charite.christo.protein
Interface ProteinViewer

All Superinterfaces:

CommandInterpreter, Disposable, HasProtein

All Known Implementing Classes:

AbstractProteinViewerProxy, ChAstex, ChAstexPROXY, ChJmol, ChJmolPROXY, Protein3d.PView, Pymol

public interface ProteinViewer
extends Disposable, HasProtein, CommandInterpreter

A protein viewer can display proteins three-dimensionally.

Field Summary

static java.lang.String	COMMAND_HIDE_EVERYTHING
static java.lang.String	COMMANDbackground
static java.lang.String	COMMANDbiomolecule
static java.lang.String	COMMANDcartoon
static java.lang.String	COMMANDcenter
static java.lang.String	COMMANDcenter_amino
static java.lang.String	COMMANDchange_object_color
static java.lang.String	COMMANDcolor
static java.lang.String	COMMANDdots
static java.lang.String	COMMANDhighlight_selected_amino_acids
static java.lang.String	COMMANDhighlight_selected_atoms
static java.lang.String	COMMANDlabel
static java.lang.String	COMMANDlabel_color
static java.lang.String	COMMANDlines
static java.lang.String	COMMANDmesh
static java.lang.String	COMMANDobject_delete
static java.lang.String	COMMANDribbons
static java.lang.String	COMMANDrotate
static java.lang.String	COMMANDsa_surface
static java.lang.String	COMMANDselect
static java.lang.String	COMMANDselection_name
static java.lang.String	COMMANDset_rotation_translation
static java.lang.String	COMMANDshowScriptPanel
static java.lang.String	COMMANDspheres
static java.lang.String	COMMANDsticks
static java.lang.String	COMMANDsurface
static java.lang.String	COMMANDsurface_color
static java.lang.String	COMMANDzoom
static java.lang.String	GET_ATOM_SELECTION_EXAMPLE
static java.lang.String	GET_AWTMASK_CONT_SELECTION
static java.lang.String	GET_AWTMASK_DISC_SELECTION
static java.lang.String	GET_CANVAS
static java.lang.String	GET_FLAGS
static java.lang.String	GET_FRAME_TITLE
static java.lang.String	GET_JMENUBAR
static java.lang.String	GET_LAST_CREATED_OBJECT
static java.lang.String	GET_SUPPORTED_COMMANDS
static java.lang.String	GET_SURFACEOBJECTS
static java.lang.String[]	INTERNAL_USE
static long	INTERPRET_NO_MSG_DIALOGS
static java.util.WeakHashMap<java.lang.Object,java.lang.Object>	mapViewer
static ProteinViewer[]	NONE
static java.lang.String	PFX_SURFACE_OBJECT
static long	PROPERTY_EXTERNAL_PROCESS
static long	PROPERTY_HAS_CONTEXTMENU
static long	PROPERTY_HAS_SCRIPT_PANEL
static long	PROPERTY_HEAVY_WEIGHT
static long	PROPERTY_MULTI_MOLECULE
static long	PROPERTY_MULTI_VIEW
static long	PROPERTY_NAMED_SELECTIONS
static long	PROPERTY_NEEDS_UPDATE_SURFACES_WHEN_ROTATED
static long	PROPERTY_OPENGL
static long	PROPERTY_RIBBON_COLOR_NO_CHANGE
static long	PROPERTY_SEQUENCE_CURSOR_DELAYED
static long	PROPERTY_TK
static java.lang.String	PROTEIN
static java.lang.String	RESIDUES
static java.lang.String	SELECTION_CURSOR
static java.lang.String	SELECTION_PICKED
static long	SET_PROTEIN_VERBOSE
static java.lang.String	SET_RUN_AFTER_INSTALLATION
static java.util.HashSet<java.lang.Class>	SHOW_CURSOR_IF_OTHER_PROTEIN
static java.lang.String[]	STYLE_COMMANDS

Method Summary

java.lang.Object	getProperty(java.lang.String id) The method may return null.
java.util.Collection<? extends ProteinViewer>	getViewersSharingViewV(boolean proxyObject) Each instance is connected with only one protein.
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 interface charite.christo.Disposable

dispose

Methods inherited from interface charite.christo.protein.HasProtein

getProtein

Methods inherited from interface charite.christo.CommandInterpreter

interpret

Field Detail

PROTEIN

static final java.lang.String PROTEIN

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Constant Field Values

RESIDUES

static final java.lang.String RESIDUES

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SELECTION_CURSOR

static final java.lang.String SELECTION_CURSOR

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SELECTION_PICKED

static final java.lang.String SELECTION_PICKED

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PROPERTY_MULTI_MOLECULE

static final long PROPERTY_MULTI_MOLECULE

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PROPERTY_MULTI_VIEW

static final long PROPERTY_MULTI_VIEW

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PROPERTY_EXTERNAL_PROCESS

static final long PROPERTY_EXTERNAL_PROCESS

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PROPERTY_TK

static final long PROPERTY_TK

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PROPERTY_HEAVY_WEIGHT

static final long PROPERTY_HEAVY_WEIGHT

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PROPERTY_OPENGL

static final long PROPERTY_OPENGL

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PROPERTY_SEQUENCE_CURSOR_DELAYED

static final long PROPERTY_SEQUENCE_CURSOR_DELAYED

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PROPERTY_HAS_SCRIPT_PANEL

static final long PROPERTY_HAS_SCRIPT_PANEL

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PROPERTY_NAMED_SELECTIONS

static final long PROPERTY_NAMED_SELECTIONS

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PROPERTY_RIBBON_COLOR_NO_CHANGE

static final long PROPERTY_RIBBON_COLOR_NO_CHANGE

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PROPERTY_HAS_CONTEXTMENU

static final long PROPERTY_HAS_CONTEXTMENU

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PROPERTY_NEEDS_UPDATE_SURFACES_WHEN_ROTATED

static final long PROPERTY_NEEDS_UPDATE_SURFACES_WHEN_ROTATED

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INTERPRET_NO_MSG_DIALOGS

static final long INTERPRET_NO_MSG_DIALOGS

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SET_PROTEIN_VERBOSE

static final long SET_PROTEIN_VERBOSE

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NONE

static final ProteinViewer[] NONE

PFX_SURFACE_OBJECT

static final java.lang.String PFX_SURFACE_OBJECT

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COMMANDhighlight_selected_atoms

static final java.lang.String COMMANDhighlight_selected_atoms

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COMMANDhighlight_selected_amino_acids

static final java.lang.String COMMANDhighlight_selected_amino_acids

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COMMANDcenter_amino

static final java.lang.String COMMANDcenter_amino

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COMMANDbiomolecule

static final java.lang.String COMMANDbiomolecule

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COMMANDzoom

static final java.lang.String COMMANDzoom

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COMMANDrotate

static final java.lang.String COMMANDrotate

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COMMANDcenter

static final java.lang.String COMMANDcenter

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COMMANDset_rotation_translation

static final java.lang.String COMMANDset_rotation_translation

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COMMANDbackground

static final java.lang.String COMMANDbackground

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COMMANDribbons

static final java.lang.String COMMANDribbons

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COMMANDspheres

static final java.lang.String COMMANDspheres

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COMMANDsticks

static final java.lang.String COMMANDsticks

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COMMANDlines

static final java.lang.String COMMANDlines

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COMMANDsurface

static final java.lang.String COMMANDsurface

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COMMANDsa_surface

static final java.lang.String COMMANDsa_surface

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COMMANDsurface_color

static final java.lang.String COMMANDsurface_color

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COMMANDmesh

static final java.lang.String COMMANDmesh

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COMMANDdots

static final java.lang.String COMMANDdots

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COMMANDcartoon

static final java.lang.String COMMANDcartoon

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COMMANDcolor

static final java.lang.String COMMANDcolor

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COMMANDchange_object_color

static final java.lang.String COMMANDchange_object_color

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COMMANDselect

static final java.lang.String COMMANDselect

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COMMANDselection_name

static final java.lang.String COMMANDselection_name

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COMMANDlabel

static final java.lang.String COMMANDlabel

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COMMANDlabel_color

static final java.lang.String COMMANDlabel_color

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COMMANDshowScriptPanel

static final java.lang.String COMMANDshowScriptPanel

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COMMANDobject_delete

static final java.lang.String COMMANDobject_delete

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COMMAND_HIDE_EVERYTHING

static final java.lang.String COMMAND_HIDE_EVERYTHING

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STYLE_COMMANDS

static final java.lang.String[] STYLE_COMMANDS

INTERNAL_USE

static final java.lang.String[] INTERNAL_USE

mapViewer

static final java.util.WeakHashMap<java.lang.Object,java.lang.Object> mapViewer

SHOW_CURSOR_IF_OTHER_PROTEIN

static final java.util.HashSet<java.lang.Class> SHOW_CURSOR_IF_OTHER_PROTEIN

GET_FRAME_TITLE

static final java.lang.String GET_FRAME_TITLE

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GET_ATOM_SELECTION_EXAMPLE

static final java.lang.String GET_ATOM_SELECTION_EXAMPLE

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GET_JMENUBAR

static final java.lang.String GET_JMENUBAR

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GET_CANVAS

static final java.lang.String GET_CANVAS

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GET_SURFACEOBJECTS

static final java.lang.String GET_SURFACEOBJECTS

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GET_LAST_CREATED_OBJECT

static final java.lang.String GET_LAST_CREATED_OBJECT

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GET_FLAGS

static final java.lang.String GET_FLAGS

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GET_SUPPORTED_COMMANDS

static final java.lang.String GET_SUPPORTED_COMMANDS

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GET_AWTMASK_CONT_SELECTION

static final java.lang.String GET_AWTMASK_CONT_SELECTION

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GET_AWTMASK_DISC_SELECTION

static final java.lang.String GET_AWTMASK_DISC_SELECTION

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SET_RUN_AFTER_INSTALLATION

static final java.lang.String SET_RUN_AFTER_INSTALLATION

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Method Detail

setProtein

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. Otherwise both methods are not important.

getViewersSharingViewV

java.util.Collection<? extends ProteinViewer> getViewersSharingViewV(boolean proxyObject)

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.

getProperty

java.lang.Object getProperty(java.lang.String id)

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

setProperty

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