Replace usage of Guava Ints utility. Integer.compare helps as well as IntStream

johnmay · egonw · commit 9bbae7a3c22f · 2022-01-01T11:32:07.000+01:00
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
@@ -27,7 +27,6 @@
 import com.google.common.collect.HashBiMap;
 import com.google.common.collect.Multimap;
 import com.google.common.collect.TreeMultimap;
-import com.google.common.primitives.Ints;
 
 import java.util.BitSet;
 import java.util.Collection;
@@ -542,7 +541,14 @@ int length() {
 
         @Override
         public int compareTo(Cycle that) {
-            return Ints.lexicographicalComparator().compare(this.path, that.path);
+            int len = Math.min(this.path.length, that.path.length);
+            for (int i = 0; i < len; i++) {
+                int result = Integer.compare(this.path[i], that.path[i]);
+                if (result != 0) {
+                    return result;
+                }
+            }
+            return this.path.length - that.path.length;
         }
     }
 
diff --git a/base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/AtomMapFilter.java b/base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/AtomMapFilter.java
@@ -25,7 +25,6 @@
 
 import com.google.common.collect.ArrayListMultimap;
 import com.google.common.collect.Multimap;
-import com.google.common.primitives.Ints;
 import org.openscience.cdk.CDKConstants;
 import org.openscience.cdk.ReactionRole;
 import org.openscience.cdk.interfaces.IAtom;
@@ -98,8 +97,8 @@ final class AtomMapFilter implements Predicate<int[]> {
 
         if (reactInvMap != null && prodInvMap != null) {
             for (Map.Entry<Integer, Collection<Integer>> e : reactInvMap.asMap().entrySet()) {
-                int[] reacMaps = Ints.toArray(e.getValue());
-                int[] prodMaps = Ints.toArray(prodInvMap.get(e.getKey()));
+                int[] reacMaps = e.getValue().stream().mapToInt(i->i).toArray();
+                int[] prodMaps = prodInvMap.get(e.getKey()).stream().mapToInt(i->i).toArray();
                 if (prodMaps.length == 0)
                     continue; // unpaired
                 mapped.add(new MappedPairs(reacMaps, prodMaps));
diff --git a/base/standard/src/main/java/org/openscience/cdk/graph/invariant/MorganNumbersTools.java b/base/standard/src/main/java/org/openscience/cdk/graph/invariant/MorganNumbersTools.java
@@ -19,10 +19,11 @@
  */
 package org.openscience.cdk.graph.invariant;
 
-import com.google.common.primitives.Ints;
 import org.openscience.cdk.interfaces.IAtomContainer;
 import org.openscience.cdk.interfaces.IBond;
 
+import java.util.Arrays;
+
 /**
  * Compute the extended connectivity values (Morgan Numbers) {@cdk.cite MOR65}.
  * The tool does not produce the lexicographic smallest labelling on the graph
@@ -75,8 +76,8 @@ public static long[] getMorganNumbers(IAtomContainer molecule) {
         for (IBond bond : molecule.bonds()) {
             int u = molecule.indexOf(bond.getBegin());
             int v = molecule.indexOf(bond.getEnd());
-            graph[u] = Ints.ensureCapacity(graph[u], degree[u] + 1, INITIAL_DEGREE);
-            graph[v] = Ints.ensureCapacity(graph[v], degree[v] + 1, INITIAL_DEGREE);
+            graph[u] = ensureCapacity(graph[u], degree[u] + 1);
+            graph[v] = ensureCapacity(graph[v], degree[v] + 1);
             graph[u][degree[u]++] = v;
             graph[v][degree[v]++] = u;
             currentInvariants[u] += nonHydrogens[v];
@@ -101,6 +102,10 @@ public static long[] getMorganNumbers(IAtomContainer molecule) {
         return currentInvariants;
     }
 
+    private static int[] ensureCapacity(int[] arr, int cap) {
+        return cap < arr.length ? arr : Arrays.copyOf(arr, cap);
+    }
+
     /**
      * Makes an array containing the morgan numbers+element symbol of the atoms
      * of {@code atomContainer}. This method puts the element symbol before the
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
@@ -25,9 +25,7 @@
 
 package org.openscience.cdk.renderer.generators.standard;
 
-import com.google.common.primitives.Ints;
 import org.openscience.cdk.config.Elements;
-import org.openscience.cdk.geometry.GeometryUtil;
 import org.openscience.cdk.graph.Cycles;
 import org.openscience.cdk.interfaces.IAtom;
 import org.openscience.cdk.interfaces.IAtomContainer;
@@ -1724,12 +1722,12 @@ public int compare(IAtomContainer ringa, IAtomContainer ringb) {
             }
 
             // order by size 6,5,7,4,3,rest
-            int sizeCmp = Ints.compare(sizePreference(ringa.getAtomCount()),
+            int sizeCmp = Integer.compare(sizePreference(ringa.getAtomCount()),
                     sizePreference(ringb.getAtomCount()));
             if (sizeCmp != 0) return sizeCmp;
 
             // now order by number of double bonds
-            int piBondCmp = Ints.compare(nDoubleBonds(ringa), nDoubleBonds(ringb));
+            int piBondCmp = Integer.compare(nDoubleBonds(ringa), nDoubleBonds(ringb));
             if (piBondCmp != 0) return -piBondCmp;
 
             // order by element frequencies, all carbon rings are preferred
@@ -1738,7 +1736,7 @@ public int compare(IAtomContainer ringa, IAtomContainer ringb) {
 
             for (Elements element : Arrays.asList(Elements.Carbon, Elements.Nitrogen, Elements.Oxygen, Elements.Sulfur,
                     Elements.Phosphorus)) {
-                int elemCmp = Ints.compare(freqA[element.number()], freqB[element.number()]);
+                int elemCmp = Integer.compare(freqA[element.number()], freqB[element.number()]);
                 if (elemCmp != 0) return -elemCmp;
             }
 
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
@@ -19,7 +19,6 @@
 package org.openscience.cdk.smiles.smarts;
 
 import com.google.common.collect.FluentIterable;
-import com.google.common.primitives.Ints;
 import org.openscience.cdk.aromaticity.Aromaticity;
 import org.openscience.cdk.aromaticity.ElectronDonation;
 import org.openscience.cdk.exception.CDKException;
@@ -49,6 +48,8 @@
 import java.util.Objects;
 import java.util.Set;
 import java.util.TreeSet;
+import java.util.stream.Collectors;
+import java.util.stream.IntStream;
 
 
 /**
@@ -383,6 +384,10 @@ public int countMatches() {
         return mappings.size();
     }
 
+    private static List<Integer> toList(int[] values) {
+        return IntStream.of(values).boxed().collect(Collectors.toList());
+    }
+
     /**
      * Get the atoms in the target molecule that match the query pattern.  Since there may be multiple matches, the
      * return value is a List of List objects. Each List object contains the indices of the atoms in the target
@@ -393,7 +398,7 @@ public int countMatches() {
     public List<List<Integer>> getMatchingAtoms() {
         List<List<Integer>> matched = new ArrayList<List<Integer>>(mappings.size());
         for (int[] mapping : mappings)
-            matched.add(Ints.asList(mapping));
+            matched.add(toList(mapping));
         return matched;
     }
 
@@ -411,7 +416,8 @@ public List<List<Integer>> getUniqueMatchingAtoms() {
             BitSet atomSet = new BitSet();
             for (int x : mapping)
                 atomSet.set(x);
-            if (atomSets.add(atomSet)) matched.add(Ints.asList(mapping));
+            if (atomSets.add(atomSet))
+                matched.add(toList(mapping));
         }
         return matched;
     }
diff --git a/legacy/src/main/java/org/openscience/cdk/smiles/smarts/SmartsAtomAtomMapFilter.java b/legacy/src/main/java/org/openscience/cdk/smiles/smarts/SmartsAtomAtomMapFilter.java
@@ -25,7 +25,6 @@
 
 import com.google.common.collect.ArrayListMultimap;
 import com.google.common.collect.Multimap;
-import com.google.common.primitives.Ints;
 import org.openscience.cdk.CDKConstants;
 import org.openscience.cdk.ReactionRole;
 import org.openscience.cdk.interfaces.IAtom;
@@ -99,8 +98,8 @@ final class SmartsAtomAtomMapFilter implements Predicate<int[]> {
 
         if (reactInvMap != null && prodInvMap != null) {
             for (Map.Entry<Integer, Collection<Integer>> e : reactInvMap.asMap().entrySet()) {
-                int[] reacMaps = Ints.toArray(e.getValue());
-                int[] prodMaps = Ints.toArray(prodInvMap.get(e.getKey()));
+                int[] reacMaps = e.getValue().stream().mapToInt(i->i).toArray();
+                int[] prodMaps = prodInvMap.get(e.getKey()).stream().mapToInt(i->i).toArray();
                 if (prodMaps.length == 0)
                     continue; // unpaired
                 mapped.add(new MappedPairs(reacMaps, prodMaps));
diff --git a/storage/smiles/src/test/java/org/openscience/cdk/smiles/SmilesParserTest.java b/storage/smiles/src/test/java/org/openscience/cdk/smiles/SmilesParserTest.java
@@ -27,7 +27,6 @@
 import java.util.Set;
 
 import com.google.common.collect.FluentIterable;
-import com.google.common.primitives.Ints;
 import org.junit.Assert;
 import org.junit.Assume;
 import org.junit.Ignore;
@@ -2226,7 +2225,7 @@ public void testNeighboringChirality() throws Exception {
 
             @Override
             public int compare(IStereoElement o1, IStereoElement o2) {
-                return Ints.compare(mol.indexOf(((ITetrahedralChirality) o1).getChiralAtom()),
+                return Integer.compare(mol.indexOf(((ITetrahedralChirality) o1).getChiralAtom()),
                         mol.indexOf(((ITetrahedralChirality) o2).getChiralAtom()));
             }
         });
diff --git a/tool/sdg/src/main/java/org/openscience/cdk/layout/NonplanarBonds.java b/tool/sdg/src/main/java/org/openscience/cdk/layout/NonplanarBonds.java
@@ -24,7 +24,6 @@
 
 package org.openscience.cdk.layout;
 
-import com.google.common.primitives.Ints;
 import org.openscience.cdk.BondRef;
 import org.openscience.cdk.CDKConstants;
 import org.openscience.cdk.geometry.GeometryUtil;
@@ -177,7 +176,7 @@ else if (element instanceof IDoubleBondStereochemistry) {
 
             @Override
             public int compare(Integer i, Integer j) {
-                return -Ints.compare(nAdjacentCentres(i), nAdjacentCentres(j));
+                return -Integer.compare(nAdjacentCentres(i), nAdjacentCentres(j));
             }
         });
 
