Package org.biojava.nbio.structure.align.gui.jmol

Class AbstractAlignmentJmol

java.lang.Object
org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol
All Implemented Interfaces:
ActionListener, MouseListener, MouseMotionListener, WindowListener, EventListener
Direct Known Subclasses:
MultipleAlignmentJmol, StructureAlignmentJmol
public abstract class AbstractAlignmentJmol extends Object implements MouseMotionListener, MouseListener, WindowListener, ActionListener
An Abstract Class to generalize the visualization of AFP and MultipleAlignment structure alignments in Jmol.
Author:
Aleix Lafita

  • Field Details

  • Constructor Details

    • AbstractAlignmentJmol

      public AbstractAlignmentJmol()

  • Method Details

    • initCoords

      protected abstract void initCoords()
      Display the structures after the variable initialization in the constructor.

    • destroy

      public void destroy()
      Set all the member variables to null.

    • resetDisplay

      public abstract void resetDisplay()
      Return to the initial state of the alignment visualization.

    • setAtoms

      public void setAtoms(Atom[] atoms)
      Create and set a new structure from a given atom array.
      Parameters:
      atoms -

    • getColorPalette

      public ColorBrewer getColorPalette()
      Return the color pattelete of the AlignmentJmol instance.

    • getJmolPanel

      public JmolPanel getJmolPanel()
      Return the jmolPanel instance of the AlignmentJmol.

    • setJmolPanel

      public void setJmolPanel(JmolPanel jmolPanel)
      Set the jmolPanel of the AlignmentJmol instance.
      Parameters:
      jmolPanel -

    • evalString

      public void evalString(String rasmolScript)
      Execute a command String in the current Jmol panel.
      Parameters:
      rasmolScript -

    • setStructure

      public void setStructure(Structure s)
      Set a new Structure to visualize in the AlignmentJmol window.
      Parameters:
      s -

    • getStructure

      public Structure getStructure()
      Return the current Structure in the AlignmentJmol instance.

    • getDistanceMatrices

      public abstract List<Matrix> getDistanceMatrices()
      Returns a List of internal Distance Matrices, one for each structure in the alignment. Returns null if no alignment is being displayed.

    • setTitle

      public void setTitle(String title)
      Set the title of the AlignmentJmol window.
      Parameters:
      label -

    • getTitle

      public String getTitle()
      Return the title of the AlignmentJmol window.

    • mouseDragged

      public void mouseDragged(MouseEvent e)
      Specified by:
      mouseDragged in interface MouseMotionListener

    • mouseMoved

      public void mouseMoved(MouseEvent e)
      Specified by:
      mouseMoved in interface MouseMotionListener

    • mouseClicked

      public void mouseClicked(MouseEvent e)
      Specified by:
      mouseClicked in interface MouseListener

    • mouseEntered

      public void mouseEntered(MouseEvent e)
      Specified by:
      mouseEntered in interface MouseListener

    • mouseExited

      public void mouseExited(MouseEvent e)
      Specified by:
      mouseExited in interface MouseListener

    • mousePressed

      public void mousePressed(MouseEvent e)
      Specified by:
      mousePressed in interface MouseListener

    • mouseReleased

      public void mouseReleased(MouseEvent e)
      Specified by:
      mouseReleased in interface MouseListener

    • windowActivated

      public void windowActivated(WindowEvent e)
      Specified by:
      windowActivated in interface WindowListener

    • windowClosed

      public void windowClosed(WindowEvent e)
      Specified by:
      windowClosed in interface WindowListener

    • windowClosing

      public void windowClosing(WindowEvent e)
      Specified by:
      windowClosing in interface WindowListener

    • windowDeactivated

      public void windowDeactivated(WindowEvent e)
      Specified by:
      windowDeactivated in interface WindowListener

    • windowDeiconified

      public void windowDeiconified(WindowEvent e)
      Specified by:
      windowDeiconified in interface WindowListener

    • windowIconified

      public void windowIconified(WindowEvent e)
      Specified by:
      windowIconified in interface WindowListener

    • windowOpened

      public void windowOpened(WindowEvent e)
      Specified by:
      windowOpened in interface WindowListener

    • actionPerformed

      public abstract void actionPerformed(ActionEvent e)
      Specified by:
      actionPerformed in interface ActionListener