edu.sdsc.mbt.viewables
Class StylesPreferences

java.lang.Object
  edu.sdsc.mbt.viewables.StylesPreferences

public class StylesPreferences

extends java.lang.Object

This class is a storage and manipulation utility to handle viewing options set through PreferencesDialog. Allows to store current configuration settings from StructureStyles, updating them and saving and restoring configuration from persistent storage.

Author:

Oleksandr V. Buzko

See Also:

StructureStyles, PreferencesDialog

Field Summary

static boolean	antialiasing
static int	ATOMIC_RADIUS
static double	atomRadiusScale
static float[]	backgroundColor Color of background in 3D viewer
static double	ballRadius
static int	ballRadiusOption
static double	bondRadiusScale
static java.awt.Color	cellBackgroundColor
static java.awt.Color[]	chainColors
static float[]	COIL_COLOR
static boolean	commonColoring
static boolean	commonRibbonColoring
static boolean	commonSelection
static int	cpkQuality
static double	cpkRadiusScale
static float	cylinderDiameter
static java.awt.Color	defaultCellBackgroundColor
static int	defaultLAF
static boolean	deriveBondOrder
static boolean	displayToolbar
static boolean	dockRama
static boolean	fastGeometry
static boolean	fogEnabled
static float[]	HELIX_COLOR Variables that define colors of the secondary structure elements.
static float	helixThickness
static boolean	indexedColor
static int	LAF
static double	lineWidth
static int	MAGNIFICATION_MOVE Constants that define modes of motion: zooming into a structure by changing the angle of view or physically moving the camera (in the latter case, fog interferes with the motion)
static int	MAGNIFICATION_ZOOM
static int	magnificationMode
static int	menuFontSize
static float[]	monitorColor Color used to display distance monitors in StructureViewer
static int	mouseFactor
static int	NATIVE_LAF
static int	POSITION_LEFT
static int	POSITION_TOP
static java.lang.String	povrayInstallationDirectoryLinux
static java.lang.String	povrayInstallationDirectoryWin
static boolean	renderBondOrder
static short	RENDERING_BALL_STICK
static short	RENDERING_BEST
static short	RENDERING_CPK
static short	RENDERING_FAST Constants that define rendering quality.
static short	RENDERING_LINES Constants that define structure rendering modes for each atom to allow different rendering of defined structure fragments.
static short	RENDERING_RIBBON
static short	RENDERING_STICK
static float	renderingBestQuality
static float	renderingFastQuality Numeric values that reflect quality of rendering.
static short	renderingMode
static int	RIBBON_CYLINDER_HELICES
static int	RIBBON_FLAT_HELICES
static int	RIBBON_LINE
static int	RIBBON_RENDERED
static int	RIBBON_UNIFORM_ROUND
static float	ribbonDiameter
static float	ribbonQuality
static int	ribbonStyle
static boolean	selectAtomLabel
static int	SELECTION_ATOM Constants that define selection modes.
static int	SELECTION_FRAGMENT
static int	SELECTION_RESIDUE
static int	SELECTION_STRUCTURE
static float[]	selectionColor
static int	selectionMode The variable that sets selection level between atom and residue
static java.awt.Color	sequenceResidueColor
static java.awt.Font	sequenceViewerFont
static boolean	showBondOrder
static boolean	showBoundWaters
static boolean	showCellGrid
static boolean	showResidueTips
static boolean	showSs
static boolean	showToolbarTips
static int	SMOOTH_LAF
static boolean	smoothRibbon
static double	sphereRadius
static int	startupMagnificationMode
static short	startupRenderingQuality
static double	stickSize
static float[]	STRAND_COLOR
static int	structureColorIndex
static java.awt.Color[]	structureColors
static boolean	structureColorSequence
static short	structureView
static int	SURFACE_DOT
static int	SURFACE_MESH
static int	SURFACE_QUALITY_HIGH
static int	SURFACE_QUALITY_LOW
static int	SURFACE_QUALITY_MEDIUM
static int	SURFACE_QUALITY_ULTRA
static int	SURFACE_SOLID
static boolean	toolbarAngle
static boolean	toolbarCenter
static boolean	toolbarChanged
static boolean	toolbarColoring
static boolean	toolbarCommon
static boolean	toolbarDihedral
static boolean	toolbarDistance
static boolean	toolbarFog
static boolean	toolbarLabels
static boolean	toolbarPDB
static int	toolbarPosition
static boolean	toolbarRendering
static boolean	toolbarSeparate
static boolean	toolbarUndo
static boolean	toolbarVisibility
static float[]	TURN_COLOR
static int	undoBufferDepth
static boolean	undoEnabled
static int	UNIFORM_RADIUS
static java.lang.String	workingDirectory
static boolean	zoomMiddle

Constructor Summary

StylesPreferences(java.lang.String location)

Method Summary

void	exportPreferences(java.io.OutputStream out)
static void	getSelectionColor(float[] color)
void	importPreferences(java.io.InputStream in)
void	readPreferences()
static void	resetStylesDefaults() This method uses hard-coded defaults to restore the configuration of the application.
void	writePreferences()

Methods inherited from class java.lang.Object

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

Field Detail

SELECTION_ATOM

public static final int SELECTION_ATOM

Constants that define selection modes.

See Also:

Constant Field Values

SELECTION_RESIDUE

public static final int SELECTION_RESIDUE

See Also:

Constant Field Values

SELECTION_FRAGMENT

public static final int SELECTION_FRAGMENT

See Also:

Constant Field Values

SELECTION_STRUCTURE

public static final int SELECTION_STRUCTURE

See Also:

Constant Field Values

POSITION_LEFT

public static final int POSITION_LEFT

See Also:

Constant Field Values

POSITION_TOP

public static final int POSITION_TOP

See Also:

Constant Field Values

RIBBON_LINE

public static final int RIBBON_LINE

See Also:

Constant Field Values

RIBBON_RENDERED

public static final int RIBBON_RENDERED

See Also:

Constant Field Values

RIBBON_CYLINDER_HELICES

public static final int RIBBON_CYLINDER_HELICES

See Also:

Constant Field Values

RIBBON_UNIFORM_ROUND

public static final int RIBBON_UNIFORM_ROUND

See Also:

Constant Field Values

RIBBON_FLAT_HELICES

public static final int RIBBON_FLAT_HELICES

See Also:

Constant Field Values

SURFACE_DOT

public static final int SURFACE_DOT

See Also:

Constant Field Values

SURFACE_MESH

public static final int SURFACE_MESH

See Also:

Constant Field Values

SURFACE_SOLID

public static final int SURFACE_SOLID

See Also:

Constant Field Values

SURFACE_QUALITY_LOW

public static final int SURFACE_QUALITY_LOW

See Also:

Constant Field Values

SURFACE_QUALITY_MEDIUM

public static final int SURFACE_QUALITY_MEDIUM

See Also:

Constant Field Values

SURFACE_QUALITY_HIGH

public static final int SURFACE_QUALITY_HIGH

See Also:

Constant Field Values

SURFACE_QUALITY_ULTRA

public static final int SURFACE_QUALITY_ULTRA

See Also:

Constant Field Values

RENDERING_LINES

public static final short RENDERING_LINES

Constants that define structure rendering modes for each atom to allow different rendering of defined structure fragments.

See Also:

Constant Field Values

RENDERING_STICK

public static final short RENDERING_STICK

See Also:

Constant Field Values

RENDERING_BALL_STICK

public static final short RENDERING_BALL_STICK

See Also:

Constant Field Values

RENDERING_CPK

public static final short RENDERING_CPK

See Also:

Constant Field Values

RENDERING_RIBBON

public static final short RENDERING_RIBBON

See Also:

Constant Field Values

RENDERING_FAST

public static final short RENDERING_FAST

Constants that define rendering quality.

See Also:

Constant Field Values

RENDERING_BEST

public static final short RENDERING_BEST

See Also:

Constant Field Values

ATOMIC_RADIUS

public static final int ATOMIC_RADIUS

See Also:

Constant Field Values

UNIFORM_RADIUS

public static final int UNIFORM_RADIUS

See Also:

Constant Field Values

MAGNIFICATION_MOVE

public static final int MAGNIFICATION_MOVE

Constants that define modes of motion: zooming into a structure by changing the angle of view or physically moving the camera (in the latter case, fog interferes with the motion)

See Also:

Constant Field Values

MAGNIFICATION_ZOOM

public static final int MAGNIFICATION_ZOOM

See Also:

Constant Field Values

SMOOTH_LAF

public static final int SMOOTH_LAF

See Also:

Constant Field Values

NATIVE_LAF

public static final int NATIVE_LAF

See Also:

Constant Field Values

defaultLAF

public static final int defaultLAF

See Also:

Constant Field Values

atomRadiusScale

public static double atomRadiusScale

cpkRadiusScale

public static double cpkRadiusScale

smoothRibbon

public static boolean smoothRibbon

helixThickness

public static float helixThickness

defaultCellBackgroundColor

public static final java.awt.Color defaultCellBackgroundColor

selectionColor

public static float[] selectionColor

backgroundColor

public static float[] backgroundColor

Color of background in 3D viewer

toolbarChanged

public static boolean toolbarChanged

toolbarPDB

public static boolean toolbarPDB

toolbarUndo

public static boolean toolbarUndo

toolbarVisibility

public static boolean toolbarVisibility

toolbarRendering

public static boolean toolbarRendering

toolbarColoring

public static boolean toolbarColoring

toolbarLabels

public static boolean toolbarLabels

toolbarCenter

public static boolean toolbarCenter

toolbarSeparate

public static boolean toolbarSeparate

toolbarCommon

public static boolean toolbarCommon

toolbarDistance

public static boolean toolbarDistance

toolbarAngle

public static boolean toolbarAngle

toolbarDihedral

public static boolean toolbarDihedral

toolbarFog

public static boolean toolbarFog

zoomMiddle

public static boolean zoomMiddle

fastGeometry

public static boolean fastGeometry

toolbarPosition

public static int toolbarPosition

selectAtomLabel

public static boolean selectAtomLabel

antialiasing

public static boolean antialiasing

povrayInstallationDirectoryWin

public static java.lang.String povrayInstallationDirectoryWin

povrayInstallationDirectoryLinux

public static java.lang.String povrayInstallationDirectoryLinux

monitorColor

public static float[] monitorColor

Color used to display distance monitors in StructureViewer

ribbonStyle

public static int ribbonStyle

renderBondOrder

public static boolean renderBondOrder

LAF

public static int LAF

structureColorIndex

public static int structureColorIndex

selectionMode

public static int selectionMode

The variable that sets selection level between atom and residue

renderingMode

public static short renderingMode

structureView

public static short structureView

cpkQuality

public static int cpkQuality

menuFontSize

public static int menuFontSize

structureColorSequence

public static boolean structureColorSequence

showCellGrid

public static boolean showCellGrid

showResidueTips

public static boolean showResidueTips

showSs

public static boolean showSs

sequenceViewerFont

public static java.awt.Font sequenceViewerFont

undoEnabled

public static boolean undoEnabled

undoBufferDepth

public static int undoBufferDepth

renderingFastQuality

public static float renderingFastQuality

Numeric values that reflect quality of rendering.

renderingBestQuality

public static float renderingBestQuality

ribbonQuality

public static float ribbonQuality

ribbonDiameter

public static float ribbonDiameter

cylinderDiameter

public static float cylinderDiameter

commonRibbonColoring

public static boolean commonRibbonColoring

commonColoring

public static boolean commonColoring

commonSelection

public static boolean commonSelection

stickSize

public static double stickSize

bondRadiusScale

public static double bondRadiusScale

sphereRadius

public static double sphereRadius

ballRadius

public static double ballRadius

ballRadiusOption

public static int ballRadiusOption

startupMagnificationMode

public static int startupMagnificationMode

startupRenderingQuality

public static short startupRenderingQuality

magnificationMode

public static int magnificationMode

workingDirectory

public static java.lang.String workingDirectory

showBondOrder

public static boolean showBondOrder

deriveBondOrder

public static boolean deriveBondOrder

showBoundWaters

public static boolean showBoundWaters

mouseFactor

public static int mouseFactor

fogEnabled

public static boolean fogEnabled

indexedColor

public static boolean indexedColor

chainColors

public static java.awt.Color[] chainColors

structureColors

public static java.awt.Color[] structureColors

lineWidth

public static double lineWidth

displayToolbar

public static boolean displayToolbar

showToolbarTips

public static boolean showToolbarTips

HELIX_COLOR

public static float[] HELIX_COLOR

Variables that define colors of the secondary structure elements.

STRAND_COLOR

public static float[] STRAND_COLOR

TURN_COLOR

public static float[] TURN_COLOR

COIL_COLOR

public static float[] COIL_COLOR

dockRama

public static boolean dockRama

sequenceResidueColor

public static java.awt.Color sequenceResidueColor

cellBackgroundColor

public static java.awt.Color cellBackgroundColor

Constructor Detail

StylesPreferences

public StylesPreferences(java.lang.String location)

Method Detail

resetStylesDefaults

public static void resetStylesDefaults()

This method uses hard-coded defaults to restore the configuration of the application. Both StructureStyles and persistent Preferences are updated.

writePreferences

public void writePreferences()

readPreferences

public void readPreferences()

importPreferences

public void importPreferences(java.io.InputStream in)
                       throws java.lang.Exception

Throws:

java.lang.Exception

exportPreferences

public void exportPreferences(java.io.OutputStream out)
                       throws java.lang.Exception

Throws:

java.lang.Exception

getSelectionColor

public static void getSelectionColor(float[] color)