Merge pull request #310 from cdk/patch/factorymalloc

Looks good to me.
cdk · Apr 29, 2017 · 10a0417 · 10a0417
2 parents baffeee + f4f069c
commit 10a0417
Show file tree

Hide file tree

Showing 8 changed files with 118 additions and 32 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
@@ -206,4 +206,27 @@ public <T extends ICDKObject> T newInstance(Class<T> clazz, Object... params) {
         return factory.ofClass(clazz, params);
     }
 
+    /**
+     * {@inheritDoc}
+     */
+    @Override
+    public IAtom newAtom() {
+        return new Atom();
+    }
+
+    /**
+     * {@inheritDoc}
+     */
+    @Override
+    public IBond newBond() {
+        return new Bond();
+    }
+
+    /**
+     * {@inheritDoc}
+     */
+    @Override
+    public IAtomContainer newAtomContainer() {
+        return new AtomContainer();
+    }
 }
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
@@ -204,4 +204,27 @@ public <T extends ICDKObject> T newInstance(Class<T> clazz, Object... params) {
         return factory.ofClass(clazz, params);
     }
 
+    /**
+     * {@inheritDoc}
+     */
+    @Override
+    public IAtom newAtom() {
+        return new DebugAtom();
+    }
+
+    /**
+     * {@inheritDoc}
+     */
+    @Override
+    public IBond newBond() {
+        return new DebugBond();
+    }
+
+    /**
+     * {@inheritDoc}
+     */
+    @Override
+    public IAtomContainer newAtomContainer() {
+        return new DebugAtomContainer();
+    }
 }
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
@@ -41,6 +41,32 @@ public interface IChemObjectBuilder {
      * @throws IllegalArgumentException Exception thrown when the {@link IChemObjectBuilder}
      *               builder cannot instantiate the <code>clazz</code> with the given parameters.
      */
-    public <T extends ICDKObject> T newInstance(Class<T> clazz, Object... params) throws IllegalArgumentException;
+    <T extends ICDKObject> T newInstance(Class<T> clazz, Object... params) throws IllegalArgumentException;
 
+    /**
+     * Create a new atom using the default constructor. This method is considerably faster
+     * than the dynamic dispatch of {@code newInstance(IAtom.class)} and should be used for
+     * high throughput applications (e.g. IO).
+     *
+     * @return new atom
+     */
+    IAtom newAtom();
+
+    /**
+     * 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
+     * high throughput applications (e.g. IO).
+     *
+     * @return new bond
+     */
+    IBond newBond();
+
+    /**
+     * 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
+     * high throughput applications (e.g. IO).
+     *
+     * @return the new atom container
+     */
+    IAtomContainer newAtomContainer();
 }
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
@@ -201,4 +201,27 @@ public <T extends ICDKObject> T newInstance(Class<T> clazz, Object... params) th
         return factory.ofClass(clazz, params);
     }
 
+    /**
+     * {@inheritDoc}
+     */
+    @Override
+    public IAtom newAtom() {
+        return new Atom();
+    }
+
+    /**
+     * {@inheritDoc}
+     */
+    @Override
+    public IBond newBond() {
+        return new Bond();
+    }
+
+    /**
+     * {@inheritDoc}
+     */
+    @Override
+    public IAtomContainer newAtomContainer() {
+        return new AtomContainer(0,0,0,0);
+    }
 }
diff --git a/storage/io/src/main/java/org/openscience/cdk/io/MDLV2000Reader.java b/storage/io/src/main/java/org/openscience/cdk/io/MDLV2000Reader.java
@@ -763,7 +763,8 @@ IBond readBondFast(String line, IChemObjectBuilder builder, IAtom[] atoms, int[]
                 throw new CDKException("invalid line length: " + length + " " + line);
         }
 
-        IBond bond = builder.newInstance(IBond.class, atoms[u], atoms[v]);
+        IBond bond = builder.newBond();
+        bond.setAtoms(new IAtom[]{atoms[u], atoms[v]});
 
         switch (type) {
             case 1: // single
@@ -1279,8 +1280,11 @@ static int length(final String str) {
      * @throws CDKException the symbol is not allowed
      */
     private IAtom createAtom(String symbol, IChemObjectBuilder builder, int lineNum) throws CDKException {
-        if (isPeriodicElement(symbol))
-            return builder.newInstance(IAtom.class, symbol);
+        if (isPeriodicElement(symbol)) {
+            IAtom atom = builder.newAtom();
+            atom.setSymbol(symbol);
+            return atom;
+        }
         if (symbol.equals("D") && interpretHydrogenIsotopes.isSet()) {
             if (mode == Mode.STRICT) throw new CDKException("invalid symbol: " + symbol);
             IAtom atom = builder.newInstance(IAtom.class, "H");

diff --git a/storage/io/src/main/java/org/openscience/cdk/io/MDLV3000Reader.java b/storage/io/src/main/java/org/openscience/cdk/io/MDLV3000Reader.java
@@ -156,7 +156,7 @@ public IAtomContainer readConnectionTable(IChemObjectBuilder builder) throws CDK
 
 
         logger.info("Reading CTAB block");
-        IAtomContainer readData = builder.newInstance(IAtomContainer.class);
+        IAtomContainer readData = builder.newAtomContainer();
         boolean foundEND = false;
         String lastLine = readHeader(readData);
         while (isReady() && !foundEND) {
@@ -256,7 +256,7 @@ public void readAtomBlock(IAtomContainer readData) throws CDKException {
                 foundEND = true;
             } else {
                 logger.debug("Parsing atom from: " + command);
-                IAtom atom = readData.getBuilder().newInstance(IAtom.class);
+                IAtom atom = readData.getBuilder().newAtom();
                 StringTokenizer tokenizer = new StringTokenizer(command);
                 // parse the index
                 try {
@@ -270,7 +270,8 @@ public void readAtomBlock(IAtomContainer readData) throws CDKException {
                 // parse the element
                 String element = tokenizer.nextToken();
                 if (isotopeFactory.isElement(element)) {
-                    atom = isotopeFactory.configure(readData.getBuilder().newInstance(IAtom.class, element));
+                    atom.setSymbol(element);
+                    isotopeFactory.configure(atom); // ?
                 } else if ("A".equals(element)) {
                     atom = readData.getBuilder().newInstance(IPseudoAtom.class, element);
                 } else if ("Q".equals(element)) {
@@ -401,7 +402,7 @@ public void readBondBlock(IAtomContainer readData) throws CDKException {
             } else {
                 logger.debug("Parsing bond from: " + command);
                 StringTokenizer tokenizer = new StringTokenizer(command);
-                IBond bond = readData.getBuilder().newInstance(IBond.class);
+                IBond bond = readData.getBuilder().newBond();
                 // parse the index
                 try {
                     String indexString = tokenizer.nextToken();

diff --git a/storage/io/src/main/java/org/openscience/cdk/io/iterator/IteratingSDFReader.java b/storage/io/src/main/java/org/openscience/cdk/io/iterator/IteratingSDFReader.java
@@ -248,7 +248,7 @@ public boolean hasNext() {
                     try {
                         ISimpleChemObjectReader reader = getReader(currentFormat);
                         reader.setReader(new StringReader(buffer.toString()));
-                        molecule = reader.read(builder.newInstance(IAtomContainer.class, 0, 0, 0, 0));
+                        molecule = reader.read(builder.newAtomContainer());
                     } catch (Exception exception) {
                         logger.error("Error while reading next molecule: " + exception.getMessage());
                         logger.debug(exception);

diff --git a/storage/smiles/src/main/java/org/openscience/cdk/smiles/BeamToCDK.java b/storage/smiles/src/main/java/org/openscience/cdk/smiles/BeamToCDK.java
@@ -490,11 +490,7 @@ private IBond.Order toCDKBondOrder(Edge edge) {
      * @return a new atom container instance
      */
     private IAtomContainer emptyContainer() {
-        try {
-            return (IAtomContainer) emptyContainer.clone();
-        } catch (CloneNotSupportedException e) {
-            return builder.newInstance(IAtomContainer.class, 0, 0, 0, 0);
-        }
+        return builder.newAtomContainer();
     }
 
     /**
@@ -506,15 +502,10 @@ private IAtomContainer emptyContainer() {
      * @return new atom with configured symbol and atomic number
      */
     private IAtom createAtom(Element element) {
-        try {
-            IAtom atom = (IAtom) templateAtom.clone();
-            atom.setSymbol(element.symbol());
-            atom.setAtomicNumber(element.atomicNumber());
-            return atom;
-        } catch (CloneNotSupportedException e) {
-            // clone is always supported if overridden but just in case :-)
-            return builder.newInstance(IAtom.class, element.symbol());
-        }
+        IAtom atom = builder.newAtom();
+        atom.setSymbol(element.symbol());
+        atom.setAtomicNumber(element.atomicNumber());
+        return atom;
     }
 
     /**
@@ -529,14 +520,9 @@ private IAtom createAtom(Element element) {
      * @return new bond instance
      */
     private IBond createBond(IAtom either, IAtom other, IBond.Order order) {
-        try {
-            IBond bond = (IBond) templateBond.clone();
-            bond.setAtoms(new IAtom[]{either, other});
-            bond.setOrder(order);
-            return bond;
-        } catch (CloneNotSupportedException e) {
-            // clone is always supported if overridden but just in case  :-)
-            return builder.newInstance(IBond.class, either, other, order);
-        }
+        IBond bond = builder.newBond();
+        bond.setAtoms(new IAtom[]{either, other});
+        bond.setOrder(order);
+        return bond;
     }
 }