Merge pull request #162 from chaubold/reduce-memory-footprint

Adjust parallelization of TwoComponentReaction node to significantly reduce memory usage

Author: ptosco

org.rdkit.knime.nodes/src/org/rdkit/knime/nodes/twocomponentreaction2/Pair.java

@@ -0,0 +1,68 @@
+/*
+ * ------------------------------------------------------------------
+ * Copyright by KNIME AG, Zurich, Switzerland
+ * Website: http://www.knime.com; Email: contact@knime.com
+ *
+ * This program is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License, Version 3, as
+ * published by the Free Software Foundation.
+ *
+ * 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 General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, see <http://www.gnu.org/licenses>.
+ *
+ * Additional permission under GNU GPL version 3 section 7:
+ *
+ * KNIME interoperates with ECLIPSE solely via ECLIPSE's plug-in APIs.
+ * Hence, KNIME and ECLIPSE are both independent programs and are not
+ * derived from each other. Should, however, the interpretation of the
+ * GNU GPL Version 3 ("License") under any applicable laws result in
+ * KNIME and ECLIPSE being a combined program, KNIME GMBH herewith grants
+ * you the additional permission to use and propagate KNIME together with
+ * ECLIPSE with only the license terms in place for ECLIPSE applying to
+ * ECLIPSE and the GNU GPL Version 3 applying for KNIME, provided the
+ * license terms of ECLIPSE themselves allow for the respective use and
+ * propagation of ECLIPSE together with KNIME.
+ *
+ * Additional permission relating to nodes for KNIME that extend the Node
+ * Extension (and in particular that are based on subclasses of NodeModel,
+ * NodeDialog, and NodeView) and that only interoperate with KNIME through
+ * standard APIs ("Nodes"):
+ * Nodes are deemed to be separate and independent programs and to not be
+ * covered works. Notwithstanding anything to the contrary in the
+ * License, the License does not apply to Nodes, you are not required to
+ * license Nodes under the License, and you are granted a license to
+ * prepare and propagate Nodes, in each case even if such Nodes are
+ * propagated with or for interoperation with KNIME. The owner of a Node
+ * may freely choose the license terms applicable to such Node, including
+ * when such Node is propagated with or for interoperation with KNIME.
+ * ---------------------------------------------------------------------
+ */
+package org.rdkit.knime.nodes.twocomponentreaction2;
+
+public class Pair<T, U> {
+ private final T first;
+ private final U second;
+
+ public Pair(T first, U second) {
+ this.first = first;
+ this.second = second;
+ }
+
+ public T getFirst() {
+ return first;
+ }
+
+ public U getSecond() {
+ return second;
+ }
+
+ @Override
+ public String toString() {
+ return "(" + first + ", " + second + ")";
+ }
+}

org.rdkit.knime.nodes/src/org/rdkit/knime/nodes/twocomponentreaction2/PairIterable.java

@@ -0,0 +1,111 @@
+/*
+ * ------------------------------------------------------------------------
+ * Copyright by KNIME AG, Zurich, Switzerland
+ * Website: http://www.knime.com; Email: contact@knime.com
+ *
+ * This program is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License, Version 3, as
+ * published by the Free Software Foundation.
+ *
+ * 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 General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, see <http://www.gnu.org/licenses>.
+ *
+ * Additional permission under GNU GPL version 3 section 7:
+ *
+ * KNIME interoperates with ECLIPSE solely via ECLIPSE's plug-in APIs.
+ * Hence, KNIME and ECLIPSE are both independent programs and are not
+ * derived from each other. Should, however, the interpretation of the
+ * GNU GPL Version 3 ("License") under any applicable laws result in
+ * KNIME and ECLIPSE being a combined program, KNIME AG herewith grants
+ * you the additional permission to use and propagate KNIME together with
+ * ECLIPSE with only the license terms in place for ECLIPSE applying to
+ * ECLIPSE and the GNU GPL Version 3 applying for KNIME, provided the
+ * license terms of ECLIPSE themselves allow for the respective use and
+ * propagation of ECLIPSE together with KNIME.
+ *
+ * Additional permission relating to nodes for KNIME that extend the Node
+ * Extension (and in particular that are based on subclasses of NodeModel,
+ * NodeDialog, and NodeView) and that only interoperate with KNIME through
+ * standard APIs ("Nodes"):
+ * Nodes are deemed to be separate and independent programs and to not be
+ * covered works. Notwithstanding anything to the contrary in the
+ * License, the License does not apply to Nodes, you are not required to
+ * license Nodes under the License, and you are granted a license to
+ * prepare and propagate Nodes, in each case even if such Nodes are
+ * propagated with or for interoperation with KNIME. The owner of a Node
+ * may freely choose the license terms applicable to such Node, including
+ * when such Node is propagated with or for interoperation with KNIME.
+ * ------------------------------------------------------------------------
+ *
+ */
+package org.rdkit.knime.nodes.twocomponentreaction2;
+
+import java.util.Iterator;
+import java.util.NoSuchElementException;
+
+/**
+ * An iterable that iterates over all pairings of two given iterables.
+ * 
+ * @author Carsten Haubold, KNIME GmbH, Konstanz, Germany
+ *
+ * @param <T> The type of the first iterable
+ * @param <U> The type of the second iterable
+ */
+class PairIterable<T, U> implements Iterable<Pair<Pair<T, Long>, Pair<U, Long>>> {
+private final Iterable<T> firstIterable;
+private final Iterable<U> secondIterable;
+
+public PairIterable(Iterable<T> firstIterable, Iterable<U> secondIterable) {
+this.firstIterable = firstIterable;
+this.secondIterable = secondIterable;
+}
+
+@Override
+public Iterator<Pair<Pair<T, Long>, Pair<U, Long>>> iterator() {
+return new PairIterator<>(firstIterable.iterator(), secondIterable);
+}
+
+private static class PairIterator<T, U> implements Iterator<Pair<Pair<T, Long>, Pair<U, Long>>> {
+private final Iterator<T> firstIterator;
+private final Iterable<U> secondIterable;
+private Iterator<U> secondIterator = null;
+private T currentFirst;
+private Long firstIndex = 0L;
+private Long secondIndex = 0L;
+
+public PairIterator(Iterator<T> firstIterator, Iterable<U> secondIterable) {
+this.firstIterator = firstIterator;
+this.secondIterable = secondIterable;
+if (firstIterator.hasNext()) {
+currentFirst = firstIterator.next();
+secondIterator = secondIterable.iterator();
+}
+}
+
+@Override
+public boolean hasNext() {
+return ((secondIterator != null && secondIterator.hasNext())) || firstIterator.hasNext();
+}
+
+@Override
+public Pair<Pair<T, Long>, Pair<U, Long>> next() {
+if (!hasNext()) {
+throw new NoSuchElementException();
+}
+
+if (!secondIterator.hasNext()) {
+currentFirst = firstIterator.next();
+firstIndex++;
+secondIterator = secondIterable.iterator();
+secondIndex = 0L;
+}
+
+return new Pair<>(new Pair<>(currentFirst, firstIndex), new Pair<>(secondIterator.next(), secondIndex++));
+}
+}
+}