//Copyright (c) 2000-2003  San Diego Supercomputer Center (SDSC),
//a facility operated by the University of California, San Diego (UCSD)
//
//Users and possessors of this source code are hereby granted a
//nonexclusive, royalty-free copyright and design patent license to
//use this code in individual software.  License is not granted for
//commercial resale, in whole or in part, without prior written
//permission from SDSC.  This source is provided "AS IS" without express
//or implied warranty of any kind.
//
//For further information, please see:  http://mbt.sdsc.edu
//

package edu.sdsc.mbt.viewables;

import java.awt.*;
import java.util.prefs.*;
import java.io.*;

/**
 * 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.
 * @see edu.sdsc.mbt.viewables.StructureStyles
 * @see edu.sdsc.sirius.dialogs.PreferencesDialog
 * @author Oleksandr V. Buzko
 */
public class StylesPreferences {
	
	/**
	 * Constants that define selection modes.
	 */
	public static final int SELECTION_ATOM = 0;
	public static final int SELECTION_RESIDUE = 1;
	public static final int SELECTION_FRAGMENT = 2;
	public static final int SELECTION_STRUCTURE = 3;
	
	public static final int POSITION_LEFT = 0;
	public static final int POSITION_TOP = 1;
		
	public static final int RIBBON_LINE = 0;
	public static final int RIBBON_RENDERED = 1;
	public static final int RIBBON_CYLINDER_HELICES = 2;
	public static final int RIBBON_UNIFORM_ROUND = 3;
	public static final int RIBBON_FLAT_HELICES = 4;
	
	public static final int SURFACE_DOT = 0;
	public static final int SURFACE_MESH = 1;
	public static final int SURFACE_SOLID = 2;
	
	public static final int SURFACE_QUALITY_LOW = 0;
	public static final int SURFACE_QUALITY_MEDIUM = 1;
	public static final int SURFACE_QUALITY_HIGH = 2;
	public static final int SURFACE_QUALITY_ULTRA = 3;

	
	/**
	 * Constants that define structure rendering modes for each atom to allow different rendering of defined structure fragments.
	 */
	public static final short RENDERING_LINES = 0;
	public static final short RENDERING_STICK = 1;
	public static final short RENDERING_BALL_STICK = 2;
	public static final short RENDERING_CPK = 3;
	public static final short RENDERING_RIBBON = 4;
	
	/**
	 * Constants that define rendering quality.
	 */
	public static final short RENDERING_FAST = 0;
	public static final short RENDERING_BEST = 1;

	public static final int ATOMIC_RADIUS = 0;
	public static final int UNIFORM_RADIUS = 1;
	
	/**
	 * 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)
	 */
	public static final int MAGNIFICATION_MOVE = 0;
	public static final int MAGNIFICATION_ZOOM = 1;
	
	public static final int SMOOTH_LAF = 0;
	public static final int NATIVE_LAF = 1;
	
	public static final int defaultLAF = SMOOTH_LAF;

	//this scale is used to generate atom radii
	public static double atomRadiusScale = 0.25;
	public static double cpkRadiusScale = 0.65;
	
	private static final double defaultLineWidth = 2.0;
	
	private static final boolean defaultIndexedColor = false;
	
	private static final int defaultRibbonStyle = RIBBON_RENDERED;
	
	private static final boolean defaultRenderBondOrder = true;
	
	private static final boolean defaultStructureColorSequence = false;//use solid colors for consecutive structure loads

	private static final int defaultToolbarPosition = POSITION_LEFT;
	
	private static final boolean defaultZoomMiddle = false;//middle button is zoom operator (otherwise, Alt-left button)
	
	private static final boolean defaultAntialiasing = false;
	
	public static boolean smoothRibbon = true;
	
	public static float helixThickness = 0.4f;

	
	//defaults
	private static final float defaultSelectionColor[] = { 1.0f, 1.0f, 0.0f };
	private static final float defaultBackgroundColor[] = { 0.0f, 0.0f, 0.0f };
	private static final float defaultMonitorColor[] = { 0.0f, 0.9f, 0.1f };
	
	private static final int defaultSelectionMode = SELECTION_ATOM;
	private static final short defaultRenderingMode = RENDERING_LINES;
	
	private static final short defaultStructureView = RENDERING_LINES;
//	private static final short defaultStructureView = RENDERING_RIBBON;
	
	private static final boolean defaultSelectAtomLabel = true;
	
	private static final boolean defaultUndoEnabled = false;
	private static final int defaultUndoBufferDepth = 10;
	
	private static final int defaultMenuFontSize = 0;//deviation from the default
	private static final int defaultCpkQuality = 10;//number of sphere divisions for rendering of CPK
	private static final float defaultRenderingFastQuality = 1.0f;
	private static final float defaultRenderingBestQuality = 3.0f;
	private static final float defaultRibbonQuality = 1.0f;
	private static final float defaultRibbonDiameter = 1.0f;
	private static final float defaultCylinderDiameter = 3.0f;
	
	private static final double defaultStickSize = 0.15;
	private static final double defaultBondRadiusScale = 0.5;
	private static final double defaultSphereRadius = 0.19;
	private static final double defaultBallRadius = 1.5;
	private static final int defaultBallRadiusOption = StylesPreferences.ATOMIC_RADIUS;

	private static final boolean defaultCommonColoring = true;
	private static final boolean defaultCommonSelection = true;
	private static final boolean defaultCommonRibbonColoring = true;
	private static final String defaultWorkingDirectory = ".";
	
	private static final float[] defaultHelixColor = new float[]{ 1.0f, 0.0f, 0.0f};
	private static final float[] defaultStrandColor = new float[]{ 1.0f, 1.0f, 0.0f};
	private static final float[] defaultTurnColor = new float[]{0.2f, 0.9f, 0.4f};
	private static final float[] defaultCoilColor = new float[]{ 0.1f, 0.4f, 0.9f };
	
	private static final int defaultMagnificationMode = MAGNIFICATION_MOVE;
	private static final int defaultStartupMagnificationMode = MAGNIFICATION_MOVE;
	private static final short defaultStartupRenderingQuality = RENDERING_FAST;
	
	private static final boolean defaultShowBondOrder = true;
	private static final boolean defaultDeriveBondOrder = false;
	
	private static final boolean defaultShowCellGrid = true;
	private static final boolean defaultShowResidueTips = false;
	private static final boolean defaultShowSs = false;//whether to show the color-coded strip on top of every sequence
	
	private static final Font defaultSequenceViewerFont = new Font("Monospaced", Font.BOLD, 16);
	
	private static final Color[] defaultChainColors = new Color[]{ Color.red, Color.YELLOW, Color.CYAN, Color.BLUE, Color.GREEN };
	
	private static final Color[] defaultStructureColors = new Color[]{ Color.red, Color.YELLOW, Color.CYAN, Color.ORANGE, Color.BLUE, Color.GREEN, Color.MAGENTA };

	private static final boolean defaultShowBoundWaters = false;
	
	private static final boolean defaultDisplayToolbar = true;
	private static final boolean defaultShowToolbarTips = true;
	
	private static final int defaultFramerate = 40;
	private static final int defaultMouseFactor = 3;
	
	private static final boolean defaultFogEnabled = true;
	
	private static final boolean defaultDockRama = true;
	
	
	private static final boolean defaultToolbarPDB = true;
	private static final boolean defaultToolbarUndo = false;
	private static final boolean defaultToolbarVisibility = true;
	private static final boolean defaultToolbarRendering = true;
	private static final boolean defaultToolbarColoring = true;
	private static final boolean defaultToolbarLabels = true;
	private static final boolean defaultToolbarCenter = true;
	private static final boolean defaultToolbarSeparate = true;
	private static final boolean defaultToolbarCommon = true;
	private static final boolean defaultToolbarDistance = false;
	private static final boolean defaultToolbarAngle = false;
	private static final boolean defaultToolbarDihedral = false;
	private static final boolean defaultToolbarFog = true;
	
	private static final boolean defaultFastGeometry = false;
		
	
	private static final Color defaultSequenceResidueColor = new Color( 0.0f, 0.0f, 0.0f );
	public static final Color defaultCellBackgroundColor = new Color( 0.7f, 0.7f, 0.7f );
		
	//instance variables
	public static float selectionColor[] = new float[3];
	
	/**
	 * Color of background in 3D viewer
	 */
	public static float backgroundColor[] = new float[3];
	
	public static boolean toolbarChanged = false;
	
	public static boolean toolbarPDB = defaultToolbarPDB;
	public static boolean toolbarUndo = defaultToolbarUndo;
	public static boolean toolbarVisibility = defaultToolbarVisibility;
	public static boolean toolbarRendering = defaultToolbarRendering;
	public static boolean toolbarColoring = defaultToolbarColoring;
	public static boolean toolbarLabels = defaultToolbarLabels;
	public static boolean toolbarCenter = defaultToolbarCenter;
	public static boolean toolbarSeparate = defaultToolbarSeparate;
	public static boolean toolbarCommon = defaultToolbarCommon;
	public static boolean toolbarDistance = defaultToolbarDistance;
	public static boolean toolbarAngle = defaultToolbarAngle;
	public static boolean toolbarDihedral = defaultToolbarDihedral;
	public static boolean toolbarFog = defaultToolbarFog;
	
	public static boolean zoomMiddle = defaultZoomMiddle;
		
	public static boolean fastGeometry = defaultFastGeometry;
	
	public static int toolbarPosition = defaultToolbarPosition;
	
	public static boolean selectAtomLabel = defaultSelectAtomLabel;
	
	public static boolean antialiasing = defaultAntialiasing;
	
	private static final String defaultPovrayInstallationDirectoryWin = "C:\\Program Files\\POV-Ray for Windows v3.6";
	private static final String defaultPovrayInstallationDirectoryLinux = "/usr/local";
	
	public static String povrayInstallationDirectoryWin = defaultPovrayInstallationDirectoryWin;
	public static String povrayInstallationDirectoryLinux = defaultPovrayInstallationDirectoryLinux;
	
	/**
	 * Color used to display distance monitors in <code>StructureViewer</code>
	 */
	public static float monitorColor[] = new float[3];
	
	public static int ribbonStyle = defaultRibbonStyle;
	
	public static boolean renderBondOrder = defaultRenderBondOrder;
	
	public static int LAF = defaultLAF;//look and feel - changeable on Mac
	
	public static int structureColorIndex = 0;
	
	/**
	 * The variable that sets selection level between atom and residue
	 */
	public static int selectionMode = defaultSelectionMode;
	public static short renderingMode = defaultRenderingMode;
	public static short structureView = defaultStructureView;
	public static int cpkQuality = defaultCpkQuality;
	
	public static int menuFontSize = defaultMenuFontSize;
	
	public static boolean structureColorSequence = defaultStructureColorSequence;
	
	public static boolean showCellGrid = defaultShowCellGrid;
	public static boolean showResidueTips = defaultShowResidueTips;
	public static boolean showSs = defaultShowSs;
	public static Font sequenceViewerFont = defaultSequenceViewerFont;
	
	public static boolean undoEnabled = defaultUndoEnabled;
	public static int undoBufferDepth = defaultUndoBufferDepth;
	
	/**
	 * Numeric values that reflect quality of rendering. 
	 */
	public static float renderingFastQuality = defaultRenderingFastQuality;
	public static float renderingBestQuality = defaultRenderingBestQuality;
	public static float ribbonQuality = defaultRibbonQuality;
	public static float ribbonDiameter = defaultRibbonDiameter;
	public static float cylinderDiameter = defaultCylinderDiameter;
	public static boolean commonRibbonColoring = defaultCommonRibbonColoring;
	public static boolean commonColoring = defaultCommonColoring;
	public static boolean commonSelection = defaultCommonSelection;
	
	public static double stickSize = defaultStickSize;//radius of sticks in stick representation
	public static double bondRadiusScale = defaultBondRadiusScale;//ratio of bond to atom radius in ball-and-stick
	public static double sphereRadius = defaultSphereRadius;
	public static double ballRadius = defaultBallRadius;
	
	public static int ballRadiusOption = defaultBallRadiusOption;
	
	public static int startupMagnificationMode = defaultStartupMagnificationMode;
	public static short startupRenderingQuality = defaultStartupRenderingQuality;
	public static int magnificationMode = startupMagnificationMode;

	public static String workingDirectory = defaultWorkingDirectory;
	
	public static boolean showBondOrder = defaultShowBondOrder;
	public static boolean deriveBondOrder = defaultDeriveBondOrder;
	
	public static boolean showBoundWaters = defaultShowBoundWaters;
	
	public static int mouseFactor = defaultMouseFactor;
	
	public static boolean fogEnabled = defaultFogEnabled;
	
	public static boolean indexedColor = defaultIndexedColor;
	
	public static Color[] chainColors = defaultChainColors;
	public static Color[] structureColors = defaultStructureColors;
	
	public static double lineWidth = defaultLineWidth;
	
	public static boolean displayToolbar = defaultDisplayToolbar;
	public static boolean showToolbarTips = defaultShowToolbarTips;
	
	/**
	 * Variables that define colors of the secondary structure elements.
	 */
	public static float[] HELIX_COLOR;
	public static float[] STRAND_COLOR;
	public static float[] TURN_COLOR;
	public static float[] COIL_COLOR;
	
	public static boolean dockRama = defaultDockRama;
	
	public static Color sequenceResidueColor = defaultSequenceResidueColor;
	public static Color cellBackgroundColor = defaultCellBackgroundColor;
	
	private String preferencesLocation = "/edu/sdsc/sirius/viewer";
	
	public StylesPreferences(String location){
		
		preferencesLocation = location;
		
		//initialize instance variables
		selectionColor[0] = defaultSelectionColor[0];
		selectionColor[1] = defaultSelectionColor[1];
		selectionColor[2] = defaultSelectionColor[2];
		
		backgroundColor[0] = defaultBackgroundColor[0];
		backgroundColor[1] = defaultBackgroundColor[1];
		backgroundColor[2] = defaultBackgroundColor[2];
	
		monitorColor[0] = defaultMonitorColor[0];
		monitorColor[1] = defaultMonitorColor[1];
		monitorColor[2] = defaultMonitorColor[2];
		
		HELIX_COLOR = new float[] {defaultHelixColor[0], defaultHelixColor[1], defaultHelixColor[2] };
		STRAND_COLOR = new float[]{defaultStrandColor[0], defaultStrandColor[1], defaultStrandColor[2]};
		TURN_COLOR = new float[]{defaultTurnColor[0], defaultTurnColor[1], defaultTurnColor[2]};
		COIL_COLOR = new float[]{defaultCoilColor[0], defaultCoilColor[1], defaultCoilColor[2]};
		
		chainColors = defaultChainColors;
		structureColors = defaultStructureColors;
		
	
		workingDirectory = (new File(defaultWorkingDirectory)).getAbsolutePath();
		if (workingDirectory.endsWith(".")){
			workingDirectory = workingDirectory.substring(0, workingDirectory.length()-1);
		}
//		System.out.println("Default: " + workingDirectory);
	}
	
	/**
	 * This method uses hard-coded defaults to restore the configuration of the application.
	 * Both StructureStyles and persistent Preferences are updated.
	 */
	public static void resetStylesDefaults(){
		
		LAF = defaultLAF;

		selectionColor[0] = defaultSelectionColor[0];
		selectionColor[1] = defaultSelectionColor[1];
		selectionColor[2] = defaultSelectionColor[2];
		
		monitorColor[0] = defaultMonitorColor[0];
		monitorColor[1] = defaultMonitorColor[1];
		monitorColor[2] = defaultMonitorColor[2];
		
		backgroundColor[0] = defaultBackgroundColor[0];
		backgroundColor[1] = defaultBackgroundColor[1];
		backgroundColor[2] = defaultBackgroundColor[2];
		
		selectionMode = defaultSelectionMode;
		renderingMode = defaultRenderingMode;
		structureView = defaultStructureView;
		cpkQuality = defaultCpkQuality;
		
		renderingFastQuality = defaultRenderingFastQuality;
		renderingBestQuality = defaultRenderingBestQuality;
		ribbonQuality = defaultRibbonQuality;
		ribbonDiameter = defaultRibbonDiameter;
		cylinderDiameter = defaultCylinderDiameter;
		
		commonRibbonColoring = defaultCommonRibbonColoring;
		commonColoring = defaultCommonColoring;
		commonSelection = defaultCommonSelection;
		
		undoEnabled = defaultUndoEnabled;
		undoBufferDepth = defaultUndoBufferDepth;
	
		stickSize = defaultStickSize;
		bondRadiusScale = defaultBondRadiusScale;
		sphereRadius = defaultSphereRadius;
		ballRadius = defaultBallRadius;
	
		ballRadiusOption = defaultBallRadiusOption;
		
		toolbarPosition = defaultToolbarPosition;
		
		selectAtomLabel = defaultSelectAtomLabel;
		
		startupMagnificationMode = defaultStartupMagnificationMode;
		startupRenderingQuality = defaultStartupRenderingQuality;
		
		workingDirectory = defaultWorkingDirectory;
		
		showBondOrder = defaultShowBondOrder;
		deriveBondOrder = defaultDeriveBondOrder;
		
		showBoundWaters = defaultShowBoundWaters;
		mouseFactor = defaultMouseFactor;
		
		fogEnabled = defaultFogEnabled;
		
		renderBondOrder = defaultRenderBondOrder;
		
		sequenceResidueColor = defaultSequenceResidueColor;
		
		structureColorSequence = defaultStructureColorSequence;
		
		showCellGrid = defaultShowCellGrid;
		showResidueTips = defaultShowResidueTips;
		showSs = defaultShowSs;
		sequenceViewerFont = defaultSequenceViewerFont;
		
		cellBackgroundColor = defaultCellBackgroundColor;
		
		sequenceViewerFont = defaultSequenceViewerFont;
		
		lineWidth = defaultLineWidth;
		
		displayToolbar = defaultDisplayToolbar;
		showToolbarTips = defaultShowToolbarTips;
		
		toolbarPDB = defaultToolbarPDB;
		toolbarUndo = defaultToolbarUndo;
		toolbarVisibility = defaultToolbarVisibility;
		toolbarRendering = defaultToolbarRendering;
		toolbarColoring = defaultToolbarColoring;
		toolbarLabels = defaultToolbarLabels;
		toolbarCenter = defaultToolbarCenter;
		toolbarSeparate = defaultToolbarSeparate;
		toolbarCommon = defaultToolbarCommon;
		toolbarDistance = defaultToolbarDistance;
		toolbarAngle = defaultToolbarAngle;
		toolbarDihedral = defaultToolbarDihedral;
		toolbarFog = defaultToolbarFog;

		fastGeometry = defaultFastGeometry;
		zoomMiddle = defaultZoomMiddle;
		
		antialiasing = defaultAntialiasing;
		
		/**
		 * Constants that define colors of the secondary structure elements.
		 */
		HELIX_COLOR = defaultHelixColor;
		STRAND_COLOR = defaultStrandColor;
		TURN_COLOR = defaultTurnColor;
		COIL_COLOR = defaultCoilColor;
		
		for (int i = 0; i < defaultChainColors.length; i++){
			chainColors[i] = defaultChainColors[i];
		}
		
		for (int i = 0; i < defaultStructureColors.length; i++){
			structureColors[i] = defaultStructureColors[i];
		}
	
		dockRama = defaultDockRama;
	}
		
	
	public void writePreferences(){
		
		Preferences root = Preferences.userRoot();
		final Preferences node = root.node(preferencesLocation);
		
		node.putInt("LAF", LAF);
		
		//start writing settings to the node
		node.putFloat("selectionColor0", selectionColor[0]);
		node.putFloat("selectionColor1", selectionColor[1]);
		node.putFloat("selectionColor2", selectionColor[2]);

		node.putFloat("monitorColor0", monitorColor[0]);
		node.putFloat("monitorColor1", monitorColor[1]);
		node.putFloat("monitorColor2", monitorColor[2]);
		
		node.putFloat("backgroundColor0", backgroundColor[0]);
		node.putFloat("backgroundColor1", backgroundColor[1]);
		node.putFloat("backgroundColor2", backgroundColor[2]);
		
		node.putInt("selectionMode", selectionMode);
		node.putInt("renderingMode", renderingMode);
		node.putInt("structureView", structureView);
		node.putInt("cpkQuality", cpkQuality);
		node.putInt("menuFontSize", menuFontSize);
		
		node.putBoolean("structureColorSequence", structureColorSequence);
		
		node.putFloat("renderingFastQuality", renderingFastQuality);
		node.putFloat("renderingBestQuality", renderingBestQuality);
		node.putFloat("ribbonQuality", ribbonQuality);
		node.putFloat("ribbonDiameter", ribbonDiameter);
		node.putFloat("cylinderDiameter", cylinderDiameter);
		
		node.putBoolean("commonRibbonColoring", commonRibbonColoring);
		node.putBoolean("commonColoring", commonColoring);
		node.putBoolean("commonSelection", commonSelection);
		
		node.putBoolean("fastGeometry", fastGeometry);
		node.putBoolean("zoomMiddle", zoomMiddle);
		
		node.putBoolean("antialiasing", antialiasing);
	
		node.putDouble("stickSize", stickSize);
		node.putDouble("bondRadiusScale", bondRadiusScale);
		node.putDouble("sphereRadius", sphereRadius);
		node.putDouble("ballRadius", ballRadius);
		
		node.putDouble("lineWidth", lineWidth);
	
		node.putInt("ballRadiusOption", ballRadiusOption);
		
		node.putInt("toolbarPosition", toolbarPosition);
		
		node.putBoolean("selectAtomLabel", selectAtomLabel);
		
		node.putInt("startupMagnificationMode", startupMagnificationMode);
		node.putInt("startupRenderingQuality", startupRenderingQuality);
		
		node.put("workingDirectory", workingDirectory);
		node.putBoolean("showBondOrder", showBondOrder);
		node.putBoolean("deriveBondOrder", deriveBondOrder);
		
		node.putBoolean("renderBondOrder", renderBondOrder);
		
		node.putBoolean("undoEnabled", undoEnabled);
		node.putInt("undoBufferDepth", undoBufferDepth);
		
		node.putBoolean("showCellGrid", showCellGrid);
		node.putBoolean("showResidueTips", showResidueTips);
		node.putBoolean("showSs", showSs);
		
		node.put("sequenceViewerFontFace", sequenceViewerFont.getFamily());
		node.putInt("sequenceViewerFontSize", sequenceViewerFont.getSize());
		node.putInt("sequenceViewerFontStyle", sequenceViewerFont.getStyle());
		
		node.putBoolean("dockRama", dockRama);
		
		node.putBoolean("showBoundWaters", showBoundWaters);
		node.putInt("mouseFactor", mouseFactor);
		
		node.putBoolean("fogEnabled", fogEnabled);
		
		node.put("povrayDirWin", povrayInstallationDirectoryWin);
		node.put("povrayDirLinux", povrayInstallationDirectoryLinux);
		
		node.putBoolean("displayToolbar", displayToolbar);
		node.putBoolean("showToolbarTips", showToolbarTips);
		
		node.putInt("sequenceResidueColor1", sequenceResidueColor.getRed());
		node.putInt("sequenceResidueColor2", sequenceResidueColor.getGreen());
		node.putInt("sequenceResidueColor3", sequenceResidueColor.getBlue());
		
		node.putBoolean("toolbarPDB", toolbarPDB);
		node.putBoolean("toolbarUndo", toolbarUndo);
		node.putBoolean("toolbarVisibility", toolbarVisibility);
		node.putBoolean("toolbarRendering", toolbarRendering);
		node.putBoolean("toolbarColoring", toolbarColoring);
		node.putBoolean("toolbarLabels", toolbarLabels);
		node.putBoolean("toolbarCenter", toolbarCenter);
		node.putBoolean("toolbarSeparate", toolbarSeparate);
		node.putBoolean("toolbarCommon", toolbarCommon);
		node.putBoolean("toolbarDistance", toolbarDistance);
		node.putBoolean("toolbarAngle", toolbarAngle);
		node.putBoolean("toolbarDihedral", toolbarDihedral);
		node.putBoolean("toolbarFog", toolbarFog);

	
		node.putFloat("helixColor0", HELIX_COLOR[0]);
		node.putFloat("helixColor1", HELIX_COLOR[1]);
		node.putFloat("helixColor2", HELIX_COLOR[2]);
		
		node.putFloat("strandColor0", STRAND_COLOR[0]);
		node.putFloat("strandColor1", STRAND_COLOR[1]);
		node.putFloat("strandColor2", STRAND_COLOR[2]);
		
		node.putFloat("turnColor0", TURN_COLOR[0]);
		node.putFloat("turnColor1", TURN_COLOR[1]);
		node.putFloat("turnColor2", TURN_COLOR[2]);
		
		node.putFloat("coilColor0", COIL_COLOR[0]);
		node.putFloat("coilColor1", COIL_COLOR[1]);
		node.putFloat("coilColor2", COIL_COLOR[2]);
		
		//save default colors
		for (int i = 0; i < chainColors.length; i++){
			Color c = chainColors[i];
			node.putInt("chainColor"+i+"_1", c.getRed());
			node.putInt("chainColor"+i+"_2", c.getGreen());
			node.putInt("chainColor"+i+"_3", c.getBlue());
		}
		
		for (int i = 0; i < structureColors.length; i++){
			Color c = structureColors[i];
			node.putInt("structureColor"+i+"_1", c.getRed());
			node.putInt("structureColor"+i+"_2", c.getGreen());
			node.putInt("structureColor"+i+"_3", c.getBlue());
		}

		try{
			node.flush();
		}
		catch (BackingStoreException ex){
			System.out.println("Unable to save preferences: " + ex);
		}
	}
	
	
	public void readPreferences(){
		
		Preferences root = Preferences.userRoot();
		final Preferences node = root.node(preferencesLocation);
		
		LAF = node.getInt("LAF", defaultLAF);
		
		selectionColor[0] = node.getFloat("selectionColor0", defaultSelectionColor[0]);
		selectionColor[1] = node.getFloat("selectionColor1", defaultSelectionColor[1]);
		selectionColor[2] = node.getFloat("selectionColor2", defaultSelectionColor[2]);
		
		selectionMode = node.getInt("selectionMode", defaultSelectionMode);
		renderingMode = (short)node.getInt("renderingMode", defaultRenderingMode);
		structureView = (short)node.getInt("structureView", defaultStructureView);
		
		//these don't have to be changed, as they are controlled only through Preferences dialog
		//and are not changed elsewhere, which may give different current and default settings
		
		monitorColor[0] = node.getFloat("monitorColor0", defaultMonitorColor[0]);
		monitorColor[1] = node.getFloat("monitorColor1", defaultMonitorColor[1]);
		monitorColor[2] = node.getFloat("monitorColor2", defaultMonitorColor[2]);
		
		backgroundColor[0] = node.getFloat("backgroundColor0", defaultBackgroundColor[0]);
		backgroundColor[1] = node.getFloat("backgroundColor1", defaultBackgroundColor[1]);
		backgroundColor[2] = node.getFloat("backgroundColor2", defaultBackgroundColor[2]);
		
		cpkQuality = node.getInt("cpkQuality", defaultCpkQuality);
		menuFontSize = node.getInt("menuFontSize", defaultMenuFontSize);
		
		renderingFastQuality = node.getFloat("renderingFastQuality", defaultRenderingFastQuality);
		renderingBestQuality = node.getFloat("renderingBestQuality", defaultRenderingBestQuality);
		ribbonQuality = node.getFloat("ribbonQuality", defaultRibbonQuality);
		ribbonDiameter = node.getFloat("ribbonDiameter", defaultRibbonDiameter);
		cylinderDiameter = node.getFloat("cylindernDiameter", defaultCylinderDiameter);

		commonRibbonColoring = node.getBoolean("commonRibbonColoring", defaultCommonRibbonColoring);
		commonColoring = node.getBoolean("commonColoring", defaultCommonColoring);
		commonSelection = node.getBoolean("commonSelection", defaultCommonSelection);
		
		undoEnabled = node.getBoolean("undoEnabled", defaultUndoEnabled);
		undoBufferDepth = node.getInt("undoBufferDepth", defaultUndoBufferDepth);
	
		stickSize = node.getDouble("stickSize", defaultStickSize);
		bondRadiusScale = node.getDouble("bondRadiusScale", defaultBondRadiusScale);
		sphereRadius = node.getDouble("sphereRadius", defaultSphereRadius);
		ballRadius = node.getDouble("ballRadius", defaultBallRadius);
		
		lineWidth = node.getDouble("lineWidth", defaultLineWidth);
		
		toolbarPosition = node.getInt("toolbarPosition", defaultToolbarPosition);
		
		selectAtomLabel = node.getBoolean("selectAtomLabel", defaultSelectAtomLabel);
	
		ballRadiusOption = node.getInt("ballRadiusOption", defaultBallRadiusOption);
		
		structureColorSequence = node.getBoolean("structureColorSequence", defaultStructureColorSequence);
		
		startupMagnificationMode = node.getInt("startupMagnificationMode", defaultStartupMagnificationMode);
		startupRenderingQuality = (short)node.getInt("startupRenderingQuality", defaultStartupRenderingQuality);
//		magnificationMode = startupMagnificationMode;
		
		//generate default values for class labels
		float[] colors = new float[4];
	
		workingDirectory = node.get("workingDirectory", defaultWorkingDirectory);
		
		showBondOrder = node.getBoolean("showBondOrder", defaultShowBondOrder);
		deriveBondOrder = node.getBoolean("deriveBondOrder", defaultDeriveBondOrder);
		showBoundWaters = node.getBoolean("showBoundWaters", defaultShowBoundWaters);
		
		mouseFactor = node.getInt("mouseFactor", defaultMouseFactor);
		fogEnabled = node.getBoolean("fogEnabled", defaultFogEnabled);
		
		povrayInstallationDirectoryWin = node.get("povrayDirWin", defaultPovrayInstallationDirectoryWin);
		povrayInstallationDirectoryLinux = node.get("povrayDirLinux", defaultPovrayInstallationDirectoryLinux);
		
		renderBondOrder = node.getBoolean("renderBondOrder", defaultRenderBondOrder);
		
		displayToolbar = node.getBoolean("displayToolbar", defaultDisplayToolbar);
		showToolbarTips = node.getBoolean("showToolbarTips", defaultShowToolbarTips);
		
		dockRama = node.getBoolean("dockRama", defaultDockRama);
		
		fastGeometry = node.getBoolean("fastGeometry", defaultFastGeometry);
		
		zoomMiddle = node.getBoolean("zoomMiddle", defaultZoomMiddle);
		
		antialiasing = node.getBoolean("antialiasing", defaultAntialiasing);
		
		sequenceResidueColor = new Color( node.getInt("sequenceResidueColor1", defaultSequenceResidueColor.getRed()), 
				node.getInt("sequenceResidueColor2", defaultSequenceResidueColor.getGreen()), 
				node.getInt("sequenceResidueColor3", defaultSequenceResidueColor.getBlue() ));
		
		for (int i = 0; i < defaultChainColors.length; i++){
			int red = node.getInt("chainColor"+i+"_1", defaultChainColors[i].getRed());
			int green = node.getInt("chainColor"+i+"_2", defaultChainColors[i].getGreen());
			int blue = node.getInt("chainColor"+i+"_3", defaultChainColors[i].getBlue());
			chainColors[i] = new Color(red, green, blue);
		}
	
		for (int i = 0; i < defaultStructureColors.length; i++){
			int red = node.getInt("structureColor"+i+"_1", defaultStructureColors[i].getRed());
			int green = node.getInt("structureColor"+i+"_2", defaultStructureColors[i].getGreen());
			int blue = node.getInt("structureColor"+i+"_3", defaultStructureColors[i].getBlue());
			structureColors[i] = new Color(red, green, blue);
		}
		
		StylesPreferences.structureColorIndex = 0;
		
		toolbarPDB = node.getBoolean("toolbarPDB", defaultToolbarPDB);
		toolbarUndo = node.getBoolean("toolbarUndo", defaultToolbarUndo);
		toolbarVisibility = node.getBoolean("toolbarVisibility", defaultToolbarVisibility);
		toolbarRendering = node.getBoolean("toolbarRendering", defaultToolbarRendering);
		toolbarColoring = node.getBoolean("toolbarColoring", defaultToolbarColoring);
		toolbarLabels = node.getBoolean("toolbarLabels", defaultToolbarLabels);
		toolbarCenter = node.getBoolean("toolbarCenter", defaultToolbarCenter);
		toolbarSeparate = node.getBoolean("toolbarSeparate", defaultToolbarSeparate);
		toolbarCommon = node.getBoolean("toolbarCommon", defaultToolbarCommon);
		toolbarDistance = node.getBoolean("toolbarDistance", defaultToolbarDistance);
		toolbarAngle = node.getBoolean("toolbarAngle", defaultToolbarAngle);
		toolbarDihedral = node.getBoolean("toolbarDihedral", defaultToolbarDihedral);
		toolbarFog = node.getBoolean("toolbarFog", defaultToolbarFog);


		showCellGrid = node.getBoolean("showCellGrid", defaultShowCellGrid);
		showResidueTips = node.getBoolean("showResidueTips", defaultShowResidueTips);
		showSs = node.getBoolean("showSs", defaultShowSs);
		
		sequenceViewerFont = new Font(node.get("sequenceViewerFontFace", defaultSequenceViewerFont.getFamily()), 
				node.getInt("sequenceViewerFontStyle", defaultSequenceViewerFont.getStyle()), 
				node.getInt("sequenceViewerFontSize", defaultSequenceViewerFont.getSize()));
		
		HELIX_COLOR = new float[]{ node.getFloat("helixColor0", defaultHelixColor[0]), node.getFloat("helixColor1", defaultHelixColor[1]), node.getFloat("helixColor2", defaultHelixColor[2]) };
		STRAND_COLOR = new float[]{ node.getFloat("strandColor0", defaultStrandColor[0]), node.getFloat("strandColor1", defaultStrandColor[1]), node.getFloat("strandColor2", defaultStrandColor[2])};
		TURN_COLOR = new float[]{ node.getFloat("turnColor0", defaultTurnColor[0]), node.getFloat("turnColor1", defaultTurnColor[1]), node.getFloat("turnColor2", defaultTurnColor[2])};
		COIL_COLOR = new float[]{ node.getFloat("coilColor0", defaultCoilColor[0]), node.getFloat("coilColor1", defaultCoilColor[1]), node.getFloat("coilColor2", defaultCoilColor[2])};
	
	}
	
	public void importPreferences(InputStream in) throws Exception{
		
		Preferences.importPreferences(in);
		readPreferences();
		
	}
	
	public void exportPreferences(OutputStream out) throws Exception{
		
		Preferences root = Preferences.userRoot();
		final Preferences node = root.node(preferencesLocation);
		
		//first, update the preferences on the disk
		writePreferences();
		
		
		node.exportSubtree(out);
		
	}
	
	public static void getSelectionColor( float[] color )
	{
		if ( color == null )
			throw new NullPointerException( "null color" );

		color[0] = selectionColor[0];
		color[1] = selectionColor[1];
		color[2] = selectionColor[2];
	}


}