From d794320d5484988a8a3e91b38aaebf87fa4dfef5 Mon Sep 17 00:00:00 2001 From: John May Date: Fri, 20 Jan 2017 15:38:04 +0000 Subject: [PATCH] Inherit doc is an inline tag --- .../org/openscience/cdk/DynamicFactory.java | 34 ++++++++-------- .../org/openscience/cdk/graph/BitMatrix.java | 2 +- .../org/openscience/cdk/graph/Cycles.java | 22 +++++----- .../cdk/graph/EssentialCycles.java | 8 ++-- .../org/openscience/cdk/graph/GraphUtil.java | 4 +- .../openscience/cdk/graph/InitialCycles.java | 12 +++--- .../openscience/cdk/graph/JumboPathGraph.java | 12 +++--- .../cdk/graph/RegularPathGraph.java | 12 +++--- .../openscience/cdk/graph/ShortestPaths.java | 12 +++--- .../cdk/graph/TripletShortCycles.java | 2 +- .../ringsearch/JumboCyclicVertexSearch.java | 10 ++--- .../ringsearch/RegularCyclicVertexSearch.java | 10 ++--- .../cdk/stereo/DoubleBondStereochemistry.java | 2 +- .../cdk/stereo/ExtendedTetrahedral.java | 6 +-- .../cdk/stereo/TetrahedralChirality.java | 4 +- .../org/openscience/cdk/AtomContainer.java | 8 ++-- .../org/openscience/cdk/AtomContainerSet.java | 2 +- .../java/org/openscience/cdk/ChemModel.java | 2 +- .../java/org/openscience/cdk/ChemObject.java | 8 ++-- .../cdk/DefaultChemObjectBuilder.java | 2 +- .../java/org/openscience/cdk/Monomer.java | 2 +- .../java/org/openscience/cdk/ReactionSet.java | 2 +- .../main/java/org/openscience/cdk/Ring.java | 2 +- .../cdk/formula/MolecularFormula.java | 4 +- .../cdk/protein/data/PDBMonomer.java | 2 +- .../cdk/protein/data/PDBPolymer.java | 2 +- .../cdk/debug/DebugAtomContainer.java | 4 +- .../cdk/debug/DebugAtomContainerSet.java | 2 +- .../openscience/cdk/debug/DebugChemModel.java | 2 +- .../cdk/debug/DebugChemObject.java | 4 +- .../cdk/debug/DebugChemObjectBuilder.java | 2 +- .../cdk/debug/DebugReactionSet.java | 2 +- .../openscience/cdk/debug/DebugSubstance.java | 2 +- .../cdk/interfaces/IAminoAcid.java | 2 +- .../org/openscience/cdk/interfaces/IAtom.java | 2 +- .../cdk/interfaces/IAtomContainer.java | 2 +- .../cdk/interfaces/IBioPolymer.java | 2 +- .../org/openscience/cdk/interfaces/IBond.java | 2 +- .../openscience/cdk/interfaces/ICrystal.java | 2 +- .../IDoubleBondStereochemistry.java | 2 +- .../openscience/cdk/interfaces/IMonomer.java | 2 +- .../cdk/interfaces/IPDBMonomer.java | 2 +- .../cdk/interfaces/IPDBPolymer.java | 2 +- .../openscience/cdk/interfaces/IPolymer.java | 2 +- .../cdk/interfaces/IPseudoAtom.java | 2 +- .../org/openscience/cdk/interfaces/IRing.java | 2 +- .../openscience/cdk/interfaces/IStrand.java | 2 +- .../cdk/interfaces/ITetrahedralChirality.java | 2 +- .../cdk/isomorphism/AbstractVFState.java | 12 +++--- .../cdk/isomorphism/AtomMatcher.java | 6 +-- .../cdk/isomorphism/BondMatcher.java | 8 ++-- .../openscience/cdk/isomorphism/Mappings.java | 8 ++-- .../cdk/isomorphism/StateStream.java | 6 +-- .../openscience/cdk/isomorphism/Ullmann.java | 2 +- .../cdk/isomorphism/UllmannState.java | 16 ++++---- .../cdk/isomorphism/UniqueAtomMatches.java | 2 +- .../cdk/isomorphism/UniqueBondMatches.java | 6 +-- .../cdk/isomorphism/VentoFoggia.java | 6 +-- .../matchers/QueryAtomContainerCreator.java | 8 ++-- .../isomorphism/matchers/QueryChemObject.java | 14 +++---- .../openscience/cdk/silent/AtomContainer.java | 8 ++-- .../cdk/silent/AtomContainerSet.java | 2 +- .../org/openscience/cdk/silent/ChemModel.java | 2 +- .../openscience/cdk/silent/ChemObject.java | 14 +++---- .../cdk/silent/MolecularFormula.java | 4 +- .../org/openscience/cdk/silent/Monomer.java | 2 +- .../openscience/cdk/silent/PDBMonomer.java | 2 +- .../openscience/cdk/silent/PDBPolymer.java | 2 +- .../openscience/cdk/silent/ReactionSet.java | 2 +- .../java/org/openscience/cdk/silent/Ring.java | 2 +- .../cdk/silent/SilentChemObjectBuilder.java | 2 +- .../cdk/aromaticity/AtomTypeModel.java | 2 +- .../cdk/aromaticity/DaylightModel.java | 2 +- .../cdk/aromaticity/PiBondModel.java | 2 +- .../cdk/graph/EdmondsMaximumMatching.java | 4 +- .../org/openscience/cdk/graph/Matching.java | 2 +- .../cdk/stereo/StereoElementFactory.java | 20 +++++----- .../cdk/fingerprint/ShortestPathWalker.java | 2 +- .../HybridizationRatioDescriptor.java | 4 +- .../cdk/renderer/SymbolVisibility.java | 2 +- .../cdk/renderer/color/UniColor.java | 4 +- .../cdk/renderer/elements/Bounds.java | 4 +- .../cdk/renderer/elements/MarkedElement.java | 2 +- .../cdk/renderer/elements/path/Close.java | 2 +- .../cdk/renderer/elements/path/CubicTo.java | 2 +- .../cdk/renderer/elements/path/LineTo.java | 2 +- .../cdk/renderer/elements/path/MoveTo.java | 2 +- .../cdk/renderer/elements/path/QuadTo.java | 2 +- .../generators/standard/ConvexHull.java | 4 +- .../generators/standard/HydrogenPosition.java | 2 +- .../standard/SelectionVisibility.java | 2 +- .../standard/StandardBondGenerator.java | 2 +- .../standard/StandardGenerator.java | 40 +++++++++---------- .../generators/standard/TextOutline.java | 2 +- .../generators/HighlightGenerator.java | 8 ++-- .../org/openscience/cdk/io/ChemObjectIO.java | 20 +++++----- .../group/AtomDiscretePartitionRefiner.java | 4 +- .../group/AtomEquitablePartitionRefiner.java | 4 +- .../group/BondDiscretePartitionRefiner.java | 4 +- .../group/BondEquitablePartitionRefiner.java | 4 +- .../org/openscience/cdk/group/Partition.java | 6 +-- .../openscience/cdk/group/Permutation.java | 6 +-- .../cdk/group/PermutationGroup.java | 2 +- .../cdk/hash/AllEquivalentCyclicSet.java | 2 +- .../openscience/cdk/hash/AtomSuppression.java | 4 +- .../cdk/hash/BasicAtomEncoder.java | 14 +++---- .../cdk/hash/BasicAtomHashGenerator.java | 2 +- .../cdk/hash/BasicMoleculeHashGenerator.java | 2 +- .../cdk/hash/ConjugatedAtomEncoder.java | 2 +- .../cdk/hash/HashGeneratorMaker.java | 2 +- .../cdk/hash/MinimumEquivalentCyclicSet.java | 2 +- .../hash/MinimumEquivalentCyclicSetUnion.java | 2 +- .../cdk/hash/PerturbedAtomHashGenerator.java | 2 +- .../openscience/cdk/hash/SeedGenerator.java | 2 +- .../org/openscience/cdk/hash/Suppressed.java | 12 +++--- .../cdk/hash/SuppressedAtomHashGenerator.java | 2 +- .../hash/stereo/BasicPermutationParity.java | 2 +- .../stereo/CombinedPermutationParity.java | 2 +- .../DoubleBondElementEncoderFactory.java | 2 +- .../cdk/hash/stereo/GeometricParity.java | 2 +- .../cdk/hash/stereo/GeometryEncoder.java | 4 +- .../cdk/hash/stereo/MultiStereoEncoder.java | 4 +- .../cdk/hash/stereo/Tetrahedral2DParity.java | 2 +- .../cdk/hash/stereo/Tetrahedral3DParity.java | 2 +- .../TetrahedralElementEncoderFactory.java | 2 +- .../matchers/smarts/ChiralityAtom.java | 2 +- .../smarts/ExplicitConnectionAtom.java | 2 +- .../matchers/smarts/LogicalOperatorAtom.java | 12 +++--- .../matchers/smarts/RingMembershipAtom.java | 2 +- .../matchers/smarts/SmallestRingAtom.java | 2 +- .../matchers/smarts/TotalConnectionAtom.java | 2 +- .../matchers/smarts/TotalHCountAtom.java | 2 +- .../smarts/TotalRingConnectionAtom.java | 2 +- .../matchers/smarts/TotalValencyAtom.java | 2 +- .../cdk/smiles/smarts/SmartsPattern.java | 2 +- 135 files changed, 322 insertions(+), 322 deletions(-) diff --git a/base/core/src/main/java/org/openscience/cdk/DynamicFactory.java b/base/core/src/main/java/org/openscience/cdk/DynamicFactory.java index 42def06c00..87f90135f0 100644 --- a/base/core/src/main/java/org/openscience/cdk/DynamicFactory.java +++ b/base/core/src/main/java/org/openscience/cdk/DynamicFactory.java @@ -831,7 +831,7 @@ private ObjectBasedKey(Class intf, Object[] params) { } /** - * @inheritDoc + *{@inheritDoc} */ @Override public Class intf() { @@ -839,7 +839,7 @@ public Class intf() { } /** - * @inheritDoc + *{@inheritDoc} */ @Override public Class type(int i) { @@ -848,7 +848,7 @@ public Class type(int i) { } /** - * @inheritDoc + *{@inheritDoc} */ @Override public int n() { @@ -880,7 +880,7 @@ private ClassBasedKey(Class intf, Class[] params) { } /** - * @inheritDoc + *{@inheritDoc} */ @Override public Class intf() { @@ -888,7 +888,7 @@ public Class intf() { } /** - * @inheritDoc + *{@inheritDoc} */ @Override public Class type(int i) { @@ -896,7 +896,7 @@ public Class type(int i) { } /** - * @inheritDoc + *{@inheritDoc} */ @Override public int n() { @@ -934,7 +934,7 @@ public static abstract class ConstructorKey implements Comparable[] getInterfaces(Class c) { @@ -1115,7 +1115,7 @@ private ModifiedCreator(Creator parent, CreationModifier modifier) { } /** - * @inheritDoc + *{@inheritDoc} */ @Override public T create(Object[] objects) throws InvocationTargetException, IllegalAccessException, @@ -1126,7 +1126,7 @@ public T create(Object[] objects) throws InvocationTargetException, IllegalAcces } /** - * @inheritDoc + *{@inheritDoc} */ @Override public Class getDeclaringClass() { @@ -1184,7 +1184,7 @@ public BasicCreator(Class c) { } /** - * @inheritDoc + *{@inheritDoc} */ @Override public Class getDeclaringClass() { @@ -1214,7 +1214,7 @@ public ArrayWrapCreator(Creator parent) { } /** - * @inheritDoc + *{@inheritDoc} */ @Override public T create(Object[] objects) throws InvocationTargetException, IllegalAccessException, @@ -1223,7 +1223,7 @@ public T create(Object[] objects) throws InvocationTargetException, IllegalAcces } /** - * @inheritDoc + *{@inheritDoc} */ @Override public Class getDeclaringClass() { @@ -1251,7 +1251,7 @@ private ReflectionCreator(Constructor constructor) { } /** - * @inheritDoc + *{@inheritDoc} */ @Override public T create(Object[] objects) throws InvocationTargetException, IllegalAccessException, @@ -1260,7 +1260,7 @@ public T create(Object[] objects) throws InvocationTargetException, IllegalAcces } /** - * @inheritDoc + *{@inheritDoc} */ @Override public Class getDeclaringClass() { diff --git a/base/core/src/main/java/org/openscience/cdk/graph/BitMatrix.java b/base/core/src/main/java/org/openscience/cdk/graph/BitMatrix.java index 294527aa2e..2abbfcca89 100644 --- a/base/core/src/main/java/org/openscience/cdk/graph/BitMatrix.java +++ b/base/core/src/main/java/org/openscience/cdk/graph/BitMatrix.java @@ -212,7 +212,7 @@ int indexOf(int x, int y) { return -1; } - /** @inheritDoc */ + /**{@inheritDoc} */ @Override public String toString() { StringBuilder sb = new StringBuilder((4 + n) * m); 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 index ea900dd593..feb8ff9848 100644 --- a/base/core/src/main/java/org/openscience/cdk/graph/Cycles.java +++ b/base/core/src/main/java/org/openscience/cdk/graph/Cycles.java @@ -819,7 +819,7 @@ int[][] apply(int[][] graph, int length) throws Intractable { */ abstract int[][] apply(int[][] graph, int length) throws Intractable; - /** @inheritDoc */ + /**{@inheritDoc} */ @Override public Cycles find(IAtomContainer molecule) throws Intractable { return find(molecule, molecule.getAtomCount()); @@ -855,7 +855,7 @@ public Cycles find(IAtomContainer molecule, int length) throws Intractable { return new Cycles(walks.toArray(new int[walks.size()][0]), molecule, bondMap); } - /** @inheritDoc */ + /**{@inheritDoc} */ @Override public Cycles find(IAtomContainer molecule, int[][] graph, int length) throws Intractable { @@ -980,19 +980,19 @@ private AllUpToLength(int length) { this.predefinedLength = length; } - /** @inheritDoc */ + /**{@inheritDoc} */ @Override public Cycles find(IAtomContainer molecule) throws Intractable { return find(molecule, molecule.getAtomCount()); } - /** @inheritDoc */ + /**{@inheritDoc} */ @Override public Cycles find(IAtomContainer molecule, int length) throws Intractable { return find(molecule, GraphUtil.toAdjList(molecule), length); } - /** @inheritDoc */ + /**{@inheritDoc} */ @Override public Cycles find(IAtomContainer molecule, int[][] graph, int length) throws Intractable { RingSearch ringSearch = new RingSearch(molecule, graph); @@ -1057,19 +1057,19 @@ private Fallback(CycleFinder primary, CycleFinder auxiliary) { this.auxiliary = auxiliary; } - /** @inheritDoc */ + /**{@inheritDoc} */ @Override public Cycles find(IAtomContainer molecule) throws Intractable { return find(molecule, molecule.getAtomCount()); } - /** @inheritDoc */ + /**{@inheritDoc} */ @Override public Cycles find(IAtomContainer molecule, int length) throws Intractable { return find(molecule, GraphUtil.toAdjList(molecule), length); } - /** @inheritDoc */ + /**{@inheritDoc} */ @Override public Cycles find(IAtomContainer molecule, int[][] graph, int length) throws Intractable { try { @@ -1098,19 +1098,19 @@ private Unchorded(CycleFinder primary) { this.primary = primary; } - /** @inheritDoc */ + /**{@inheritDoc} */ @Override public Cycles find(IAtomContainer molecule) throws Intractable { return find(molecule, molecule.getAtomCount()); } - /** @inheritDoc */ + /**{@inheritDoc} */ @Override public Cycles find(IAtomContainer molecule, int length) throws Intractable { return find(molecule, GraphUtil.toAdjList(molecule), length); } - /** @inheritDoc */ + /**{@inheritDoc} */ @Override public Cycles find(IAtomContainer molecule, int[][] graph, int length) throws Intractable { diff --git a/base/core/src/main/java/org/openscience/cdk/graph/EssentialCycles.java b/base/core/src/main/java/org/openscience/cdk/graph/EssentialCycles.java index 9c4e9f55c7..be5191238d 100644 --- a/base/core/src/main/java/org/openscience/cdk/graph/EssentialCycles.java +++ b/base/core/src/main/java/org/openscience/cdk/graph/EssentialCycles.java @@ -195,25 +195,25 @@ private MyCycle(int[] path) { super(null, path); } - /** @inheritDoc */ + /**{@inheritDoc} */ @Override BitSet edges(int[] path) { return initial.toEdgeVector(path); } - /** @inheritDoc */ + /**{@inheritDoc} */ @Override int[][] family() { return new int[][]{path()}; } - /** @inheritDoc */ + /**{@inheritDoc} */ @Override int sizeOfFamily() { return 1; } - /** @inheritDoc */ + /**{@inheritDoc} */ @Override public String toString() { return Arrays.toString(path()); 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 index c60b90ab9d..810a158bb9 100644 --- a/base/core/src/main/java/org/openscience/cdk/graph/GraphUtil.java +++ b/base/core/src/main/java/org/openscience/cdk/graph/GraphUtil.java @@ -372,7 +372,7 @@ private Tuple(int u, int v) { } /** - * @inheritDoc + *{@inheritDoc} */ @Override public boolean equals(Object o) { @@ -385,7 +385,7 @@ public boolean equals(Object o) { } /** - * @inheritDoc + *{@inheritDoc} */ @Override public int hashCode() { diff --git a/base/core/src/main/java/org/openscience/cdk/graph/InitialCycles.java b/base/core/src/main/java/org/openscience/cdk/graph/InitialCycles.java index 355efb69ac..4479d512fa 100644 --- a/base/core/src/main/java/org/openscience/cdk/graph/InitialCycles.java +++ b/base/core/src/main/java/org/openscience/cdk/graph/InitialCycles.java @@ -563,13 +563,13 @@ class EvenCycle extends Cycle { this.y = y; } - /** @inheritDoc */ + /**{@inheritDoc} */ @Override BitSet edges(int[] path) { return toEdgeVector(path); } - /** @inheritDoc */ + /**{@inheritDoc} */ @Override int[][] family() { @@ -586,7 +586,7 @@ int[][] family() { return paths; } - /** @inheritDoc */ + /**{@inheritDoc} */ @Override int sizeOfFamily() { return paths.nPathsTo(p) * paths.nPathsTo(q); @@ -609,13 +609,13 @@ class OddCycle extends Cycle { z = pathToZ[pathToY.length - 1]; } - /** @inheritDoc */ + /**{@inheritDoc} */ @Override BitSet edges(int[] path) { return toEdgeVector(path); } - /** @inheritDoc */ + /**{@inheritDoc} */ @Override int[][] family() { int[][] pathsToY = paths.pathsTo(y); @@ -631,7 +631,7 @@ int[][] family() { return paths; } - /** @inheritDoc */ + /**{@inheritDoc} */ @Override int sizeOfFamily() { return paths.nPathsTo(y) * paths.nPathsTo(z); diff --git a/base/core/src/main/java/org/openscience/cdk/graph/JumboPathGraph.java b/base/core/src/main/java/org/openscience/cdk/graph/JumboPathGraph.java index 9282b6c75d..3374eb3354 100644 --- a/base/core/src/main/java/org/openscience/cdk/graph/JumboPathGraph.java +++ b/base/core/src/main/java/org/openscience/cdk/graph/JumboPathGraph.java @@ -116,7 +116,7 @@ private void add(final PathEdge edge) { graph[v].add(edge); } - /** @inheritDoc */ + /**{@inheritDoc} */ @Override public int degree(final int x) { return graph[x].size(); @@ -159,7 +159,7 @@ private List combine(final List edges, final int x) { return reduced; } - /** @inheritDoc */ + /**{@inheritDoc} */ @Override void remove(final int x, final List cycles) { @@ -285,13 +285,13 @@ static final class SimpleEdge extends PathEdge { super(u, v, EMPTY_SET); } - /** @inheritDoc */ + /**{@inheritDoc} */ @Override ArrayBuilder reconstruct(ArrayBuilder ab) { return ab.append(other(ab.prev())); } - /** @inheritDoc */ + /**{@inheritDoc} */ @Override int len() { return 2; @@ -321,13 +321,13 @@ static final class ReducedEdge extends PathEdge { this.f = f; } - /** @inheritDoc */ + /**{@inheritDoc} */ @Override ArrayBuilder reconstruct(ArrayBuilder ab) { return u == ab.prev() ? f.reconstruct(e.reconstruct(ab)) : e.reconstruct(f.reconstruct(ab)); } - /** @inheritDoc */ + /**{@inheritDoc} */ @Override int len() { return xs.cardinality() + 2; diff --git a/base/core/src/main/java/org/openscience/cdk/graph/RegularPathGraph.java b/base/core/src/main/java/org/openscience/cdk/graph/RegularPathGraph.java index f0119f344d..fe73e5c332 100644 --- a/base/core/src/main/java/org/openscience/cdk/graph/RegularPathGraph.java +++ b/base/core/src/main/java/org/openscience/cdk/graph/RegularPathGraph.java @@ -116,7 +116,7 @@ private void add(final PathEdge edge) { graph[v].add(edge); } - /** @inheritDoc */ + /**{@inheritDoc} */ @Override public int degree(final int x) { return graph[x].size(); @@ -159,7 +159,7 @@ private List combine(final List edges, final int x) { return reduced; } - /** @inheritDoc */ + /**{@inheritDoc} */ @Override void remove(final int x, final List cycles) { @@ -285,13 +285,13 @@ static final class SimpleEdge extends PathEdge { super(u, v, EMPTY_SET); } - /** @inheritDoc */ + /**{@inheritDoc} */ @Override ArrayBuilder reconstruct(ArrayBuilder ab) { return ab.append(other(ab.prev())); } - /** @inheritDoc */ + /**{@inheritDoc} */ @Override int len() { return 2; @@ -321,13 +321,13 @@ static final class ReducedEdge extends PathEdge { this.f = f; } - /** @inheritDoc */ + /**{@inheritDoc} */ @Override ArrayBuilder reconstruct(ArrayBuilder ab) { return u == ab.prev() ? f.reconstruct(e.reconstruct(ab)) : e.reconstruct(f.reconstruct(ab)); } - /** @inheritDoc */ + /**{@inheritDoc} */ @Override int len() { return Long.bitCount(xs) + 2; 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 index 3cfcb783f4..130df8e451 100644 --- a/base/core/src/main/java/org/openscience/cdk/graph/ShortestPaths.java +++ b/base/core/src/main/java/org/openscience/cdk/graph/ShortestPaths.java @@ -654,14 +654,14 @@ public Source(int v) { this.v = v; } - /** @inheritDoc */ + /**{@inheritDoc} */ @Override public int[][] toPaths(int n) { // only every one shortest path at source return new int[][]{toPath(n)}; } - /** @inheritDoc */ + /**{@inheritDoc} */ @Override public int[] toPath(int n) { // create the path of the given length @@ -691,7 +691,7 @@ private SequentialRoute(Route parent, int v) { this.parent = parent; } - /** @inheritDoc */ + /**{@inheritDoc} */ @Override public int[][] toPaths(int n) { @@ -706,7 +706,7 @@ public int[][] toPaths(int n) { } - /** @inheritDoc */ + /**{@inheritDoc} */ @Override public int[] toPath(int n) { int[] path = parent.toPath(n); @@ -737,7 +737,7 @@ private Branch(Route left, Route right) { this.right = right; } - /** @inheritDoc */ + /**{@inheritDoc} */ @Override public int[][] toPaths(int n) { @@ -754,7 +754,7 @@ public int[][] toPaths(int n) { return paths; } - /** @inheritDoc */ + /**{@inheritDoc} */ @Override public int[] toPath(int n) { // use the left as the first path diff --git a/base/core/src/main/java/org/openscience/cdk/graph/TripletShortCycles.java b/base/core/src/main/java/org/openscience/cdk/graph/TripletShortCycles.java index 48cdd4d830..134771f474 100644 --- a/base/core/src/main/java/org/openscience/cdk/graph/TripletShortCycles.java +++ b/base/core/src/main/java/org/openscience/cdk/graph/TripletShortCycles.java @@ -545,7 +545,7 @@ private int[] toArray() { return p; } - /** @inheritDoc */ + /**{@inheritDoc} */ @Override public int compareTo(final Path that) { if (this.len() > that.len()) return +1; diff --git a/base/core/src/main/java/org/openscience/cdk/ringsearch/JumboCyclicVertexSearch.java b/base/core/src/main/java/org/openscience/cdk/ringsearch/JumboCyclicVertexSearch.java index 0ff09035e9..cc5e6c6712 100644 --- a/base/core/src/main/java/org/openscience/cdk/ringsearch/JumboCyclicVertexSearch.java +++ b/base/core/src/main/java/org/openscience/cdk/ringsearch/JumboCyclicVertexSearch.java @@ -180,7 +180,7 @@ private int[] buildVertexColor() { } /** - * @inheritDoc + *{@inheritDoc} */ @Override public boolean cyclic(int v) { @@ -188,7 +188,7 @@ public boolean cyclic(int v) { } /** - * @inheritDoc + *{@inheritDoc} */ @Override public boolean cyclic(int u, int v) { @@ -215,7 +215,7 @@ public boolean cyclic(int u, int v) { } /** - * @inheritDoc + *{@inheritDoc} */ @Override public int[] cyclic() { @@ -223,7 +223,7 @@ public int[] cyclic() { } /** - * @inheritDoc + *{@inheritDoc} */ @Override public int[][] isolated() { @@ -235,7 +235,7 @@ public int[][] isolated() { } /** - * @inheritDoc + *{@inheritDoc} */ @Override public int[][] fused() { diff --git a/base/core/src/main/java/org/openscience/cdk/ringsearch/RegularCyclicVertexSearch.java b/base/core/src/main/java/org/openscience/cdk/ringsearch/RegularCyclicVertexSearch.java index 202726e14a..5fec574408 100644 --- a/base/core/src/main/java/org/openscience/cdk/ringsearch/RegularCyclicVertexSearch.java +++ b/base/core/src/main/java/org/openscience/cdk/ringsearch/RegularCyclicVertexSearch.java @@ -268,7 +268,7 @@ private int[] buildVertexColor() { } /** - * @inheritDoc + *{@inheritDoc} */ @Override public boolean cyclic(int v) { @@ -276,7 +276,7 @@ public boolean cyclic(int v) { } /** - * @inheritDoc + *{@inheritDoc} */ @Override public boolean cyclic(int u, int v) { @@ -306,7 +306,7 @@ public boolean cyclic(int u, int v) { } /** - * @inheritDoc + *{@inheritDoc} */ @Override public int[] cyclic() { @@ -314,7 +314,7 @@ public int[] cyclic() { } /** - * @inheritDoc + *{@inheritDoc} */ @Override public int[][] isolated() { @@ -326,7 +326,7 @@ public int[][] isolated() { } /** - * @inheritDoc + *{@inheritDoc} */ @Override public int[][] fused() { diff --git a/base/core/src/main/java/org/openscience/cdk/stereo/DoubleBondStereochemistry.java b/base/core/src/main/java/org/openscience/cdk/stereo/DoubleBondStereochemistry.java index 67af05615b..8905e3b440 100644 --- a/base/core/src/main/java/org/openscience/cdk/stereo/DoubleBondStereochemistry.java +++ b/base/core/src/main/java/org/openscience/cdk/stereo/DoubleBondStereochemistry.java @@ -93,7 +93,7 @@ public Conformation getStereo() { } /** - * @inheritDoc + *{@inheritDoc} */ @Override public boolean contains(IAtom atom) { diff --git a/base/core/src/main/java/org/openscience/cdk/stereo/ExtendedTetrahedral.java b/base/core/src/main/java/org/openscience/cdk/stereo/ExtendedTetrahedral.java index ae14ae0aba..9de8553f9b 100644 --- a/base/core/src/main/java/org/openscience/cdk/stereo/ExtendedTetrahedral.java +++ b/base/core/src/main/java/org/openscience/cdk/stereo/ExtendedTetrahedral.java @@ -180,7 +180,7 @@ public IAtom[] findTerminalAtoms(IAtomContainer container) { } /** - * @inheritDoc + *{@inheritDoc} */ @Override public boolean contains(IAtom atom) { @@ -190,7 +190,7 @@ public boolean contains(IAtom atom) { } /** - * @inheritDoc + *{@inheritDoc} */ @Override public IStereoElement map(Map atoms, Map bonds) { @@ -199,7 +199,7 @@ public IStereoElement map(Map atoms, Map bonds) { } /** - * @inheritDoc + *{@inheritDoc} */ @Override public IChemObjectBuilder getBuilder() { diff --git a/base/core/src/main/java/org/openscience/cdk/stereo/TetrahedralChirality.java b/base/core/src/main/java/org/openscience/cdk/stereo/TetrahedralChirality.java index 93a2234c65..bac6dfc230 100644 --- a/base/core/src/main/java/org/openscience/cdk/stereo/TetrahedralChirality.java +++ b/base/core/src/main/java/org/openscience/cdk/stereo/TetrahedralChirality.java @@ -113,7 +113,7 @@ public IChemObjectBuilder getBuilder() { } /** - * @inheritDoc + *{@inheritDoc} */ @Override public boolean contains(IAtom atom) { @@ -124,7 +124,7 @@ public boolean contains(IAtom atom) { } /** - * @inheritDoc + *{@inheritDoc} */ @Override public ITetrahedralChirality map(Map atoms, Map bonds) { diff --git a/base/data/src/main/java/org/openscience/cdk/AtomContainer.java b/base/data/src/main/java/org/openscience/cdk/AtomContainer.java index f338db5d42..fb2868f367 100644 --- a/base/data/src/main/java/org/openscience/cdk/AtomContainer.java +++ b/base/data/src/main/java/org/openscience/cdk/AtomContainer.java @@ -198,7 +198,7 @@ public void addStereoElement(IStereoElement element) { } /** - * @inheritDoc + *{@inheritDoc} */ @Override public void setStereoElements(List elements) { @@ -1278,7 +1278,7 @@ else if (electronContainer instanceof ISingleElectron) removeSingleElectron((ISingleElectron) electronContainer); } - /** @inheritDoc */ + /**{@inheritDoc} */ @Override public void removeAtomAndConnectedElectronContainers(IAtom atom) { int position = getAtomNumber(atom); @@ -1312,7 +1312,7 @@ public void removeAtomAndConnectedElectronContainers(IAtom atom) { } /** - * @inheritDoc + *{@inheritDoc} */ @Override public void removeAllElements() { @@ -1698,7 +1698,7 @@ public void stateChanged(IChemObjectChangeEvent event) { } /** - * @inheritDoc + *{@inheritDoc} */ @Override public boolean isEmpty() { diff --git a/base/data/src/main/java/org/openscience/cdk/AtomContainerSet.java b/base/data/src/main/java/org/openscience/cdk/AtomContainerSet.java index cd6148fc15..acbc542631 100644 --- a/base/data/src/main/java/org/openscience/cdk/AtomContainerSet.java +++ b/base/data/src/main/java/org/openscience/cdk/AtomContainerSet.java @@ -439,7 +439,7 @@ public int compare(Integer o1, Integer o2) { } /** - * @inheritDoc + *{@inheritDoc} */ @Override public boolean isEmpty() { diff --git a/base/data/src/main/java/org/openscience/cdk/ChemModel.java b/base/data/src/main/java/org/openscience/cdk/ChemModel.java index 7d65b68f92..1eba57cf82 100644 --- a/base/data/src/main/java/org/openscience/cdk/ChemModel.java +++ b/base/data/src/main/java/org/openscience/cdk/ChemModel.java @@ -253,7 +253,7 @@ public void stateChanged(IChemObjectChangeEvent event) { } /** - * @inheritDoc + *{@inheritDoc} */ @Override public boolean isEmpty() { diff --git a/base/data/src/main/java/org/openscience/cdk/ChemObject.java b/base/data/src/main/java/org/openscience/cdk/ChemObject.java index 8a51abfd67..4e4629a73b 100644 --- a/base/data/src/main/java/org/openscience/cdk/ChemObject.java +++ b/base/data/src/main/java/org/openscience/cdk/ChemObject.java @@ -265,7 +265,7 @@ public T getProperty(Object description) { } /** - * @inheritDoc + *{@inheritDoc} */ @Override public T getProperty(Object description, Class c) { @@ -379,7 +379,7 @@ public void setFlag(int mask, boolean value) { } /** - * @inheritDoc + *{@inheritDoc} */ @Override public boolean getFlag(int mask) { @@ -387,14 +387,14 @@ public boolean getFlag(int mask) { } /** - * @inheritDoc + *{@inheritDoc} */ @Override public Short getFlagValue() { return flags; } - /** @inheritDoc */ + /**{@inheritDoc} */ @Override public void setProperties(Map properties) { this.properties = null; diff --git a/base/data/src/main/java/org/openscience/cdk/DefaultChemObjectBuilder.java b/base/data/src/main/java/org/openscience/cdk/DefaultChemObjectBuilder.java index 74e8237935..3c0592156d 100644 --- a/base/data/src/main/java/org/openscience/cdk/DefaultChemObjectBuilder.java +++ b/base/data/src/main/java/org/openscience/cdk/DefaultChemObjectBuilder.java @@ -199,7 +199,7 @@ public static IChemObjectBuilder getInstance() { } /** - * @inheritDoc + *{@inheritDoc} */ @Override public T newInstance(Class clazz, Object... params) { diff --git a/base/data/src/main/java/org/openscience/cdk/Monomer.java b/base/data/src/main/java/org/openscience/cdk/Monomer.java index a7c0fa89c6..b1d1130a3b 100644 --- a/base/data/src/main/java/org/openscience/cdk/Monomer.java +++ b/base/data/src/main/java/org/openscience/cdk/Monomer.java @@ -120,7 +120,7 @@ public void setMonomerType(String cMonomerType) { } /** - * @inheritDoc + *{@inheritDoc} */ @Override public IMonomer clone() throws CloneNotSupportedException { diff --git a/base/data/src/main/java/org/openscience/cdk/ReactionSet.java b/base/data/src/main/java/org/openscience/cdk/ReactionSet.java index 4f3dd8a5de..fba939165f 100644 --- a/base/data/src/main/java/org/openscience/cdk/ReactionSet.java +++ b/base/data/src/main/java/org/openscience/cdk/ReactionSet.java @@ -249,7 +249,7 @@ public void removeReaction(IReaction relevantReaction) { } /** - * @inheritDoc + *{@inheritDoc} */ @Override public boolean isEmpty() { diff --git a/base/data/src/main/java/org/openscience/cdk/Ring.java b/base/data/src/main/java/org/openscience/cdk/Ring.java index b1ccc1142a..149f169537 100644 --- a/base/data/src/main/java/org/openscience/cdk/Ring.java +++ b/base/data/src/main/java/org/openscience/cdk/Ring.java @@ -139,7 +139,7 @@ public int getBondOrderSum() { } /** - * @inheritDoc + *{@inheritDoc} */ @Override public IRing clone() throws CloneNotSupportedException { diff --git a/base/data/src/main/java/org/openscience/cdk/formula/MolecularFormula.java b/base/data/src/main/java/org/openscience/cdk/formula/MolecularFormula.java index 0dc7a96fe0..7cc8c2f283 100644 --- a/base/data/src/main/java/org/openscience/cdk/formula/MolecularFormula.java +++ b/base/data/src/main/java/org/openscience/cdk/formula/MolecularFormula.java @@ -308,7 +308,7 @@ public void removeProperty(Object description) { } /** - * @inheritDoc + *{@inheritDoc} */ @Override public T getProperty(Object description) { @@ -320,7 +320,7 @@ public T getProperty(Object description) { } /** - * @inheritDoc + *{@inheritDoc} */ @Override public T getProperty(Object description, Class c) { diff --git a/base/data/src/main/java/org/openscience/cdk/protein/data/PDBMonomer.java b/base/data/src/main/java/org/openscience/cdk/protein/data/PDBMonomer.java index 5022d50e66..c3d9334d46 100644 --- a/base/data/src/main/java/org/openscience/cdk/protein/data/PDBMonomer.java +++ b/base/data/src/main/java/org/openscience/cdk/protein/data/PDBMonomer.java @@ -105,7 +105,7 @@ public String getResSeq() { } /** - * @inheritDoc + *{@inheritDoc} */ @Override public IPDBMonomer clone() throws CloneNotSupportedException { diff --git a/base/data/src/main/java/org/openscience/cdk/protein/data/PDBPolymer.java b/base/data/src/main/java/org/openscience/cdk/protein/data/PDBPolymer.java index b3b425db48..f49769ca58 100644 --- a/base/data/src/main/java/org/openscience/cdk/protein/data/PDBPolymer.java +++ b/base/data/src/main/java/org/openscience/cdk/protein/data/PDBPolymer.java @@ -122,7 +122,7 @@ public Collection getMonomerNamesInSequentialOrder() { } /** - * @inheritDoc + *{@inheritDoc} */ @Override public IPDBPolymer clone() throws CloneNotSupportedException { diff --git a/base/datadebug/src/main/java/org/openscience/cdk/debug/DebugAtomContainer.java b/base/datadebug/src/main/java/org/openscience/cdk/debug/DebugAtomContainer.java index 1cd4d30c0b..4eb34aeb8c 100644 --- a/base/datadebug/src/main/java/org/openscience/cdk/debug/DebugAtomContainer.java +++ b/base/datadebug/src/main/java/org/openscience/cdk/debug/DebugAtomContainer.java @@ -69,7 +69,7 @@ public void addStereoElement(IStereoElement parity) { } /** - * @inheritDoc + *{@inheritDoc} */ @Override public void setStereoElements(List elements) { @@ -729,7 +729,7 @@ public IChemObjectBuilder getBuilder() { } /** - * @inheritDoc + *{@inheritDoc} */ @Override public boolean isEmpty() { diff --git a/base/datadebug/src/main/java/org/openscience/cdk/debug/DebugAtomContainerSet.java b/base/datadebug/src/main/java/org/openscience/cdk/debug/DebugAtomContainerSet.java index 96a7a84b9d..3a5a9bbe2c 100644 --- a/base/datadebug/src/main/java/org/openscience/cdk/debug/DebugAtomContainerSet.java +++ b/base/datadebug/src/main/java/org/openscience/cdk/debug/DebugAtomContainerSet.java @@ -286,7 +286,7 @@ public int getAtomContainerCount() { } /** - * @inheritDoc + *{@inheritDoc} */ @Override public boolean isEmpty() { diff --git a/base/datadebug/src/main/java/org/openscience/cdk/debug/DebugChemModel.java b/base/datadebug/src/main/java/org/openscience/cdk/debug/DebugChemModel.java index 9529b27e3c..3580369162 100644 --- a/base/datadebug/src/main/java/org/openscience/cdk/debug/DebugChemModel.java +++ b/base/datadebug/src/main/java/org/openscience/cdk/debug/DebugChemModel.java @@ -233,7 +233,7 @@ public void setReactionSet(IReactionSet sor) { } /** - * @inheritDoc + *{@inheritDoc} */ @Override public boolean isEmpty() { diff --git a/base/datadebug/src/main/java/org/openscience/cdk/debug/DebugChemObject.java b/base/datadebug/src/main/java/org/openscience/cdk/debug/DebugChemObject.java index 3ec291bb33..50cdd31a82 100644 --- a/base/datadebug/src/main/java/org/openscience/cdk/debug/DebugChemObject.java +++ b/base/datadebug/src/main/java/org/openscience/cdk/debug/DebugChemObject.java @@ -108,7 +108,7 @@ public T getProperty(Object description) { } /** - * @inheritDoc + *{@inheritDoc} */ @Override public T getProperty(Object description, Class c) { @@ -151,7 +151,7 @@ public boolean getFlag(int flagType) { return super.getFlag(flagType); } - /** @inheritDoc */ + /**{@inheritDoc} */ @Override public void setProperties(Map properties) { logger.debug("Setting properties: ", properties); diff --git a/base/datadebug/src/main/java/org/openscience/cdk/debug/DebugChemObjectBuilder.java b/base/datadebug/src/main/java/org/openscience/cdk/debug/DebugChemObjectBuilder.java index f63f53046b..e5295dc7c5 100644 --- a/base/datadebug/src/main/java/org/openscience/cdk/debug/DebugChemObjectBuilder.java +++ b/base/datadebug/src/main/java/org/openscience/cdk/debug/DebugChemObjectBuilder.java @@ -197,7 +197,7 @@ public static IChemObjectBuilder getInstance() { } /** - * @inheritDoc + *{@inheritDoc} */ @Override public T newInstance(Class clazz, Object... params) { diff --git a/base/datadebug/src/main/java/org/openscience/cdk/debug/DebugReactionSet.java b/base/datadebug/src/main/java/org/openscience/cdk/debug/DebugReactionSet.java index e743d74ea9..1caceb0cdf 100644 --- a/base/datadebug/src/main/java/org/openscience/cdk/debug/DebugReactionSet.java +++ b/base/datadebug/src/main/java/org/openscience/cdk/debug/DebugReactionSet.java @@ -216,7 +216,7 @@ public void removeReaction(IReaction reaction) { } /** - * @inheritDoc + *{@inheritDoc} */ @Override public boolean isEmpty() { diff --git a/base/datadebug/src/main/java/org/openscience/cdk/debug/DebugSubstance.java b/base/datadebug/src/main/java/org/openscience/cdk/debug/DebugSubstance.java index 6210b115fc..42d2bd8ee2 100644 --- a/base/datadebug/src/main/java/org/openscience/cdk/debug/DebugSubstance.java +++ b/base/datadebug/src/main/java/org/openscience/cdk/debug/DebugSubstance.java @@ -287,7 +287,7 @@ public int getAtomContainerCount() { } /** - * @inheritDoc + *{@inheritDoc} */ @Override public boolean isEmpty() { diff --git a/base/interfaces/src/main/java/org/openscience/cdk/interfaces/IAminoAcid.java b/base/interfaces/src/main/java/org/openscience/cdk/interfaces/IAminoAcid.java index b2cea50035..b746987e70 100644 --- a/base/interfaces/src/main/java/org/openscience/cdk/interfaces/IAminoAcid.java +++ b/base/interfaces/src/main/java/org/openscience/cdk/interfaces/IAminoAcid.java @@ -72,7 +72,7 @@ public interface IAminoAcid extends IMonomer { public void addCTerminus(IAtom atom); /** - * @inheritDoc + *{@inheritDoc} */ @Override public IAminoAcid clone() throws CloneNotSupportedException; diff --git a/base/interfaces/src/main/java/org/openscience/cdk/interfaces/IAtom.java b/base/interfaces/src/main/java/org/openscience/cdk/interfaces/IAtom.java index 94d746e332..d16677b4ab 100644 --- a/base/interfaces/src/main/java/org/openscience/cdk/interfaces/IAtom.java +++ b/base/interfaces/src/main/java/org/openscience/cdk/interfaces/IAtom.java @@ -182,7 +182,7 @@ public interface IAtom extends IAtomType { void setIsInRing(boolean ring); /** - * @inheritDoc + *{@inheritDoc} */ @Override public IAtom clone() throws CloneNotSupportedException; diff --git a/base/interfaces/src/main/java/org/openscience/cdk/interfaces/IAtomContainer.java b/base/interfaces/src/main/java/org/openscience/cdk/interfaces/IAtomContainer.java index 52dfb6bb29..0f8a5ea07f 100644 --- a/base/interfaces/src/main/java/org/openscience/cdk/interfaces/IAtomContainer.java +++ b/base/interfaces/src/main/java/org/openscience/cdk/interfaces/IAtomContainer.java @@ -631,7 +631,7 @@ public interface IAtomContainer extends IChemObject, IChemObjectListener { public boolean isEmpty(); /** - * @inheritDoc + *{@inheritDoc} */ @Override public IAtomContainer clone() throws CloneNotSupportedException; diff --git a/base/interfaces/src/main/java/org/openscience/cdk/interfaces/IBioPolymer.java b/base/interfaces/src/main/java/org/openscience/cdk/interfaces/IBioPolymer.java index e1e902c1b5..673f6723df 100644 --- a/base/interfaces/src/main/java/org/openscience/cdk/interfaces/IBioPolymer.java +++ b/base/interfaces/src/main/java/org/openscience/cdk/interfaces/IBioPolymer.java @@ -136,7 +136,7 @@ public interface IBioPolymer extends IPolymer { public Map getStrands(); /** - * @inheritDoc + *{@inheritDoc} */ @Override public IBioPolymer clone() throws CloneNotSupportedException; diff --git a/base/interfaces/src/main/java/org/openscience/cdk/interfaces/IBond.java b/base/interfaces/src/main/java/org/openscience/cdk/interfaces/IBond.java index ca17511e8d..b3a223750f 100644 --- a/base/interfaces/src/main/java/org/openscience/cdk/interfaces/IBond.java +++ b/base/interfaces/src/main/java/org/openscience/cdk/interfaces/IBond.java @@ -284,7 +284,7 @@ public enum Stereo { */ void setIsInRing(boolean ring); - /** @inheritDoc */ + /**{@inheritDoc} */ @Override public IBond clone() throws CloneNotSupportedException; } diff --git a/base/interfaces/src/main/java/org/openscience/cdk/interfaces/ICrystal.java b/base/interfaces/src/main/java/org/openscience/cdk/interfaces/ICrystal.java index 0b37245ee0..fe909f67bc 100644 --- a/base/interfaces/src/main/java/org/openscience/cdk/interfaces/ICrystal.java +++ b/base/interfaces/src/main/java/org/openscience/cdk/interfaces/ICrystal.java @@ -138,7 +138,7 @@ public interface ICrystal extends IAtomContainer { public void setZ(Integer value); /** - * @inheritDoc + *{@inheritDoc} */ @Override public ICrystal clone() throws CloneNotSupportedException; diff --git a/base/interfaces/src/main/java/org/openscience/cdk/interfaces/IDoubleBondStereochemistry.java b/base/interfaces/src/main/java/org/openscience/cdk/interfaces/IDoubleBondStereochemistry.java index a007cfeca2..7a72d94f2c 100644 --- a/base/interfaces/src/main/java/org/openscience/cdk/interfaces/IDoubleBondStereochemistry.java +++ b/base/interfaces/src/main/java/org/openscience/cdk/interfaces/IDoubleBondStereochemistry.java @@ -85,7 +85,7 @@ public Conformation invert() { public Conformation getStereo(); /** - * @inheritDoc + *{@inheritDoc} */ @Override public IDoubleBondStereochemistry map(Map atoms, Map bonds); diff --git a/base/interfaces/src/main/java/org/openscience/cdk/interfaces/IMonomer.java b/base/interfaces/src/main/java/org/openscience/cdk/interfaces/IMonomer.java index a3b35b4545..5f8dcfb999 100644 --- a/base/interfaces/src/main/java/org/openscience/cdk/interfaces/IMonomer.java +++ b/base/interfaces/src/main/java/org/openscience/cdk/interfaces/IMonomer.java @@ -69,7 +69,7 @@ public interface IMonomer extends IAtomContainer { public void setMonomerType(String cMonomerType); /** - * @inheritDoc + *{@inheritDoc} */ @Override public IMonomer clone() throws CloneNotSupportedException; diff --git a/base/interfaces/src/main/java/org/openscience/cdk/interfaces/IPDBMonomer.java b/base/interfaces/src/main/java/org/openscience/cdk/interfaces/IPDBMonomer.java index 378b66d61b..961fefed6a 100644 --- a/base/interfaces/src/main/java/org/openscience/cdk/interfaces/IPDBMonomer.java +++ b/base/interfaces/src/main/java/org/openscience/cdk/interfaces/IPDBMonomer.java @@ -74,7 +74,7 @@ public interface IPDBMonomer extends IMonomer { public void setResSeq(String newResSeq); /** - * @inheritDoc + *{@inheritDoc} */ @Override public IPDBMonomer clone() throws CloneNotSupportedException; diff --git a/base/interfaces/src/main/java/org/openscience/cdk/interfaces/IPDBPolymer.java b/base/interfaces/src/main/java/org/openscience/cdk/interfaces/IPDBPolymer.java index 8f0de07564..6de625e4b5 100644 --- a/base/interfaces/src/main/java/org/openscience/cdk/interfaces/IPDBPolymer.java +++ b/base/interfaces/src/main/java/org/openscience/cdk/interfaces/IPDBPolymer.java @@ -73,7 +73,7 @@ public interface IPDBPolymer extends IBioPolymer { public Collection getStructures(); /** - * @inheritDoc + *{@inheritDoc} */ @Override public IPDBPolymer clone() throws CloneNotSupportedException; diff --git a/base/interfaces/src/main/java/org/openscience/cdk/interfaces/IPolymer.java b/base/interfaces/src/main/java/org/openscience/cdk/interfaces/IPolymer.java index 2d23be9111..40e615f16e 100644 --- a/base/interfaces/src/main/java/org/openscience/cdk/interfaces/IPolymer.java +++ b/base/interfaces/src/main/java/org/openscience/cdk/interfaces/IPolymer.java @@ -86,7 +86,7 @@ public interface IPolymer extends IAtomContainer { public void removeMonomer(String name); /** - * @inheritDoc + *{@inheritDoc} */ @Override public IPolymer clone() throws CloneNotSupportedException; diff --git a/base/interfaces/src/main/java/org/openscience/cdk/interfaces/IPseudoAtom.java b/base/interfaces/src/main/java/org/openscience/cdk/interfaces/IPseudoAtom.java index e18a019b01..a8021072be 100644 --- a/base/interfaces/src/main/java/org/openscience/cdk/interfaces/IPseudoAtom.java +++ b/base/interfaces/src/main/java/org/openscience/cdk/interfaces/IPseudoAtom.java @@ -68,7 +68,7 @@ public interface IPseudoAtom extends IAtom { void setAttachPointNum(int ap); /** - * @inheritDoc + *{@inheritDoc} */ @Override public IPseudoAtom clone() throws CloneNotSupportedException; diff --git a/base/interfaces/src/main/java/org/openscience/cdk/interfaces/IRing.java b/base/interfaces/src/main/java/org/openscience/cdk/interfaces/IRing.java index 9d6e0d4eb6..b8302168a0 100644 --- a/base/interfaces/src/main/java/org/openscience/cdk/interfaces/IRing.java +++ b/base/interfaces/src/main/java/org/openscience/cdk/interfaces/IRing.java @@ -58,7 +58,7 @@ public interface IRing extends IAtomContainer { public int getBondOrderSum(); /** - * @inheritDoc + *{@inheritDoc} */ @Override public IRing clone() throws CloneNotSupportedException; diff --git a/base/interfaces/src/main/java/org/openscience/cdk/interfaces/IStrand.java b/base/interfaces/src/main/java/org/openscience/cdk/interfaces/IStrand.java index 3d62326ad5..a097017000 100644 --- a/base/interfaces/src/main/java/org/openscience/cdk/interfaces/IStrand.java +++ b/base/interfaces/src/main/java/org/openscience/cdk/interfaces/IStrand.java @@ -123,7 +123,7 @@ public interface IStrand extends IAtomContainer { public Map getMonomers(); /** - * @inheritDoc + *{@inheritDoc} */ @Override public IStrand clone() throws CloneNotSupportedException; diff --git a/base/interfaces/src/main/java/org/openscience/cdk/interfaces/ITetrahedralChirality.java b/base/interfaces/src/main/java/org/openscience/cdk/interfaces/ITetrahedralChirality.java index a96bb37e13..4e92766c96 100644 --- a/base/interfaces/src/main/java/org/openscience/cdk/interfaces/ITetrahedralChirality.java +++ b/base/interfaces/src/main/java/org/openscience/cdk/interfaces/ITetrahedralChirality.java @@ -94,7 +94,7 @@ public Stereo invert() { void setStereo(Stereo stereo); /** - * @inheritDoc + *{@inheritDoc} */ @Override public ITetrahedralChirality map(Map atoms, Map bonds); diff --git a/base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/AbstractVFState.java b/base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/AbstractVFState.java index 2be2ae4e18..a6a18b3128 100644 --- a/base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/AbstractVFState.java +++ b/base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/AbstractVFState.java @@ -111,19 +111,19 @@ final int nextM(int n, int m) { return mMax(); } - /** @inheritDoc */ + /**{@inheritDoc} */ @Override final int nMax() { return g1.length; } - /** @inheritDoc */ + /**{@inheritDoc} */ @Override final int mMax() { return g2.length; } - /** @inheritDoc */ + /**{@inheritDoc} */ @Override final boolean add(int n, int m) { if (!feasible(n, m)) return false; @@ -137,7 +137,7 @@ final boolean add(int n, int m) { return true; } - /** @inheritDoc */ + /**{@inheritDoc} */ @Override final void remove(int n, int m) { m1[n] = m2[m] = UNMAPPED; @@ -158,13 +158,13 @@ final void remove(int n, int m) { */ abstract boolean feasible(int n, int m); - /** @inheritDoc */ + /**{@inheritDoc} */ @Override int[] mapping() { return Arrays.copyOf(m1, m1.length); } - /** @inheritDoc */ + /**{@inheritDoc} */ @Override int size() { return size; diff --git a/base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/AtomMatcher.java b/base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/AtomMatcher.java index 21fd3cc9ae..8a626be63c 100644 --- a/base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/AtomMatcher.java +++ b/base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/AtomMatcher.java @@ -76,7 +76,7 @@ public static AtomMatcher forQuery() { /** A matcher defines all atoms as compatible. */ private static final class AnyMatcher extends AtomMatcher { - /** @inheritDoc */ + /**{@inheritDoc} */ @Override public boolean matches(IAtom atom1, IAtom atom2) { return true; @@ -89,7 +89,7 @@ public boolean matches(IAtom atom1, IAtom atom2) { */ private static final class QueryMatcher extends AtomMatcher { - /** @inheritDoc */ + /**{@inheritDoc} */ @Override public boolean matches(IAtom atom1, IAtom atom2) { return ((IQueryAtom) atom1).matches(atom2); @@ -102,7 +102,7 @@ public boolean matches(IAtom atom1, IAtom atom2) { */ private static final class ElementMatcher extends AtomMatcher { - /** @inheritDoc */ + /**{@inheritDoc} */ @Override public boolean matches(IAtom atom1, IAtom atom2) { return atomicNumber(atom1) == atomicNumber(atom2); diff --git a/base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/BondMatcher.java b/base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/BondMatcher.java index 3ab7b770e6..53bad20a7e 100644 --- a/base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/BondMatcher.java +++ b/base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/BondMatcher.java @@ -93,7 +93,7 @@ public static BondMatcher forQuery() { */ private static final class OrderMatcher extends BondMatcher { - /** @inheritDoc */ + /**{@inheritDoc} */ @Override public boolean matches(IBond bond1, IBond bond2) { return bond1.getFlag(ISAROMATIC) && bond2.getFlag(ISAROMATIC) || bond1.getOrder() == bond2.getOrder(); @@ -107,7 +107,7 @@ public boolean matches(IBond bond1, IBond bond2) { */ private static final class StrictOrderMatcher extends BondMatcher { - /** @inheritDoc */ + /**{@inheritDoc} */ @Override public boolean matches(IBond bond1, IBond bond2) { return bond1.getFlag(ISAROMATIC) == bond2.getFlag(ISAROMATIC) @@ -118,7 +118,7 @@ public boolean matches(IBond bond1, IBond bond2) { /** All bonds are considered compatible. */ private static final class AnyMatcher extends BondMatcher { - /** @inheritDoc */ + /**{@inheritDoc} */ @Override public boolean matches(IBond bond1, IBond bond2) { return true; @@ -131,7 +131,7 @@ public boolean matches(IBond bond1, IBond bond2) { */ private static final class QueryMatcher extends BondMatcher { - /** @inheritDoc */ + /**{@inheritDoc} */ @Override public boolean matches(IBond bond1, IBond bond2) { return ((IQueryBond) bond1).matches(bond2); diff --git a/base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/Mappings.java b/base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/Mappings.java index 527d379dfa..536e0683fc 100644 --- a/base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/Mappings.java +++ b/base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/Mappings.java @@ -524,7 +524,7 @@ public int countUnique() { return uniqueAtoms().count(); } - /** @inheritDoc */ + /**{@inheritDoc} */ @Override public Iterator iterator() { return iterable.iterator(); @@ -547,7 +547,7 @@ private ToAtomMap(IAtomContainer query, IAtomContainer target) { this.target = target; } - /** @inheritDoc */ + /**{@inheritDoc} */ @Override public Map apply(int[] mapping) { ImmutableMap.Builder map = ImmutableMap.builder(); @@ -579,7 +579,7 @@ private ToBondMap(IAtomContainer query, IAtomContainer target) { GraphUtil.toAdjList(target, bonds2); } - /** @inheritDoc */ + /**{@inheritDoc} */ @Override public Map apply(int[] mapping) { ImmutableMap.Builder map = ImmutableMap.builder(); @@ -616,7 +616,7 @@ private ToAtomBondMap(IAtomContainer query, IAtomContainer target) { GraphUtil.toAdjList(target, bonds2); } - /** @inheritDoc */ + /**{@inheritDoc} */ @Override public Map apply(int[] mapping) { ImmutableMap.Builder map = ImmutableMap.builder(); diff --git a/base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/StateStream.java b/base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/StateStream.java index 3bc6d2f871..d454341819 100644 --- a/base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/StateStream.java +++ b/base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/StateStream.java @@ -61,13 +61,13 @@ final class StateStream implements Iterator { this.next = state.nMax() == 0 || state.mMax() == 0 ? null : findNext(); // first-mapping } - /** @inheritDoc */ + /**{@inheritDoc} */ @Override public boolean hasNext() { return next != null; } - /** @inheritDoc */ + /**{@inheritDoc} */ @Override public int[] next() { int[] ret = next; @@ -75,7 +75,7 @@ public int[] next() { return ret; } - /** @inheritDoc */ + /**{@inheritDoc} */ @Override public void remove() { throw new UnsupportedOperationException("a graph matching cannot be removed"); diff --git a/base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/Ullmann.java b/base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/Ullmann.java index 85f250088f..fc01e6cd70 100644 --- a/base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/Ullmann.java +++ b/base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/Ullmann.java @@ -175,7 +175,7 @@ private UllmannIterable(IAtomContainer container1, IAtomContainer container2, in this.bondMatcher = bondMatcher; } - /** @inheritDoc */ + /**{@inheritDoc} */ @Override public Iterator iterator() { return new StateStream(new UllmannState(container1, container2, g1, g2, bonds1, bonds2, atomMatcher, diff --git a/base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/UllmannState.java b/base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/UllmannState.java index ae4089b7a3..9b78e9b4bb 100644 --- a/base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/UllmannState.java +++ b/base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/UllmannState.java @@ -101,13 +101,13 @@ public UllmannState(IAtomContainer container1, IAtomContainer container2, int[][ } } - /** @inheritDoc */ + /**{@inheritDoc} */ @Override int nextN(int n) { return size; // we progress down the rows of the matrix } - /** @inheritDoc */ + /**{@inheritDoc} */ @Override int nextM(int n, int m) { for (int i = m + 1; i < g2.length; i++) @@ -115,19 +115,19 @@ int nextM(int n, int m) { return g2.length; } - /** @inheritDoc */ + /**{@inheritDoc} */ @Override int nMax() { return g1.length; } - /** @inheritDoc */ + /**{@inheritDoc} */ @Override int mMax() { return g2.length; } - /** @inheritDoc */ + /**{@inheritDoc} */ @Override boolean add(int n, int m) { @@ -150,7 +150,7 @@ boolean add(int n, int m) { } } - /** @inheritDoc */ + /**{@inheritDoc} */ @Override void remove(int n, int m) { size--; @@ -229,13 +229,13 @@ private boolean hasCandidate(int n) { return false; } - /** @inheritDoc */ + /**{@inheritDoc} */ @Override int[] mapping() { return Arrays.copyOf(m1, m1.length); } - /** @inheritDoc */ + /**{@inheritDoc} */ @Override int size() { return size; diff --git a/base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/UniqueAtomMatches.java b/base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/UniqueAtomMatches.java index e4b0af5c92..827466e130 100644 --- a/base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/UniqueAtomMatches.java +++ b/base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/UniqueAtomMatches.java @@ -67,7 +67,7 @@ public UniqueAtomMatches() { } /** - * @inheritDoc + *{@inheritDoc} */ @Override public boolean apply(int[] input) { diff --git a/base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/UniqueBondMatches.java b/base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/UniqueBondMatches.java index e825ad6b42..16873b52a1 100644 --- a/base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/UniqueBondMatches.java +++ b/base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/UniqueBondMatches.java @@ -68,7 +68,7 @@ public UniqueBondMatches(int[][] g) { this(g, 10); } - /** @inheritDoc */ + /**{@inheritDoc} */ @Override public boolean apply(int[] input) { return unique.add(toEdgeSet(input)); @@ -107,13 +107,13 @@ private Tuple(int u, int v) { this.v = v; } - /** @inheritDoc */ + /**{@inheritDoc} */ @Override public int hashCode() { return u ^ v; } - /** @inheritDoc */ + /**{@inheritDoc} */ @Override public boolean equals(Object o) { if (this == o) return true; diff --git a/base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/VentoFoggia.java b/base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/VentoFoggia.java index 893a31dfee..e818b2f488 100644 --- a/base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/VentoFoggia.java +++ b/base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/VentoFoggia.java @@ -112,13 +112,13 @@ private VentoFoggia(IAtomContainer query, AtomMatcher atomMatcher, BondMatcher b this.queryMatching = query instanceof IQueryAtomContainer; } - /** @inheritDoc */ + /**{@inheritDoc} */ @Override public int[] match(IAtomContainer target) { return matchAll(target).stereochemistry().first(); } - /** @inheritDoc */ + /**{@inheritDoc} */ @Override public Mappings matchAll(final IAtomContainer target) { EdgeToBondMap bonds2 = EdgeToBondMap.withSpaceFor(target); @@ -229,7 +229,7 @@ private VFIterable(IAtomContainer container1, IAtomContainer container2, int[][] this.subgraph = subgraph; } - /** @inheritDoc */ + /**{@inheritDoc} */ @Override public Iterator iterator() { if (subgraph) { diff --git a/base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/matchers/QueryAtomContainerCreator.java b/base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/matchers/QueryAtomContainerCreator.java index 42ef3cf82a..a59e4e4127 100644 --- a/base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/matchers/QueryAtomContainerCreator.java +++ b/base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/matchers/QueryAtomContainerCreator.java @@ -243,7 +243,7 @@ private AnyAtom(IChemObjectBuilder builder) { super(builder); } - /** @inheritDoc */ + /**{@inheritDoc} */ @Override public boolean matches(IAtom atom) { return true; @@ -257,7 +257,7 @@ private AromaticAtom(IChemObjectBuilder builder) { super(builder); } - /** @inheritDoc */ + /**{@inheritDoc} */ @Override public boolean matches(IAtom atom) { return atom.getFlag(CDKConstants.ISAROMATIC); @@ -271,7 +271,7 @@ private AnyOrderBond(IAtom either, IAtom other, IChemObjectBuilder builder) { super(either, other, Order.UNSET, builder); } - /** @inheritDoc */ + /**{@inheritDoc} */ @Override public boolean matches(IBond bond) { return bond != null && bond.getOrder() != Order.UNSET; @@ -285,7 +285,7 @@ private AromaticQueryBond(IAtom either, IAtom other, IChemObjectBuilder builder) super(either, other, Order.UNSET, builder); } - /** @inheritDoc */ + /**{@inheritDoc} */ @Override public boolean matches(IBond bond) { return bond.getFlag(CDKConstants.ISAROMATIC); diff --git a/base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/matchers/QueryChemObject.java b/base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/matchers/QueryChemObject.java index e1984c7d84..4078058521 100644 --- a/base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/matchers/QueryChemObject.java +++ b/base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/matchers/QueryChemObject.java @@ -229,7 +229,7 @@ public T getProperty(Object description) { } /** - * @inheritDoc + *{@inheritDoc} */ @Override public T getProperty(Object description, Class c) { @@ -285,7 +285,7 @@ public void setID(String identifier) { } /** - * @inheritDoc + *{@inheritDoc} */ @Override public void setFlag(int mask, boolean value) { @@ -298,14 +298,14 @@ public void setFlag(int mask, boolean value) { } /** - * @inheritDoc + *{@inheritDoc} */ @Override public boolean getFlag(int mask) { return (flags & mask) != 0; } - /** @inheritDoc */ + /**{@inheritDoc} */ @Override public void setProperties(Map properties) { this.properties = null; @@ -328,7 +328,7 @@ public void addProperties(Map properties) { private boolean doNotification = true; /** - * @inheritDoc + *{@inheritDoc} */ @Override public void setFlags(boolean[] flagsNew) { @@ -337,7 +337,7 @@ public void setFlags(boolean[] flagsNew) { } /** - * @inheritDoc + *{@inheritDoc} */ @Override public boolean[] getFlags() { @@ -351,7 +351,7 @@ public boolean[] getFlags() { } /** - * @inheritDoc + *{@inheritDoc} */ @Override public Short getFlagValue() { diff --git a/base/silent/src/main/java/org/openscience/cdk/silent/AtomContainer.java b/base/silent/src/main/java/org/openscience/cdk/silent/AtomContainer.java index 2a83f708ff..add9d3e549 100644 --- a/base/silent/src/main/java/org/openscience/cdk/silent/AtomContainer.java +++ b/base/silent/src/main/java/org/openscience/cdk/silent/AtomContainer.java @@ -194,7 +194,7 @@ public void addStereoElement(IStereoElement element) { } /** - * @inheritDoc + *{@inheritDoc} */ @Override public void setStereoElements(List elements) { @@ -1247,7 +1247,7 @@ else if (electronContainer instanceof ISingleElectron) removeSingleElectron((ISingleElectron) electronContainer); } - /** @inheritDoc */ + /**{@inheritDoc} */ @Override public void removeAtomAndConnectedElectronContainers(IAtom atom) { int position = getAtomNumber(atom); @@ -1280,7 +1280,7 @@ public void removeAtomAndConnectedElectronContainers(IAtom atom) { } /** - * @inheritDoc + *{@inheritDoc} */ @Override public void removeAllElements() { @@ -1641,7 +1641,7 @@ private void growSingleElectronArray() { public void stateChanged(IChemObjectChangeEvent event) {} /** - * @inheritDoc + *{@inheritDoc} */ @Override public boolean isEmpty() { diff --git a/base/silent/src/main/java/org/openscience/cdk/silent/AtomContainerSet.java b/base/silent/src/main/java/org/openscience/cdk/silent/AtomContainerSet.java index 4650571f93..5bdfe497ab 100644 --- a/base/silent/src/main/java/org/openscience/cdk/silent/AtomContainerSet.java +++ b/base/silent/src/main/java/org/openscience/cdk/silent/AtomContainerSet.java @@ -421,7 +421,7 @@ public int compare(Integer o1, Integer o2) { } /** - * @inheritDoc + *{@inheritDoc} */ @Override public boolean isEmpty() { diff --git a/base/silent/src/main/java/org/openscience/cdk/silent/ChemModel.java b/base/silent/src/main/java/org/openscience/cdk/silent/ChemModel.java index 97e437aedd..0ef6595c4b 100644 --- a/base/silent/src/main/java/org/openscience/cdk/silent/ChemModel.java +++ b/base/silent/src/main/java/org/openscience/cdk/silent/ChemModel.java @@ -239,7 +239,7 @@ public Object clone() throws CloneNotSupportedException { public void stateChanged(IChemObjectChangeEvent event) {} /** - * @inheritDoc + *{@inheritDoc} */ @Override public boolean isEmpty() { diff --git a/base/silent/src/main/java/org/openscience/cdk/silent/ChemObject.java b/base/silent/src/main/java/org/openscience/cdk/silent/ChemObject.java index b49f68af98..0ce71438e1 100644 --- a/base/silent/src/main/java/org/openscience/cdk/silent/ChemObject.java +++ b/base/silent/src/main/java/org/openscience/cdk/silent/ChemObject.java @@ -210,7 +210,7 @@ public T getProperty(Object description) { } /** - * @inheritDoc + *{@inheritDoc} */ @Override public T getProperty(Object description, Class c) { @@ -307,7 +307,7 @@ private boolean isPowerOfTwo(int num) { } /** - * @inheritDoc + *{@inheritDoc} */ @Override public void setFlag(int mask, boolean value) { @@ -322,7 +322,7 @@ public void setFlag(int mask, boolean value) { } /** - * @inheritDoc + *{@inheritDoc} */ @Override public boolean getFlag(int mask) { @@ -330,14 +330,14 @@ public boolean getFlag(int mask) { } /** - * @inheritDoc + *{@inheritDoc} */ @Override public Short getFlagValue() { return flags; // auto-boxing } - /** @inheritDoc */ + /**{@inheritDoc} */ @Override public void setProperties(Map properties) { this.properties = null; @@ -357,7 +357,7 @@ public void addProperties(Map properties) { } /** - * @inheritDoc + *{@inheritDoc} */ @Override public void setFlags(boolean[] flagsNew) { @@ -366,7 +366,7 @@ public void setFlags(boolean[] flagsNew) { } /** - * @inheritDoc + *{@inheritDoc} */ @Override public boolean[] getFlags() { diff --git a/base/silent/src/main/java/org/openscience/cdk/silent/MolecularFormula.java b/base/silent/src/main/java/org/openscience/cdk/silent/MolecularFormula.java index cb614f937c..c9d1952204 100644 --- a/base/silent/src/main/java/org/openscience/cdk/silent/MolecularFormula.java +++ b/base/silent/src/main/java/org/openscience/cdk/silent/MolecularFormula.java @@ -305,7 +305,7 @@ public void removeProperty(Object description) { } /** - * @inheritDoc + *{@inheritDoc} */ @Override public T getProperty(Object description) { @@ -317,7 +317,7 @@ public T getProperty(Object description) { } /** - * @inheritDoc + *{@inheritDoc} */ @Override public T getProperty(Object description, Class c) { diff --git a/base/silent/src/main/java/org/openscience/cdk/silent/Monomer.java b/base/silent/src/main/java/org/openscience/cdk/silent/Monomer.java index 80e4e22885..33502f7105 100644 --- a/base/silent/src/main/java/org/openscience/cdk/silent/Monomer.java +++ b/base/silent/src/main/java/org/openscience/cdk/silent/Monomer.java @@ -118,7 +118,7 @@ public void setMonomerType(String cMonomerType) { } /** - * @inheritDoc + *{@inheritDoc} */ @Override public IMonomer clone() throws CloneNotSupportedException { diff --git a/base/silent/src/main/java/org/openscience/cdk/silent/PDBMonomer.java b/base/silent/src/main/java/org/openscience/cdk/silent/PDBMonomer.java index 56d72f90bd..3b432c6298 100644 --- a/base/silent/src/main/java/org/openscience/cdk/silent/PDBMonomer.java +++ b/base/silent/src/main/java/org/openscience/cdk/silent/PDBMonomer.java @@ -104,7 +104,7 @@ public String getResSeq() { } /** - * @inheritDoc + *{@inheritDoc} */ @Override public IPDBMonomer clone() throws CloneNotSupportedException { diff --git a/base/silent/src/main/java/org/openscience/cdk/silent/PDBPolymer.java b/base/silent/src/main/java/org/openscience/cdk/silent/PDBPolymer.java index 188f11782f..099ff2a290 100644 --- a/base/silent/src/main/java/org/openscience/cdk/silent/PDBPolymer.java +++ b/base/silent/src/main/java/org/openscience/cdk/silent/PDBPolymer.java @@ -121,7 +121,7 @@ public Collection getMonomerNamesInSequentialOrder() { } /** - * @inheritDoc + *{@inheritDoc} */ @Override public IPDBPolymer clone() throws CloneNotSupportedException { diff --git a/base/silent/src/main/java/org/openscience/cdk/silent/ReactionSet.java b/base/silent/src/main/java/org/openscience/cdk/silent/ReactionSet.java index e3d2989153..bebf40301a 100644 --- a/base/silent/src/main/java/org/openscience/cdk/silent/ReactionSet.java +++ b/base/silent/src/main/java/org/openscience/cdk/silent/ReactionSet.java @@ -245,7 +245,7 @@ public void removeReaction(IReaction relevantReaction) { } /** - * @inheritDoc + *{@inheritDoc} */ @Override public boolean isEmpty() { diff --git a/base/silent/src/main/java/org/openscience/cdk/silent/Ring.java b/base/silent/src/main/java/org/openscience/cdk/silent/Ring.java index 513b2c2e9b..4b1c7f83bd 100644 --- a/base/silent/src/main/java/org/openscience/cdk/silent/Ring.java +++ b/base/silent/src/main/java/org/openscience/cdk/silent/Ring.java @@ -139,7 +139,7 @@ public int getBondOrderSum() { } /** - * @inheritDoc + *{@inheritDoc} */ @Override public IRing clone() throws CloneNotSupportedException { diff --git a/base/silent/src/main/java/org/openscience/cdk/silent/SilentChemObjectBuilder.java b/base/silent/src/main/java/org/openscience/cdk/silent/SilentChemObjectBuilder.java index 5c1e7b7e8b..9eef242035 100644 --- a/base/silent/src/main/java/org/openscience/cdk/silent/SilentChemObjectBuilder.java +++ b/base/silent/src/main/java/org/openscience/cdk/silent/SilentChemObjectBuilder.java @@ -194,7 +194,7 @@ public static IChemObjectBuilder getInstance() { } /** - * @inheritDoc + *{@inheritDoc} */ @Override public T newInstance(Class clazz, Object... params) throws IllegalArgumentException { diff --git a/base/standard/src/main/java/org/openscience/cdk/aromaticity/AtomTypeModel.java b/base/standard/src/main/java/org/openscience/cdk/aromaticity/AtomTypeModel.java index e6f81ccceb..2411499c67 100644 --- a/base/standard/src/main/java/org/openscience/cdk/aromaticity/AtomTypeModel.java +++ b/base/standard/src/main/java/org/openscience/cdk/aromaticity/AtomTypeModel.java @@ -77,7 +77,7 @@ final class AtomTypeModel extends ElectronDonation { this.exocyclic = exocyclic; } - /** @inheritDoc */ + /**{@inheritDoc} */ @Override int[] contribution(IAtomContainer container, RingSearch ringSearch) { diff --git a/base/standard/src/main/java/org/openscience/cdk/aromaticity/DaylightModel.java b/base/standard/src/main/java/org/openscience/cdk/aromaticity/DaylightModel.java index 7b07cb6e8e..ee821cbc32 100644 --- a/base/standard/src/main/java/org/openscience/cdk/aromaticity/DaylightModel.java +++ b/base/standard/src/main/java/org/openscience/cdk/aromaticity/DaylightModel.java @@ -75,7 +75,7 @@ final class DaylightModel extends ElectronDonation { private static final int ARSENIC = 33; private static final int SELENIUM = 34; - /** @inheritDoc */ + /**{@inheritDoc} */ @Override int[] contribution(IAtomContainer container, RingSearch ringSearch) { diff --git a/base/standard/src/main/java/org/openscience/cdk/aromaticity/PiBondModel.java b/base/standard/src/main/java/org/openscience/cdk/aromaticity/PiBondModel.java index 3761811ad6..a4d942341f 100644 --- a/base/standard/src/main/java/org/openscience/cdk/aromaticity/PiBondModel.java +++ b/base/standard/src/main/java/org/openscience/cdk/aromaticity/PiBondModel.java @@ -41,7 +41,7 @@ */ final class PiBondModel extends ElectronDonation { - /** @inheritDoc */ + /**{@inheritDoc} */ @Override int[] contribution(IAtomContainer container, RingSearch ringSearch) { diff --git a/base/standard/src/main/java/org/openscience/cdk/graph/EdmondsMaximumMatching.java b/base/standard/src/main/java/org/openscience/cdk/graph/EdmondsMaximumMatching.java index c6aa6596b6..3f1587afff 100644 --- a/base/standard/src/main/java/org/openscience/cdk/graph/EdmondsMaximumMatching.java +++ b/base/standard/src/main/java/org/openscience/cdk/graph/EdmondsMaximumMatching.java @@ -412,13 +412,13 @@ private Tuple(int first, int second) { this.second = second; } - /** @inheritDoc */ + /**{@inheritDoc} */ @Override public int hashCode() { return 31 * first + second; } - /** @inheritDoc */ + /**{@inheritDoc} */ @Override public boolean equals(Object o) { if (this == o) return true; diff --git a/base/standard/src/main/java/org/openscience/cdk/graph/Matching.java b/base/standard/src/main/java/org/openscience/cdk/graph/Matching.java index 4984e65f9a..e34e7dcc80 100644 --- a/base/standard/src/main/java/org/openscience/cdk/graph/Matching.java +++ b/base/standard/src/main/java/org/openscience/cdk/graph/Matching.java @@ -225,7 +225,7 @@ public static Matching withCapacity(final int capacity) { return new Matching(capacity); } - /** @inheritDoc */ + /**{@inheritDoc} */ @Override public String toString() { StringBuilder sb = new StringBuilder(4 * match.length); diff --git a/base/standard/src/main/java/org/openscience/cdk/stereo/StereoElementFactory.java b/base/standard/src/main/java/org/openscience/cdk/stereo/StereoElementFactory.java index dc1568c2d2..5cd0f08d51 100644 --- a/base/standard/src/main/java/org/openscience/cdk/stereo/StereoElementFactory.java +++ b/base/standard/src/main/java/org/openscience/cdk/stereo/StereoElementFactory.java @@ -347,20 +347,20 @@ static final class StereoElementFactory2D extends StereoElementFactory { super(container, graph, bondMap); } - /** @inheritDoc */ + /**{@inheritDoc} */ @Override ITetrahedralChirality createTetrahedral(IAtom atom, Stereocenters stereocenters) { return createTetrahedral(container.getAtomNumber(atom), stereocenters); } - /** @inheritDoc */ + /**{@inheritDoc} */ @Override IDoubleBondStereochemistry createGeometric(IBond bond, Stereocenters stereocenters) { return createGeometric(container.getAtomNumber(bond.getAtom(0)), container.getAtomNumber(bond.getAtom(1)), stereocenters); } - /** @inheritDoc */ + /**{@inheritDoc} */ @Override ITetrahedralChirality createTetrahedral(int v, Stereocenters stereocenters) { @@ -431,7 +431,7 @@ ITetrahedralChirality createTetrahedral(int v, Stereocenters stereocenters) { return new TetrahedralChirality(focus, neighbors, winding); } - /** @inheritDoc */ + /**{@inheritDoc} */ @Override IDoubleBondStereochemistry createGeometric(int u, int v, Stereocenters stereocenters) { @@ -472,7 +472,7 @@ IDoubleBondStereochemistry createGeometric(int u, int v, Stereocenters stereocen conformation); } - /** @inheritDoc */ + /**{@inheritDoc} */ @Override ExtendedTetrahedral createExtendedTetrahedral(int v, Stereocenters stereocenters) { @@ -691,20 +691,20 @@ private static final class StereoElementFactory3D extends StereoElementFactory { super(container, graph, bondMap); } - /** @inheritDoc */ + /**{@inheritDoc} */ @Override ITetrahedralChirality createTetrahedral(IAtom atom, Stereocenters stereocenters) { return createTetrahedral(container.getAtomNumber(atom), stereocenters); } - /** @inheritDoc */ + /**{@inheritDoc} */ @Override IDoubleBondStereochemistry createGeometric(IBond bond, Stereocenters stereocenters) { return createGeometric(container.getAtomNumber(bond.getAtom(0)), container.getAtomNumber(bond.getAtom(1)), stereocenters); } - /** @inheritDoc */ + /**{@inheritDoc} */ @Override ITetrahedralChirality createTetrahedral(int v, Stereocenters stereocenters) { @@ -736,7 +736,7 @@ ITetrahedralChirality createTetrahedral(int v, Stereocenters stereocenters) { return new TetrahedralChirality(focus, neighbors, winding); } - /** @inheritDoc */ + /**{@inheritDoc} */ @Override IDoubleBondStereochemistry createGeometric(int u, int v, Stereocenters stereocenters) { @@ -767,7 +767,7 @@ IDoubleBondStereochemistry createGeometric(int u, int v, Stereocenters stereocen return new DoubleBondStereochemistry(bond, new IBond[]{bondMap.get(u, x), bondMap.get(v, w),}, conformation); } - /** @inheritDoc */ + /**{@inheritDoc} */ @Override ExtendedTetrahedral createExtendedTetrahedral(int v, Stereocenters stereocenters) { diff --git a/descriptor/fingerprint/src/main/java/org/openscience/cdk/fingerprint/ShortestPathWalker.java b/descriptor/fingerprint/src/main/java/org/openscience/cdk/fingerprint/ShortestPathWalker.java index 6f629c070e..a3f2c08801 100644 --- a/descriptor/fingerprint/src/main/java/org/openscience/cdk/fingerprint/ShortestPathWalker.java +++ b/descriptor/fingerprint/src/main/java/org/openscience/cdk/fingerprint/ShortestPathWalker.java @@ -217,7 +217,7 @@ private boolean isSP2Bond(IBond bond) { } /** - * @inheritDoc + *{@inheritDoc} */ @Override public String toString() { diff --git a/descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/HybridizationRatioDescriptor.java b/descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/HybridizationRatioDescriptor.java index ed4768eda4..a526facfa4 100644 --- a/descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/HybridizationRatioDescriptor.java +++ b/descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/HybridizationRatioDescriptor.java @@ -57,7 +57,7 @@ public HybridizationRatioDescriptor() {} /** * Returns a {@link DescriptorSpecification} which specifies which descriptor is implemented by this class. * - * @inheritDoc + *{@inheritDoc} * @return An object containing the descriptor specification */ @Override @@ -98,7 +98,7 @@ public String[] getDescriptorNames() { } /** - * @inheritDoc + *{@inheritDoc} * * @param e the exception * @return a dummy value diff --git a/display/render/src/main/java/org/openscience/cdk/renderer/SymbolVisibility.java b/display/render/src/main/java/org/openscience/cdk/renderer/SymbolVisibility.java index 9dd65abcca..dc8ed6131b 100644 --- a/display/render/src/main/java/org/openscience/cdk/renderer/SymbolVisibility.java +++ b/display/render/src/main/java/org/openscience/cdk/renderer/SymbolVisibility.java @@ -104,7 +104,7 @@ private IupacVisibility(boolean terminal) { } /** - * @inheritDoc + *{@inheritDoc} */ @Override public boolean visible(IAtom atom, List bonds, RendererModel model) { diff --git a/display/render/src/main/java/org/openscience/cdk/renderer/color/UniColor.java b/display/render/src/main/java/org/openscience/cdk/renderer/color/UniColor.java index 27bb85a725..1c784d6ca3 100644 --- a/display/render/src/main/java/org/openscience/cdk/renderer/color/UniColor.java +++ b/display/render/src/main/java/org/openscience/cdk/renderer/color/UniColor.java @@ -47,7 +47,7 @@ public UniColor(Color color) { } /** - * @inheritDoc + *{@inheritDoc} */ @Override public Color getAtomColor(IAtom atom) { @@ -55,7 +55,7 @@ public Color getAtomColor(IAtom atom) { } /** - * @inheritDoc + *{@inheritDoc} */ @Override public Color getAtomColor(IAtom atom, Color defaultColor) { diff --git a/display/renderbasic/src/main/java/org/openscience/cdk/renderer/elements/Bounds.java b/display/renderbasic/src/main/java/org/openscience/cdk/renderer/elements/Bounds.java index 36b502a2ed..c7544f7631 100644 --- a/display/renderbasic/src/main/java/org/openscience/cdk/renderer/elements/Bounds.java +++ b/display/renderbasic/src/main/java/org/openscience/cdk/renderer/elements/Bounds.java @@ -220,7 +220,7 @@ public final boolean isEmpty() { } /** - * @inheritDoc + *{@inheritDoc} */ @Override public void accept(IRenderingVisitor visitor) { @@ -228,7 +228,7 @@ public void accept(IRenderingVisitor visitor) { } /** - * @inheritDoc + *{@inheritDoc} */ @Override public String toString() { diff --git a/display/renderbasic/src/main/java/org/openscience/cdk/renderer/elements/MarkedElement.java b/display/renderbasic/src/main/java/org/openscience/cdk/renderer/elements/MarkedElement.java index efd69401f4..9c41632096 100644 --- a/display/renderbasic/src/main/java/org/openscience/cdk/renderer/elements/MarkedElement.java +++ b/display/renderbasic/src/main/java/org/openscience/cdk/renderer/elements/MarkedElement.java @@ -99,7 +99,7 @@ public List getClasses() { } /** - * @inheritDoc + *{@inheritDoc} */ @Override public void accept(IRenderingVisitor visitor) { diff --git a/display/renderbasic/src/main/java/org/openscience/cdk/renderer/elements/path/Close.java b/display/renderbasic/src/main/java/org/openscience/cdk/renderer/elements/path/Close.java index 491b09a483..c51f713d7c 100644 --- a/display/renderbasic/src/main/java/org/openscience/cdk/renderer/elements/path/Close.java +++ b/display/renderbasic/src/main/java/org/openscience/cdk/renderer/elements/path/Close.java @@ -45,7 +45,7 @@ public float[] points() { return new float[0]; } - /** @inheritDoc */ + /**{@inheritDoc} */ @Override public void points(double[] coords) { // N/A diff --git a/display/renderbasic/src/main/java/org/openscience/cdk/renderer/elements/path/CubicTo.java b/display/renderbasic/src/main/java/org/openscience/cdk/renderer/elements/path/CubicTo.java index 0778ecde37..15b1bd0424 100644 --- a/display/renderbasic/src/main/java/org/openscience/cdk/renderer/elements/path/CubicTo.java +++ b/display/renderbasic/src/main/java/org/openscience/cdk/renderer/elements/path/CubicTo.java @@ -86,7 +86,7 @@ public float[] points() { (float) coords[4], (float) coords[5]}; } - /** @inheritDoc */ + /**{@inheritDoc} */ @Override public void points(double[] coords) { coords[0] = this.coords[0]; diff --git a/display/renderbasic/src/main/java/org/openscience/cdk/renderer/elements/path/LineTo.java b/display/renderbasic/src/main/java/org/openscience/cdk/renderer/elements/path/LineTo.java index d5940d9cdf..26673f67e1 100644 --- a/display/renderbasic/src/main/java/org/openscience/cdk/renderer/elements/path/LineTo.java +++ b/display/renderbasic/src/main/java/org/openscience/cdk/renderer/elements/path/LineTo.java @@ -75,7 +75,7 @@ public float[] points() { return new float[]{(float) coords[0], (float) coords[1]}; } - /** @inheritDoc */ + /**{@inheritDoc} */ @Override public void points(double[] coords) { coords[0] = this.coords[0]; diff --git a/display/renderbasic/src/main/java/org/openscience/cdk/renderer/elements/path/MoveTo.java b/display/renderbasic/src/main/java/org/openscience/cdk/renderer/elements/path/MoveTo.java index 3718174bce..108469a266 100644 --- a/display/renderbasic/src/main/java/org/openscience/cdk/renderer/elements/path/MoveTo.java +++ b/display/renderbasic/src/main/java/org/openscience/cdk/renderer/elements/path/MoveTo.java @@ -76,7 +76,7 @@ public float[] points() { return new float[]{(float) coords[0], (float) coords[1]}; } - /** @inheritDoc */ + /**{@inheritDoc} */ @Override public void points(double[] coords) { coords[0] = this.coords[0]; diff --git a/display/renderbasic/src/main/java/org/openscience/cdk/renderer/elements/path/QuadTo.java b/display/renderbasic/src/main/java/org/openscience/cdk/renderer/elements/path/QuadTo.java index 62278887c8..be926203c1 100644 --- a/display/renderbasic/src/main/java/org/openscience/cdk/renderer/elements/path/QuadTo.java +++ b/display/renderbasic/src/main/java/org/openscience/cdk/renderer/elements/path/QuadTo.java @@ -81,7 +81,7 @@ public float[] points() { return new float[]{(float) coords[0], (float) coords[1], (float) coords[2], (float) coords[3]}; } - /** @inheritDoc */ + /**{@inheritDoc} */ @Override public void points(double[] coords) { coords[0] = this.coords[0]; diff --git a/display/renderbasic/src/main/java/org/openscience/cdk/renderer/generators/standard/ConvexHull.java b/display/renderbasic/src/main/java/org/openscience/cdk/renderer/generators/standard/ConvexHull.java index 227b36512d..9f81a62e41 100644 --- a/display/renderbasic/src/main/java/org/openscience/cdk/renderer/generators/standard/ConvexHull.java +++ b/display/renderbasic/src/main/java/org/openscience/cdk/renderer/generators/standard/ConvexHull.java @@ -277,7 +277,7 @@ static final class PolarComparator implements Comparator { this.reference = reference; } - /** @inheritDoc */ + /**{@inheritDoc} */ @Override public int compare(Point2D a, Point2D b) { final double deltaX1 = a.getX() - reference.getX(); @@ -306,7 +306,7 @@ else if (deltaX2 >= 0 && deltaX1 < 0) */ static final class CompareYThenX implements Comparator { - /** @inheritDoc */ + /**{@inheritDoc} */ @Override public int compare(Point2D a, Point2D b) { if (a.getY() < b.getY()) return -1; diff --git a/display/renderbasic/src/main/java/org/openscience/cdk/renderer/generators/standard/HydrogenPosition.java b/display/renderbasic/src/main/java/org/openscience/cdk/renderer/generators/standard/HydrogenPosition.java index c1d2263206..29aca4ed50 100644 --- a/display/renderbasic/src/main/java/org/openscience/cdk/renderer/generators/standard/HydrogenPosition.java +++ b/display/renderbasic/src/main/java/org/openscience/cdk/renderer/generators/standard/HydrogenPosition.java @@ -201,7 +201,7 @@ private OffsetExtent(double extent, double offset) { this.offset = offset; } - /** @inheritDoc */ + /**{@inheritDoc} */ @Override public String toString() { return String.format("%.2f, %.2f", extent, offset); diff --git a/display/renderbasic/src/main/java/org/openscience/cdk/renderer/generators/standard/SelectionVisibility.java b/display/renderbasic/src/main/java/org/openscience/cdk/renderer/generators/standard/SelectionVisibility.java index 47bd32eb92..4315f7ff93 100644 --- a/display/renderbasic/src/main/java/org/openscience/cdk/renderer/generators/standard/SelectionVisibility.java +++ b/display/renderbasic/src/main/java/org/openscience/cdk/renderer/generators/standard/SelectionVisibility.java @@ -82,7 +82,7 @@ public static SymbolVisibility all(SymbolVisibility visibility) { } /** - * @inheritDoc + *{@inheritDoc} */ @Override public boolean visible(IAtom atom, List neighbors, RendererModel model) { diff --git a/display/renderbasic/src/main/java/org/openscience/cdk/renderer/generators/standard/StandardBondGenerator.java b/display/renderbasic/src/main/java/org/openscience/cdk/renderer/generators/standard/StandardBondGenerator.java index f1fc297cb5..0416ff9ec0 100644 --- a/display/renderbasic/src/main/java/org/openscience/cdk/renderer/generators/standard/StandardBondGenerator.java +++ b/display/renderbasic/src/main/java/org/openscience/cdk/renderer/generators/standard/StandardBondGenerator.java @@ -1331,7 +1331,7 @@ static final class RingBondOffsetComparator implements Comparator> getParameters() { @@ -822,7 +822,7 @@ static void unhide(IChemObject chemobj) { public static final class AtomColor extends AbstractGeneratorParameter { /** - * @inheritDoc + *{@inheritDoc} */ @Override public IAtomColorer getDefault() { @@ -839,7 +839,7 @@ public IAtomColorer getDefault() { public static final class Visibility extends AbstractGeneratorParameter { /** - * @inheritDoc + *{@inheritDoc} */ @Override public SymbolVisibility getDefault() { @@ -854,7 +854,7 @@ public SymbolVisibility getDefault() { public static final class StrokeRatio extends AbstractGeneratorParameter { /** - * @inheritDoc + *{@inheritDoc} */ @Override public Double getDefault() { @@ -869,7 +869,7 @@ public Double getDefault() { public static final class BondSeparation extends AbstractGeneratorParameter { /** - * @inheritDoc + *{@inheritDoc} */ @Override public Double getDefault() { @@ -884,7 +884,7 @@ public Double getDefault() { public static final class SymbolMarginRatio extends AbstractGeneratorParameter { /** - * @inheritDoc + *{@inheritDoc} */ @Override public Double getDefault() { @@ -898,7 +898,7 @@ public Double getDefault() { public static final class WedgeRatio extends AbstractGeneratorParameter { /** - * @inheritDoc + *{@inheritDoc} */ @Override public Double getDefault() { @@ -913,7 +913,7 @@ public Double getDefault() { public static final class HashSpacing extends AbstractGeneratorParameter { /** - * @inheritDoc + *{@inheritDoc} */ @Override public Double getDefault() { @@ -927,7 +927,7 @@ public Double getDefault() { public static final class WaveSpacing extends AbstractGeneratorParameter { /** - * @inheritDoc + *{@inheritDoc} */ @Override public Double getDefault() { @@ -941,7 +941,7 @@ public Double getDefault() { public static final class DashSection extends AbstractGeneratorParameter { /** - * @inheritDoc + *{@inheritDoc} */ @Override public Integer getDefault() { @@ -954,7 +954,7 @@ public Integer getDefault() { */ public static final class FancyBoldWedges extends AbstractGeneratorParameter { - /** @inheritDoc */ + /**{@inheritDoc} */ @Override public Boolean getDefault() { return true; @@ -966,7 +966,7 @@ public Boolean getDefault() { */ public static final class FancyHashedWedges extends AbstractGeneratorParameter { - /** @inheritDoc */ + /**{@inheritDoc} */ @Override public Boolean getDefault() { return true; @@ -980,7 +980,7 @@ public Boolean getDefault() { */ public static final class OuterGlowWidth extends AbstractGeneratorParameter { - /** @inheritDoc */ + /**{@inheritDoc} */ @Override public Double getDefault() { return 2d; @@ -993,7 +993,7 @@ public Double getDefault() { */ public static final class Highlighting extends AbstractGeneratorParameter { - /** @inheritDoc */ + /**{@inheritDoc} */ @Override public HighlightStyle getDefault() { return HighlightStyle.Colored; @@ -1006,7 +1006,7 @@ public HighlightStyle getDefault() { */ public static final class AnnotationColor extends AbstractGeneratorParameter { - /** @inheritDoc */ + /**{@inheritDoc} */ @Override public Color getDefault() { return Color.RED; @@ -1019,7 +1019,7 @@ public Color getDefault() { */ public static final class AnnotationDistance extends AbstractGeneratorParameter { - /** @inheritDoc */ + /**{@inheritDoc} */ @Override public Double getDefault() { return 0.25; @@ -1031,7 +1031,7 @@ public Double getDefault() { */ public static final class AnnotationFontScale extends AbstractGeneratorParameter { - /** @inheritDoc */ + /**{@inheritDoc} */ @Override public Double getDefault() { return 0.5; @@ -1043,7 +1043,7 @@ public Double getDefault() { */ public static final class SgroupBracketDepth extends AbstractGeneratorParameter { - /** @inheritDoc */ + /**{@inheritDoc} */ @Override public Double getDefault() { return 0.18; @@ -1055,7 +1055,7 @@ public Double getDefault() { */ public static final class SgroupFontScale extends AbstractGeneratorParameter { - /** @inheritDoc */ + /**{@inheritDoc} */ @Override public Double getDefault() { return 0.6; diff --git a/display/renderbasic/src/main/java/org/openscience/cdk/renderer/generators/standard/TextOutline.java b/display/renderbasic/src/main/java/org/openscience/cdk/renderer/generators/standard/TextOutline.java index d87361a886..4ee9fdbaff 100644 --- a/display/renderbasic/src/main/java/org/openscience/cdk/renderer/generators/standard/TextOutline.java +++ b/display/renderbasic/src/main/java/org/openscience/cdk/renderer/generators/standard/TextOutline.java @@ -241,7 +241,7 @@ TextOutline translate(final double translateX, final double translateY) { } /** - * @inheritDoc + *{@inheritDoc} */ @Override public String toString() { diff --git a/display/renderextra/src/main/java/org/openscience/cdk/renderer/generators/HighlightGenerator.java b/display/renderextra/src/main/java/org/openscience/cdk/renderer/generators/HighlightGenerator.java index 8ab930ea88..220d5cb2e1 100644 --- a/display/renderextra/src/main/java/org/openscience/cdk/renderer/generators/HighlightGenerator.java +++ b/display/renderextra/src/main/java/org/openscience/cdk/renderer/generators/HighlightGenerator.java @@ -118,7 +118,7 @@ public final class HighlightGenerator implements IGenerator { /** Property key. */ public static final String ID_MAP = "cdk.highlight.id"; - /** @inheritDoc */ + /**{@inheritDoc} */ @Override public IRenderingElement generate(IAtomContainer container, RendererModel model) { @@ -225,7 +225,7 @@ private static Shape createBondHighlight(IBond bond, double radius) { return AffineTransform.getRotateInstance(theta, x1, y1).createTransformedShape(s); } - /** @inheritDoc */ + /**{@inheritDoc} */ @Override public List> getParameters() { return Arrays.asList(new IGeneratorParameter[]{highlightRadius, highlightPalette}); @@ -325,7 +325,7 @@ public FixedPalette(Color[] colors) { } /** - * @inheritDoc + *{@inheritDoc} */ @Override public Color color(int id) { @@ -404,7 +404,7 @@ private void fill(Color[] colors, int from, int to) { } } - /** @inheritDoc */ + /**{@inheritDoc} */ @Override public Color color(int id) { if (id < 0) throw new IllegalArgumentException("id should be positive"); diff --git a/storage/io/src/main/java/org/openscience/cdk/io/ChemObjectIO.java b/storage/io/src/main/java/org/openscience/cdk/io/ChemObjectIO.java index e70900c251..06df2c2a31 100644 --- a/storage/io/src/main/java/org/openscience/cdk/io/ChemObjectIO.java +++ b/storage/io/src/main/java/org/openscience/cdk/io/ChemObjectIO.java @@ -54,7 +54,7 @@ public abstract class ChemObjectIO implements IChemObjectIO { private SettingManager settings = new SettingManager(); /** - * @inheritDoc + *{@inheritDoc} */ @Override public List getListeners() { @@ -62,7 +62,7 @@ public List getListeners() { } /** - * @inheritDoc + *{@inheritDoc} */ @Override public void addChemObjectIOListener(IChemObjectIOListener listener) { @@ -70,7 +70,7 @@ public void addChemObjectIOListener(IChemObjectIOListener listener) { } /** - * @inheritDoc + *{@inheritDoc} */ @Override public void removeChemObjectIOListener(IChemObjectIOListener listener) { @@ -78,7 +78,7 @@ public void removeChemObjectIOListener(IChemObjectIOListener listener) { } /** - * @inheritDoc + *{@inheritDoc} */ @Override public S addSetting(IOSetting setting) { @@ -86,7 +86,7 @@ public S addSetting(IOSetting setting) { } /** - * @inheritDoc + *{@inheritDoc} */ @Override public void addSettings(Collection settings) { @@ -105,7 +105,7 @@ public void addSettings(Collection settings) { } /** - * @inheritDoc + *{@inheritDoc} */ @Override public boolean hasSetting(String name) { @@ -113,7 +113,7 @@ public boolean hasSetting(String name) { } /** - * @inheritDoc + *{@inheritDoc} */ @Override public S getSetting(String name) { @@ -121,7 +121,7 @@ public S getSetting(String name) { } /** - * @inheritDoc + *{@inheritDoc} */ @Override public S getSetting(String name, Class c) { @@ -129,7 +129,7 @@ public S getSetting(String name, Class c) { } /** - * @inheritDoc + *{@inheritDoc} */ @Override public IOSetting[] getIOSettings() { @@ -137,7 +137,7 @@ public IOSetting[] getIOSettings() { } /** - * @inheritDoc + *{@inheritDoc} */ @Override public Collection getSettings() { diff --git a/tool/group/src/main/java/org/openscience/cdk/group/AtomDiscretePartitionRefiner.java b/tool/group/src/main/java/org/openscience/cdk/group/AtomDiscretePartitionRefiner.java index d8120ce154..c566b609a1 100644 --- a/tool/group/src/main/java/org/openscience/cdk/group/AtomDiscretePartitionRefiner.java +++ b/tool/group/src/main/java/org/openscience/cdk/group/AtomDiscretePartitionRefiner.java @@ -126,7 +126,7 @@ public AtomDiscretePartitionRefiner(boolean ignoreElements, boolean ignoreBondOr } /** - * @inheritDoc + *{@inheritDoc} */ @Override public int getVertexCount() { @@ -134,7 +134,7 @@ public int getVertexCount() { } /** - * @inheritDoc + *{@inheritDoc} */ @Override public int getConnectivity(int i, int j) { diff --git a/tool/group/src/main/java/org/openscience/cdk/group/AtomEquitablePartitionRefiner.java b/tool/group/src/main/java/org/openscience/cdk/group/AtomEquitablePartitionRefiner.java index f05052ad7f..681c212074 100644 --- a/tool/group/src/main/java/org/openscience/cdk/group/AtomEquitablePartitionRefiner.java +++ b/tool/group/src/main/java/org/openscience/cdk/group/AtomEquitablePartitionRefiner.java @@ -45,7 +45,7 @@ public AtomEquitablePartitionRefiner(AtomDiscretePartitionRefiner discreteRefine } /** - * @inheritDoc + *{@inheritDoc} */ @Override public int neighboursInBlock(Set block, int atomIndex) { @@ -59,7 +59,7 @@ public int neighboursInBlock(Set block, int atomIndex) { } /** - * @inheritDoc + *{@inheritDoc} */ @Override public int getVertexCount() { diff --git a/tool/group/src/main/java/org/openscience/cdk/group/BondDiscretePartitionRefiner.java b/tool/group/src/main/java/org/openscience/cdk/group/BondDiscretePartitionRefiner.java index c88f7b9a09..b2585eb5ed 100644 --- a/tool/group/src/main/java/org/openscience/cdk/group/BondDiscretePartitionRefiner.java +++ b/tool/group/src/main/java/org/openscience/cdk/group/BondDiscretePartitionRefiner.java @@ -112,7 +112,7 @@ public BondDiscretePartitionRefiner(boolean ignoreBondOrders) { } /** - * @inheritDoc + *{@inheritDoc} */ @Override public int getVertexCount() { @@ -120,7 +120,7 @@ public int getVertexCount() { } /** - * @inheritDoc + *{@inheritDoc} */ @Override public int getConnectivity(int i, int j) { diff --git a/tool/group/src/main/java/org/openscience/cdk/group/BondEquitablePartitionRefiner.java b/tool/group/src/main/java/org/openscience/cdk/group/BondEquitablePartitionRefiner.java index e82dd129c8..37b0d0edda 100644 --- a/tool/group/src/main/java/org/openscience/cdk/group/BondEquitablePartitionRefiner.java +++ b/tool/group/src/main/java/org/openscience/cdk/group/BondEquitablePartitionRefiner.java @@ -51,7 +51,7 @@ public BondEquitablePartitionRefiner(BondDiscretePartitionRefiner discreteRefine } /** - * @inheritDoc + *{@inheritDoc} */ @Override public int neighboursInBlock(Set block, int bondIndex) { @@ -65,7 +65,7 @@ public int neighboursInBlock(Set block, int bondIndex) { } /** - * @inheritDoc + *{@inheritDoc} */ @Override public int getVertexCount() { diff --git a/tool/group/src/main/java/org/openscience/cdk/group/Partition.java b/tool/group/src/main/java/org/openscience/cdk/group/Partition.java index 7f82beb962..8ecaa2bf83 100644 --- a/tool/group/src/main/java/org/openscience/cdk/group/Partition.java +++ b/tool/group/src/main/java/org/openscience/cdk/group/Partition.java @@ -94,7 +94,7 @@ public static Partition unit(int size) { } /** - * @inheritDoc + *{@inheritDoc} */ @Override public boolean equals(Object o) { @@ -109,7 +109,7 @@ public boolean equals(Object o) { } /** - * @inheritDoc + *{@inheritDoc} */ @Override public int hashCode() { @@ -415,7 +415,7 @@ public boolean inSameCell(int elementI, int elementJ) { } /** - * @inheritDoc + *{@inheritDoc} */ @Override public String toString() { diff --git a/tool/group/src/main/java/org/openscience/cdk/group/Permutation.java b/tool/group/src/main/java/org/openscience/cdk/group/Permutation.java index d8eebf767c..1dcb6db9b9 100644 --- a/tool/group/src/main/java/org/openscience/cdk/group/Permutation.java +++ b/tool/group/src/main/java/org/openscience/cdk/group/Permutation.java @@ -75,7 +75,7 @@ public Permutation(Permutation other) { } /** - * @inheritDoc + *{@inheritDoc} */ @Override public boolean equals(Object other) { @@ -88,7 +88,7 @@ public boolean equals(Object other) { } /** - * @inheritDoc + *{@inheritDoc} */ @Override public int hashCode() { @@ -253,7 +253,7 @@ public String toCycleString() { } /** - * @inheritDoc + *{@inheritDoc} */ @Override public String toString() { diff --git a/tool/group/src/main/java/org/openscience/cdk/group/PermutationGroup.java b/tool/group/src/main/java/org/openscience/cdk/group/PermutationGroup.java index 979a0785fc..811dc9f832 100644 --- a/tool/group/src/main/java/org/openscience/cdk/group/PermutationGroup.java +++ b/tool/group/src/main/java/org/openscience/cdk/group/PermutationGroup.java @@ -403,7 +403,7 @@ public int test(Permutation permutation) { } /** - * @inheritDoc + *{@inheritDoc} */ @Override public String toString() { diff --git a/tool/hash/src/main/java/org/openscience/cdk/hash/AllEquivalentCyclicSet.java b/tool/hash/src/main/java/org/openscience/cdk/hash/AllEquivalentCyclicSet.java index 8812fdb715..c2bcdaa2cf 100644 --- a/tool/hash/src/main/java/org/openscience/cdk/hash/AllEquivalentCyclicSet.java +++ b/tool/hash/src/main/java/org/openscience/cdk/hash/AllEquivalentCyclicSet.java @@ -61,7 +61,7 @@ final class AllEquivalentCyclicSet extends EquivalentSetFinder { /** - * @inheritDoc + *{@inheritDoc} */ @Override Set find(long[] invariants, IAtomContainer container, int[][] graph) { diff --git a/tool/hash/src/main/java/org/openscience/cdk/hash/AtomSuppression.java b/tool/hash/src/main/java/org/openscience/cdk/hash/AtomSuppression.java index 6a0ee55a16..31141ee7c8 100644 --- a/tool/hash/src/main/java/org/openscience/cdk/hash/AtomSuppression.java +++ b/tool/hash/src/main/java/org/openscience/cdk/hash/AtomSuppression.java @@ -63,7 +63,7 @@ Suppressed suppress(IAtomContainer container) { */ private static final class AnyHydrogens extends AtomSuppression { - /** @inheritDoc */ + /**{@inheritDoc} */ @Override Suppressed suppress(IAtomContainer container) { BitSet hydrogens = new BitSet(); @@ -78,7 +78,7 @@ Suppressed suppress(IAtomContainer container) { /** Suppresses any pseudo atom. */ private static final class AnyPseudos extends AtomSuppression { - /** @inheritDoc */ + /**{@inheritDoc} */ @Override Suppressed suppress(IAtomContainer container) { BitSet hydrogens = new BitSet(); diff --git a/tool/hash/src/main/java/org/openscience/cdk/hash/BasicAtomEncoder.java b/tool/hash/src/main/java/org/openscience/cdk/hash/BasicAtomEncoder.java index 5aa630bd72..84fdcd00c8 100644 --- a/tool/hash/src/main/java/org/openscience/cdk/hash/BasicAtomEncoder.java +++ b/tool/hash/src/main/java/org/openscience/cdk/hash/BasicAtomEncoder.java @@ -54,7 +54,7 @@ public enum BasicAtomEncoder implements AtomEncoder { ATOMIC_NUMBER { /** - * @inheritDoc + *{@inheritDoc} */ @Override public int encode(IAtom atom, IAtomContainer container) { @@ -70,7 +70,7 @@ public int encode(IAtom atom, IAtomContainer container) { MASS_NUMBER { /** - * @inheritDoc + *{@inheritDoc} */ @Override public int encode(IAtom atom, IAtomContainer container) { @@ -87,7 +87,7 @@ public int encode(IAtom atom, IAtomContainer container) { FORMAL_CHARGE { /** - * @inheritDoc + *{@inheritDoc} */ @Override public int encode(IAtom atom, IAtomContainer container) { @@ -103,7 +103,7 @@ public int encode(IAtom atom, IAtomContainer container) { N_CONNECTED_ATOMS { /** - * @inheritDoc + *{@inheritDoc} */ @Override public int encode(IAtom atom, IAtomContainer container) { @@ -118,7 +118,7 @@ public int encode(IAtom atom, IAtomContainer container) { BOND_ORDER_SUM { /** - * @inheritDoc + *{@inheritDoc} */ @Override public int encode(IAtom atom, IAtomContainer container) { @@ -133,7 +133,7 @@ public int encode(IAtom atom, IAtomContainer container) { ORBITAL_HYBRIDIZATION { /** - * @inheritDoc + *{@inheritDoc} */ @Override public int encode(IAtom atom, IAtomContainer container) { @@ -149,7 +149,7 @@ public int encode(IAtom atom, IAtomContainer container) { FREE_RADICALS { /** - * @inheritDoc + *{@inheritDoc} */ @Override public int encode(IAtom atom, IAtomContainer container) { diff --git a/tool/hash/src/main/java/org/openscience/cdk/hash/BasicAtomHashGenerator.java b/tool/hash/src/main/java/org/openscience/cdk/hash/BasicAtomHashGenerator.java index 871036a5ab..80eb81811a 100644 --- a/tool/hash/src/main/java/org/openscience/cdk/hash/BasicAtomHashGenerator.java +++ b/tool/hash/src/main/java/org/openscience/cdk/hash/BasicAtomHashGenerator.java @@ -123,7 +123,7 @@ public BasicAtomHashGenerator(AtomHashGenerator seedGenerator, Pseudorandom pseu } /** - * @inheritDoc + *{@inheritDoc} */ @Override public long[] generate(IAtomContainer container) { diff --git a/tool/hash/src/main/java/org/openscience/cdk/hash/BasicMoleculeHashGenerator.java b/tool/hash/src/main/java/org/openscience/cdk/hash/BasicMoleculeHashGenerator.java index 508d02c5a7..459b03bd85 100644 --- a/tool/hash/src/main/java/org/openscience/cdk/hash/BasicMoleculeHashGenerator.java +++ b/tool/hash/src/main/java/org/openscience/cdk/hash/BasicMoleculeHashGenerator.java @@ -83,7 +83,7 @@ public BasicMoleculeHashGenerator(AtomHashGenerator generator) { } /** - * @inheritDoc + *{@inheritDoc} */ @Override public long generate(IAtomContainer container) { diff --git a/tool/hash/src/main/java/org/openscience/cdk/hash/ConjugatedAtomEncoder.java b/tool/hash/src/main/java/org/openscience/cdk/hash/ConjugatedAtomEncoder.java index 8274e370a4..d87d55238f 100644 --- a/tool/hash/src/main/java/org/openscience/cdk/hash/ConjugatedAtomEncoder.java +++ b/tool/hash/src/main/java/org/openscience/cdk/hash/ConjugatedAtomEncoder.java @@ -81,7 +81,7 @@ public ConjugatedAtomEncoder(List encoders) { } /** - * @inheritDoc + *{@inheritDoc} */ @Override public int encode(IAtom atom, IAtomContainer container) { diff --git a/tool/hash/src/main/java/org/openscience/cdk/hash/HashGeneratorMaker.java b/tool/hash/src/main/java/org/openscience/cdk/hash/HashGeneratorMaker.java index db5919c3c3..a8f77fd3c4 100644 --- a/tool/hash/src/main/java/org/openscience/cdk/hash/HashGeneratorMaker.java +++ b/tool/hash/src/main/java/org/openscience/cdk/hash/HashGeneratorMaker.java @@ -367,7 +367,7 @@ private ConjugatedEncoderFactory(StereoEncoderFactory left, StereoEncoderFactory } /** - * @inheritDoc + *{@inheritDoc} */ @Override public StereoEncoder create(IAtomContainer container, int[][] graph) { diff --git a/tool/hash/src/main/java/org/openscience/cdk/hash/MinimumEquivalentCyclicSet.java b/tool/hash/src/main/java/org/openscience/cdk/hash/MinimumEquivalentCyclicSet.java index 53f0402fa4..d79c65167a 100644 --- a/tool/hash/src/main/java/org/openscience/cdk/hash/MinimumEquivalentCyclicSet.java +++ b/tool/hash/src/main/java/org/openscience/cdk/hash/MinimumEquivalentCyclicSet.java @@ -76,7 +76,7 @@ final class MinimumEquivalentCyclicSet extends EquivalentSetFinder { /** - * @inheritDoc + *{@inheritDoc} */ @Override Set find(long[] invariants, IAtomContainer container, int[][] graph) { diff --git a/tool/hash/src/main/java/org/openscience/cdk/hash/MinimumEquivalentCyclicSetUnion.java b/tool/hash/src/main/java/org/openscience/cdk/hash/MinimumEquivalentCyclicSetUnion.java index 4fa784ff04..6f293cf413 100644 --- a/tool/hash/src/main/java/org/openscience/cdk/hash/MinimumEquivalentCyclicSetUnion.java +++ b/tool/hash/src/main/java/org/openscience/cdk/hash/MinimumEquivalentCyclicSetUnion.java @@ -82,7 +82,7 @@ final class MinimumEquivalentCyclicSetUnion extends EquivalentSetFinder { /** - * @inheritDoc + *{@inheritDoc} */ @Override public Set find(long[] invariants, IAtomContainer container, int[][] graph) { diff --git a/tool/hash/src/main/java/org/openscience/cdk/hash/PerturbedAtomHashGenerator.java b/tool/hash/src/main/java/org/openscience/cdk/hash/PerturbedAtomHashGenerator.java index ad95ca9d22..47077f0d5f 100644 --- a/tool/hash/src/main/java/org/openscience/cdk/hash/PerturbedAtomHashGenerator.java +++ b/tool/hash/src/main/java/org/openscience/cdk/hash/PerturbedAtomHashGenerator.java @@ -110,7 +110,7 @@ public PerturbedAtomHashGenerator(SeedGenerator seeds, AbstractAtomHashGenerator } /** - * @inheritDoc + *{@inheritDoc} */ @Override public long[] generate(IAtomContainer container) { diff --git a/tool/hash/src/main/java/org/openscience/cdk/hash/SeedGenerator.java b/tool/hash/src/main/java/org/openscience/cdk/hash/SeedGenerator.java index 08f526d3c1..6d38fb8c12 100644 --- a/tool/hash/src/main/java/org/openscience/cdk/hash/SeedGenerator.java +++ b/tool/hash/src/main/java/org/openscience/cdk/hash/SeedGenerator.java @@ -102,7 +102,7 @@ public SeedGenerator(AtomEncoder encoder, AtomSuppression suppression) { } /** - * @inheritDoc + *{@inheritDoc} */ @Override public long[] generate(IAtomContainer container) { diff --git a/tool/hash/src/main/java/org/openscience/cdk/hash/Suppressed.java b/tool/hash/src/main/java/org/openscience/cdk/hash/Suppressed.java index ac642a8009..05bed12880 100644 --- a/tool/hash/src/main/java/org/openscience/cdk/hash/Suppressed.java +++ b/tool/hash/src/main/java/org/openscience/cdk/hash/Suppressed.java @@ -61,19 +61,19 @@ abstract class Suppressed { /** Default 'empty' implementation always returns false. */ private static final class Empty extends Suppressed { - /** @inheritDoc */ + /**{@inheritDoc} */ @Override boolean contains(int i) { return false; } - /** @inheritDoc */ + /**{@inheritDoc} */ @Override int count() { return 0; } - /** @inheritDoc */ + /**{@inheritDoc} */ @Override int[] toArray() { return new int[0]; @@ -99,19 +99,19 @@ private SuppressedBitSet(BitSet set) { this.set = set; } - /** @inheritDoc */ + /**{@inheritDoc} */ @Override boolean contains(int i) { return set.get(i); } - /** @inheritDoc */ + /**{@inheritDoc} */ @Override int count() { return set.cardinality(); } - /** @inheritDoc */ + /**{@inheritDoc} */ @Override int[] toArray() { int[] xs = new int[count()]; diff --git a/tool/hash/src/main/java/org/openscience/cdk/hash/SuppressedAtomHashGenerator.java b/tool/hash/src/main/java/org/openscience/cdk/hash/SuppressedAtomHashGenerator.java index 0a93e4f1b1..731d983a76 100644 --- a/tool/hash/src/main/java/org/openscience/cdk/hash/SuppressedAtomHashGenerator.java +++ b/tool/hash/src/main/java/org/openscience/cdk/hash/SuppressedAtomHashGenerator.java @@ -109,7 +109,7 @@ public SuppressedAtomHashGenerator(AtomHashGenerator seedGenerator, Pseudorandom } /** - * @inheritDoc + *{@inheritDoc} */ @Override public long[] generate(IAtomContainer container) { diff --git a/tool/hash/src/main/java/org/openscience/cdk/hash/stereo/BasicPermutationParity.java b/tool/hash/src/main/java/org/openscience/cdk/hash/stereo/BasicPermutationParity.java index f44294d951..9fd8f9b244 100644 --- a/tool/hash/src/main/java/org/openscience/cdk/hash/stereo/BasicPermutationParity.java +++ b/tool/hash/src/main/java/org/openscience/cdk/hash/stereo/BasicPermutationParity.java @@ -56,7 +56,7 @@ public BasicPermutationParity(int[] indices) { * The number values to check is typically small ({@literal < 5}) and thus * we use brute-force to count the number of inversions. * - * @inheritDoc + *{@inheritDoc} */ @Override public int parity(long[] current) { diff --git a/tool/hash/src/main/java/org/openscience/cdk/hash/stereo/CombinedPermutationParity.java b/tool/hash/src/main/java/org/openscience/cdk/hash/stereo/CombinedPermutationParity.java index 60494a6316..fe0fc96786 100644 --- a/tool/hash/src/main/java/org/openscience/cdk/hash/stereo/CombinedPermutationParity.java +++ b/tool/hash/src/main/java/org/openscience/cdk/hash/stereo/CombinedPermutationParity.java @@ -50,7 +50,7 @@ public CombinedPermutationParity(PermutationParity left, PermutationParity right } /** - * @inheritDoc + *{@inheritDoc} */ @Override public int parity(long[] current) { diff --git a/tool/hash/src/main/java/org/openscience/cdk/hash/stereo/DoubleBondElementEncoderFactory.java b/tool/hash/src/main/java/org/openscience/cdk/hash/stereo/DoubleBondElementEncoderFactory.java index 51ef6c2f27..ed93050d3e 100644 --- a/tool/hash/src/main/java/org/openscience/cdk/hash/stereo/DoubleBondElementEncoderFactory.java +++ b/tool/hash/src/main/java/org/openscience/cdk/hash/stereo/DoubleBondElementEncoderFactory.java @@ -48,7 +48,7 @@ public final class DoubleBondElementEncoderFactory implements StereoEncoderFactory { /** - * @inheritDoc + *{@inheritDoc} */ @Override public StereoEncoder create(IAtomContainer container, int[][] graph) { diff --git a/tool/hash/src/main/java/org/openscience/cdk/hash/stereo/GeometricParity.java b/tool/hash/src/main/java/org/openscience/cdk/hash/stereo/GeometricParity.java index fc73cad37e..df05b56e24 100644 --- a/tool/hash/src/main/java/org/openscience/cdk/hash/stereo/GeometricParity.java +++ b/tool/hash/src/main/java/org/openscience/cdk/hash/stereo/GeometricParity.java @@ -59,7 +59,7 @@ private Predefined(int parity) { this.parity = parity; } - /** @inheritDoc */ + /**{@inheritDoc} */ @Override int parity() { return parity; diff --git a/tool/hash/src/main/java/org/openscience/cdk/hash/stereo/GeometryEncoder.java b/tool/hash/src/main/java/org/openscience/cdk/hash/stereo/GeometryEncoder.java index 75d50baa4a..ded9484c01 100644 --- a/tool/hash/src/main/java/org/openscience/cdk/hash/stereo/GeometryEncoder.java +++ b/tool/hash/src/main/java/org/openscience/cdk/hash/stereo/GeometryEncoder.java @@ -87,7 +87,7 @@ public GeometryEncoder(int centre, PermutationParity permutation, GeometricParit * parity this may changed with the next {@code current[]} values and so * 'false' is returned. * - * @inheritDoc + *{@inheritDoc} */ @Override public boolean encode(long[] current, long[] next) { @@ -119,7 +119,7 @@ public boolean encode(long[] current, long[] next) { } /** - * @inheritDoc + *{@inheritDoc} */ @Override public void reset() { diff --git a/tool/hash/src/main/java/org/openscience/cdk/hash/stereo/MultiStereoEncoder.java b/tool/hash/src/main/java/org/openscience/cdk/hash/stereo/MultiStereoEncoder.java index cfb4a2037c..fba7967467 100644 --- a/tool/hash/src/main/java/org/openscience/cdk/hash/stereo/MultiStereoEncoder.java +++ b/tool/hash/src/main/java/org/openscience/cdk/hash/stereo/MultiStereoEncoder.java @@ -58,7 +58,7 @@ public MultiStereoEncoder(List encoders) { } /** - * @inheritDoc + *{@inheritDoc} */ @Override public boolean encode(long[] current, long[] next) { @@ -75,7 +75,7 @@ public boolean encode(long[] current, long[] next) { } /** - * @inheritDoc + *{@inheritDoc} */ @Override public void reset() { diff --git a/tool/hash/src/main/java/org/openscience/cdk/hash/stereo/Tetrahedral2DParity.java b/tool/hash/src/main/java/org/openscience/cdk/hash/stereo/Tetrahedral2DParity.java index 7bd948bf38..467f19a888 100644 --- a/tool/hash/src/main/java/org/openscience/cdk/hash/stereo/Tetrahedral2DParity.java +++ b/tool/hash/src/main/java/org/openscience/cdk/hash/stereo/Tetrahedral2DParity.java @@ -70,7 +70,7 @@ public Tetrahedral2DParity(Point2d[] coordinates, int[] elevations) { } /** - * @inheritDoc + *{@inheritDoc} */ @Override public int parity() { diff --git a/tool/hash/src/main/java/org/openscience/cdk/hash/stereo/Tetrahedral3DParity.java b/tool/hash/src/main/java/org/openscience/cdk/hash/stereo/Tetrahedral3DParity.java index 629fb8b5e6..cc65d0d80c 100644 --- a/tool/hash/src/main/java/org/openscience/cdk/hash/stereo/Tetrahedral3DParity.java +++ b/tool/hash/src/main/java/org/openscience/cdk/hash/stereo/Tetrahedral3DParity.java @@ -60,7 +60,7 @@ public Tetrahedral3DParity(Point3d[] coordinates) { } /** - * @inheritDoc + *{@inheritDoc} */ @Override public int parity() { diff --git a/tool/hash/src/main/java/org/openscience/cdk/hash/stereo/TetrahedralElementEncoderFactory.java b/tool/hash/src/main/java/org/openscience/cdk/hash/stereo/TetrahedralElementEncoderFactory.java index 0683c08145..d1ad8a6477 100644 --- a/tool/hash/src/main/java/org/openscience/cdk/hash/stereo/TetrahedralElementEncoderFactory.java +++ b/tool/hash/src/main/java/org/openscience/cdk/hash/stereo/TetrahedralElementEncoderFactory.java @@ -48,7 +48,7 @@ public final class TetrahedralElementEncoderFactory implements StereoEncoderFactory { /** - * @inheritDoc + *{@inheritDoc} */ @Override public StereoEncoder create(IAtomContainer container, int[][] graph) { diff --git a/tool/smarts/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/ChiralityAtom.java b/tool/smarts/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/ChiralityAtom.java index 2d34b229d0..2f7db6fd41 100644 --- a/tool/smarts/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/ChiralityAtom.java +++ b/tool/smarts/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/ChiralityAtom.java @@ -84,7 +84,7 @@ public boolean matches(IAtom atom) { return true; } - /** @inheritDoc */ + /**{@inheritDoc} */ @Override public boolean chiralityMatches(IAtom target, int tParity, int permParity) { int qParity = permParity * (clockwise ? 1 : -1); diff --git a/tool/smarts/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/ExplicitConnectionAtom.java b/tool/smarts/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/ExplicitConnectionAtom.java index 18f0c65a7e..61958810c6 100644 --- a/tool/smarts/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/ExplicitConnectionAtom.java +++ b/tool/smarts/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/ExplicitConnectionAtom.java @@ -44,7 +44,7 @@ public ExplicitConnectionAtom(int degree, IChemObjectBuilder builder) { this.degree = degree; } - /** @inheritDoc */ + /**{@inheritDoc} */ @Override public boolean matches(IAtom atom) { // XXX: this is incorrect but bug 824 expects this behaviour. The reason diff --git a/tool/smarts/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/LogicalOperatorAtom.java b/tool/smarts/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/LogicalOperatorAtom.java index 7bdcb25ab0..947ca37cbf 100644 --- a/tool/smarts/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/LogicalOperatorAtom.java +++ b/tool/smarts/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/LogicalOperatorAtom.java @@ -206,13 +206,13 @@ private Conjunction(IChemObjectBuilder builder, IQueryAtom left, IQueryAtom righ throw new UnsupportedOperationException("create a new logical atom"); } - /** @inheritDoc */ + /**{@inheritDoc} */ @Override public boolean matches(IAtom atom) { return left.matches(atom) && right.matches(atom); } - /** @inheritDoc */ + /**{@inheritDoc} */ @Override public boolean chiralityMatches(IAtom target, int tParity, int permParity) { // contract dictates that left.matches() & right.matches() are known to be true @@ -255,13 +255,13 @@ private Disjunction(IChemObjectBuilder builder, IQueryAtom left, IQueryAtom righ throw new UnsupportedOperationException("create a new logical atom"); } - /** @inheritDoc */ + /**{@inheritDoc} */ @Override public boolean matches(IAtom atom) { return left.matches(atom) || right.matches(atom); } - /** @inheritDoc */ + /**{@inheritDoc} */ @Override public boolean chiralityMatches(IAtom target, int tParity, int permParity) { // we know the left or right was true, for each side which matched try to verify @@ -306,13 +306,13 @@ private Negation(IChemObjectBuilder builder, IQueryAtom expression) { throw new UnsupportedOperationException("create a new logical atom"); } - /** @inheritDoc */ + /**{@inheritDoc} */ @Override public boolean matches(IAtom atom) { return chiral || !expression.matches(atom); } - /** @inheritDoc */ + /**{@inheritDoc} */ @Override public boolean chiralityMatches(IAtom target, int tParity, int permParity) { return !expression.chiralityMatches(target, tParity, permParity); diff --git a/tool/smarts/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/RingMembershipAtom.java b/tool/smarts/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/RingMembershipAtom.java index 4010fc237e..afd8784727 100644 --- a/tool/smarts/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/RingMembershipAtom.java +++ b/tool/smarts/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/RingMembershipAtom.java @@ -53,7 +53,7 @@ public RingMembershipAtom(int num, IChemObjectBuilder builder) { this.ringNumber = num; } - /** @inheritDoc */ + /**{@inheritDoc} */ @Override public boolean matches(IAtom atom) { return ringNumber < 0 ? invariants(atom).ringConnectivity() > 0 : ringNumber == invariants(atom).ringNumber(); diff --git a/tool/smarts/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/SmallestRingAtom.java b/tool/smarts/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/SmallestRingAtom.java index d1e46dc2a1..f3bf45c0cf 100644 --- a/tool/smarts/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/SmallestRingAtom.java +++ b/tool/smarts/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/SmallestRingAtom.java @@ -54,7 +54,7 @@ public SmallestRingAtom(int ringSize, IChemObjectBuilder builder) { this.ringSize = ringSize; } - /** @inheritDoc */ + /**{@inheritDoc} */ @Override public boolean matches(IAtom atom) { return ringSize < 0 ? invariants(atom).ringConnectivity() > 0 diff --git a/tool/smarts/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/TotalConnectionAtom.java b/tool/smarts/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/TotalConnectionAtom.java index dd22aa56c3..4d35789e2c 100644 --- a/tool/smarts/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/TotalConnectionAtom.java +++ b/tool/smarts/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/TotalConnectionAtom.java @@ -47,7 +47,7 @@ public TotalConnectionAtom(int connectivity, IChemObjectBuilder builder) { this.connectivity = connectivity; } - /** @inheritDoc */ + /**{@inheritDoc} */ @Override public boolean matches(IAtom atom) { return invariants(atom).connectivity() == connectivity; diff --git a/tool/smarts/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/TotalHCountAtom.java b/tool/smarts/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/TotalHCountAtom.java index 778ab2b098..22d937ad73 100644 --- a/tool/smarts/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/TotalHCountAtom.java +++ b/tool/smarts/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/TotalHCountAtom.java @@ -53,7 +53,7 @@ public boolean matches(final IAtom atom) { return invariants(atom).totalHydrogenCount() == totalHCount; } - /** @inheritDoc */ + /**{@inheritDoc} */ @Override public String toString() { return "H" + totalHCount; diff --git a/tool/smarts/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/TotalRingConnectionAtom.java b/tool/smarts/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/TotalRingConnectionAtom.java index 42869c6f21..c5428ad60a 100644 --- a/tool/smarts/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/TotalRingConnectionAtom.java +++ b/tool/smarts/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/TotalRingConnectionAtom.java @@ -51,7 +51,7 @@ public TotalRingConnectionAtom(int ringConnectivity, IChemObjectBuilder builder) this.ringConnectivity = ringConnectivity; } - /** @inheritDoc */ + /**{@inheritDoc} */ @Override public boolean matches(IAtom atom) { return invariants(atom).ringConnectivity() == ringConnectivity; diff --git a/tool/smarts/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/TotalValencyAtom.java b/tool/smarts/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/TotalValencyAtom.java index de51ee1c75..8a07283b88 100644 --- a/tool/smarts/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/TotalValencyAtom.java +++ b/tool/smarts/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/TotalValencyAtom.java @@ -47,7 +47,7 @@ public TotalValencyAtom(int valence, IChemObjectBuilder builder) { } /** - * @inheritDoc + *{@inheritDoc} */ @Override public boolean matches(IAtom atom) { diff --git a/tool/smarts/src/main/java/org/openscience/cdk/smiles/smarts/SmartsPattern.java b/tool/smarts/src/main/java/org/openscience/cdk/smiles/smarts/SmartsPattern.java index 2ddf6c55dd..b163583e20 100644 --- a/tool/smarts/src/main/java/org/openscience/cdk/smiles/smarts/SmartsPattern.java +++ b/tool/smarts/src/main/java/org/openscience/cdk/smiles/smarts/SmartsPattern.java @@ -114,7 +114,7 @@ private SmartsPattern(final String smarts, IChemObjectBuilder builder) throws IO } /** - * @inheritDoc + *{@inheritDoc} */ @Override public int[] match(IAtomContainer container) {