Fix bad or malformed HTML warnings.

johnmay · Jan 20, 2017 · fe077e3 · fe077e3
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commit fe077e3
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diff --git a/base/core/src/main/java/org/openscience/cdk/config/Elements.java b/base/core/src/main/java/org/openscience/cdk/config/Elements.java
@@ -298,7 +298,7 @@ public int group() {
      * size of an atom that forms part of one covalent bond.
      *
      * @return covalent radius - null if not available
-     * @see <a href="http://en.wikipedia.org/wiki/Covalent_radius>Covalent radius</a>
+     * @see <a href="http://en.wikipedia.org/wiki/Covalent_radius">Covalent radius</a>
      */
     public Double covalentRadius() {
         return rCov;
@@ -310,7 +310,7 @@ public Double covalentRadius() {
      * atom.
      *
      * @return van der Waals radius - null if not available
-     * @see <a href="http://en.wikipedia.org/wiki/Van_der_Waals_radius>Van de Waals radius</a>
+     * @see <a href="http://en.wikipedia.org/wiki/Van_der_Waals_radius">Van de Waals radius</a>
      */
     public Double vdwRadius() {
         return rW;
@@ -324,7 +324,7 @@ public Double vdwRadius() {
      * available 'null' is returned.
      *
      * @return Pauling electronegativity - null if not available
-     * @see <a href="http://en.wikipedia.org/wiki/Electronegativity#Pauling_electronegativity>Pauling Electronegativity</a>
+     * @see <a href="http://en.wikipedia.org/wiki/Electronegativity#Pauling_electronegativity">Pauling Electronegativity</a>
      */
     public Double electronegativity() {
         return electronegativity;

diff --git a/base/core/src/main/java/org/openscience/cdk/graph/ConnectedComponents.java b/base/core/src/main/java/org/openscience/cdk/graph/ConnectedComponents.java
@@ -5,13 +5,13 @@
 /**
  * Compute the connected components of an adjacency list.
  *
- * <blockquote><pre>
+ * <blockquote><pre>{@code
  *     int[][]             g          = GraphUtil.toAdjList(container(l
  *     ConnectedComponents cc         = new ConnectedComponents(g);
  *     int[]               components = cc.components();
  *     for (int v = 0; v < g.length; v++)
  *         components[v];
- * </pre></blockquote>
+ * }</pre></blockquote>
  *
  * @author John May
  * @cdk.module core

diff --git a/base/core/src/main/java/org/openscience/cdk/graph/Cycles.java b/base/core/src/main/java/org/openscience/cdk/graph/Cycles.java
@@ -453,10 +453,10 @@ public static void markRingAtomsAndBonds(IAtomContainer mol, int[][] adjList, Ed
     /**
      * Use an auxiliary cycle finder if the primary method was intractable.
      *
-     * <blockquote><pre>
+     * <blockquote><pre>{@code
      * // all cycles or all cycles size <= 6
      * CycleFinder cf = Cycles.or(Cycles.all(), Cycles.all(6));
-     * </pre></blockquote>
+     * }</pre></blockquote>
      *
      * It is possible to nest multiple levels.
      *

diff --git a/base/core/src/main/java/org/openscience/cdk/graph/GraphUtil.java b/base/core/src/main/java/org/openscience/cdk/graph/GraphUtil.java
@@ -190,7 +190,7 @@ public static int[][] toAdjList(IAtomContainer container, EdgeToBondMap bondMap)
      * graph} to {@literal include} in the subgraph. The provided vertices also
      * provide the mapping between vertices in the subgraph and the original.
      *
-     * <blockquote><pre>
+     * <blockquote><pre>{@code
      * int[][] g  = toAdjList(naphthalene);
      * int[]   vs = new int[]{0, 1, 2, 3, 4, 5};
      *
@@ -199,7 +199,7 @@ public static int[][] toAdjList(IAtomContainer container, EdgeToBondMap bondMap)
      * for(int v = 0; v < h.length; v++) {
      *     // vs[v] is 'v' in 'g'
      * }
-     * </pre></blockquote>
+     * }</pre></blockquote>
      *
      * @param graph   adjacency list graph
      * @param include the vertices of he graph to include in the subgraph

diff --git a/base/core/src/main/java/org/openscience/cdk/graph/RelevantCycles.java b/base/core/src/main/java/org/openscience/cdk/graph/RelevantCycles.java
@@ -40,7 +40,7 @@
  * in number but can be checked (see {@link #size()}) before construction
  * {@cdk.cite Vismara97}.
  *
- * <blockquote><pre>
+ * <blockquote><pre>{@code
  * // import static org.openscience.cdk.graph.GraphUtil.*;
  * IAtomContainer m = ...;
  *
@@ -69,7 +69,7 @@
  *         }
  *     }
  * }
- *
+ * }
  * </pre></blockquote>
  *
  * @author John May
@@ -139,7 +139,7 @@ private List<Cycle> independent(final Collection<Cycle> cycles) {
     /**
      * Reconstruct the paths of all relevant cycles.
      *
-     * <blockquote><pre>
+     * <blockquote><pre>{@code
      * RelevantCycles relevant = ...
      *
      * // ensure the number is manageable
@@ -148,7 +148,7 @@ private List<Cycle> independent(final Collection<Cycle> cycles) {
      *     // process the path
      *   }
      * }
-     * </pre></blockquote>
+     * }</pre></blockquote>
      *
      * @return array of vertex paths
      */

diff --git a/base/core/src/main/java/org/openscience/cdk/graph/ShortestPaths.java b/base/core/src/main/java/org/openscience/cdk/graph/ShortestPaths.java
@@ -35,7 +35,7 @@
  * the paths. When no path is found (i.e. not-connected) an empty path is always
  * returned. 
  *
- * <blockquote><pre>
+ * <blockquote><pre>{@code
  * IAtomContainer benzene = MoleculeFactory.makeBenzene();
  *
  * IAtom c1 = benzene.getAtom(0);
@@ -57,6 +57,7 @@
  * int[][] paths = sp.pathsTo(c4);
  * int[] org = paths[0];  // paths[0] == path
  * int[] alt = paths[1];
+ * }
  * </pre></blockquote>
  *
  *  If shortest paths from multiple start atoms are required {@link
@@ -273,7 +274,7 @@ private void compute(final int[][] adjacent, final int[] ordering) {
      * is a member of a different fragment, or the vertex is not present in the
      * container at all.
      *
-     * <pre>
+     * <pre>{@code
      * ShortestPaths sp = ...;
      *
      * // reconstruct first path
@@ -283,7 +284,7 @@ private void compute(final int[][] adjacent, final int[] ordering) {
      * if(sp.nPathsTo(5) == 1){
      *     int[] path = sp.pathTo(5); // reconstruct the path
      * }
-     * </pre>
+     * }</pre>
      *
      * @param end the <i>end</i> vertex to find a path to
      * @return path from the <i>start</i> to the <i>end</i> vertex
@@ -307,7 +308,7 @@ public int[] pathTo(int end) {
      * a member of a different fragment, or the atom is not present in the
      * container at all.
      *
-     * <pre>
+     * <pre>{@code
      * ShortestPaths sp   = ...;
      * IAtom         end  = ...;
      *
@@ -318,7 +319,7 @@ public int[] pathTo(int end) {
      * if(sp.nPathsTo(end) == 1){
      *     int[] path = sp.pathTo(end); // reconstruct the path
      * }
-     * </pre>
+     * }</pre>
      *
      * @param end the <i>end</i> vertex to find a path to
      * @return path from the <i>start</i> to the <i>end</i> vertex
@@ -358,7 +359,7 @@ public boolean isPrecedingPathTo(int end) {
      * at maximum 1024 paths). It is safer to check the number of paths ({@link
      * #nPathsTo(int)}) before attempting to reconstruct all shortest paths.
      *
-     * <pre>
+     * <pre>{@code
      * int           threshold = 20;
      * ShortestPaths sp        = ...;
      *
@@ -369,7 +370,7 @@ public boolean isPrecedingPathTo(int end) {
      * if(sp.nPathsTo(5) < threshold){
      *     int[][] path = sp.pathsTo(5); // reconstruct shortest paths
      * }
-     * </pre>
+     * }</pre>
      *
      * @param end the end vertex
      * @return all shortest paths from the start to the end vertex
@@ -387,15 +388,15 @@ public int[][] pathsTo(int end) {
      * size arrays of vertex indices. When there is no path an empty array is
      * returned. It is considered there to be no path if the end vertex belongs
      * to the same container but is a member of a different fragment, or the
-     * vertex is not present in the container at all. 
+     * vertex is not present in the container at all.
      *
      * <b>Important:</b> for every possible branch the number of possible paths
      * doubles and could be in the order of tens of thousands. Although the
      * chance of finding such a molecule is highly unlikely (C720 fullerene has
      * at maximum 1024 paths). It is safer to check the number of paths ({@link
      * #nPathsTo(int)}) before attempting to reconstruct all shortest paths.
      *
-     * <pre>
+     * <pre>{@code
      * int           threshold = 20;
      * ShortestPaths sp        = ...;
      * IAtom         end       = ...;
@@ -407,7 +408,7 @@ public int[][] pathsTo(int end) {
      * if(sp.nPathsTo(end) < threshold){
      *     int[][] path = sp.pathsTo(end); // reconstruct shortest paths
      * }
-     * </pre>
+     * }</pre>
      *
      * @param end the end atom
      * @return all shortest paths from the start to the end vertex
@@ -425,7 +426,7 @@ public int[][] pathsTo(IAtom end) {
      * is a member of a different fragment, or the vertex is not present in the
      * container at all.
      *
-     * <pre>
+     * <pre>{@code
      * ShortestPaths sp = ...;
      *
      * // reconstruct a shortest path
@@ -435,7 +436,7 @@ public int[][] pathsTo(IAtom end) {
      * if(sp.nPathsTo(5) == 1){
      *     IAtom[] path = sp.atomsTo(5); // reconstruct shortest path
      * }
-     * </pre>
+     * }</pre>
      *
      * @param end the <i>end</i> vertex to find a path to
      * @return path from the <i>start</i> to the <i>end</i> atoms as fixed size
@@ -467,7 +468,7 @@ public IAtom[] atomsTo(int end) {
      * container at all.
      *
      *
-     * <pre>
+     * <pre>{@code
      * ShortestPaths sp   = ...;
      * IAtom         end  = ...;
      *
@@ -478,7 +479,7 @@ public IAtom[] atomsTo(int end) {
      * if(sp.nPathsTo(end) == 1){
      *     IAtom[] path = sp.atomsTo(end); // reconstruct shortest path
      * }
-     * </pre>
+     * }</pre>
      *
      * @param end the <i>end</i> atom to find a path to
      * @return path from the <i>start</i> to the <i>end</i> atoms as fixed size
@@ -497,13 +498,13 @@ public IAtom[] atomsTo(IAtom end) {
      * vertex belongs to the same container but is a member of a different
      * fragment, or the vertex is not present in the container at all.
      *
-     * <pre>
+     * <pre>{@code
      * ShortestPaths sp   = ...;
      *
      * sp.nPathsTo(5); // number of paths
      *
      * sp.nPathsTo(-1); // returns 0 - there are no paths
-     * </pre>
+     * }</pre>
      *
      * @param end the <i>end</i> vertex to which the number of paths will be
      *            returned
@@ -519,15 +520,15 @@ public int nPathsTo(int end) {
      * atom belongs to the same container but is a member of a different
      * fragment, or the atom is not present in the container at all.
      *
-     * <pre>
+     * <pre>{@code
      * ShortestPaths sp   = ...;
      * IAtom         end  = ...l
      *
      * sp.nPathsTo(end); // number of paths
      *
      * sp.nPathsTo(null);           // returns 0 - there are no paths
      * sp.nPathsTo(new Atom("C"));  // returns 0 - there are no paths
-     * </pre>
+     * }</pre>
      *
      * @param end the <i>end</i> vertex to which the number of paths will be
      *            returned
@@ -543,7 +544,7 @@ public int nPathsTo(IAtom end) {
      * Formally, there is a path if the distance is less then the number of
      * vertices.
      *
-     * <pre>
+     * <pre>{@code
      * IAtomContainer container = ...;
      * ShortestPaths  sp        = ...; // start = 0
      *
@@ -552,7 +553,7 @@ public int nPathsTo(IAtom end) {
      * if(sp.distanceTo(5) < n) {
      *     // these is a path from 0 to 5
      * }
-     * </pre>
+     * }</pre>
      *
      * Conveniently the distance is also the index of the last vertex in the
      * path.
@@ -582,7 +583,7 @@ public int distanceTo(int end) {
      * Formally, there is a path if the distance is less then the number of
      * atoms.
      *
-     * <pre>
+     * <pre>{@code
      * IAtomContainer container = ...;
      * ShortestPaths  sp        = ...; // start atom
      * IAtom          end       = ...;
@@ -592,21 +593,21 @@ public int distanceTo(int end) {
      * if( sp.distanceTo(end) < n ) {
      *     // these is a path from start to end
      * }
-     *
+     * }
      * </pre>
      *
      * Conveniently the distance is also the index of the last vertex in the
      * path.
      *
-     * <pre>
+     * <pre>{@code
      * IAtomContainer container = ...;
      * ShortestPaths  sp        = ...; // start atom
      * IAtom          end       = ...;
      *
      * int atoms = sp.atomsTo(end);
      * // end == atoms[sp.distanceTo(end)];
      *
-     * </pre>
+     * }</pre>
      *
      * @param end atom to measure the distance to
      * @return distance to the given atom