Replace Guava Predicate/Function with the JDK 1.8 versions. This tech…

…nically breaks the API but is very easy to update thanks to the :: operator. We will be revisiting the Mappings.java to use the Streams API
cdk · Jan 1, 2022 · 40dabd1 · 40dabd1
1 parent 92a03c1
commit 40dabd1
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Showing 11 changed files with 112 additions and 40 deletions.
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
@@ -23,7 +23,6 @@
 
 package org.openscience.cdk.isomorphism;
 
-import com.google.common.base.Predicate;
 import com.google.common.collect.ArrayListMultimap;
 import com.google.common.collect.Multimap;
 import com.google.common.primitives.Ints;
@@ -39,6 +38,7 @@
 import java.util.List;
 import java.util.Map;
 import java.util.Set;
+import java.util.function.Predicate;
 
 /**
  * A filter for substructure matches implementing the logic for Atom-Atom Mapping matching. The following
@@ -141,7 +141,7 @@ private ReactionRole role(IAtom atom) {
      * @return whether the match should be accepted
      */
     @Override
-    public boolean apply(int[] perm) {
+    public boolean test(int[] perm) {
         for (MappedPairs mpair : mapped) {
 
             // possibly 'or' of query maps, need to use a set
@@ -178,6 +178,16 @@ public boolean apply(int[] perm) {
         return true;
     }
 
+    /**
+     * Backwards compatible method from when we used GUAVA predicates.
+     * @param ints atom index bijection
+     * @return true/false
+     * @see #test(int[])
+     */
+    public boolean apply(int[] ints) {
+        return test(ints);
+    }
+
     /**
      * Helper class list all reactant atom indices (rIdxs) and product
      * atom indices (pIdxs) that are in the same Atom-Atom-Mapping class.

diff --git a/base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/ComponentFilter.java b/base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/ComponentFilter.java
@@ -25,13 +25,13 @@
 
 package org.openscience.cdk.isomorphism;
 
-import com.google.common.base.Predicate;
 import org.openscience.cdk.CDKConstants;
 import org.openscience.cdk.graph.ConnectedComponents;
 import org.openscience.cdk.graph.GraphUtil;
 import org.openscience.cdk.interfaces.IAtomContainer;
 
 import java.util.Arrays;
+import java.util.function.Predicate;
 
 /**
  * A predicate for verifying component level grouping in query/target structure
@@ -135,7 +135,7 @@ public ComponentFilter(int[] grouping, int[] targetComponents) {
      * @return the mapping preserves the specified grouping
      */
     @Override
-    public boolean apply(final int[] mapping) {
+    public boolean test(final int[] mapping) {
 
         // no grouping required
         if (queryComponents == null) return true;
@@ -168,4 +168,14 @@ public boolean apply(final int[] mapping) {
 
         return true;
     }
+
+    /**
+     * Backwards compatible method from when we used GUAVA predicates.
+     * @param ints atom index bijection
+     * @return true/false
+     * @see #test(int[])
+     */
+    public boolean apply(int[] ints) {
+        return test(ints);
+    }
 }
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
@@ -24,8 +24,6 @@
 
 package org.openscience.cdk.isomorphism;
 
-import com.google.common.base.Function;
-import com.google.common.base.Predicate;
 import com.google.common.collect.FluentIterable;
 import com.google.common.collect.ImmutableMap;
 import com.google.common.collect.Iterables;
@@ -40,6 +38,8 @@
 import java.util.Arrays;
 import java.util.Iterator;
 import java.util.Map;
+import java.util.function.Function;
+import java.util.function.Predicate;
 
 /**
  * A fluent interface for handling (sub)-graph mappings from a query to a target
@@ -202,7 +202,7 @@ public final class Mappings implements Iterable<int[]> {
      * @return fluent-api reference
      */
     public Mappings filter(final Predicate<int[]> predicate) {
-        return new Mappings(query, target, Iterables.filter(iterable, predicate));
+        return new Mappings(query, target, Iterables.filter(iterable, predicate::test));
     }
 
     /**
@@ -238,7 +238,7 @@ public Mappings filter(final Predicate<int[]> predicate) {
      * @return iterable of the transformed type
      */
     public <T> Iterable<T> map(final Function<int[], T> f) {
-        return Iterables.transform(iterable, f);
+        return Iterables.transform(iterable, f::apply);
     }
 
     /**
@@ -282,7 +282,7 @@ public Mappings uniqueAtoms() {
 
             @Override
             public Iterator<int[]> iterator() {
-                return Iterators.filter(iterable.iterator(), new UniqueAtomMatches());
+                return Iterators.filter(iterable.iterator(), new UniqueAtomMatches()::test);
             }
         });
     }
@@ -302,7 +302,7 @@ public Mappings uniqueBonds() {
 
             @Override
             public Iterator<int[]> iterator() {
-                return Iterators.filter(iterable.iterator(), new UniqueBondMatches(g));
+                return Iterators.filter(iterable.iterator(), new UniqueBondMatches(g)::test);
             }
         });
     }
@@ -435,12 +435,7 @@ public Iterable<Map<IChemObject, IChemObject>> toAtomBondMap() {
      */
     public Iterable<IChemObject> toChemObjects() {
         return FluentIterable.from(map(new ToAtomBondMap(query, target)))
-                             .transformAndConcat(new Function<Map<IChemObject, IChemObject>, Iterable<? extends IChemObject>>() {
-            @Override
-            public Iterable<? extends IChemObject> apply(Map<IChemObject, IChemObject> map) {
-                return map.values();
-            }
-        });
+                             .transformAndConcat(map -> map.values());
     }
 
     /**
@@ -462,9 +457,7 @@ public Iterable<? extends IChemObject> apply(Map<IChemObject, IChemObject> map)
      */
     public Iterable<IAtomContainer> toSubstructures() {
         return FluentIterable.from(map(new ToAtomBondMap(query, target)))
-                             .transform(new Function<Map<IChemObject, IChemObject>, IAtomContainer>() {
-                                 @Override
-                                 public IAtomContainer apply(Map<IChemObject, IChemObject> map) {
+                             .transform(map -> {
                                      final IAtomContainer submol = target.getBuilder()
                                                                          .newInstance(IAtomContainer.class,
                                                                                       query.getAtomCount(), target.getBondCount(), 0, 0);
@@ -473,7 +466,6 @@ public IAtomContainer apply(Map<IChemObject, IChemObject> map) {
                                      for (IBond bond : query.bonds())
                                          submol.addBond((IBond)map.get(bond));
                                      return submol;
-                                 }
                              });
     }
 

diff --git a/base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/QueryStereoFilter.java b/base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/QueryStereoFilter.java
@@ -25,7 +25,6 @@
 
 package org.openscience.cdk.isomorphism;
 
-import com.google.common.base.Predicate;
 import com.google.common.collect.Maps;
 import org.openscience.cdk.interfaces.IAtom;
 import org.openscience.cdk.interfaces.IAtomContainer;
@@ -40,6 +39,7 @@
 
 import java.util.Arrays;
 import java.util.Map;
+import java.util.function.Predicate;
 
 import static org.openscience.cdk.interfaces.IDoubleBondStereochemistry.Conformation;
 import static org.openscience.cdk.interfaces.IDoubleBondStereochemistry.Conformation.TOGETHER;
@@ -115,7 +115,7 @@ public QueryStereoFilter(IAtomContainer query, IAtomContainer target) {
      * @return the stereo chemistry is value
      */
     @Override
-    public boolean apply(final int[] mapping) {
+    public boolean test(final int[] mapping) {
 
         // reset augment group config if it was initialised
         if (groupConfigAdjust != null)
@@ -432,6 +432,16 @@ private int parity(Conformation conformation) {
         return conformation == TOGETHER ? 1 : -1;
     }
 
+    /**
+     * Backwards compatible method from when we used GUAVA predicates.
+     * @param ints atom index bijection
+     * @return true/false
+     * @see #test(int[])
+     */
+    public boolean apply(int[] ints) {
+        return test(ints);
+    }
+
     // could be moved into the IStereoElement to allow faster introspection
     private static enum Type {
         Tetrahedral, Geometric

diff --git a/base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/StereoMatch.java b/base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/StereoMatch.java
@@ -24,7 +24,6 @@
 
 package org.openscience.cdk.isomorphism;
 
-import com.google.common.base.Predicate;
 import com.google.common.collect.Maps;
 import org.openscience.cdk.interfaces.IAtom;
 import org.openscience.cdk.interfaces.IAtomContainer;
@@ -35,6 +34,7 @@
 
 import java.util.Arrays;
 import java.util.Map;
+import java.util.function.Predicate;
 
 import static org.openscience.cdk.interfaces.IDoubleBondStereochemistry.Conformation;
 import static org.openscience.cdk.interfaces.IDoubleBondStereochemistry.Conformation.TOGETHER;
@@ -109,7 +109,7 @@ final class StereoMatch implements Predicate<int[]> {
      * @return the stereo chemistry is value
      */
     @Override
-    public boolean apply(final int[] mapping) {
+    public boolean test(final int[] mapping) {
 
         // n.b. not true for unspecified queries e.g. [C@?H](*)(*)*
         if (queryStereoIndices.length > targetStereoIndices.length) return false;
@@ -131,6 +131,16 @@ public boolean apply(final int[] mapping) {
         return true;
     }
 
+    /**
+     * Backwards compatible method from when we used GUAVA predicates.
+     * @param ints atom index bijection
+     * @return true/false
+     * @see #test(int[])
+     */
+    public boolean apply(int[] ints) {
+        return test(ints);
+    }
+
     /**
      * Verify the tetrahedral stereochemistry (clockwise/anticlockwise) of atom
      * {@code u} is preserved in the target when the {@code mapping} is used.

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
@@ -24,11 +24,11 @@
 
 package org.openscience.cdk.isomorphism;
 
-import com.google.common.base.Predicate;
 import com.google.common.collect.Sets;
 
 import java.util.BitSet;
 import java.util.Set;
+import java.util.function.Predicate;
 
 /**
  * A predicate for filtering atom-mapping results. This class is intended for
@@ -70,10 +70,20 @@ public UniqueAtomMatches() {
      *{@inheritDoc}
      */
     @Override
-    public boolean apply(int[] input) {
+    public boolean test(int[] input) {
         return unique.add(toBitSet(input));
     }
 
+    /**
+     * Backwards compatible method from when we used GUAVA predicates.
+     * @param ints atom index bijection
+     * @return true/false
+     * @see #test(int[])
+     */
+    public boolean apply(int[] ints) {
+        return test(ints);
+    }
+
     /**
      * Convert a mapping to a bitset.
      *

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
@@ -24,11 +24,11 @@
 
 package org.openscience.cdk.isomorphism;
 
-import com.google.common.base.Predicate;
 import com.google.common.collect.Sets;
 
 import java.util.HashSet;
 import java.util.Set;
+import java.util.function.Predicate;
 
 /**
  * A predicate for filtering atom-mapping results for those which cover unique
@@ -70,10 +70,20 @@ public UniqueBondMatches(int[][] g) {
 
     /**{@inheritDoc} */
     @Override
-    public boolean apply(int[] input) {
+    public boolean test(int[] input) {
         return unique.add(toEdgeSet(input));
     }
 
+    /**
+     * Backwards compatible method from when we used GUAVA predicates.
+     * @param ints atom index bijection
+     * @return true/false
+     * @see #test(int[])
+     */
+    public boolean apply(int[] ints) {
+        return test(ints);
+    }
+
     /**
      * Convert a mapping to a bitset.
      *

diff --git a/legacy/src/main/java/org/openscience/cdk/isomorphism/SmartsStereoMatch.java b/legacy/src/main/java/org/openscience/cdk/isomorphism/SmartsStereoMatch.java
@@ -24,7 +24,6 @@
 
 package org.openscience.cdk.isomorphism;
 
-import com.google.common.base.Predicate;
 import com.google.common.collect.Maps;
 import org.openscience.cdk.interfaces.IAtom;
 import org.openscience.cdk.interfaces.IAtomContainer;
@@ -39,6 +38,7 @@
 
 import java.util.Arrays;
 import java.util.Map;
+import java.util.function.Predicate;
 
 import static org.openscience.cdk.interfaces.IDoubleBondStereochemistry.Conformation;
 import static org.openscience.cdk.interfaces.IDoubleBondStereochemistry.Conformation.TOGETHER;
@@ -107,7 +107,7 @@ public SmartsStereoMatch(IAtomContainer query, IAtomContainer target) {
      * @return the stereo chemistry is value
      */
     @Override
-    public boolean apply(final int[] mapping) {
+    public boolean test(final int[] mapping) {
         for (final int u : queryStereoIndices) {
             switch (queryTypes[u]) {
                 case Tetrahedral:
@@ -121,6 +121,16 @@ public boolean apply(final int[] mapping) {
         return true;
     }
 
+    /**
+     * Backwards compatible method from when we used GUAVA predicates.
+     * @param ints atom index bijection
+     * @return true/false
+     * @see #test(int[])
+     */
+    public boolean apply(int[] ints) {
+        return test(ints);
+    }
+
     /**
      * Verify the tetrahedral stereochemistry (clockwise/anticlockwise) of atom
      * {@code u} is preserved in the target when the {@code mapping} is used.