We can replace checkNotNull with requireNonNull (since JDK 1.7)

johnmay · egonw · commit 5e46d9c0b34f · 2022-01-01T11:32:07.000+01:00
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
@@ -29,8 +29,8 @@
 import java.util.Collection;
 import java.util.LinkedList;
 import java.util.List;
+import java.util.Objects;
 
-import static com.google.common.base.Preconditions.checkNotNull;
 import static org.openscience.cdk.graph.InitialCycles.Cycle;
 
 /**
@@ -94,8 +94,8 @@ public EssentialCycles(final int[][] graph) {
      * @param initial a molecule graph
      */
     EssentialCycles(final RelevantCycles relevant, final InitialCycles initial) {
-        checkNotNull(relevant, "No RelevantCycles provided");
-        this.initial = checkNotNull(initial, "No InitialCycles provided");
+        Objects.requireNonNull(relevant, "No RelevantCycles provided");
+        this.initial = Objects.requireNonNull(initial, "No InitialCycles provided");
         this.basis = new GreedyBasis(initial.numberOfCycles(), initial.numberOfEdges());
         this.essential = new ArrayList<Cycle>();
 
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
@@ -31,8 +31,8 @@
 
 import java.util.BitSet;
 import java.util.Collection;
+import java.util.Objects;
 
-import static com.google.common.base.Preconditions.checkNotNull;
 import static java.util.Arrays.copyOf;
 
 /**
@@ -113,7 +113,7 @@ final class InitialCycles {
      * @throws NullPointerException the graph was null
      */
     private InitialCycles(final int[][] graph, final int limit, boolean biconnected) {
-        this.graph = checkNotNull(graph, "no graph provided");
+        this.graph = Objects.requireNonNull(graph, "no graph provided");
 
         // ordering ensures the number of initial cycles is polynomial
         this.biconnected = biconnected;
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
@@ -29,9 +29,9 @@
 import java.util.BitSet;
 import java.util.Collections;
 import java.util.List;
+import java.util.Objects;
 
 import static com.google.common.base.Preconditions.checkArgument;
-import static com.google.common.base.Preconditions.checkNotNull;
 
 /**
  * A path graph (<b>P-Graph</b>) for graphs with more than 64 vertices - the
@@ -78,8 +78,8 @@ final class JumboPathGraph extends PathGraph {
     @SuppressWarnings("unchecked")
     JumboPathGraph(final int[][] mGraph, final int[] rank, final int limit) {
 
-        checkNotNull(mGraph, "no molecule graph");
-        checkNotNull(rank, "no rank provided");
+        Objects.requireNonNull(mGraph, "no molecule graph");
+        Objects.requireNonNull(rank, "no rank provided");
 
         this.graph = new List[mGraph.length];
         this.rank = rank;
diff --git a/base/core/src/main/java/org/openscience/cdk/graph/MinimumCycleBasis.java b/base/core/src/main/java/org/openscience/cdk/graph/MinimumCycleBasis.java
@@ -23,7 +23,8 @@
  */
 package org.openscience.cdk.graph;
 
-import static com.google.common.base.Preconditions.checkNotNull;
+import java.util.Objects;
+
 import static org.openscience.cdk.graph.InitialCycles.Cycle;
 
 /**
@@ -85,7 +86,7 @@ public final class MinimumCycleBasis {
      * @see GraphUtil#subgraph(int[][], int[])
      */
     public MinimumCycleBasis(final int[][] graph) {
-        this(new InitialCycles(checkNotNull(graph, "No graph provided")));
+        this(new InitialCycles(Objects.requireNonNull(graph, "No graph provided")));
     }
 
     /**
@@ -111,7 +112,7 @@ public MinimumCycleBasis(final int[][] graph) {
      */
     MinimumCycleBasis(final InitialCycles initial, boolean connected) {
 
-        checkNotNull(initial, "No InitialCycles provided");
+        Objects.requireNonNull(initial, "No InitialCycles provided");
 
         this.graph = initial.graph();
         this.basis = new GreedyBasis(initial.numberOfCycles(), initial.numberOfEdges());
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
@@ -28,9 +28,9 @@
 import java.util.ArrayList;
 import java.util.Collections;
 import java.util.List;
+import java.util.Objects;
 
 import static com.google.common.base.Preconditions.checkArgument;
-import static com.google.common.base.Preconditions.checkNotNull;
 
 /**
  * A path graph (<b>P-Graph</b>) for graphs with less than 64 vertices - the
@@ -77,8 +77,8 @@ final class RegularPathGraph extends PathGraph {
     @SuppressWarnings("unchecked")
     RegularPathGraph(final int[][] mGraph, final int[] rank, final int limit) {
 
-        checkNotNull(mGraph, "no molecule graph");
-        checkNotNull(rank, "no rank provided");
+        Objects.requireNonNull(mGraph, "no molecule graph");
+        Objects.requireNonNull(rank, "no rank provided");
 
         this.graph = new List[mGraph.length];
         this.rank = rank;
diff --git a/base/core/src/main/java/org/openscience/cdk/graph/RelevantCycles.java b/base/core/src/main/java/org/openscience/cdk/graph/RelevantCycles.java
@@ -27,8 +27,8 @@
 import java.util.ArrayList;
 import java.util.Collection;
 import java.util.List;
+import java.util.Objects;
 
-import static com.google.common.base.Preconditions.checkNotNull;
 import static org.openscience.cdk.graph.InitialCycles.Cycle;
 
 /**
@@ -111,7 +111,7 @@ public RelevantCycles(final int[][] graph) {
      */
     RelevantCycles(final InitialCycles initial) {
 
-        checkNotNull(initial, "No InitialCycles provided");
+        Objects.requireNonNull(initial, "No InitialCycles provided");
 
         this.basis = new GreedyBasis(initial.numberOfCycles(), initial.numberOfEdges());
 
diff --git a/base/standard/src/main/java/org/openscience/cdk/aromaticity/Aromaticity.java b/base/standard/src/main/java/org/openscience/cdk/aromaticity/Aromaticity.java
@@ -35,9 +35,9 @@
 import org.openscience.cdk.ringsearch.RingSearch;
 
 import java.util.Arrays;
+import java.util.Objects;
 import java.util.Set;
 
-import static com.google.common.base.Preconditions.checkNotNull;
 import static org.openscience.cdk.CDKConstants.ISAROMATIC;
 import static org.openscience.cdk.graph.GraphUtil.EdgeToBondMap;
 
@@ -151,8 +151,8 @@ public final class Aromaticity {
      * @see org.openscience.cdk.graph.Cycles
      */
     public Aromaticity(ElectronDonation model, CycleFinder cycles) {
-        this.model = checkNotNull(model);
-        this.cycles = checkNotNull(cycles);
+        this.model = Objects.requireNonNull(model);
+        this.cycles = Objects.requireNonNull(cycles);
     }
 
     /**
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
@@ -37,8 +37,8 @@
 
 import java.util.Arrays;
 import java.util.Map;
+import java.util.Objects;
 
-import static com.google.common.base.Preconditions.checkNotNull;
 import static org.openscience.cdk.interfaces.IAtomType.Hybridization;
 
 /**
@@ -98,7 +98,7 @@ int[] contribution(IAtomContainer container, RingSearch ringSearch) {
 
             Hybridization hyb = atom.getHybridization();
 
-            checkNotNull(atom.getAtomTypeName(), "atom has unset atom type");
+            Objects.requireNonNull(atom.getAtomTypeName(), "atom has unset atom type");
 
             // atom has been assigned an atom type but we don't know the hybrid state,
             // typically for atom type 'X' (unknown)
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
@@ -33,8 +33,7 @@
 
 import java.util.Arrays;
 import java.util.Map;
-
-import static com.google.common.base.Preconditions.checkNotNull;
+import java.util.Objects;
 
 /**
  * Electron donation model closely mirroring the Daylight model for use in
@@ -98,8 +97,8 @@ int[] contribution(IAtomContainer container, RingSearch ringSearch) {
         for (int i = 0; i < n; i++) {
             IAtom a = container.getAtom(i);
             atomIndex.put(a, i);
-            int implH = checkNotNull(a.getImplicitHydrogenCount(),
-                                     "Aromaticity model requires implicit hydrogen count is set.");
+            int implH = Objects.requireNonNull(a.getImplicitHydrogenCount(),
+                                      "Aromaticity model requires implicit hydrogen count is set.");
             degree[i] = implH;
             valence[i] = implH;
         }
@@ -114,7 +113,7 @@ int[] contribution(IAtomContainer container, RingSearch ringSearch) {
             degree[u]++;
             degree[v]++;
 
-            IBond.Order order = checkNotNull(bond.getOrder(), "Aromaticity model requires that bond orders must be set");
+            IBond.Order order = Objects.requireNonNull(bond.getOrder(), "Aromaticity model requires that bond orders must be set");
 
             switch (order) {
                 case UNSET:
diff --git a/legacy/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/AtomicNumberAtom.java b/legacy/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/AtomicNumberAtom.java
@@ -23,10 +23,11 @@
  */
 package org.openscience.cdk.isomorphism.matchers.smarts;
 
-import com.google.common.base.Preconditions;
 import org.openscience.cdk.interfaces.IAtom;
 import org.openscience.cdk.interfaces.IChemObjectBuilder;
 
+import java.util.Objects;
+
 /**
  * This matches an atom using the atomic number.
  *
@@ -55,7 +56,7 @@ public AtomicNumberAtom(int atomicNumber, IChemObjectBuilder builder) {
      */
     @Override
     public boolean matches(IAtom atom) {
-        return Preconditions.checkNotNull(atom.getAtomicNumber(), "Atomic number is not set.").equals(
+        return Objects.requireNonNull(atom.getAtomicNumber(), "Atomic number is not set.").equals(
                 this.getAtomicNumber());
     }
 }
diff --git a/legacy/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/SMARTSAtomInvariants.java b/legacy/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/SMARTSAtomInvariants.java
@@ -34,9 +34,9 @@
 
 import java.util.Arrays;
 import java.util.Collections;
+import java.util.Objects;
 import java.util.Set;
 
-import static com.google.common.base.Preconditions.checkNotNull;
 import static org.openscience.cdk.graph.GraphUtil.EdgeToBondMap;
 
 /**
@@ -290,7 +290,7 @@ private static void configureDaylight(IAtomContainer container, int[][] graph, E
 
             IAtom atom = container.getAtom(v);
 
-            int implHCount = checkNotNull(atom.getImplicitHydrogenCount(), "Implicit hydrogen count was not set.");
+            int implHCount = Objects.requireNonNull(atom.getImplicitHydrogenCount(), "Implicit hydrogen count was not set.");
 
             int totalHCount = implHCount;
             int valence = implHCount;
diff --git a/legacy/src/main/java/org/openscience/cdk/smiles/smarts/SMARTSQueryTool.java b/legacy/src/main/java/org/openscience/cdk/smiles/smarts/SMARTSQueryTool.java
@@ -46,10 +46,10 @@
 import java.util.LinkedHashMap;
 import java.util.List;
 import java.util.Map;
+import java.util.Objects;
 import java.util.Set;
 import java.util.TreeSet;
 
-import static com.google.common.base.Preconditions.checkNotNull;
 
 /**
  * This class provides a easy to use wrapper around SMARTS matching functionality.  User code that wants to do
@@ -284,7 +284,7 @@ public void useEssentialRings() {
      * @see Cycles
      */
     public void setAromaticity(Aromaticity aromaticity) {
-        this.aromaticity = checkNotNull(aromaticity, "aromaticity was not provided");
+        this.aromaticity = Objects.requireNonNull(aromaticity, "aromaticity was not provided");
     }
 
     /**
diff --git a/storage/smiles/src/main/java/org/openscience/cdk/smiles/CDKToBeam.java b/storage/smiles/src/main/java/org/openscience/cdk/smiles/CDKToBeam.java
@@ -50,11 +50,10 @@
 import uk.ac.ebi.beam.GraphBuilder;
 
 import java.io.IOException;
-import java.util.Arrays;
 import java.util.Map;
+import java.util.Objects;
 
 import static com.google.common.base.Preconditions.checkArgument;
-import static com.google.common.base.Preconditions.checkNotNull;
 import static org.openscience.cdk.CDKConstants.ATOM_ATOM_MAPPING;
 import static org.openscience.cdk.interfaces.IDoubleBondStereochemistry.Conformation.TOGETHER;
 import static org.openscience.cdk.interfaces.ITetrahedralChirality.Stereo.CLOCKWISE;
@@ -209,7 +208,7 @@ static Atom toBeamAtom(final IAtom a, final int flavour) {
 
         final boolean aromatic = SmiFlavor.isSet(flavour, SmiFlavor.UseAromaticSymbols) && a.getFlag(CDKConstants.ISAROMATIC);
         final Integer charge = a.getFormalCharge();
-        final String symbol = checkNotNull(a.getSymbol(), "An atom had an undefined symbol");
+        final String symbol = Objects.requireNonNull(a.getSymbol(), "An atom had an undefined symbol");
 
         Element element = Element.ofSymbol(symbol);
         if (element == null) element = Element.Unknown;
@@ -221,7 +220,7 @@ static Atom toBeamAtom(final IAtom a, final int flavour) {
         if (element == Element.Unknown) {
             ab.hydrogens(hCount != null ? hCount : 0);
         } else {
-            ab.hydrogens(checkNotNull(hCount, "One or more atoms had an undefined number of implicit hydrogens"));
+            ab.hydrogens(Objects.requireNonNull(hCount, "One or more atoms had an undefined number of implicit hydrogens"));
         }
 
         if (charge != null) ab.charge(charge);

Original file line number	Diff line number	Diff line change
`@@ -23,10 +23,11 @@`
`23`	`23`	`*/`
`24`	`24`	`package org.openscience.cdk.isomorphism.matchers.smarts;`
`25`	`25`
`26`		`-import com.google.common.base.Preconditions;`
`27`	`26`	`import org.openscience.cdk.interfaces.IAtom;`
`28`	`27`	`import org.openscience.cdk.interfaces.IChemObjectBuilder;`
`29`	`28`
	`29`	`+import java.util.Objects;`
	`30`	`+`
`30`	`31`	`/**`
`31`	`32`	`* This matches an atom using the atomic number.`
`32`	`33`	`*`
`@@ -55,7 +56,7 @@ public AtomicNumberAtom(int atomicNumber, IChemObjectBuilder builder) {`
`55`	`56`	`*/`
`56`	`57`	`@Override`
`57`	`58`	`public boolean matches(IAtom atom) {`
`58`		`- return Preconditions.checkNotNull(atom.getAtomicNumber(), "Atomic number is not set.").equals(`
	`59`	`+ return Objects.requireNonNull(atom.getAtomicNumber(), "Atomic number is not set.").equals(`
`59`	`60`	`this.getAtomicNumber());`
`60`	`61`	`}`
`61`	`62`	`}`