--- /dev/null
+/*
+ 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
git://source.jalview.org / jalview.git / blobdiff