Resolvers review comments - also ensure correct copyright.

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

src/main/org/openscience/cdk/graph/BitMatrix.java

@@ -1,3 +1,26 @@
+/*
+ * Copyright (c) 2013 European Bioinformatics Institute (EMBL-EBI)
+ *                    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.graph;
 
 import org.openscience.cdk.annotations.TestClass;
@@ -176,6 +199,10 @@ private int eliminate(int x, int y) {
                 swap(i, y);
 
             // xor row with all vectors that have x set
+            // note: rows above y are not touched, this isn't an issue in
+            //       it's current use (cycle basis) as we only care about
+            //       new additions being independent. However starting from
+            //       j = 0 allows you to change this but of course is slower.
             for (int j = y + 1; j < m; j++)
                 if (rows[j].get(x))
                     rows[j] = xor(rows[j], rows[y]);

src/main/org/openscience/cdk/graph/EssentialCycles.java

@@ -1,3 +1,26 @@
+/*
+ * Copyright (c) 2013 European Bioinformatics Institute (EMBL-EBI)
+ *                    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.graph;
 
 import org.openscience.cdk.annotations.TestClass;
@@ -21,11 +44,11 @@
  *
  * @author John May
  * @cdk.module core
- * @cdk.keyword Essential Rings
- * @cdk.keyword Essential Cycles
- * @cdk.keyword Graph
- * @cdk.keyword Cycles
- * @cdk.keyword Rings
+ * @cdk.keyword essential rings
+ * @cdk.keyword essential cycles
+ * @cdk.keyword graph
+ * @cdk.keyword cycles
+ * @cdk.keyword rings
  * @see RelevantCycles
  * @see MinimumCycleBasis
  * @see org.openscience.cdk.ringsearch.SSSRFinder#findEssentialRings()

src/main/org/openscience/cdk/graph/GraphUtil.java

@@ -1,5 +1,6 @@
 /*
- * Copyright (c) 2013 John May <jwmay@users.sf.net>
+ * Copyright (c) 2013 European Bioinformatics Institute (EMBL-EBI)
+ *                    John May <jwmay@users.sf.net>
  *
  * Contact: cdk-devel@lists.sourceforge.net
  *
@@ -20,7 +21,6 @@
  * 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.graph;
 
 import org.openscience.cdk.annotations.TestClass;
@@ -123,10 +123,10 @@ public static int[][] subgraph(int[][] graph, int[] include) {
         int n = graph.length;
         int m = include.length;
 
-        // lookup from graph to subgraph
-        int[] lookup = new int[n];
+        // mapping from vertex in 'graph' to 'subgraph'
+        int[] mapping = new int[n];
         for (int i = 0; i < m; i++) {
-            lookup[include[i]] = i + 1;
+            mapping[include[i]] = i + 1;
         }
 
         // initialise the subgraph
@@ -137,12 +137,12 @@ public static int[][] subgraph(int[][] graph, int[] include) {
         // vertices p and q. If p or q is less then 0 then it is not
         // in the subgraph
         for (int v = 0; v < n; v++) {
-            int p = lookup[v] - 1;
+            int p = mapping[v] - 1;
             if (p < 0)
                 continue;
 
             for (int w : graph[v]) {
-                int q = lookup[w] - 1;
+                int q = mapping[w] - 1;
                 if (q < 0)
                     continue;
                 if (degree[p] == subgraph[p].length)

src/main/org/openscience/cdk/graph/GreedyBasis.java

@@ -1,5 +1,6 @@
 /*
- * Copyright (c) 2013 John May <jwmay@users.sf.net>
+ * Copyright (c) 2013 European Bioinformatics Institute (EMBL-EBI)
+ *                    John May <jwmay@users.sf.net>
  *
  * Contact: cdk-devel@lists.sourceforge.net
  *

src/main/org/openscience/cdk/graph/InitialCycles.java

@@ -1,5 +1,6 @@
 /*
- * Copyright (c) 2013 John May <jwmay@users.sf.net>
+ * Copyright (c) 2013 European Bioinformatics Institute (EMBL-EBI)
+ *                    John May <jwmay@users.sf.net>
  *
  * Contact: cdk-devel@lists.sourceforge.net
  *
@@ -20,7 +21,6 @@
  * 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.graph;
 
 import org.openscience.cdk.annotations.TestClass;
@@ -66,7 +66,15 @@ final class InitialCycles {
     private final Map<Edge, Integer> edgeToIndex;
     private final List<Edge> edges;
 
-    /** The degree indicates the start count for the key-value counting. */
+    /**
+     * Initial array size for 'ordering()'. This method sorts vertices by degree
+     * by counting how many of each degree there is then putting values in place
+     * directly. This is known as key-value counting and is used in radix
+     * sorts.
+     *
+     * @see <a href="https://en.wikipedia.org/wiki/Radix_sort#Least_significant_digit_radix_sorts">Radix
+     *      Sort</a>
+     */
     private final static int DEFAULT_DEGREE = 4;
 
     /**
@@ -499,6 +507,12 @@ int length() {
         }
     }
 
+    /**
+     * An even cycle is formed from two shortest paths of the same length
+     * and 'two' edges to a common vertex. The cycle formed by these is
+     * even, 2n + 2 = even.
+     * @see #compute()
+     */
     class EvenCycle extends Cycle {
         int p, q, y;
 
@@ -537,6 +551,12 @@ class EvenCycle extends Cycle {
         }
     }
 
+    /**
+     * An odd cycle is formed from two shortest paths of the same length
+     * and 'one' edge to a common vertex. The cycle formed by these is odd,
+     * 2n + 1 = odd.
+     * @see #compute()
+     */
     class OddCycle extends Cycle {
         int y, z;
 

src/main/org/openscience/cdk/graph/MinimumCycleBasis.java

@@ -1,3 +1,26 @@
+/*
+ * Copyright (c) 2013 European Bioinformatics Institute (EMBL-EBI)
+ *                    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.graph;
 
 import org.openscience.cdk.annotations.TestClass;
@@ -22,26 +45,27 @@
  * with MCB although traditionally their meaning was different {@cdk.cite
  * Berger04}. Although the MCB can be used to generate all other cycles of a
  * graph it may not be unique. A compound with a bridged ring system, such as <a
- * href="http://bit.ly/11sBxYr"><i>3-quinuclidinol</i></a>, has three equally
- * valid minimum cycle bases. From any two six member rings the third ring can
- * be generated by &oplus;-sum (xoring) their edges. As there may be more than
- * one MCB it should not be used as a <i>unique</i> descriptor. The smallest
- * (but potentially exponential) <i>unique</i> set of short cycles which
- * generates the cycle space is the union of all minimum cycle bases. This set
- * is known as the {@link RelevantCycles}. The intersect of all minimum cycle
- * bases ({@link EssentialCycles}) is also unique. Although the number of {@link
+ * href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:115239">
+ * <i>3-quinuclidinol</i></a>, has three equally valid minimum cycle bases. From
+ * any two six member rings the third ring can be generated by &oplus;-sum
+ * (xoring) their edges. As there may be more than one MCB it should not be used
+ * as a <i>unique</i> descriptor. The smallest (but potentially exponential)
+ * <i>unique</i> set of short cycles which generates the cycle space is the
+ * union of all minimum cycle bases. This set is known as the {@link
+ * RelevantCycles}. The intersect of all minimum cycle bases ({@link
+ * EssentialCycles}) is also unique. Although the number of {@link
  * EssentialCycles} is polynomial it can not always be used to generate the
  * cycle space.
  *
  * @author John May
  * @cdk.module core
- * @cdk.keyword SSSR
- * @cdk.keyword Smallest Set of Smallest Rings
- * @cdk.keyword MCB
- * @cdk.keyword Minimum Cycle Basis
- * @cdk.keyword Cycle
- * @cdk.keyword Ring
- * @cdk.keyword Ring Perception
+ * @cdk.keyword sssr
+ * @cdk.keyword smallest set of smallest rings
+ * @cdk.keyword mcb
+ * @cdk.keyword minimum cycle basis
+ * @cdk.keyword cycle
+ * @cdk.keyword ring
+ * @cdk.keyword ring perception
  * @see RelevantCycles
  * @see org.openscience.cdk.ringsearch.SSSRFinder#findSSSR()
  * @see <a href="http://en.wikipedia.org/wiki/Cycle_space">Cycle Basis</a>

src/main/org/openscience/cdk/graph/RelevantCycles.java

@@ -1,5 +1,6 @@
 /*
- * Copyright (c) 2013 John May <jwmay@users.sf.net>
+ * Copyright (c) 2013 European Bioinformatics Institute (EMBL-EBI)
+ *                    John May <jwmay@users.sf.net>
  *
  * Contact: cdk-devel@lists.sourceforge.net
  *
@@ -74,13 +75,13 @@
  *
  * @author John May
  * @cdk.module core
- * @cdk.keyword Relevant Cycles
- * @cdk.keyword Relevant Rings
+ * @cdk.keyword relevant cycles
+ * @cdk.keyword relevant rings
  * @cdk.keyword R(G)
- * @cdk.keyword Union of all Minimum Cycles Bases
- * @cdk.keyword Cycle
- * @cdk.keyword Ring
- * @cdk.keyword Ring Perception
+ * @cdk.keyword union of all minimum cycles bases
+ * @cdk.keyword cycle
+ * @cdk.keyword ring
+ * @cdk.keyword ring perception
  * @cdk.githash
  * @see org.openscience.cdk.ringsearch.RingSearch
  * @see org.openscience.cdk.ringsearch.SSSRFinder#findRelevantRings()

src/test/org/openscience/cdk/graph/BitMatrixTest.java

@@ -1,5 +1,6 @@
 /*
- * Copyright (c) 2013 John May <jwmay@users.sf.net>
+ * Copyright (c) 2013 European Bioinformatics Institute (EMBL-EBI)
+ *                    John May <jwmay@users.sf.net>
  *
  * Contact: cdk-devel@lists.sourceforge.net
  *

src/test/org/openscience/cdk/graph/EssentialCyclesTest.java

@@ -1,5 +1,6 @@
 /*
- * Copyright (c) 2013 John May <jwmay@users.sf.net>
+ * Copyright (c) 2013 European Bioinformatics Institute (EMBL-EBI)
+ *                    John May <jwmay@users.sf.net>
  *
  * Contact: cdk-devel@lists.sourceforge.net
  *
@@ -20,7 +21,6 @@
  * 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.graph;
 
 import org.junit.Test;

src/test/org/openscience/cdk/graph/GraphUtilTest.java

@@ -1,3 +1,26 @@
+/*
+ * Copyright (c) 2013 European Bioinformatics Institute (EMBL-EBI)
+ *                    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.graph;
 
 import org.junit.Test;
@@ -202,6 +225,7 @@ public void testToAdjList_Null() throws Exception {
 
     /**
      * 2,2-dimethylpropane
+     * @cdk.inchi InChI=1S/C5H12/c1-5(2,3)4/h1-4H3
      */
     private static IAtomContainer simple() {
 

src/test/org/openscience/cdk/graph/GreedyBasisTest.java

@@ -1,5 +1,6 @@
 /*
- * Copyright (c) 2013 John May <jwmay@users.sf.net>
+ * Copyright (c) 2013 European Bioinformatics Institute (EMBL-EBI)
+ *                    John May <jwmay@users.sf.net>
  *
  * Contact: cdk-devel@lists.sourceforge.net
  *

src/test/org/openscience/cdk/graph/InitialCyclesTest.java

@@ -1,5 +1,6 @@
 /*
- * Copyright (c) 2013 John May <jwmay@users.sf.net>
+ * Copyright (c) 2013 European Bioinformatics Institute (EMBL-EBI)
+ *                    John May <jwmay@users.sf.net>
  *
  * Contact: cdk-devel@lists.sourceforge.net
  *
@@ -20,7 +21,6 @@
  * 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.graph;
 
 import org.junit.Test;