Alt input mode (ring sprout, bond sprout, kekule/tautomer shifting)

.gitignore

@@ -4,8 +4,9 @@ dist/
 *~
 lib-licenses.txt
 MANIFEST.MF
-.gitignore
 .classpath
 .project
 build.xml
+**/*.class
+**/target/
 maven/jchempaint-nodeps/target/

.vscode/settings.json

@@ -0,0 +1,3 @@
+{
+    "java.configuration.updateBuildConfiguration": "interactive"
+}

app-osx/src/main/resources/org/openscience/jchempaint/resources/JCPShort_Cuts.properties

@@ -34,11 +34,13 @@ new=meta N
 open=meta O
 saveAs=meta shift S
 export=meta E
-zoomin=typed +
-zoomout=typed -
+zoomin=meta EQUALS
+zoomout=meta MINUS
+plus=EQUALS
+minus=MINUS
 renderOptions=alt E
 print=meta P
-close=alt C
+close=alt W
 cut=meta X
 copy=meta C
 eraser=pressed DELETE

core/pom.xml

@@ -48,10 +48,6 @@
             <version>1.2</version>
         </dependency>
 
-        <dependency>
-            <groupId>org.openscience.cdk</groupId>
-            <artifactId>cdk-annotation</artifactId>
-        </dependency>
         <dependency>
             <groupId>org.openscience.cdk</groupId>
             <artifactId>cdk-atomtype</artifactId>
@@ -172,6 +168,11 @@
                         <artifactId>gettext-commons</artifactId>
                         <version>0.9.8</version>
                     </dependency>
+                    <dependency>
+                        <groupId>com.google.guava</groupId>
+                        <artifactId>guava</artifactId>
+                        <version>30.0-jre</version> 
+                    </dependency>
                 </dependencies>
             </plugin>
         </plugins>

core/src/main/java/org/openscience/jchempaint/AbstractJChemPaintPanel.java

@@ -99,8 +99,6 @@ public abstract class AbstractJChemPaintPanel extends JPanel{
     private JComponent lastActionButton;
     protected JMenuItem undoMenu;
     protected JMenuItem redoMenu;
-    protected JMenu atomMenu;
-    protected JMenu bondMenu;
     protected JMenu rgroupMenu;
     protected boolean debug=false;
     protected boolean modified = false;

core/src/main/java/org/openscience/jchempaint/AtomBondSet.java

@@ -0,0 +1,84 @@
+package org.openscience.jchempaint;
+
+import org.openscience.cdk.AtomRef;
+import org.openscience.cdk.BondRef;
+import org.openscience.cdk.interfaces.IAtom;
+import org.openscience.cdk.interfaces.IAtomContainer;
+import org.openscience.cdk.interfaces.IBond;
+
+import java.util.ArrayList;
+import java.util.List;
+
+/**
+ * CDK 2.10 onwards enforces an invariant on AtomContainer's that a bond
+ * can not be stored unless it's atoms are also stored (a dangling bond).
+ * You must also add atoms before bonds in AtomContainer now.
+ * <br/>
+ * This class allows arbitrary sets of atoms and bonds to be stored without
+ * the no dangling bonds constraint. This is required because sometimes we merge
+ * /delete/update bonds.
+ */
+public class AtomBondSet {
+
+    private final List<IAtom> atoms = new ArrayList<>();
+    private final List<IBond> bonds = new ArrayList<>();
+
+    public AtomBondSet() {
+    }
+
+    public AtomBondSet(IAtomContainer mol) {
+        for (IAtom atom : mol.atoms())
+            atoms.add(AtomRef.deref(atom));
+        for (IBond bond : mol.bonds())
+            bonds.add(BondRef.deref(bond));
+    }
+
+    public Iterable<IAtom> atoms() {
+        return atoms;
+    }
+
+    public Iterable<IBond> bonds() {
+        return bonds;
+    }
+
+    public int getAtomCount() {
+        return atoms.size();
+    }
+
+    public int getBondCount() {
+        return bonds.size();
+    }
+
+    public void add(IAtom atom) {
+        atoms.add(atom);
+    }
+
+    public void add(IBond bond) {
+        bonds.add(bond);
+    }
+
+    public void remove(IBond bond) {
+        bonds.remove(bond);
+    }
+
+    public void remove(IAtom atom) {
+        atoms.remove(atom);
+    }
+
+    public boolean contains(IAtom atom) {
+        return atoms.contains(atom);
+    }
+
+    public boolean contains(IBond bond) {
+        return bonds.contains(bond);
+    }
+
+    public boolean isEmpty() {
+        return atoms.isEmpty() && bonds.isEmpty();
+    }
+
+    public IAtom getSingleAtom() {
+        if (atoms.size() != 1) throw new IllegalArgumentException();
+        return atoms.get(0);
+    }
+}

core/src/main/java/org/openscience/jchempaint/InsertTextPanel.java

@@ -81,8 +81,7 @@ public InsertTextPanel(AbstractJChemPaintPanel jChemPaintPanel, JFrame closeafte
         textCombo = new JComboBox<String>(oldText.toArray(new String[]{}));
         textCombo.setEditable(true);
         textCombo.setToolTipText(GT.get("Enter a CAS, SMILES or InChI string"));
-
-        textCombo.addActionListener(this);
+        // textCombo.addActionListener(this); // this can cause double inserts
         editor = (JTextComponent) textCombo.getEditor().getEditorComponent();
 
         button.addActionListener(this);
@@ -116,7 +115,7 @@ public void actionPerformed(ActionEvent actionEvent) {
             if (molecule == null)
                 return;
             try {
-                JChemPaint.generateModel(jChemPaintPanel, molecule, true, false);
+                JChemPaint.generateModel(jChemPaintPanel, molecule, true, true);
             } catch (CDKException e) {
                 e.printStackTrace();
                 return;

core/src/main/java/org/openscience/jchempaint/JCPPropertyHandler.java

@@ -286,11 +286,11 @@ public ResourceBundle getResources()
 
 
 	/**
-	 *  Returns an URL build from the path of this object and another part that is
-	 *  searched in the properties file. Used to find the images for the buttons.
+	 * Returns an URL build from the path of this object and another part that is
+	 * searched in the properties file. Used to find the images for the buttons.
 	 *
-	 *@param  key  String The String that says which image is searched
-	 *@return      URL The URL where the image is located
+	 * @param  key  String The String that says which image is searched
+	 * @return      URL The URL where the image is located
 	 */
 	public URL getResource(String key)
 	{
@@ -307,13 +307,29 @@ public URL getResource(String key)
 		return null;
 	}
 
+	/**
+	 * Returns the resource URL from the properties file that follows the given
+	 * String, if the resource is not found, no log message is emitted.
+	 *
+	 * @param  key  String The String to be looked after
+	 * @return      URL The URL where the image is located
+	 */
+	public URL getOptionalResource(String key)
+	{
+		try {
+			return getClass().getResource(getResources().getString(key));
+		} catch (MissingResourceException ignore) {
+			return null;
+		}
+	}
+
 
 	/**
-	 *  Returns the ResourceString from the properties file that follows the given
-	 *  String.
+	 * Returns the ResourceString from the properties file that follows the given
+	 * String.
 	 *
-	 *@param  key  String The String to be looked after
-	 *@return      String The String that follows the key in the properties file
+	 * @param  key  String The String to be looked after
+	 * @return      String The String that follows the key in the properties file
 	 */
 	public String getResourceString(String key)
 	{

core/src/main/java/org/openscience/jchempaint/JCPToolBar.java

@@ -64,6 +64,7 @@ public class JCPToolBar
     private static ILoggingTool logger =
         LoggingToolFactory.createLoggingTool(JCPToolBar.class);
     public static Color BUTTON_INACTIVE_COLOR=Color.WHITE;//new Color(230,230,230);
+    public static Color BUTON_ACTIVE_COLOR=new Color(98, 182, 207, 111);
     /**
      *  Gets the toolbar attribute of the MainContainerPanel object
      *
@@ -173,7 +174,7 @@ public float getAlignmentY()
             logger.warn("Could not find Tooltip resource for: ", key);
             logger.debug(e);
         }
-        URL disabledurl = jcpph.getResource(key + JCPAction.disabled_imageSuffix);
+        URL disabledurl = jcpph.getOptionalResource(key + JCPAction.disabled_imageSuffix);
         logger.debug("Trying to find resource: ", url);
         if (disabledurl != null){
             ImageIcon disabledimage = new ImageIcon(disabledurl);
@@ -247,13 +248,15 @@ public static Component createToolbar(int orientation, String kind, AbstractJChe
                     if (toolKeys[i].equals("bondTool")) {
                         //button.setBackground(Color.GRAY);
                         button.setBackground(new Color(238, 238, 238));
+                        button.setOpaque(true);
                         chemPaintPanel.setLastActionButton(button);
                         AddBondDragModule activeModule = new AddBondDragModule(chemPaintPanel.get2DHub(), IBond.Stereo.NONE, true);
                         activeModule.setID(toolKeys[i]);
                         chemPaintPanel.get2DHub().setActiveDrawModule(activeModule);
                     } else if (toolKeys[i].equals("C")) {
                         button.setBackground(Color.GRAY);
                         chemPaintPanel.setLastSecondaryButton(button);
+                        button.setOpaque(true);
                     } else {
                         button.setBackground(BUTTON_INACTIVE_COLOR);
                     }

core/src/main/java/org/openscience/jchempaint/JChemPaintMenuHelper.java

@@ -21,6 +21,7 @@
 import javax.swing.event.MenuListener;
 
 import org.openscience.cdk.config.XMLIsotopeFactory;
+import org.openscience.cdk.interfaces.IAtom;
 import org.openscience.cdk.interfaces.IIsotope;
 import org.openscience.cdk.tools.ILoggingTool;
 import org.openscience.cdk.tools.LoggingToolFactory;
@@ -132,14 +133,6 @@ else if (itemKeys[i].startsWith("@")) {
 	            }
         	}
         }
-        if(key.equals("atomMenu")){
-            jcpPanel.atomMenu=(JMenu)menu;
-            jcpPanel.enOrDisableMenus((JMenu)menu, false);
-        }
-        if(key.equals("bondMenu")){
-            jcpPanel.bondMenu=(JMenu)menu;
-            jcpPanel.enOrDisableMenus((JMenu)menu, false);
-        }
 
         if(key.equals("isotopeChange")){
             ((JMenu)menu).addMenuListener(new MenuListener(){
@@ -155,11 +148,11 @@ public void menuSelected(MenuEvent arg0) {
                     //is empty, various commands return null
                     if((SwingPopupModule.lastAtomPopupedFor!=null && SwingPopupModule.lastAtomPopupedFor.getSymbol()!=null)
                             || (jcpPanel.getRenderPanel().getRenderer().getRenderer2DModel().getSelection()!=null && 
-                                    jcpPanel.getRenderPanel().getRenderer().getRenderer2DModel().getSelection().getConnectedAtomContainer()!=null &&
-                                    jcpPanel.getRenderPanel().getRenderer().getRenderer2DModel().getSelection().getConnectedAtomContainer().getAtomCount()>0)){
+                                    !jcpPanel.getRenderPanel().getRenderer().getRenderer2DModel().getSelection().elements(IAtom.class).isEmpty())){
                         try {
                             String symbol;
-                            if(jcpPanel.getRenderPanel().getRenderer().getRenderer2DModel().getSelection().getConnectedAtomContainer()!=null && jcpPanel.getRenderPanel().getRenderer().getRenderer2DModel().getSelection().getConnectedAtomContainer().getAtomCount()>0)
+                            if(jcpPanel.getRenderPanel().getRenderer().getRenderer2DModel().getSelection().getConnectedAtomContainer()!=null &&
+                               !jcpPanel.getRenderPanel().getRenderer().getRenderer2DModel().getSelection().elements(IAtom.class).isEmpty())
                                 symbol = jcpPanel.getRenderPanel().getRenderer().getRenderer2DModel().getSelection().getConnectedAtomContainer().getAtom(0).getSymbol();
                             else
                                 symbol = SwingPopupModule.lastAtomPopupedFor.getSymbol();
@@ -259,14 +252,14 @@ protected JMenuItem createMenuItem(AbstractJChemPaintPanel jcpPanel, String cmd,
             mi = new JMenuItem(translation);
         }
         JCPPropertyHandler jcpph = JCPPropertyHandler.getInstance(true);
-        URL url = jcpph.getResource(cmd + JCPAction.imageSuffix);
+        URL url = jcpph.getOptionalResource(cmd + JCPAction.imageSuffix);
         if (url != null)
         {
             ImageIcon image = new ImageIcon(url);
             Image img = image.getImage();
             Image newimg = img.getScaledInstance(16, 16, java.awt.Image.SCALE_SMOOTH);
             mi.setIcon(new ImageIcon(newimg));
-            URL disabledurl = jcpph.getResource(cmd + JCPAction.disabled_imageSuffix);
+            URL disabledurl = jcpph.getOptionalResource(cmd + JCPAction.disabled_imageSuffix);
             if (disabledurl != null){
                 ImageIcon disabledimage = new ImageIcon(disabledurl);
                 if (image != null){
@@ -317,7 +310,7 @@ protected JMenuItem createMenuItem(AbstractJChemPaintPanel jcpPanel, String cmd,
      *  for zooming is problematic.<br>
      *  More here: http://bugs.sun.com/bugdatabase/view_bug.do?bug_id=4262044
      *
-     * @param  cmd  String The Strin to identify the MenuItem.
+     * @param  cmd  String The String to identify the MenuItem.
      * @param  mi   the regarding MenuItem.
      * @param  jcp  The JChemPaintPanel this menu is used for.
      */