charite.christo.protein
Class ChJmol

java.lang.Object
  charite.christo.protein.ChJmol

All Implemented Interfaces:

ChRunnable, CommandInterpreter, Disposable, PaintHook, HasProtein, ProteinViewer, org.jmol.api.JmolCallbackListener

public class ChJmol
extends java.lang.Object
implements ProteinViewer, ChRunnable, PaintHook, org.jmol.api.JmolCallbackListener

Jmol Home: http://jmol.sourceforge.net/
License: WIKI:LGPL

Field Summary

static ChJmol[]

NONE

Fields inherited from interface charite.christo.protein.ProteinViewer

COMMAND_HIDE_EVERYTHING, COMMANDbackground, COMMANDbiomolecule, COMMANDcartoon, COMMANDcenter, COMMANDcenter_amino, COMMANDchange_object_color, COMMANDcolor, COMMANDdots, COMMANDhighlight_selected_amino_acids, COMMANDhighlight_selected_atoms, COMMANDlabel, COMMANDlabel_color, COMMANDlines, COMMANDmesh, COMMANDobject_delete, COMMANDribbons, COMMANDrotate, COMMANDsa_surface, COMMANDselect, COMMANDselection_name, COMMANDset_rotation_translation, COMMANDshowScriptPanel, COMMANDspheres, COMMANDsticks, COMMANDsurface, COMMANDsurface_color, COMMANDzoom, GET_ATOM_SELECTION_EXAMPLE, GET_AWTMASK_CONT_SELECTION, GET_AWTMASK_DISC_SELECTION, GET_CANVAS, GET_FLAGS, GET_FRAME_TITLE, GET_JMENUBAR, GET_LAST_CREATED_OBJECT, GET_SUPPORTED_COMMANDS, GET_SURFACEOBJECTS, INTERNAL_USE, INTERPRET_NO_MSG_DIALOGS, mapViewer, PFX_SURFACE_OBJECT, PROPERTY_EXTERNAL_PROCESS, PROPERTY_HAS_CONTEXTMENU, PROPERTY_HAS_SCRIPT_PANEL, PROPERTY_HEAVY_WEIGHT, PROPERTY_MULTI_MOLECULE, PROPERTY_MULTI_VIEW, PROPERTY_NAMED_SELECTIONS, PROPERTY_NEEDS_UPDATE_SURFACES_WHEN_ROTATED, PROPERTY_OPENGL, PROPERTY_RIBBON_COLOR_NO_CHANGE, PROPERTY_SEQUENCE_CURSOR_DELAYED, PROPERTY_TK, PROTEIN, RESIDUES, SELECTION_CURSOR, SELECTION_PICKED, SET_PROTEIN_VERBOSE, SET_RUN_AFTER_INSTALLATION, SHOW_CURSOR_IF_OTHER_PROTEIN, STYLE_COMMANDS

Fields inherited from interface charite.christo.ChRunnable

APPEND, COLUMN_TITLE, DOWNLOAD_FINISHED, GET_PANEL, ICON, INTERPRET_LINE, IS_DRAG4XY, ITEM_TEXT, MODIFY_RENDERER_COMPONENT, PROGRESS, REPAINT_CURSOR, SAY_DOWNLOADING, SET_ICON_IMAGE, SET_TREE_VALUE, SHOW_IN_FRAME, TAB_TEXT, TIP_TEXT

Constructor Summary

ChJmol()

Method Summary

void	dispose()
org.jmol.viewer.Viewer	getJmolViewer()
java.lang.Object	getProperty(java.lang.String getID) The method may return null.
Protein	getProtein()
UniqueList<ProteinViewer>	getViewersSharingViewV(boolean proxies) Each instance is connected with only one protein.
void	highlightAtoms(Selection3D[] atoms, java.lang.String type)
void	interpret(long options, java.lang.String command0)
void	mayDeleteJmol()
void	notifyCallback(org.jmol.constant.EnumCallback type, java.lang.Object[] data)
boolean	notifyEnabled(org.jmol.constant.EnumCallback type)
boolean	paintHook(javax.swing.JComponent c, java.awt.Graphics g, boolean after)
java.lang.Object	run(java.lang.String id, java.lang.Object arg)
void	setCallbackFunction(java.lang.String callbackType, java.lang.String callbackFunction)
void	setProperty(java.lang.String id, java.lang.Object value)
boolean	setProtein(long options, Protein p, ProteinViewer inSameView) The only use of the setProtein and getProtein methods are to to keep a reference to the protein object.

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

NONE

public static final ChJmol[] NONE

Constructor Detail

ChJmol

public ChJmol()

Method Detail

setProperty

public void setProperty(java.lang.String id,
                        java.lang.Object value)

Specified by:

setProperty in interface ProteinViewer

getProperty

public java.lang.Object getProperty(java.lang.String getID)

Description copied from interface: ProteinViewer

The method may return null. GET_JMENUBAR: javax.swing.JMenuBar GET_CANVAS: java.awt.Component GET_SURFACEOBJECTS: List GET_FLAGS: long-bit-mask with properties A generic command like COMMANDcolor: Boolean.TRUE if command is supported

Specified by:

getProperty in interface ProteinViewer

getProtein

public Protein getProtein()

Specified by:

getProtein in interface HasProtein

setProtein

public boolean setProtein(long options,
                          Protein p,
                          ProteinViewer inSameView)

Description copied from interface: ProteinViewer

The only use of the setProtein and getProtein methods are to to keep a reference to the protein object. Otherwise both methods are not important.

Specified by:

setProtein in interface ProteinViewer

highlightAtoms

public void highlightAtoms(Selection3D[] atoms,
                           java.lang.String type)

run

public java.lang.Object run(java.lang.String id,
                            java.lang.Object arg)

Specified by:

run in interface ChRunnable

interpret

public void interpret(long options,
                      java.lang.String command0)

Specified by:

interpret in interface CommandInterpreter

dispose

public void dispose()

Specified by:

dispose in interface Disposable

mayDeleteJmol

public void mayDeleteJmol()

getViewersSharingViewV

public UniqueList<ProteinViewer> getViewersSharingViewV(boolean proxies)

Description copied from interface: ProteinViewer

Each instance is connected with only one protein. But several instances can share the view such that several proteins are displayed in the same panel.

Specified by:

getViewersSharingViewV in interface ProteinViewer

paintHook

public boolean paintHook(javax.swing.JComponent c,
                         java.awt.Graphics g,
                         boolean after)

Specified by:

paintHook in interface PaintHook

after - This method is called once before and once after super.paintComponent.

Returns:

means do not call super.paintComponent

getJmolViewer

public org.jmol.viewer.Viewer getJmolViewer()

setCallbackFunction

public void setCallbackFunction(java.lang.String callbackType,
                                java.lang.String callbackFunction)

Specified by:

setCallbackFunction in interface org.jmol.api.JmolCallbackListener

notifyCallback

public void notifyCallback(org.jmol.constant.EnumCallback type,
                           java.lang.Object[] data)

Specified by:

notifyCallback in interface org.jmol.api.JmolCallbackListener

notifyEnabled

public boolean notifyEnabled(org.jmol.constant.EnumCallback type)

Specified by:

notifyEnabled in interface org.jmol.api.JmolCallbackListener