Introducing new abstract super class to allow default implementations…

… - mirrors the preexisting abstract classes for atom/bond descriptors.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>

src/main/org/openscience/cdk/qsar/AbstractAtomPairDescriptor.java

@@ -0,0 +1,36 @@
+/*
+ * Copyright (c) 2013 John May <jwmay@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 U
+ */
+
+package org.openscience.cdk.qsar;
+
+/**
+ * A super class for atom pair descriptors allowing default implementations for
+ * interface methods.
+ *
+ * @author John May
+ * @cdk.module qsar
+ */
+public abstract class AbstractAtomPairDescriptor extends AbstractDescriptor
+        implements IAtomPairDescriptor {
+
+}

src/main/org/openscience/cdk/qsar/AbstractAtomicDescriptor.java

@@ -39,12 +39,12 @@
  * @cdk.module qsar
  * @cdk.githash
  */
-public abstract class AbstractAtomicDescriptor implements IAtomicDescriptor {
+public abstract class AbstractAtomicDescriptor extends AbstractDescriptor implements IAtomicDescriptor {
 
 	private static final String PREVIOUS_ATOMCONTAINER = "previousAtomContainer";
 
 	private Map cachedDescriptorValues = null;
-	
+
 	/**
 	 * Returns true if the cached IDescriptorResult's are for the given IAtomContainer.
 	 * 

src/main/org/openscience/cdk/qsar/AbstractBondDescriptor.java

@@ -28,7 +28,6 @@
 
 import org.openscience.cdk.interfaces.IAtomContainer;
 import org.openscience.cdk.interfaces.IBond;
-import org.openscience.cdk.qsar.result.DoubleResult;
 import org.openscience.cdk.qsar.result.IDescriptorResult;
 
 /**
@@ -40,7 +39,7 @@
  * @cdk.module qsar
  * @cdk.githash
  */
-public abstract class AbstractBondDescriptor implements IBondDescriptor {
+public abstract class AbstractBondDescriptor extends AbstractDescriptor implements IBondDescriptor {
 
 	private static final String PREVIOUS_ATOMCONTAINER = "previousAtomContainer";
 

src/main/org/openscience/cdk/qsar/AbstractDescriptor.java

@@ -0,0 +1,46 @@
+/*
+ * Copyright (c) 2013 John May <jwmay@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 U
+ */
+
+package org.openscience.cdk.qsar;
+
+import org.openscience.cdk.interfaces.IChemObjectBuilder;
+
+/**
+ * A super class for molecular descriptors allowing default implementations for
+ * interface methods.
+ *
+ * @author John May
+ * @cdk.module qsar
+ */
+abstract class AbstractDescriptor implements IDescriptor {
+
+    /**
+     * Default implementation of initialise allows optional override.
+     *
+     * @param builder chem object build
+     */
+    @Override public void initialise(IChemObjectBuilder builder) {
+        // do nothing
+    }
+
+}

src/main/org/openscience/cdk/qsar/AbstractMolecularDescriptor.java

@@ -0,0 +1,35 @@
+/*
+ * Copyright (c) 2013 John May <jwmay@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 U
+ */
+
+package org.openscience.cdk.qsar;
+
+/**
+ * A super class for molecular descriptors allowing default implementations for
+ * interface methods.
+ *
+ * @author John May
+ * @cdk.module qsar
+ */
+public abstract class AbstractMolecularDescriptor extends AbstractDescriptor implements IMolecularDescriptor {
+
+}

src/main/org/openscience/cdk/qsar/IDescriptor.java

@@ -22,6 +22,7 @@
 
 import org.openscience.cdk.IImplementationSpecification;
 import org.openscience.cdk.exception.CDKException;
+import org.openscience.cdk.interfaces.IChemObjectBuilder;
 import org.openscience.cdk.qsar.result.IDescriptorResult;
 
 /**
@@ -86,6 +87,16 @@
  */
 public interface IDescriptor {
 
+    /**
+     * Initialise the descriptor with the specified chem object builder. This
+     * allows descriptors that required domain objects, such as for SMARTS queries
+     * to initialise correctly. If you do not need domain objects then this method
+     * does not need to be implemented.
+     *
+     * @param builder chem object builder to use with this descriptor
+     */
+    void initialise(IChemObjectBuilder builder);
+
    /**
    * Returns a <code>IImplementationSpecification</code> which specifies which descriptor
    * is implemented by this class.