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

Packages that use Mapping
fr.orsay.lri.varna   
fr.orsay.lri.varna.models.rna   
fr.orsay.lri.varna.models.treealign   
 

Uses of Mapping in fr.orsay.lri.varna
 

Methods in fr.orsay.lri.varna with parameters of type Mapping
 void VARNAPanel.drawRNAInterpolated(RNA target, int drawMode, Mapping m)
          Draws a secondary structure of RNA using a given drawing algorithm and displays it, using an interpolated transition between the previous one and the new one.
 void VARNAPanel.drawRNAInterpolated(RNA target, Mapping m)
          Draws a secondary structure of RNA using the default drawing algorithm and displays it, using an interpolated transition between the previous one and the new one.
 void VARNAPanel.drawRNAInterpolated(String seq, String str, int drawMode, Mapping m)
          Draws a secondary structure of RNA using a given drawing algorithm and displays it, using an interpolated transition between the previous one and the new one.
 void VARNAPanel.drawRNAInterpolated(String seq, String str, Mapping m)
          Draws a secondary structure of RNA using the default drawing algorithm and displays it, using an interpolated transition between the previous one and the new one.
 void VARNAPanel.showRNAInterpolated(RNA target, Mapping m)
          Simply displays (does not redraw) a secondary structure , using an interpolated transition between the previous one and the new one.
 void VARNAPanel.showRNAInterpolated(RNA target, VARNAConfig cfg, Mapping m)
           
 

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

Methods in fr.orsay.lri.varna.models.rna that return Mapping
static Mapping Mapping.DefaultMapping(int n, int m)
           
static Mapping Mapping.DefaultOutermostMapping(int n, int m)
           
static Mapping Mapping.readMappingFromAlignment(String m, String n)
           
 

Uses of Mapping in fr.orsay.lri.varna.models.treealign
 

Fields in fr.orsay.lri.varna.models.treealign declared as Mapping
private  Mapping RNATree2.ConvertToMapping.m
           
private  Mapping RNATree.ConvertToMapping.m
           
 

Methods in fr.orsay.lri.varna.models.treealign that return Mapping
 Mapping RNATree2.ConvertToMapping.convert(Tree<AlignedNode<RNANodeValue2,RNANodeValue2>> tree)
           
 Mapping RNATree.ConvertToMapping.convert(Tree<AlignedNode<RNANodeValue,RNANodeValue>> tree)
           
static Mapping RNATree2.mappingFromAlignment(Tree<AlignedNode<RNANodeValue2,RNANodeValue2>> alignment)
          Convert an RNA tree (with RNANodeValue2) alignment into a Mapping.
static Mapping RNATree.mappingFromAlignment(Tree<AlignedNode<RNANodeValue,RNANodeValue>> alignment)
          Convert an RNA tree alignment into a Mapping.