Merged in the cdk-1.4.x branch

cdk · Dec 10, 2011 · 46f2ad0 · 46f2ad0
2 parents d8d6eee + 1142dc6
commit 46f2ad0
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Showing 10 changed files with 292 additions and 30 deletions.
diff --git a/AUTHORS b/AUTHORS
@@ -33,6 +33,7 @@ Jonty Lawson
 Daniel Leidert
 Edgar Luttmann
 Todd Martin
+John May
 Nathanaël Mazuir
 Stephan Michels
 Scooter Morris

diff --git a/src/main/org/openscience/cdk/controller/IMouseEventRelay.java b/src/main/org/openscience/cdk/controller/IMouseEventRelay.java
@@ -1,6 +1,5 @@
-/* $Revision$ $Author$ $Date$
- * 
- * Copyright (C) 2007  Niels Out <nielsout@users.sf.net>
+/* Copyright (C) 2007  Niels Out <nielsout@users.sf.net>
+ *               2011  Egon Willighagen <egonw@users.sf.net>
  * 
  * Contact: cdk-devel@lists.sourceforge.net or nout@science.uva.nl
  * 
@@ -25,54 +24,99 @@
 package org.openscience.cdk.controller;
 
 /**
+ * Widget toolkit-independent interface to relay for mouse events.
  * 
  * @cdk.module control
  */
 public interface IMouseEventRelay {
+
 	/**
+	 * Event to signal that the left mouse button has been released.
 	 * 
-	 * @param screenCoordX
-	 * @param screenCoordY
+	 * @param screenCoordX the x part of the screen coordinate where the event happened.
+	 * @param screenCoordY the y part of the screen coordinate where the event happened.
 	 */
 	public abstract void mouseClickedUp(int screenCoordX, int screenCoordY);
+
 	/**
+     * Event to signal that the left mouse button has been pushed but not released yet.
 	 * 
-	 * @param screenCoordX
-	 * @param screenCoordY
+     * @param screenCoordX the x part of the screen coordinate where the event happened.
+     * @param screenCoordY the y part of the screen coordinate where the event happened.
 	 */
 	public abstract void mouseClickedDown(int screenCoordX, int screenCoordY);
+
+    /**
+     * Event to signal that the right mouse button has been pushed but not released yet.
+     * 
+     * @param screenCoordX the x part of the screen coordinate where the event happened.
+     * @param screenCoordY the y part of the screen coordinate where the event happened.
+     */
+	public abstract void mouseClickedDownRight(int x, int y);
+
+	/**
+     * Event to signal that the right mouse button has been released.
+     * 
+     * @param screenCoordX the x part of the screen coordinate where the event happened.
+     * @param screenCoordY the y part of the screen coordinate where the event happened.
+     */
+	public abstract void mouseClickedUpRight(int x, int y);
+
 	/**
+     * Event to signal that a mouse button has been double clicked.
 	 * 
-	 * @param screenCoordX
-	 * @param screenCoordY
+     * @param screenCoordX the x part of the screen coordinate where the event happened.
+     * @param screenCoordY the y part of the screen coordinate where the event happened.
 	 */
 	public abstract void mouseClickedDouble(int screenCoordX, int screenCoordY);
+
 	/**
+     * Event to signal that a mouse has been moved to the new coordinates.
 	 * 
-	 * @param screenCoordX
-	 * @param screenCoordY
+     * @param screenCoordX the x part of the latest screen coordinate.
+     * @param screenCoordY the y part of the latest screen coordinate.
 	 */
 	public abstract void mouseMove(int screenCoordX, int screenCoordY);
+
 	/**
 	 * 
-	 * @param screenCoordX
-	 * @param screenCoordY
+     * @param screenCoordX
+     * @param screenCoordY
 	 */
 	public abstract void mouseEnter(int screenCoordX, int screenCoordY);
+
 	/**
 	 * 
-	 * @param screenCoordX
-	 * @param screenCoordY
+     * @param screenCoordX
+     * @param screenCoordY
 	 */
 	public abstract void mouseExit(int screenCoordX, int screenCoordY);
+
 	/**
+     * Event to signal that a mouse has been dragged from one point to
+     * a next.
 	 * 
-	 * @param screenCoordXFrom
-	 * @param screenCoordYFrom
-	 * @param screenCoordXTo
-	 * @param screenCoordYTo
+	 * @param screenCoordXFrom the x part of the screen coordinate dragged from.
+	 * @param screenCoordYFrom the y part of the screen coordinate dragged from.
+	 * @param screenCoordXTo   the x part of the screen coordinate dragged to.
+	 * @param screenCoordYTo   the y part of the screen coordinate dragged to.
 	 */
 	public abstract void mouseDrag(int screenCoordXFrom, int screenCoordYFrom, int screenCoordXTo, int screenCoordYTo);
 
+    /**
+     * Event to signal that the mouse wheel has been rotated a certain amount forward.
+     * 
+     * @param rotation an platform-specific amount of rotation of the wheel
+     * @see #mouseWheelMovedBackward(int)
+     */
+	public abstract void mouseWheelMovedForward(int rotation);
+
+	/**
+     * Event to signal that the mouse wheel has been rotated a certain amount backward.
+     * 
+     * @param rotation an platform-specific amount of rotation of the wheel
+     * @see #mouseWheelMovedForward(int)
+     */
+	public abstract void mouseWheelMovedBackward(int rotation);
 
 }
diff --git a/src/main/org/openscience/cdk/io/MDLV2000Reader.java b/src/main/org/openscience/cdk/io/MDLV2000Reader.java
@@ -752,12 +752,19 @@ private IAtomContainer readAtomContainer(IAtomContainer molecule) throws CDKExce
             		int aliasAtomNumber = Integer.parseInt(line.replaceFirst("A\\s{1,4}", "")) - RGroupCounter;
             		line = input.readLine(); linecount++;
 					String[] aliasArray = line.split("\\\\");
-					// name of the alias atom like R1 odr R2 etc. 
+					// name of the alias atom like R1 or R2 etc. 
 					String alias = "";
 					for (int i = 0; i < aliasArray.length; i++) {
 						alias += aliasArray[i];
 					}
 					IAtom aliasAtom = outputContainer.getAtom(aliasAtomNumber);
+
+                    // skip if already a pseudoatom
+                    if(aliasAtom instanceof IPseudoAtom){
+                        ((IPseudoAtom) aliasAtom).setLabel(alias);
+                        continue;
+                    }
+
 					IAtom newPseudoAtom = molecule.getBuilder().newInstance(IPseudoAtom.class,alias);
 					if(aliasAtom.getPoint2d() != null) {
 						newPseudoAtom.setPoint2d(aliasAtom.getPoint2d());

diff --git a/src/main/org/openscience/cdk/renderer/visitor/AWTDrawVisitor.java b/src/main/org/openscience/cdk/renderer/visitor/AWTDrawVisitor.java
@@ -85,13 +85,43 @@ public class AWTDrawVisitor extends AbstractAWTDrawVisitor {
 
 	private final Map<Integer, BasicStroke> strokeMap = 
 	    new HashMap<Integer, BasicStroke>();
-
+
+	/**
+	 * Returns the current {@link RendererModel}.
+	 *
+	 * @return the current model
+	 */
+    @TestMethod("testGetRendererModel")
+	public RendererModel getRendererModel() {
+		return rendererModel;
+	}
+
+	/**
+	 * Returns the current stroke map.
+	 *
+	 * @return a {@link Map} with Integer as keys and {@link BasicStroke}s.
+	 */
+    @TestMethod("testGetStrokeMap")
+	public Map<Integer, BasicStroke> getStrokeMap() {
+		return strokeMap;
+	}
+
 	private final Map<TextAttribute, Object> map = 
         new Hashtable<TextAttribute, Object>();
 
 	private final Graphics2D graphics;
 
-    /**
+	/**
+	 * Returns the {@link Graphics2D} for for this visitor.
+	 *
+	 * @return the {@link Graphics2D} object
+	 */
+    @TestMethod("testGetGraphics")
+	public Graphics2D getGraphics() {
+		return graphics;
+	}
+
+	/**
      * Constructs a new {@link IDrawVisitor} using the AWT widget toolkit,
      * taking a {@link Graphics2D} object to which the chemical content
      * is drawn.

diff --git a/src/main/org/openscience/cdk/tools/AtomicProperties.java b/src/main/org/openscience/cdk/tools/AtomicProperties.java
@@ -27,6 +27,9 @@
 import java.util.Hashtable;
 import java.util.Map;
 
+import org.openscience.cdk.annotations.TestClass;
+import org.openscience.cdk.annotations.TestMethod;
+
 /**
  * Provides atomic property values for descriptor calculations.
  *
@@ -37,6 +40,7 @@
  * @cdk.module qsar
  * @cdk.githash
  */
+@TestClass("org.openscience.cdk.tools.AtomicPropertiesTest")
 public class AtomicProperties {
 
     private static AtomicProperties ap=null;
@@ -72,41 +76,47 @@ private AtomicProperties() throws IOException {
 		bufferedReader.close();
 	}
 
-
-
+    @TestMethod("testGetVdWVolume")
 	public double getVdWVolume(String symbol) {
 		return htVdWVolume.get(symbol);
 	}
 
+    @TestMethod("testGetNormalizedVdWVolume")
 	public double getNormalizedVdWVolume(String symbol) {
 		return this.getVdWVolume(symbol)/this.getVdWVolume("C");
 	}
 
+    @TestMethod("testGetElectronegativity")
 	public double getElectronegativity(String symbol) {
 		return htElectronegativity.get(symbol);
 	}
 
+    @TestMethod("testGetNormalizedElectronegativity")
 	public double getNormalizedElectronegativity(String symbol) {
 		return this.getElectronegativity(symbol)/this.getElectronegativity("C");
 	}
-	public double getPolarizability(String symbol) {
+
+    @TestMethod("testGetPolarizability")
+    public double getPolarizability(String symbol) {
 		return htPolarizability.get(symbol);
 	}
 
+    @TestMethod("testGetNormalizedPolarizability")
 	public double getNormalizedPolarizability(String symbol) {
 		return this.getPolarizability(symbol)/this.getPolarizability("C");
 	}
 
+    @TestMethod("testGetMass")
     public double getMass(String symbol) {
 		return htMass.get(symbol);
 	}
 
+    @TestMethod("testGetNormalizedMass")
 	public double getNormalizedMass(String symbol) {
 		return this.getMass(symbol)/this.getMass("C");
 	}
 
-
-
+	@TestMethod("testGetInstance")
 	public static AtomicProperties getInstance() throws IOException
 	{
 		if (ap == null) {

diff --git a/src/test/data/mdl/mol_testAliasAtomNaming.mol b/src/test/data/mdl/mol_testAliasAtomNaming.mol
@@ -0,0 +1,16 @@
+"a carbonyl group"
+  biocyc  0628111714
+
+  4  3  0  0  0  0  0  0  0  0999 V2000
+  332.4620  333.2690    0.0000 R#  0  0  0  0  0  0  0
+ -999.0000  333.2690    0.0000 R#  0  0  0  0  0  0  0
+ -333.2690  333.2690    0.0000 C   0  0  0  0  0  0  0
+ -333.2690  999.0000    0.0000 O   0  0  0  0  0  0  0
+  3  1  1  0  0  0  0
+  3  2  1  0  0  0  0
+  3  4  2  0  0  0  0
+A    2
+R1
+A    1
+R1
+M  END
diff --git a/src/test/org/openscience/cdk/io/MDLV2000ReaderTest.java b/src/test/org/openscience/cdk/io/MDLV2000ReaderTest.java
@@ -925,6 +925,25 @@ public void testQueryBondType6() throws Exception {
         MDLV2000Reader reader = new MDLV2000Reader(in);
         IMolecule molecule = DefaultChemObjectBuilder.getInstance().newInstance(IMolecule.class);
         reader.read(molecule);
-        Assert.assertEquals("R", molecule.getAtom(55).getSymbol() );
+        Assert.assertEquals("R", molecule.getAtom(55).getSymbol());
+    }
+
+    @Test
+    public void testAliasAtomNaming() throws Exception {
+        InputStream in = ClassLoader.getSystemResourceAsStream("data/mdl/mol_testAliasAtomNaming.mol");
+        MDLV2000Reader reader = new MDLV2000Reader(in);
+        IMolecule molecule = DefaultChemObjectBuilder.getInstance().newInstance(IMolecule.class);
+        reader.read(molecule);
+
+        IAtom[] atoms = AtomContainerManipulator.getAtomArray(molecule);
+
+        int r1Count = 0;
+        for (IAtom atom : atoms) {
+            if (atom instanceof IPseudoAtom) {
+                Assert.assertEquals("R1", ((IPseudoAtom) atom).getLabel());
+                r1Count++;
+            }
+        }
+        Assert.assertEquals(2, r1Count);
     }
 }
diff --git a/src/test/org/openscience/cdk/modulesuites/MqsarTests.java b/src/test/org/openscience/cdk/modulesuites/MqsarTests.java
@@ -23,6 +23,7 @@
 import org.junit.runners.Suite.SuiteClasses;
 import org.openscience.cdk.coverage.QsarCoverageTest;
 import org.openscience.cdk.qsar.DescriptorExceptionTest;
+import org.openscience.cdk.tools.AtomicPropertiesTest;
 
 /**
  * TestSuite that runs all the sample tests.
@@ -34,6 +35,7 @@
 @RunWith(value=Suite.class)
 @SuiteClasses(value={
     QsarCoverageTest.class,
-    DescriptorExceptionTest.class
+    DescriptorExceptionTest.class,
+    AtomicPropertiesTest.class
 })
 public class MqsarTests {}
diff --git a/src/test/org/openscience/cdk/renderer/visitor/AWTDrawVisitorTest.java b/src/test/org/openscience/cdk/renderer/visitor/AWTDrawVisitorTest.java
@@ -71,7 +71,29 @@ public void testSetRendererModel() {
 		Assert.assertNotNull(visitor);
 	}
 
-	@Test
+    @Test
+    public void testGetRendererModel() {
+        Image image = new BufferedImage(
+            100, 100, BufferedImage.TYPE_INT_RGB
+        );
+        Graphics2D g2d = (Graphics2D)image.getGraphics();
+        AWTDrawVisitor visitor = new AWTDrawVisitor(g2d);
+        RendererModel model = new RendererModel();
+        visitor.setRendererModel(model);
+        Assert.assertEquals(model, visitor.getRendererModel());
+    }
+
+    @Test
+    public void testGetStrokeMap() {
+        Image image = new BufferedImage(
+            100, 100, BufferedImage.TYPE_INT_RGB
+        );
+        Graphics2D g2d = (Graphics2D)image.getGraphics();
+        AWTDrawVisitor visitor = new AWTDrawVisitor(g2d);
+        Assert.assertNotNull(visitor.getStrokeMap());
+    }
+
+    @Test
 	public void testVisit() {
 		Image image = new BufferedImage(
 			100, 100, BufferedImage.TYPE_INT_RGB
@@ -84,4 +106,14 @@ public void testVisit() {
 		// at least we now know it did not crash...
 		Assert.assertNotNull(visitor);
 	}
+
+    @Test
+    public void testGetGraphics() {
+        Image image = new BufferedImage(
+            100, 100, BufferedImage.TYPE_INT_RGB
+        );
+        Graphics2D g2d = (Graphics2D)image.getGraphics();
+        AWTDrawVisitor visitor = new AWTDrawVisitor(g2d);
+        Assert.assertEquals(g2d, visitor.getGraphics());
+    }
 }