double newRadius)
           
 

Method parameters in fr.orsay.lri.varna with type arguments of type ModeleBP
 void VARNAPanel.fireStructureChanged(Set<ModeleBP> current, Set<ModeleBP> addedBasePairs, Set<ModeleBP> removedBasePairs)
           
 void VARNAPanel.fireStructureChanged(Set<ModeleBP> current, Set<ModeleBP> addedBasePairs, Set<ModeleBP> removedBasePairs)
           
 void VARNAPanel.fireStructureChanged(Set<ModeleBP> current, Set<ModeleBP> addedBasePairs, Set<ModeleBP> removedBasePairs)
           
 

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

Method parameters in fr.orsay.lri.varna.interfaces with type arguments of type ModeleBP
 void InterfaceVARNARNAListener.onStructureChanged(Set<ModeleBP> current, Set<ModeleBP> addedBasePairs, Set<ModeleBP> removedBasePairs)
          Reacts to modification of the structure (Base-pair addition/removal).
 void InterfaceVARNARNAListener.onStructureChanged(Set<ModeleBP> current, Set<ModeleBP> addedBasePairs, Set<ModeleBP> removedBasePairs)
          Reacts to modification of the structure (Base-pair addition/removal).
 void InterfaceVARNARNAListener.onStructureChanged(Set<ModeleBP> current, Set<ModeleBP> addedBasePairs, Set<ModeleBP> removedBasePairs)
          Reacts to modification of the structure (Base-pair addition/removal).
 

Uses of ModeleBP in fr.orsay.lri.varna.models
 

Fields in fr.orsay.lri.varna.models declared as ModeleBP
private  ModeleBP VARNAEdits.AddBPEdit._msbp
           
private  ModeleBP VARNAEdits.RemoveBPEdit._msbp
           
 

Constructors in fr.orsay.lri.varna.models with parameters of type ModeleBP
VARNAEdits.AddBPEdit(int i, int j, ModeleBP msbp, VARNAPanel vp)
           
VARNAEdits.RemoveBPEdit(int i, int j, ModeleBP msbp, VARNAPanel vp)
           
 

Uses of ModeleBP in fr.orsay.lri.varna.models.rna
 

Fields in fr.orsay.lri.varna.models.rna declared as ModeleBP
private  ModeleBP ModeleBase._BP
           
 

Fields in fr.orsay.lri.varna.models.rna with type parameters of type ModeleBP
private  ArrayList<ModeleBP> RNA._structureAux
          Additional bonds and info can be specified here.
 

Methods in fr.orsay.lri.varna.models.rna that return ModeleBP
 ModeleBP RNAMLParser.BPTemp.createBPStyle(ModeleBase mb5, ModeleBase mb3)
           
 ModeleBP RNA.getBPStyle(int i, int j)
           
 ModeleBP ModeleBase.getStyleBP()
          Gets the base pair type for this element.
 

Methods in fr.orsay.lri.varna.models.rna that return types with arguments of type ModeleBP
 ArrayList<ModeleBP> RNA.getAllBPs()
           
 ArrayList<ModeleBP> RNA.getAuxBPs()
           
 ArrayList<ModeleBP> RNA.getAuxBPs(int i)
           
 ArrayList<ModeleBP> RNA.getBPsAt(int i)
           
 ArrayList<ModeleBP> RNA.getSecStrBPs()
           
 ArrayList<ModeleBP> RNA.getStructureAux()
           
 

Methods in fr.orsay.lri.varna.models.rna with parameters of type ModeleBP
 void RNA.addBP(int i, int j, ModeleBP msbp)
           
 void RNA.addBPAux(int i, int j, ModeleBP msbp)
           
 void RNA.addBPToStructure(int index5, int index3, ModeleBP msbp)
           
 void RNA.addBPToStructureUsingNumbers(int number5, int number3, ModeleBP msbp)
          Adds a base pair to this RNA's structure.
 int ModeleBP.compareTo(ModeleBP mb)
           
private  void RNA.drawBasePair(SecStrDrawingProducer out, Point2D.Double orig, Point2D.Double dest, ModeleBP style, VARNAConfig conf)
           
 Color RNA.getBasePairColor(ModeleBP bp, VARNAConfig conf)
           
 double RNA.getBasePairThickness(ModeleBP bp, VARNAConfig conf)
           
 void RNA.removeBP(ModeleBP ms)
           
 void ModeleBase.setElementStructure(int structure, ModeleBP type)
          Sets this InterfaceBase associated structure element.
 void ModeleBase.setStyleBP(ModeleBP type)
          Sets the base pair type for this element.
 

Method parameters in fr.orsay.lri.varna.models.rna with type arguments of type ModeleBP
private  void RNA.applyBPs(ArrayList<ModeleBP> allbps)
           
static void RNAMLParser.planarize(ArrayList<ModeleBP> input, ArrayList<ModeleBP> planar, ArrayList<ModeleBP> others, int length)
           
static void RNAMLParser.planarize(ArrayList<ModeleBP> input, ArrayList<ModeleBP> planar, ArrayList<ModeleBP> others, int length)
           
static void RNAMLParser.planarize(ArrayList<ModeleBP> input, ArrayList<ModeleBP> planar, ArrayList<ModeleBP> others, int length)
           
 

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

Fields in fr.orsay.lri.varna.views declared as ModeleBP
(package private)  ModeleBP VueBPType._msbp
           
 

Fields in fr.orsay.lri.varna.views with type parameters of type ModeleBP
(package private)  ArrayList<ModeleBP> VueBPThickness._msbp
           
private  ArrayList<ModeleBP> VueBPList.data
           
 

Methods in fr.orsay.lri.varna.views with parameters of type ModeleBP
 void VueUI.UIAddBP(int i, int j, ModeleBP ms)
           
 void VueUI.UIRemoveBP(ModeleBP ms)
           
 

Constructors in fr.orsay.lri.varna.views with parameters of type ModeleBP
VueBPType(VARNAPanel vp, ModeleBP msbp)
           
 

Constructor parameters in fr.orsay.lri.varna.views with type arguments of type ModeleBP
VueBPThickness(VARNAPanel vp, ArrayList<ModeleBP> msbp)