+++ /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