Uses of Class
fr.orsay.lri.varna.models.naView.Loop

Packages that use Loop
fr.orsay.lri.varna.models.naView   
 

Uses of Loop in fr.orsay.lri.varna.models.naView
 

Fields in fr.orsay.lri.varna.models.naView declared as Loop
private  Loop Connection.loop
           
private  Loop NAView.root
           
 

Fields in fr.orsay.lri.varna.models.naView with type parameters of type Loop
private  ArrayList<Loop> NAView.loops
           
 

Methods in fr.orsay.lri.varna.models.naView that return Loop
private  Loop NAView.construct_loop(int ibase)
          Starting at residue ibase, recursively constructs the loop containing said base and all deeper bases.
 Loop Connection.getLoop()
           
 

Methods in fr.orsay.lri.varna.models.naView with parameters of type Loop
private  int NAView.depth(Loop lp)
          Determines the depth of loop, lp.
private  void NAView.determine_radius(Loop lp, double lencut)
          For the loop pointed to by lp, determine the radius of the loop that will ensure that each base around the loop will have a separation of at least lencut around the circle.
private  int NAView.find_ic_middle(int icstart, int icend, Connection anchor_connection, Connection acp, Loop lp)
          Finds the middle of a set of connected connectors.
 void Connection.setLoop(Loop loop)
           
private  void NAView.traverse_loop(Loop lp, Connection anchor_connection)
          This is the workhorse of the display program.