Module pdb
Package de.grogra.ext.pdb.view

Class BallStickVisualizer

java.lang.Object
de.grogra.ext.pdb.view.BallStickVisualizer
All Implemented Interfaces:
Visualizer, Command
public class BallStickVisualizer extends Object implements Visualizer, Command
Author:
fdill, mdube This class is responsible for visualizing the data model as a ball and stick model. The ball and stick model shows the atoms and their bonds. RH20060629 changed AColor to RGBAShader RH20060629 changed Appereance to Shader RH20060629 changed EdgeSet to Edge RH20060629 changed EdgeSet.BRANCH to Graph.BRANCH_EDGE RH20060629 changed EdgeSet.GEOMETRY to Graph.BRANCH_EDGE RH20060629 changed EdgeSet.SUCCESSOR to Graph.SUCCESSOR_EDGE RH20060629 changed sphere.basis.set to sphere.setTransform RH20060629 changed stick.basis.set to stick.setTransform RH20060629 changed "stick.radius = ..." to "stick.setRadius(...)" RH20060629 changed "stick.appearance = ..." to "stick.setShader(...)" RH20060629 changed "stick.axis" to "stick.getAxis()"

  • Field Details

  • Constructor Details

    • BallStickVisualizer

      public BallStickVisualizer(IProtein protein)
      Creation of HashMaps for coloring the atoms and for bonding of them. The latter one is realized with the @link StickTupel which holds the indices of the two atoms to be bonded.
      Parameters:
      protein - - the data model representing the read *.pdb file.

  • Method Details

    • createGraph

      public Node createGraph()
      Description copied from interface: Visualizer
      Creates a graph by iterating through the 3 hierarchy layers of the protein model.
      Specified by:
      createGraph in interface Visualizer
      Returns:
      Node - representing the graph of the according model of the given protein
      See Also:
      • de.grogra.ext.pdb.Visualizer#createGraph()

    • getCommandName

      public String getCommandName()
      Description copied from interface: Command
      Returns a name which can be used in the graphical user interface to represent this command.
      Specified by:
      getCommandName in interface Command
      Returns:
      this commands's name

    • run

      public void run(Object info, Context ctx)
      This method is executed by choosing the corresponding menu entry "Ball&Stick Model"
      Specified by:
      run in interface Command
      Parameters:
      info - an argument
      ctx - a context