X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=srcjar%2Ffr%2Forsay%2Flri%2Fvarna%2Fviews%2FVueMenu.java;fp=srcjar%2Ffr%2Forsay%2Flri%2Fvarna%2Fviews%2FVueMenu.java;h=f7ee43f87b88b9f2c9742bacc8db19ff4920a7d2;hb=2d6292c0377bc6b773c6844a45d3f2c5fac352c7;hp=0000000000000000000000000000000000000000;hpb=954af328a2a6a0055572cd1a09ee035301222574;p=jalview.git

diff --git a/srcjar/fr/orsay/lri/varna/views/VueMenu.java b/srcjar/fr/orsay/lri/varna/views/VueMenu.java
new file mode 100644
index 0000000..f7ee43f
--- /dev/null
+++ b/srcjar/fr/orsay/lri/varna/views/VueMenu.java
@@ -0,0 +1,495 @@
+/*
+ VARNA is a tool for the automated drawing, visualization and annotation of the secondary structure of RNA, designed as a companion software for web servers and databases.
+ Copyright (C) 2008  Kevin Darty, Alain Denise and Yann Ponty.
+ electronic mail : Yann.Ponty@lri.fr
+ paper mail : LRI, bat 490 Universit� Paris-Sud 91405 Orsay Cedex France
+
+ This file is part of VARNA version 3.1.
+ VARNA version 3.1 is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License
+ as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+
+ VARNA version 3.1 is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY;
+ without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+ See the GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License along with VARNA version 3.1.
+ If not, see http://www.gnu.org/licenses.
+ */
+package fr.orsay.lri.varna.views;
+
+import java.awt.Color;
+import java.awt.Component;
+import java.awt.Container;
+import java.awt.Font;
+import java.awt.Point;
+import java.awt.event.KeyEvent;
+import java.util.ArrayList;
+
+import javax.swing.JCheckBoxMenuItem;
+import javax.swing.JComponent;
+import javax.swing.JLabel;
+import javax.swing.JMenu;
+import javax.swing.JMenuItem;
+import javax.swing.JPopupMenu;
+import javax.swing.JSeparator;
+import javax.swing.KeyStroke;
+
+import fr.orsay.lri.varna.VARNAPanel;
+import fr.orsay.lri.varna.controlers.ControleurMenu;
+import fr.orsay.lri.varna.models.rna.RNA;
+
+public class VueMenu extends JPopupMenu {
+	/**
+	 * 
+	 */
+	private static final long serialVersionUID = 1L;
+
+	private VARNAPanel _vp;
+
+	private ControleurMenu _controlerMenu;
+
+	private JCheckBoxMenuItem _itemOptionSpecialBaseColored = new JCheckBoxMenuItem(
+			"Custom colored", false);
+	private JCheckBoxMenuItem _itemShowWarnings = new JCheckBoxMenuItem(
+			"Show warnings", false);
+	private JCheckBoxMenuItem _itemDrawBackbone = new JCheckBoxMenuItem(
+			"Draw backbone", true);
+	private JCheckBoxMenuItem _itemOptionGapsBaseColored = new JCheckBoxMenuItem(
+			"Custom colored", false);
+	private JCheckBoxMenuItem _itemOptionBondsColored = new JCheckBoxMenuItem(
+			"Use base color for base-pairs", false);
+	private JCheckBoxMenuItem _itemShowNCBP = new JCheckBoxMenuItem(
+			"Show non-canonical BPs", true);
+	private JCheckBoxMenuItem _itemShowOnlyPlanar = new JCheckBoxMenuItem(
+			"Hide tertiary BPs", false);
+	private JCheckBoxMenuItem _itemFlatExteriorLoop = new JCheckBoxMenuItem(
+			"Flat exterior loop", false);
+	
+	private JCheckBoxMenuItem _itemShowColorMap = new JCheckBoxMenuItem(
+			"Show color map", false);
+	private JMenuItem _dashBasesColor;
+
+	private ArrayList<JComponent> _disabled = new ArrayList<JComponent>();
+
+	private JMenuItem _rotation;
+	private JMenuItem _bpHeightIncrement;
+
+	private Point _spawnOrigin = new Point(-1,-1);
+	
+	public VueMenu(VARNAPanel vp) {
+		_vp = vp;
+		_controlerMenu = new ControleurMenu(_vp, this);
+	}
+
+	private void addTitle(String title, boolean keep) {
+		// TOD BH SwingJS -- this should not be necessary
+		JSeparator sep = new JPopupMenu.Separator(); // BH SWingJS needs JPopupMenu.Separator
+		//JSeparator sep = new JSeparator();
+		JMenuItem titleItem = new JMenuItem(" " + title);//BH SwingJS was JLabel -- need to be able to do this.
+		// titleItem.setAlignmentX(0.5f);
+		Font previousFont = titleItem.getFont();
+		Font futureFont = previousFont.deriveFont(Font.BOLD).deriveFont(
+				(float) previousFont.getSize() + 1.0f);
+
+		titleItem.setFont(futureFont);
+		Color current = titleItem.getForeground();
+		Color future = current.brighter().brighter();
+		// titleItem.setBackground(future);
+		titleItem.setForeground(future);
+		add(titleItem);
+		add(sep);
+		if (!keep) {
+			_disabled.add(sep);
+			_disabled.add(titleItem);
+		}
+	}
+	
+	private void configMenuItem(JMenuItem mi, String command, String keyStroke, Container par)
+	{ configMenuItem(mi,command,keyStroke,par,false); }
+
+	private void configMenuItem(JMenuItem mi, String command, String keyStroke, Container par, boolean disabled)
+	{ 
+		mi.setActionCommand(command);
+		mi.addActionListener(_controlerMenu);
+		if (keyStroke!=null)
+			if (!keyStroke.equals(""))
+				mi.setAccelerator(KeyStroke.getKeyStroke(keyStroke));
+		if (disabled)
+		{ _disabled.add(mi);}
+		par.add(mi);
+	}
+	
+	private JMenuItem createMenuItem(String caption, String command, String keyStroke, Container par, boolean disabled)
+	{
+		JMenuItem mi = new JMenuItem(caption);
+		configMenuItem(mi, command,keyStroke, par, disabled);
+		return mi;
+	}
+
+	private JMenuItem createMenuItem(String caption, String command, String keyStroke, Container par)
+	{ return createMenuItem(caption, command, keyStroke, par,false); }
+
+
+	public void updateDialog() {
+		for (int i = 0; i < _disabled.size(); i++) {
+			JComponent j = _disabled.get(i);
+			j.setVisible(_vp.isModifiable());
+		}
+		_itemOptionSpecialBaseColored.setState(_vp.getColorSpecialBases());
+		_itemShowWarnings.setState(_vp.getShowWarnings());
+		_itemOptionGapsBaseColored.setState(_vp.getColorGapsBases());
+		_itemOptionGapsBaseColored.setEnabled(_vp.isComparisonMode());
+		_dashBasesColor.setEnabled(_vp.isComparisonMode());
+		
+		_rotation.setEnabled(_vp.getDrawMode() != RNA.DRAW_MODE_LINEAR);
+		_bpHeightIncrement.setEnabled(_vp.getDrawMode() == RNA.DRAW_MODE_LINEAR);
+
+		_itemOptionBondsColored.setState(_vp.getUseBaseColorsForBPs());
+		_itemShowNCBP.setState(_vp.getShowNonCanonicalBP());
+		_itemShowOnlyPlanar.setState(!_vp.getShowNonPlanarBP());
+		_itemShowColorMap.setState(_vp.getColorMapVisible());
+		_itemFlatExteriorLoop.setState(_vp.getFlatExteriorLoop());
+		_itemFlatExteriorLoop.setEnabled(_vp.getDrawMode() == RNA.DRAW_MODE_RADIATE);
+	}
+
+	/**
+	 * Builds the popup menu
+	 */
+	public void buildPopupMenu() {
+		addTitle("File", true);
+		fileMenu();
+		exportMenu();
+		createMenuItem("Print...", "print", "control P", this);
+		addSeparator();
+
+		addTitle("Display", true);
+		viewMenu();
+		displayMenu();
+		//JSeparator sep = new JSeparator();
+		// TODO BH SwingJS - this should not be necessary
+		JSeparator sep = new JPopupMenu.Separator(); // BH SWingJS needs JPopupMenu.Separator
+		add(sep);
+		_disabled.add(sep);
+
+		addTitle("Edit", false);
+		editRNAMenu();
+		redrawMenu();
+		colorClassesMenu();
+		annotationMenu();
+		_disabled.add(_itemShowNCBP);
+		_disabled.add(_itemShowOnlyPlanar);
+		aboutMenu();
+	}
+
+	private void annotationMenu() {
+		JMenu submenuAnnotations = new JMenu("Annotations");
+		JMenu addAnnotations = new JMenu("New");
+		createMenuItem("Here", "annotationsaddPosition", "", addAnnotations);
+		createMenuItem("Base", "annotationsaddBase", "", addAnnotations);
+		createMenuItem("Loop", "annotationsaddLoop", "", addAnnotations);
+		createMenuItem("Helix", "annotationsaddHelix", "", addAnnotations);
+		//JSeparator sep = new JSeparator();
+		JSeparator sep = new JPopupMenu.Separator(); // BH SWingJS needs JPopupMenu.Separator
+
+		addAnnotations.add(sep);
+		createMenuItem("Region", "annotationsaddRegion", "", addAnnotations);
+		createMenuItem("Chem. prob.", "annotationsaddChemProb", "", addAnnotations);
+		submenuAnnotations.add(addAnnotations);
+		createMenuItem("Edit from list...", "annotationsedit", "", submenuAnnotations);
+		createMenuItem("Remove from list...", "annotationsremove", "", submenuAnnotations);
+		submenuAnnotations.addSeparator();
+		createMenuItem("Auto 5'/3'", "annotationsautoextremites", "control alt Q", submenuAnnotations);
+		createMenuItem("Auto helices", "annotationsautohelices", "control Q", submenuAnnotations);
+		createMenuItem("Auto interior loops", "annotationsautointerior", "alt shift Q", submenuAnnotations);
+		createMenuItem("Auto terminal loops", "annotationsautoterminal", "control shift Q", submenuAnnotations);
+		add(submenuAnnotations);
+	}
+
+	private void fileMenu() {
+		createMenuItem("New...", "userInput", "control N", this,true);
+		createMenuItem("Open...", "file", "control O", this,true);
+		createMenuItem("Save...", "saveas", "control S", this,true);
+		JMenu submenuSave = new JMenu("Save as");
+		createMenuItem("DBN (Vienna)", "dbn", "", submenuSave);
+		createMenuItem("BPSEQ", "bpseq", "", submenuSave);
+		createMenuItem("CT", "ct", "", submenuSave);
+		add(submenuSave);
+	}
+
+	private void exportMenu() {
+		// Export menu
+		JMenu submenuExport = new JMenu("Export");
+		createMenuItem("SVG", "svg", "", submenuExport);
+		createMenuItem("PGF/TIKZ", "tikz", "", submenuExport);
+		createMenuItem("XFIG", "xfig", "", submenuExport);
+		submenuExport.addSeparator();
+		createMenuItem("EPS", "eps", "", submenuExport);
+		submenuExport.addSeparator();
+		createMenuItem("PNG", "png", "", submenuExport);
+		createMenuItem("JPEG", "jpeg", "", submenuExport);
+		add(submenuExport);
+	}
+
+
+	private void displayMenu() {
+		
+		// SubMenu Base-pairs
+		JMenu subMenuBasePairs = new JMenu("Base Pairs");
+		createMenuItem("BP style...", "bpstyle", "control shift P", subMenuBasePairs);
+		configMenuItem(_itemShowNCBP, "shownc", "control W", subMenuBasePairs);
+		configMenuItem(_itemShowOnlyPlanar, "shownp", "control E", subMenuBasePairs);
+		// SubMenu Non standard Bases
+		JMenu subMenuNSBases = new JMenu("Non-standard bases");
+		configMenuItem(_itemOptionSpecialBaseColored, "specialbasecolored", "control J", subMenuNSBases);
+		createMenuItem("Color", "specialBasesColor", "control shift J", subMenuNSBases);
+		// SubMenu Gaps Bases
+		JMenu subMenuGapsBases = new JMenu("'Gaps' bases");
+		configMenuItem(_itemOptionGapsBaseColored, "dashbasecolored", "control D", subMenuGapsBases);		
+		_dashBasesColor = createMenuItem("Color", "dashBasesColor", "control shift D", subMenuGapsBases);
+		// Removable separator 
+		//JSeparator sep = new JSeparator();
+		JSeparator sep = new JPopupMenu.Separator(); // BH SWingJS needs JPopupMenu.Separator
+		_disabled.add(sep);
+		
+		// Style menu
+		JMenu submenuStyle = new JMenu("RNA style");
+		createMenuItem("Toggle draw bases", "gaspin", "alt G", submenuStyle,true);
+		submenuStyle.add(subMenuBasePairs);
+		submenuStyle.addSeparator();
+		submenuStyle.add(subMenuNSBases);
+		submenuStyle.add(subMenuGapsBases);
+		submenuStyle.add(sep);
+		createMenuItem("Backbone color", "backbone", "control K", submenuStyle,true);
+		configMenuItem(_itemDrawBackbone, "showbackbone", "alt B", submenuStyle);
+		
+		// Submenu Title
+		JMenu submenuTitle = new JMenu("Title");		
+		createMenuItem("Set Title", "setTitle", "control T", submenuTitle, true);
+		createMenuItem("Font", "titleDisplay", "control shift T", submenuTitle, true);
+		createMenuItem("Color", "titleColor", "control alt T", submenuTitle, true);
+		_disabled.add(submenuTitle);
+
+		// Color map menu
+		JMenu submenuColorMap = new JMenu("Color map");
+		configMenuItem(_itemShowColorMap, "toggleshowcolormap", "control shift L", submenuColorMap, false);
+		createMenuItem("Caption", "colormapcaption", "control shift C", submenuColorMap,true);
+		createMenuItem("Style...", "colormapstyle", "control L", submenuColorMap,false);
+		submenuColorMap.addSeparator();
+		createMenuItem("Edit values...", "colormapvalues", "shift L", submenuColorMap,true);
+		createMenuItem("Load values...", "colormaploadvalues", "control shift K", submenuColorMap,true);
+		_disabled.add(submenuColorMap);
+		
+		// Menu Misc
+		JMenu submenuMisc = new JMenu("Misc");
+		createMenuItem("Num. period.", "numPeriod", "control M", submenuMisc);
+		createMenuItem("Background color", "background", "control G", submenuMisc);
+		submenuMisc.add(submenuTitle);
+		
+		// Main menu
+		add(submenuStyle);		
+		add(submenuColorMap);
+		add(submenuMisc);
+
+	}
+	
+	private void editRNAMenu()
+	{
+		createMenuItem("Bases...","editallbases","",this,true);
+		createMenuItem("BasePairs...","editallbps","",this,true);
+	}
+
+	private void redrawMenu() {
+		JMenu submenuRedraw = new JMenu("Redraw");
+		_disabled.add(submenuRedraw);
+
+		JMenu submenuAlgorithms = new JMenu("Algorithm");
+		_disabled.add(submenuAlgorithms);
+
+		createMenuItem("Linear","line","control 1",submenuAlgorithms,true);
+		createMenuItem("Circular","circular","control 2",submenuAlgorithms,true);
+		createMenuItem("Radiate","radiate","control 3",submenuAlgorithms,true);
+		createMenuItem("NAView","naview","control 4",submenuAlgorithms,true);
+		//createMenuItem("VARNAView","varnaview","control 5",submenuAlgorithms,true);
+		//createMenuItem("MOTIFView","motifview","control 6",submenuAlgorithms,true);
+		submenuRedraw.add(submenuAlgorithms);
+		
+		// Sets the height increment in LINEAR_MODE type of drawing
+		_bpHeightIncrement = createMenuItem("BP height increment","bpheightincrement","control H",submenuRedraw);
+		configMenuItem(_itemFlatExteriorLoop, "flat", "control F", submenuRedraw, true);
+
+		// Item pour le r�glage de l'espace entre chaques bases
+		createMenuItem("Space between bases","spaceBetweenBases","control shift S",submenuRedraw,true);		
+		createMenuItem("Reset","reset","control shift R",submenuRedraw,true);		
+
+		add(submenuRedraw);
+	}
+
+	@SuppressWarnings("unused")
+	private void warningMenu() {
+		// Menu showWarning
+		configMenuItem(_itemShowWarnings, "showwarnings", "", this, true);
+	}
+
+	private void viewMenu() {
+		// View menu
+		JMenu submenuView = new JMenu("View");
+
+		// Zoom submenu
+		JMenu zoomDisplay = new JMenu("Zoom");
+		createMenuItem("25%","zoom25","",zoomDisplay);
+		createMenuItem("50%","zoom50","",zoomDisplay);
+		createMenuItem("100%","zoom100","",zoomDisplay);
+		createMenuItem("150%","zoom150","",zoomDisplay);
+		createMenuItem("200%","zoom200","",zoomDisplay);
+		createMenuItem("Custom","zoom","control Z",zoomDisplay);
+		submenuView.add(zoomDisplay);		
+		_rotation = createMenuItem("Rotation...","rotation","control R",submenuView);
+		createMenuItem("Rescale...","rescale","",submenuView);
+		submenuView.addSeparator();		
+		createMenuItem("Border size","borderSize","control B",submenuView);
+		
+		add(submenuView);
+
+	}
+
+	JMenu _subMenuBases;
+
+	private Component _selectionMenuIndex = null;
+
+	public void addSelectionMenu(JMenuItem s) {
+		_selectionMenuIndex = s;
+		_disabled.add(s);
+		insert(s, getComponentCount() - 2);
+	}
+
+	public void removeSelectionMenu() {
+		if (_selectionMenuIndex != null) {
+			this.remove(_selectionMenuIndex);
+			_selectionMenuIndex = null;
+		}
+	}
+
+	private void colorClassesMenu() {
+		// Menu Bases
+		_subMenuBases = new JMenu("Colors");
+		_disabled.add(_subMenuBases);
+		createMenuItem("By Base","eachKind","control U",_subMenuBases,true);
+		createMenuItem("By BP","eachCouple","shift U",_subMenuBases,true);
+		createMenuItem("By Position","eachBase","alt U",_subMenuBases,true);
+		add(_subMenuBases);
+	}
+
+	/**
+	 * add default color options to a menu
+	 */
+	public void addColorOptions(JMenu submenu) {
+		createMenuItem("Fill Color",submenu.getActionCommand() + ",InnerColor","",submenu,true);
+		createMenuItem("Stroke Color",submenu.getActionCommand() + ",OutlineColor","",submenu,true);
+		createMenuItem("Label Color",submenu.getActionCommand() + ",NameColor","",submenu,true);		
+		submenu.addSeparator();
+		createMenuItem("BP Color",submenu.getActionCommand() + ",BPColor","",submenu,true);		
+		createMenuItem("BP Thickness",submenu.getActionCommand() + ",BPThickness","",submenu,true);		
+		submenu.addSeparator();
+		createMenuItem("Number Color",submenu.getActionCommand() + ",NumberColor","",submenu,true);		
+	}
+
+	private void aboutMenu() {
+		addSeparator();
+		createMenuItem("About VARNA", "about", "control A", this);
+	}
+
+	public void addAnnotationMenu(JMenu menu) {
+		addAnnotationMenu(menu, false);
+	}	
+	
+	public void addAnnotationMenu(JMenu menu, boolean existingAnnot) {
+		String title = "Annotation";
+		if (existingAnnot)
+		{
+			String debut = "";
+			String texte = _vp.get_selectedAnnotation().getTexte();
+			if (texte.length() < 5)
+				debut = texte;
+			else
+				debut = texte.substring(0, 5) + "...";
+			title = "Annotation: " + debut;			
+		}
+		JMenu menuAnnotation = new JMenu(title);
+		if (!existingAnnot)
+			createMenuItem("Add",menu.getActionCommand() + "annotationadd","",menuAnnotation,true);		
+		createMenuItem("Edit",menu.getActionCommand() + "annotationedit","",menuAnnotation,true);		
+		createMenuItem("Remove",menu.getActionCommand() + "annotationremove","",menuAnnotation,true);		
+		menu.add(menuAnnotation);
+	}	
+	
+	
+	public static long getSerialVersionUID() {
+		return serialVersionUID;
+	}
+
+	public VARNAPanel get_vp() {
+		return _vp;
+	}
+
+	public ControleurMenu get_controleurMenu() {
+		return _controlerMenu;
+	}
+
+	public JCheckBoxMenuItem get_itemOptionSpecialBaseColored() {
+		return _itemOptionSpecialBaseColored;
+	}
+
+	public JCheckBoxMenuItem get_itemShowWarnings() {
+		return _itemShowWarnings;
+	}
+
+	public JCheckBoxMenuItem get_itemOptionDashBaseColored() {
+		return _itemOptionGapsBaseColored;
+	}
+
+	public void set_controleurMenu(ControleurMenu menu) {
+		_controlerMenu = menu;
+	}
+
+	public void set_itemOptionSpecialBaseColored(
+			JCheckBoxMenuItem optionSpecialBaseColored) {
+		_itemOptionSpecialBaseColored = optionSpecialBaseColored;
+	}
+
+	public void set_itemShowWarnings(JCheckBoxMenuItem showWarnings) {
+		_itemShowWarnings = showWarnings;
+	}
+
+	public void set_itemOptionDashBaseColored(
+			JCheckBoxMenuItem optionDashBaseColored) {
+		_itemOptionGapsBaseColored = optionDashBaseColored;
+	}
+
+	public JMenuItem get_rotation() {
+		return _rotation;
+	}
+
+	public void set_rotation(JMenuItem _rotation) {
+		this._rotation = _rotation;
+	}
+
+	public JCheckBoxMenuItem get_itemOptionBondsColored() {
+		return _itemOptionBondsColored;
+	}
+
+	public void set_itemOptionBondsColored(JCheckBoxMenuItem optionBondsColored) {
+		_itemOptionBondsColored = optionBondsColored;
+	}
+
+
+	public void show(Component invoker,int x,int y) {
+		 _spawnOrigin = new Point(x,y);
+		 super.show(invoker,x,y); 
+	 }
+	
+	public Point getSpawnPoint()
+	{
+		return _spawnOrigin ;
+	}
+
+}
\ No newline at end of file