Documentation updates and deprecation marking.

cdk · Oct 11, 2018 · 9a3990c · 9a3990c
1 parent 4f37be8
commit 9a3990c
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Showing 92 changed files with 104 additions and 16 deletions.
diff --git a/base/core/src/main/java/org/openscience/cdk/config/Isotopes.java b/base/core/src/main/java/org/openscience/cdk/config/Isotopes.java
@@ -114,7 +114,7 @@ private static boolean isMajor(IIsotope atom) {
 
     /**
      * Clear the isotope information from atoms that are major isotopes (e.g.
-     * <sup>12</sup>C, <sub>1</sup>H, etc).
+     * <sup>12</sup>C, <sup>1</sup>H, etc).
      * @param mol the molecule
      */
     public static void clearMajorIsotopes(IAtomContainer mol) {
@@ -128,7 +128,7 @@ public static void clearMajorIsotopes(IAtomContainer mol) {
 
     /**
      * Clear the isotope information from istopes that are major (e.g.
-     * <sup>12</sup>C, <sub>1</sup>H, etc).
+     * <sup>12</sup>C, <sup>1</sup>H, etc).
      * @param formula the formula
      */
     public static void clearMajorIsotopes(IMolecularFormula formula) {

diff --git a/legacy/src/main/java/org/openscience/cdk/geometry/GeometryTools.java b/legacy/src/main/java/org/openscience/cdk/geometry/GeometryTools.java
@@ -67,7 +67,9 @@
  *
  * @cdk.module    standard
  * @cdk.githash
+ * @deprecated use {@link GeometryUtil} moved for dependency reorganisation
  */
+@Deprecated
 public class GeometryTools {
 
     private static ILoggingTool logger = LoggingToolFactory.createLoggingTool(GeometryTools.class);

diff --git a/legacy/src/main/java/org/openscience/cdk/graph/BFSShortestPath.java b/legacy/src/main/java/org/openscience/cdk/graph/BFSShortestPath.java
@@ -40,7 +40,9 @@
  * @cdk.module  standard
  * @cdk.githash
  * @cdk.created 2004-10-19
+ * @deprecated Use {@link ShortestPaths}
  */
+@Deprecated
 public final class BFSShortestPath {
 
     private BFSShortestPath() {} // ensure non-instantiability.

diff --git a/legacy/src/main/java/org/openscience/cdk/graph/BiconnectivityInspector.java b/legacy/src/main/java/org/openscience/cdk/graph/BiconnectivityInspector.java
@@ -42,6 +42,7 @@
 import org._3pq.jgrapht.event.GraphVertexChangeEvent;
 import org._3pq.jgrapht.graph.SimpleGraph;
 import org._3pq.jgrapht.graph.Subgraph;
+import org.openscience.cdk.interfaces.IAtomContainer;
 
 /**
  * Finds the biconnected components of a graph.
@@ -52,8 +53,10 @@
  *
  * @cdk.module standard
  * @cdk.githash
- *
+ * @deprecated Use {@link org.openscience.cdk.ringsearch.RingSearch} or
+ *             {@link Cycles#markRingAtomsAndBonds(IAtomContainer)}
  */
+@Deprecated
 public class BiconnectivityInspector {
 
     private List            biconnectedSets;

diff --git a/legacy/src/main/java/org/openscience/cdk/graph/MinimalPathIterator.java b/legacy/src/main/java/org/openscience/cdk/graph/MinimalPathIterator.java
@@ -47,8 +47,9 @@
  *
  * @cdk.module standard
  * @cdk.githash
- *
+ * @deprecated use {@link ShortestPaths}
  */
+@Deprecated
 public class MinimalPathIterator implements Iterator {
 
     private Object        sourceVertex, targetVertex;

diff --git a/legacy/src/main/java/org/openscience/cdk/graph/MoleculeGraphs.java b/legacy/src/main/java/org/openscience/cdk/graph/MoleculeGraphs.java
@@ -39,6 +39,7 @@
  * @cdk.githash
  *
  */
+@Deprecated
 public class MoleculeGraphs {
 
     // make class non-instantiable

diff --git a/legacy/src/main/java/org/openscience/cdk/isomorphism/SmartsStereoMatch.java b/legacy/src/main/java/org/openscience/cdk/isomorphism/SmartsStereoMatch.java
@@ -55,6 +55,7 @@
  * @cdk.module smarts
  * @cdk.githash
  */
+@Deprecated
 public final class SmartsStereoMatch implements Predicate<int[]> {
 
     /** Query and target contains. */

diff --git a/legacy/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/AliphaticAtom.java b/legacy/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/AliphaticAtom.java
@@ -30,6 +30,7 @@
  * @cdk.githash
  * @cdk.keyword SMARTS
  */
+@Deprecated
 public class AliphaticAtom extends SMARTSAtom {
 
     private static final long serialVersionUID = 5145049891214205622L;

diff --git a/...cy/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/AliphaticSymbolAtom.java b/...cy/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/AliphaticSymbolAtom.java
@@ -28,6 +28,7 @@
  * @cdk.githash
  * @cdk.keyword SMARTS
  */
+@Deprecated
 public class AliphaticSymbolAtom extends SMARTSAtom {
 
     /**

diff --git a/legacy/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/AnyAtom.java b/legacy/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/AnyAtom.java
@@ -28,6 +28,7 @@
  * @cdk.githash
  * @cdk.keyword SMARTS
  */
+@Deprecated
 public class AnyAtom extends SMARTSAtom {
 
     private static final long serialVersionUID = -2061241755106011847L;

diff --git a/legacy/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/AnyOrderQueryBond.java b/legacy/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/AnyOrderQueryBond.java
@@ -29,6 +29,7 @@
  * @cdk.githash
  * @cdk.keyword SMARTS
  */
+@Deprecated
 public class AnyOrderQueryBond extends SMARTSBond {
 
     private static final long serialVersionUID = -826100570208878645L;

diff --git a/legacy/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/AromaticAtom.java b/legacy/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/AromaticAtom.java
@@ -30,6 +30,7 @@
 * @cdk.githash
 * @cdk.keyword SMARTS
 */
+@Deprecated
 public class AromaticAtom extends SMARTSAtom {
 
     private static final long serialVersionUID = -3345204886992669829L;

diff --git a/.../main/java/org/openscience/cdk/isomorphism/matchers/smarts/AromaticOrSingleQueryBond.java b/.../main/java/org/openscience/cdk/isomorphism/matchers/smarts/AromaticOrSingleQueryBond.java
@@ -30,6 +30,7 @@
  * @cdk.githash
  * @cdk.keyword SMARTS
  */
+@Deprecated
 public class AromaticOrSingleQueryBond extends SMARTSBond {
 
     private static final long serialVersionUID = 6941220923564432716L;

diff --git a/legacy/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/AromaticQueryBond.java b/legacy/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/AromaticQueryBond.java
@@ -30,6 +30,7 @@
  * @cdk.githash
  * @cdk.keyword SMARTS
  */
+@Deprecated
 public class AromaticQueryBond extends SMARTSBond {
 
     private static final long serialVersionUID = 6941220923564432716L;

diff --git a/legacy/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/AromaticSymbolAtom.java b/legacy/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/AromaticSymbolAtom.java
@@ -28,6 +28,7 @@
  * @cdk.githash
  * @cdk.keyword SMARTS
  */
+@Deprecated
 public class AromaticSymbolAtom extends SMARTSAtom {
 
     public AromaticSymbolAtom(String symbol, IChemObjectBuilder builder) {

diff --git a/legacy/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/AtomicNumberAtom.java b/legacy/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/AtomicNumberAtom.java
@@ -34,6 +34,7 @@
  * @cdk.githash
  * @cdk.keyword SMARTS
  */
+@Deprecated
 public class AtomicNumberAtom extends SMARTSAtom {
 
     /**

diff --git a/legacy/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/ChiralityAtom.java b/legacy/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/ChiralityAtom.java
@@ -29,6 +29,7 @@
  * @cdk.githash
  * @cdk.keyword SMARTS
  */
+@Deprecated
 public class ChiralityAtom extends SMARTSAtom {
 
     /**

diff --git a/...src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/ExplicitConnectionAtom.java b/...src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/ExplicitConnectionAtom.java
@@ -30,6 +30,7 @@
  * @cdk.keyword SMARTS
  * @cdk.githash
  */
+@Deprecated
 public final class ExplicitConnectionAtom extends SMARTSAtom {
 
     /** Number of explicit connections. */

diff --git a/legacy/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/FormalChargeAtom.java b/legacy/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/FormalChargeAtom.java
@@ -30,6 +30,7 @@
  * @cdk.githash
  * @cdk.keyword SMARTS
  */
+@Deprecated
 public class FormalChargeAtom extends SMARTSAtom {
 
     private static final long serialVersionUID = 1203658471548492071L;

diff --git a/...rc/main/java/org/openscience/cdk/isomorphism/matchers/smarts/HybridizationNumberAtom.java b/...rc/main/java/org/openscience/cdk/isomorphism/matchers/smarts/HybridizationNumberAtom.java
@@ -35,6 +35,7 @@
  * @cdk.keyword SMARTS
  */
 
+@Deprecated
 public class HybridizationNumberAtom extends SMARTSAtom {
 
     /**

diff --git a/legacy/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/HydrogenAtom.java b/legacy/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/HydrogenAtom.java
@@ -30,6 +30,7 @@
  * @cdk.githash
  * @cdk.keyword SMARTS
  */
+@Deprecated
 public class HydrogenAtom extends SMARTSAtom {
 
     /** Creates a new instance. */

diff --git a/legacy/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/ImplicitHCountAtom.java b/legacy/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/ImplicitHCountAtom.java
@@ -28,6 +28,7 @@
  * @cdk.githash
  * @cdk.keyword SMARTS
  */
+@Deprecated
 public class ImplicitHCountAtom extends SMARTSAtom {
 
     private static final long serialVersionUID = 6752937431492584928L;

diff --git a/...cy/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/LogicalOperatorAtom.java b/...cy/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/LogicalOperatorAtom.java
@@ -29,6 +29,7 @@
  * @cdk.githash
  * @cdk.keyword SMARTS
  */
+@Deprecated
 public class LogicalOperatorAtom extends SMARTSAtom {
 
     /**

diff --git a/...cy/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/LogicalOperatorBond.java b/...cy/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/LogicalOperatorBond.java
@@ -29,6 +29,7 @@
  * @cdk.githash
  * @cdk.keyword SMARTS
  */
+@Deprecated
 public class LogicalOperatorBond extends SMARTSBond {
 
     private static final long serialVersionUID = 7508020488830371461L;

diff --git a/legacy/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/MassAtom.java b/legacy/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/MassAtom.java
@@ -32,6 +32,7 @@
  * @cdk.githash
  * @cdk.keyword SMARTS
  */
+@Deprecated
 public class MassAtom extends SMARTSAtom {
 
     private final int mass;

diff --git a/legacy/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/NonCHHeavyAtom.java b/legacy/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/NonCHHeavyAtom.java
@@ -28,6 +28,7 @@
  * @cdk.githash
  * @cdk.keyword SMARTS
  */
+@Deprecated
 public class NonCHHeavyAtom extends SMARTSAtom {
 
     private static final long serialVersionUID = 5145049891214205622L;

diff --git a/legacy/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/OrderQueryBond.java b/legacy/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/OrderQueryBond.java
@@ -32,6 +32,7 @@
  * @cdk.githash
  * @cdk.keyword SMARTS
  */
+@Deprecated
 public class OrderQueryBond extends SMARTSBond {
 
     private static final long serialVersionUID = -5139538872961160661L;

diff --git a/...rc/main/java/org/openscience/cdk/isomorphism/matchers/smarts/PeriodicGroupNumberAtom.java b/...rc/main/java/org/openscience/cdk/isomorphism/matchers/smarts/PeriodicGroupNumberAtom.java
@@ -35,6 +35,7 @@
  * @cdk.keyword SMARTS
  */
 
+@Deprecated
 public class PeriodicGroupNumberAtom extends SMARTSAtom {
 
     int groupNumber;

diff --git a/.../src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/ReactionRoleQueryAtom.java b/.../src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/ReactionRoleQueryAtom.java
@@ -30,6 +30,7 @@
 /**
  * Matches atoms with a particular role in a reaction.
  */
+@Deprecated
 public class ReactionRoleQueryAtom extends SMARTSAtom {
 
     public static final int ROLE_REACTANT = 0x1;

diff --git a/...cy/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/RecursiveSmartsAtom.java b/...cy/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/RecursiveSmartsAtom.java
@@ -39,6 +39,7 @@
  * @cdk.githash
  * @cdk.keyword SMARTS
  */
+@Deprecated
 public final class RecursiveSmartsAtom extends SMARTSAtom {
 
     /** The IQueryAtomContainer created by parsing the recursive smarts */

diff --git a/legacy/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/RingBond.java b/legacy/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/RingBond.java
@@ -28,6 +28,7 @@
  * @cdk.githash
  * @cdk.keyword SMARTS
  */
+@Deprecated
 public class RingBond extends SMARTSBond {
 
     private static final long serialVersionUID = -8670609649648985629L;

diff --git a/legacy/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/RingIdentifierAtom.java b/legacy/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/RingIdentifierAtom.java
@@ -30,6 +30,7 @@
  * @cdk.githash
  * @cdk.keyword SMARTS
  */
+@Deprecated
 public class RingIdentifierAtom extends SMARTSAtom {
 
     private static final long serialVersionUID = -6812146026923460637L;

diff --git a/legacy/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/RingMembershipAtom.java b/legacy/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/RingMembershipAtom.java
@@ -31,6 +31,7 @@
  * @cdk.keyword SMARTS
  * @cdk.githash
  */
+@Deprecated
 public class RingMembershipAtom extends SMARTSAtom {
 
     /**

diff --git a/legacy/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/SMARTSAtom.java b/legacy/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/SMARTSAtom.java
@@ -30,6 +30,7 @@
  * @cdk.githash
  * @cdk.keyword SMARTS
  */
+@Deprecated
 public abstract class SMARTSAtom extends QueryAtom implements IQueryAtom {
 
     public SMARTSAtom(IChemObjectBuilder builder) {

diff --git a/...y/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/SMARTSAtomInvariants.java b/...y/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/SMARTSAtomInvariants.java
@@ -58,6 +58,7 @@
  * @author John May
  * @cdk.module smarts
  */
+@Deprecated
 final class SMARTSAtomInvariants {
 
     /** Property key to index the class by. */

diff --git a/legacy/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/SMARTSBond.java b/legacy/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/SMARTSBond.java
@@ -31,6 +31,7 @@
  * @cdk.githash
  * @cdk.keyword SMARTS
  */
+@Deprecated
 public class SMARTSBond extends QueryBond implements IQueryBond {
 
     private static final long serialVersionUID = 6164978147730140061L;

diff --git a/legacy/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/SmallestRingAtom.java b/legacy/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/SmallestRingAtom.java
@@ -39,6 +39,7 @@
  * @cdk.keyword SMARTS
  * @cdk.githash
  */
+@Deprecated
 public final class SmallestRingAtom extends SMARTSAtom {
 
     /** Ring size to check. */

diff --git a/legacy/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/SmartsMatchers.java b/legacy/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/SmartsMatchers.java
@@ -37,6 +37,7 @@
  * @cdk.module smarts
  * @cdk.githash
  */
+@Deprecated
 public final class SmartsMatchers {
 
     /**

diff --git a/legacy/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/StereoBond.java b/legacy/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/StereoBond.java
@@ -28,6 +28,7 @@
  * @cdk.githash
  * @cdk.keyword SMARTS
  */
+@Deprecated
 public class StereoBond extends SMARTSBond {
 
     private final boolean   unspecified;

diff --git a/...cy/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/TotalConnectionAtom.java b/...cy/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/TotalConnectionAtom.java
@@ -36,6 +36,7 @@
  * @cdk.githash
  * @cdk.keyword SMARTS
  */
+@Deprecated
 public final class TotalConnectionAtom extends SMARTSAtom {
 
     /** Total number of connections from an atom including H count. */

diff --git a/legacy/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/TotalHCountAtom.java b/legacy/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/TotalHCountAtom.java
@@ -31,6 +31,7 @@
  * @cdk.keyword SMARTS
  * @cdk.githash
  */
+@Deprecated
 public final class TotalHCountAtom extends SMARTSAtom {
 
     /** The total hydrogen count to match. */

diff --git a/...rc/main/java/org/openscience/cdk/isomorphism/matchers/smarts/TotalRingConnectionAtom.java b/...rc/main/java/org/openscience/cdk/isomorphism/matchers/smarts/TotalRingConnectionAtom.java
@@ -36,6 +36,7 @@
  * @cdk.githash
  * @cdk.keyword SMARTS
  */
+@Deprecated
 public final class TotalRingConnectionAtom extends SMARTSAtom {
 
     /** Number of rings. */

diff --git a/legacy/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/TotalValencyAtom.java b/legacy/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/TotalValencyAtom.java
@@ -29,6 +29,7 @@
  * @cdk.keyword SMARTS
  * @cdk.githash
  */
+@Deprecated
 public final class TotalValencyAtom extends SMARTSAtom {
 
     /**

diff --git a/legacy/src/main/java/org/openscience/cdk/smiles/smarts/SMARTSQueryTool.java b/legacy/src/main/java/org/openscience/cdk/smiles/smarts/SMARTSQueryTool.java
@@ -108,7 +108,9 @@
  * @cdk.githash
  * @cdk.keyword SMARTS
  * @cdk.keyword substructure search
+ * @deprecated use {@link org.openscience.cdk.smarts.SmartsPattern}
  */
+@Deprecated
 public class SMARTSQueryTool {
 
     private static ILoggingTool logger        = LoggingToolFactory.createLoggingTool(SMARTSQueryTool.class);

diff --git a/legacy/src/main/java/org/openscience/cdk/smiles/smarts/SmartsAtomAtomMapFilter.java b/legacy/src/main/java/org/openscience/cdk/smiles/smarts/SmartsAtomAtomMapFilter.java
@@ -66,6 +66,7 @@
  *
  * @see <a href="http://www.daylight.com/dayhtml/doc/theory/theory.smarts.html">Daylight Theory Manual</a>
  */
+@Deprecated
 final class SmartsAtomAtomMapFilter implements Predicate<int[]> {
 
     private final List<MappedPairs> mapped = new ArrayList<>();

diff --git a/legacy/src/main/java/org/openscience/cdk/smiles/smarts/parser/ASTAliphatic.java b/legacy/src/main/java/org/openscience/cdk/smiles/smarts/parser/ASTAliphatic.java
@@ -26,6 +26,7 @@
  * @cdk.githash
  * @cdk.keyword SMARTS AST
  */
+@Deprecated
 class ASTAliphatic extends SimpleNode {
 
     /**