Merge pull request #888 from uli-f/add_newreaction_to_ichemobjectbuilder

added dedicated method newReaction() for instantiation of Reaction ob…
cdk · Sep 5, 2022 · 244a3a4 · 244a3a4
2 parents 9e89820 + c780f42
commit 244a3a4
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Showing 8 changed files with 71 additions and 10 deletions.
diff --git a/base/data/src/main/java/org/openscience/cdk/DefaultChemObjectBuilder.java b/base/data/src/main/java/org/openscience/cdk/DefaultChemObjectBuilder.java
@@ -239,6 +239,14 @@ public IAtomContainer newAtomContainer() {
                 return new AtomContainer2(0, 0, 0, 0);
 
         }
+
+        /**
+         * {@inheritDoc}
+         */
+        @Override
+        public IReaction newReaction() {
+            return new Reaction();
+        }
     }
 
     /**
@@ -294,4 +302,12 @@ public IBond newBond() {
     public IAtomContainer newAtomContainer() {
         return Holder.INSTANCE.newAtomContainer();
     }
+
+    /**
+     * {@inheritDoc}
+     */
+    @Override
+    public IReaction newReaction() {
+        return Holder.INSTANCE.newReaction();
+    }
 }
diff --git a/base/data/src/test/java/org/openscience/cdk/DefaultChemObjectBuilderTest.java b/base/data/src/test/java/org/openscience/cdk/DefaultChemObjectBuilderTest.java
@@ -25,8 +25,7 @@
 import org.openscience.cdk.test.AbstractChemObjectBuilderTest;
 
 /**
- * Checks the functionality of the {@link IChemObjectBuilder}
- * {@link SilentChemObjectBuilder} implementation.
+ * Checks the functionality of the {@link IChemObjectBuilder} {@link DefaultChemObjectBuilder} implementation.
  *
  * @cdk.module test-data
  */

diff --git a/base/datadebug/src/main/java/org/openscience/cdk/debug/DebugChemObjectBuilder.java b/base/datadebug/src/main/java/org/openscience/cdk/debug/DebugChemObjectBuilder.java
@@ -68,7 +68,6 @@
  * implementation. The factory create debug objects which will log their
  * behaviour when used.
  *
- * 
  * <pre>{@code
  *     IChemObjectBuilder builder = DebugChemObjectBuilder.getInstance();
  *
@@ -197,6 +196,14 @@ public IBond newBond() {
         public IAtomContainer newAtomContainer() {
             return new DebugAtomContainer(0, 0, 0, 0);
         }
+
+        /**
+         * {@inheritDoc}
+         */
+        @Override
+        public IReaction newReaction() {
+            return new DebugReaction();
+        }
     }
 
     /**
@@ -252,4 +259,12 @@ public IBond newBond() {
     public IAtomContainer newAtomContainer() {
         return Holder.INSTANCE.newAtomContainer();
     }
+
+    /**
+     * {@inheritDoc}
+     */
+    @Override
+    public IReaction newReaction() {
+        return Holder.INSTANCE.newReaction();
+    }
 }
diff --git a/base/datadebug/src/test/java/org/openscience/cdk/debug/DebugChemObjectBuilderTest.java b/base/datadebug/src/test/java/org/openscience/cdk/debug/DebugChemObjectBuilderTest.java
@@ -25,8 +25,7 @@
 import org.openscience.cdk.interfaces.IChemObjectBuilder;
 
 /**
- * Checks the functionality of the {@link IChemObjectBuilder}
- * {@link DebugChemObjectBuilder} implementation.
+ * Checks the functionality of the {@link IChemObjectBuilder} {@link DebugChemObjectBuilder} implementation.
  *
  * @cdk.module test-datadebug
  */

diff --git a/base/interfaces/src/main/java/org/openscience/cdk/interfaces/IChemObjectBuilder.java b/base/interfaces/src/main/java/org/openscience/cdk/interfaces/IChemObjectBuilder.java
@@ -54,7 +54,7 @@ public interface IChemObjectBuilder {
 
     /**
      * Create a new bond using the default constructor. This method is considerably faster
-     * than the dynamic dispatch of {@code newInstance(IAtom.class)} and should be used for
+     * than the dynamic dispatch of {@code newInstance(IBond.class)} and should be used for
      * high throughput applications (e.g. IO).
      *
      * @return new bond
@@ -63,10 +63,20 @@ public interface IChemObjectBuilder {
 
     /**
      * Create a new atom container using the default constructor. This method is considerably faster
-     * than the dynamic dispatch of {@code newInstance(IAtom.class)} and should be used for
+     * than the dynamic dispatch of {@code newInstance(IAtomContainer.class)} and should be used for
      * high throughput applications (e.g. IO).
      *
      * @return the new atom container
      */
     IAtomContainer newAtomContainer();
+
+    /**
+     * Create a new reaction using the default constructor. This method is considerably faster
+     * than the dynamic dispatch of {@code newInstance(IReaction.class)} and should be used for
+     * high throughput applications (e.g. IO).
+     *
+     * @return the new reaction
+     */
+    IReaction newReaction();
+
 }
diff --git a/base/silent/src/main/java/org/openscience/cdk/silent/SilentChemObjectBuilder.java b/base/silent/src/main/java/org/openscience/cdk/silent/SilentChemObjectBuilder.java
@@ -234,6 +234,14 @@ public IAtomContainer newAtomContainer() {
                 return new AtomContainer2(0, 0, 0, 0);
 
         }
+
+        /**
+         * {@inheritDoc}
+         */
+        @Override
+        public IReaction newReaction() {
+            return new Reaction();
+        }
     }
 
     /**
@@ -289,4 +297,12 @@ public IBond newBond() {
     public IAtomContainer newAtomContainer() {
         return Holder.INSTANCE.newAtomContainer();
     }
+
+    /**
+     * {@inheritDoc}
+     */
+    @Override
+    public IReaction newReaction() {
+        return Holder.INSTANCE.newReaction();
+    }
 }
diff --git a/base/silent/src/test/java/org/openscience/cdk/silent/SilentChemObjectBuilderTest.java b/base/silent/src/test/java/org/openscience/cdk/silent/SilentChemObjectBuilderTest.java
@@ -25,8 +25,7 @@
 import org.openscience.cdk.interfaces.IChemObjectBuilder;
 
 /**
- * Checks the functionality of the {@link IChemObjectBuilder}
- * {@link SilentChemObjectBuilder} implementation.
+ * Checks the functionality of the {@link IChemObjectBuilder} {@link SilentChemObjectBuilder} implementation.
  *
  * @cdk.module test-silent
  */

diff --git a/base/test/src/main/java/org/openscience/cdk/test/AbstractChemObjectBuilderTest.java b/base/test/src/main/java/org/openscience/cdk/test/AbstractChemObjectBuilderTest.java
@@ -69,7 +69,7 @@ public static void setRootObject(IChemObject rootObject) {
     }
 
     @Test(expected = IllegalArgumentException.class)
-    public void testNewInstance_Class_arrayObject() throws Exception {
+    public void testNewInstance_Class_arrayObject() {
         // throw random stuff; it should fail
         IChemObjectBuilder builder = rootObject.getBuilder();
         builder.newInstance(IAtom.class, new Object[2]);
@@ -660,4 +660,11 @@ public void testSubstance() {
         Assert.assertNotNull(substance);
     }
 
+    @Test
+    public void testNewReaction_dedicatedMethod() {
+        IChemObjectBuilder builder = rootObject.getBuilder();
+        IReaction reaction = builder.newReaction();
+        Assert.assertNotNull(reaction);
+    }
+
 }