Merged in cdk-1.4.x with the 1.4.3 changes

cdk · Sep 18, 2011 · 191ea5d · 191ea5d
2 parents a1894f2 + f5f9d23
commit 191ea5d
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Showing 7 changed files with 196 additions and 1 deletion.
diff --git a/src/main/org/openscience/cdk/ReactionScheme.java b/src/main/org/openscience/cdk/ReactionScheme.java
@@ -25,7 +25,10 @@
 package org.openscience.cdk;
 
 import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.Iterator;
 import java.util.List;
+import java.util.Map;
 
 import org.openscience.cdk.annotations.TestMethod;
 import org.openscience.cdk.interfaces.IReaction;
@@ -125,6 +128,18 @@ public Object clone() throws CloneNotSupportedException {
 		for (IReaction reaction : reactions()) {
 			clone.addReaction((IReaction)reaction.clone());
 		}
+        // clone the properties
+        if (getProperties() != null) {
+            Map<Object, Object> properties = getProperties();
+            Map<Object, Object> clonedHashtable = new HashMap<Object, Object>();
+            Iterator<Object> keys = properties.keySet().iterator();
+            while (keys.hasNext()) {
+                Object key = keys.next();
+                Object value = properties.get(key);
+                clonedHashtable.put(key, value);
+            }
+            clone.setProperties(clonedHashtable);
+        }
 
 		return clone;
 	}

diff --git a/src/main/org/openscience/cdk/renderer/elements/ArrowElement.java b/src/main/org/openscience/cdk/renderer/elements/ArrowElement.java
@@ -0,0 +1,66 @@
+/* Copyright (C) 2009  Stefan Kuhn <shk3@users.sf.net>
+ *               2011  Egon Willighagen <egonw@users.sf.net>
+ *  
+ * Contact: cdk-devel@list.sourceforge.net
+ * 
+ *  This program is free software; you can redistribute it and/or
+ *  modify it under the terms of the GNU Lesser General Public License
+ *  as published by the Free Software Foundation; either version 2.1
+ *  of the License, or (at your option) any later version.
+ *
+ *  This program 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 Lesser General Public License for more details.
+ *
+ *  You should have received a copy of the GNU Lesser General Public License
+ *  along with this program; if not, write to the Free Software
+ *  Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA.
+ */
+package org.openscience.cdk.renderer.elements;
+
+import java.awt.Color;
+
+/**
+ * {@link IRenderingElement} for linear arrows. 
+ *
+ * @cdk.module renderbasic
+ */
+public class ArrowElement implements IRenderingElement {
+
+    public final double startX;
+    public final double startY;
+    public final double endX;
+    public final double endY;
+    public final double width;
+    public final Color color;
+    public final boolean direction;
+
+    /**
+     * Constructor for an arrow element, based on starting point, end point, width,
+     * direction, and color.
+     *
+     * @param startX    X coordinate of the point where the arrow starts.
+     * @param startY    Y coodrinate of the point where the arrow starts.
+     * @param endX      X coordinate of the point where the arrow ends.
+     * @param endY      Y coordinate of the point where the arrow ends.
+     * @param width     width of the arrow line.
+     * @param direction true is the arrow points from start to end, false if from end to start
+     * @param color     {@link Color} of the arrow
+     */
+    public ArrowElement(double startX, double startY, double endX, double endY,
+            double width, boolean direction, Color color) {
+        this.endX = startX;
+        this.endY = startY;
+        this.startX = endX;
+        this.startY = endY;
+        this.width = width;
+        this.color = color;
+        this.direction = direction;
+    }
+
+    /** {@inheritDoc} */
+    public void accept(IRenderingVisitor v) {
+        v.visit(this);
+    }
+}
diff --git a/src/main/org/openscience/cdk/renderer/generators/BasicSceneGenerator.java b/src/main/org/openscience/cdk/renderer/generators/BasicSceneGenerator.java
@@ -42,6 +42,22 @@
 @TestClass("org.openscience.cdk.renderer.generators.BasicSceneGeneratorTest")
 public class BasicSceneGenerator implements IGenerator<IAtomContainer> {
 
+	/**
+	 * The width of the head of arrows.
+	 *
+	 * @author egonw
+	 */
+    public static class ArrowHeadWidth extends
+    AbstractGeneratorParameter<Double> {
+    	/** Returns the default arrow head width.
+    	 * @return 10.0 */
+    	public Double getDefault() {
+    		return 10.0;
+    	}
+    }
+    private IGeneratorParameter<Double> arrowHeadWidth =
+    	new ArrowHeadWidth();
+
 	/**
 	 * Determines if tooltips are to be shown.
 	 */
@@ -216,7 +232,8 @@ public List<IGeneratorParameter<?>> getParameters() {
                         scale,
                         fitToScreen,
                         showMoleculeTitle,
-                        showTooltip
+                        showTooltip,
+                        arrowHeadWidth
                 }
         );
     }

diff --git a/src/main/org/openscience/cdk/renderer/visitor/AWTDrawVisitor.java b/src/main/org/openscience/cdk/renderer/visitor/AWTDrawVisitor.java
@@ -39,6 +39,7 @@
 import org.openscience.cdk.annotations.TestClass;
 import org.openscience.cdk.annotations.TestMethod;
 import org.openscience.cdk.renderer.RendererModel;
+import org.openscience.cdk.renderer.elements.ArrowElement;
 import org.openscience.cdk.renderer.elements.AtomSymbolElement;
 import org.openscience.cdk.renderer.elements.ElementGroup;
 import org.openscience.cdk.renderer.elements.GeneralPath;
@@ -55,6 +56,7 @@
 import org.openscience.cdk.renderer.font.IFontManager;
 import org.openscience.cdk.renderer.generators.BasicBondGenerator.WedgeWidth;
 import org.openscience.cdk.renderer.generators.BasicSceneGenerator;
+import org.openscience.cdk.renderer.generators.BasicSceneGenerator.ArrowHeadWidth;
 import org.openscience.cdk.renderer.generators.BasicSceneGenerator.Scale;
 import org.openscience.cdk.renderer.generators.BasicSceneGenerator.UseAntiAliasing;
 
@@ -375,6 +377,41 @@ public int currentSegment( float[] coords ) {
         };
     }
 
+    private void visit(ArrowElement line) {
+    	double scale = rendererModel.getParameter(
+    			Scale.class).getValue();
+    	Stroke savedStroke = graphics.getStroke();
+
+    	int w = (int) (line.width * scale);
+    	if (strokeMap.containsKey(w)) {
+    		graphics.setStroke(strokeMap.get(w));
+    	} else {
+    		BasicStroke stroke = new BasicStroke(w);
+    		graphics.setStroke(stroke);
+    		strokeMap.put(w, stroke);
+    	}
+
+    	graphics.setColor(line.color);
+    	int[] a = this.transformPoint(line.startX, line.startY);
+    	int[] b = this.transformPoint(line.endX, line.endY);
+    	graphics.drawLine(a[0], a[1], b[0], b[1]);
+    	double aW = rendererModel.getParameter(
+    			ArrowHeadWidth.class
+    	).getValue() / scale;
+    	if(line.direction){
+    		int[] c = this.transformPoint(line.startX-aW, line.startY-aW);
+    		int[] d = this.transformPoint(line.startX-aW, line.startY+aW);
+    		graphics.drawLine(a[0], a[1], c[0], c[1]);
+    		graphics.drawLine(a[0], a[1], d[0], d[1]);
+    	}else{
+    		int[] c = this.transformPoint(line.endX+aW, line.endY-aW);
+    		int[] d = this.transformPoint(line.endX+aW, line.endY+aW);
+    		graphics.drawLine(b[0], b[1], c[0], c[1]);
+    		graphics.drawLine(b[0], b[1], d[0], d[1]);
+    	}        
+    	graphics.setStroke(savedStroke);
+    }
+
     private void visit(TextGroupElement textGroup) {
         this.graphics.setFont(this.fontManager.getFont());
         Point point = 
@@ -476,6 +513,8 @@ else if (element instanceof PathElement)
             visit((PathElement) element);
         else if (element instanceof GeneralPath)
             visit((GeneralPath)element);
+        else if (element instanceof ArrowElement)
+            visit((ArrowElement) element);
         else
             System.err.println("Visitor method for "
                     + element.getClass().getName() + " is not implemented");

diff --git a/src/main/org/openscience/cdk/silent/ReactionScheme.java b/src/main/org/openscience/cdk/silent/ReactionScheme.java
@@ -19,7 +19,10 @@
 package org.openscience.cdk.silent;
 
 import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.Iterator;
 import java.util.List;
+import java.util.Map;
 
 import org.openscience.cdk.annotations.TestMethod;
 import org.openscience.cdk.interfaces.IReaction;
@@ -119,6 +122,18 @@ public Object clone() throws CloneNotSupportedException {
 		for (IReaction reaction : reactions()) {
 			clone.addReaction((IReaction)reaction.clone());
 		}
+        // clone the properties
+        if (getProperties() != null) {
+            Map<Object, Object> properties = getProperties();
+            Map<Object, Object> clonedHashtable = new HashMap<Object, Object>();
+            Iterator<Object> keys = properties.keySet().iterator();
+            while (keys.hasNext()) {
+                Object key = keys.next();
+                Object value = properties.get(key);
+                clonedHashtable.put(key, value);
+            }
+            clone.setProperties(clonedHashtable);
+        }
 
 		return clone;
 	}

diff --git a/src/test/org/openscience/cdk/modulesuites/MrenderbasicTests.java b/src/test/org/openscience/cdk/modulesuites/MrenderbasicTests.java
@@ -23,6 +23,7 @@
 import org.junit.runners.Suite.SuiteClasses;
 import org.openscience.cdk.coverage.RenderbasicCoverageTest;
 import org.openscience.cdk.renderer.AtomContainerRendererTest;
+import org.openscience.cdk.renderer.elements.ArrowElementTest;
 import org.openscience.cdk.renderer.elements.AtomSymbolElementTest;
 import org.openscience.cdk.renderer.elements.GeneralPathTest;
 import org.openscience.cdk.renderer.elements.LineElementTest;
@@ -62,6 +63,7 @@
 	RingElementTest.class,
 	AtomSymbolElementTest.class,
 	RectangleElementTest.class,
+	ArrowElementTest.class,
 	GeneralPathTest.class,
 	AWTFontManagerTest.class,
 	LineToTest.class,

diff --git a/src/test/org/openscience/cdk/renderer/elements/ArrowElementTest.java b/src/test/org/openscience/cdk/renderer/elements/ArrowElementTest.java
@@ -0,0 +1,41 @@
+/* Copyright (C) 2011  Egon Willighagen <egonw@users.sf.net>
+ * 
+ * Contact: cdk-devel@lists.sourceforge.net
+ * 
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2.1 of the License, or (at your option)
+ * any later version. All we ask is that proper credit is given for our work,
+ * which includes - but is not limited to - adding the above copyright notice to
+ * the beginning of your source code files, and to any copyright notice that you
+ * may distribute with programs based on this work.
+ * 
+ * This program 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 Lesser General Public License for more
+ * details.
+ * 
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this program; if not, write to the Free Software Foundation, Inc.,
+ * 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA.
+ */
+package org.openscience.cdk.renderer.elements;
+
+import java.awt.Color;
+
+import org.junit.BeforeClass;
+
+/**
+ * @cdk.module test-renderbasic
+ */
+public class ArrowElementTest extends AbstractElementTest {
+
+    @BeforeClass
+    public static void setup() {
+        IRenderingElement element = new ArrowElement(
+            0, 0, 1, 1, 1.0, true, Color.orange
+        );
+        setRenderingElement(element);
+    }
+
+}