Skip to content

Commit b3f0f8d

Browse files
johnmayegonw
johnmay
authored and
egonw
committed
Remove usage of FluentIterable using the Stream API. Some usages are more verbose but OK and perhaps indicate a List should have been consumed/returned in the first place.
1 parent 314cd4b commit b3f0f8d

File tree

11 files changed

+134
-101
lines changed

11 files changed

+134
-101
lines changed

‎app/depict/src/main/java/org/openscience/cdk/depict/DepictionGenerator.java

Lines changed: 8 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -18,7 +18,6 @@
1818
*/
1919
package org.openscience.cdk.depict;
2020

21-
import com.google.common.collect.FluentIterable;
2221
import org.openscience.cdk.CDKConstants;
2322
import org.openscience.cdk.exception.CDKException;
2423
import org.openscience.cdk.geometry.GeometryUtil;
@@ -61,6 +60,7 @@
6160
import java.util.Map;
6261
import java.util.Set;
6362
import java.util.TreeMap;
63+
import java.util.stream.StreamSupport;
6464

6565
/**
6666
* A high-level API for depicting molecules and reactions.
@@ -321,8 +321,8 @@ public Depiction depict(final IAtomContainer mol) throws CDKException {
321321
* @see #depict(Iterable, int, int)
322322
*/
323323
public Depiction depict(Iterable<IAtomContainer> mols) throws CDKException {
324-
int nMols = FluentIterable.from(mols).size();
325-
Dimension grid = Dimensions.determineGrid(nMols);
324+
int count = (int) StreamSupport.stream(mols.spliterator(), false).count();
325+
Dimension grid = Dimensions.determineGrid(count);
326326
return depict(mols, grid.height, grid.width);
327327
}
328328

@@ -358,7 +358,8 @@ public Depiction depict(Iterable<IAtomContainer> mols, int nrow, int ncol) throw
358358
e.getKey().setProperty(StandardGenerator.HIGHLIGHT_COLOR, e.getValue());
359359

360360
// setup the model scale
361-
List<IAtomContainer> molList = FluentIterable.from(mols).toList();
361+
List<IAtomContainer> molList = new ArrayList<>();
362+
mols.forEach(molList::add);
362363
DepictionGenerator copy = this.withParam(BasicSceneGenerator.Scale.class,
363364
caclModelScale(molList));
364365

@@ -603,7 +604,9 @@ private Bounds generatePlusSymbol(double scale, Color fgcol) {
603604
}
604605

605606
private List<IAtomContainer> toList(IAtomContainerSet set) {
606-
return FluentIterable.from(set.atomContainers()).toList();
607+
List<IAtomContainer> mols = new ArrayList<>();
608+
set.atomContainers().forEach(mols::add);
609+
return mols;
607610
}
608611

609612
private IRenderingElement generate(IAtomContainer molecule, RendererModel model, int atomNum) throws CDKException {

‎base/core/src/main/java/org/openscience/cdk/config/Isotopes.java

Lines changed: 16 additions & 15 deletions
Original file line numberDiff line numberDiff line change
@@ -30,10 +30,8 @@
3030
import java.nio.channels.Channels;
3131
import java.nio.channels.ReadableByteChannel;
3232
import java.util.ArrayList;
33-
import java.util.HashMap;
3433
import java.util.List;
3534

36-
import com.google.common.collect.FluentIterable;
3735
import org.openscience.cdk.interfaces.IAtom;
3836
import org.openscience.cdk.interfaces.IAtomContainer;
3937
import org.openscience.cdk.interfaces.IIsotope;
@@ -132,19 +130,22 @@ public static void clearMajorIsotopes(IAtomContainer mol) {
132130
* @param formula the formula
133131
*/
134132
public static void clearMajorIsotopes(IMolecularFormula formula) {
135-
for (IIsotope iso : FluentIterable.from(formula.isotopes()).toList())
136-
if (isMajor(iso)) {
137-
int count = formula.getIsotopeCount(iso);
138-
formula.removeIsotope(iso);
139-
iso.setMassNumber(null);
140-
// may be immutable
141-
if (iso.getMassNumber() != null) {
142-
iso = formula.getBuilder().newInstance(IIsotope.class, iso.getSymbol());
143-
iso.setAtomicNumber(iso.getAtomicNumber());
144-
}
145-
iso.setExactMass(null);
146-
iso.setNaturalAbundance(null);
147-
formula.addIsotope(iso, count);
133+
List<IIsotope> majorIsotopes = new ArrayList<>();
134+
formula.isotopes().forEach(i -> {
135+
if (isMajor(i)) majorIsotopes.add(i);
136+
});
137+
for (IIsotope iso : majorIsotopes) {
138+
int count = formula.getIsotopeCount(iso);
139+
formula.removeIsotope(iso);
140+
iso.setMassNumber(null);
141+
// may be immutable
142+
if (iso.getMassNumber() != null) {
143+
iso = formula.getBuilder().newInstance(IIsotope.class, iso.getSymbol());
144+
iso.setAtomicNumber(iso.getAtomicNumber());
148145
}
146+
iso.setExactMass(null);
147+
iso.setNaturalAbundance(null);
148+
formula.addIsotope(iso, count);
149+
}
149150
}
150151
}

‎base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/Mappings.java

Lines changed: 56 additions & 32 deletions
Original file line numberDiff line numberDiff line change
@@ -24,7 +24,6 @@
2424

2525
package org.openscience.cdk.isomorphism;
2626

27-
import com.google.common.collect.FluentIterable;
2827
import com.google.common.collect.ImmutableMap;
2928
import com.google.common.collect.Iterables;
3029
import org.openscience.cdk.graph.GraphUtil;
@@ -39,6 +38,8 @@
3938
import java.util.Map;
4039
import java.util.function.Function;
4140
import java.util.function.Predicate;
41+
import java.util.stream.Collectors;
42+
import java.util.stream.Stream;
4243
import java.util.stream.StreamSupport;
4344

4445
/**
@@ -278,14 +279,7 @@ public Mappings stereochemistry() {
278279
public Mappings uniqueAtoms() {
279280
// we need the unique predicate to be reset for each new iterator -
280281
// otherwise multiple iterations are always filtered (seen before)
281-
return new Mappings(query, target, new Iterable<int[]>() {
282-
283-
@Override
284-
public Iterator<int[]> iterator() {
285-
return StreamSupport.stream(iterable.spliterator(), false)
286-
.filter(new UniqueAtomMatches()).iterator();
287-
}
288-
});
282+
return new Mappings(query, target, () -> stream().filter(new UniqueAtomMatches()).iterator());
289283
}
290284

291285
/**
@@ -299,14 +293,7 @@ public Mappings uniqueBonds() {
299293
// we need the unique predicate to be reset for each new iterator -
300294
// otherwise multiple iterations are always filtered (seen before)
301295
final int[][] g = GraphUtil.toAdjList(query);
302-
return new Mappings(query, target, new Iterable<int[]>() {
303-
304-
@Override
305-
public Iterator<int[]> iterator() {
306-
return StreamSupport.stream(iterable.spliterator(), false)
307-
.filter(new UniqueBondMatches(g)).iterator();
308-
}
309-
});
296+
return new Mappings(query, target, () -> stream().filter(new UniqueBondMatches(g)).iterator());
310297
}
311298

312299
/**
@@ -422,6 +409,18 @@ public Iterable<Map<IChemObject, IChemObject>> toAtomBondMap() {
422409
return map(new ToAtomBondMap(query, target));
423410
}
424411

412+
/**
413+
* Convert the Mappings to a Java 8 {@link java.util.stream.Stream}. The Stream API was written after
414+
* this class and provides much of the functionality (e.g. {@link #map} is {@link
415+
* Stream#map(java.util.function.Function)} etc. Unlike an Iterable, a stream cannot be traversed more
416+
* than once.
417+
*
418+
* @return the stream
419+
*/
420+
public Stream<int[]> stream() {
421+
return StreamSupport.stream(this.spliterator(), false);
422+
}
423+
425424
/**
426425
* Obtain the chem objects (atoms and bonds) that have 'hit' in the target molecule.
427426
*
@@ -433,11 +432,46 @@ public Iterable<Map<IChemObject, IChemObject>> toAtomBondMap() {
433432
* }
434433
* </pre></blockquote>
435434
*
436-
* @return lazy iterable of chem objects
435+
* @return non-lazy iterable of chem objects
437436
*/
438437
public Iterable<IChemObject> toChemObjects() {
439-
return FluentIterable.from(map(new ToAtomBondMap(query, target)))
440-
.transformAndConcat(map -> map.values());
438+
return stream()
439+
.map(new ToAtomBondMap(query, target))
440+
.flatMap(map -> map.values().stream())
441+
.collect(Collectors.toList());
442+
}
443+
444+
/**
445+
* Obtain the mapped substructures (atoms/bonds) of the target compound. The atoms
446+
* and bonds are the same as in the target molecule but there may be less of them.
447+
*
448+
* <blockquote><pre>
449+
* IAtomContainer query, target
450+
* Mappings mappings = ...;
451+
* for (IAtomContainer mol : mol.toSubstructures()) {
452+
* for (IAtom atom : mol.atoms())
453+
* target.contains(atom); // always true
454+
* for (IAtom atom : target.atoms())
455+
* mol.contains(atom): // not always true
456+
* }
457+
* </pre></blockquote>
458+
*
459+
* @return lazy stream iterable of molecules
460+
*/
461+
public Stream<IAtomContainer> toSubstructuresStream() {
462+
return stream()
463+
.map(new ToAtomBondMap(query, target))
464+
.map(map -> {
465+
final IAtomContainer submol = target.getBuilder()
466+
.newInstance(IAtomContainer.class,
467+
query.getAtomCount(), target.getBondCount(), 0, 0);
468+
for (IAtom atom : query.atoms())
469+
submol.addAtom((IAtom)map.get(atom));
470+
for (IBond bond : query.bonds())
471+
submol.addBond((IBond)map.get(bond));
472+
return submol;
473+
});
474+
441475
}
442476

443477
/**
@@ -455,20 +489,10 @@ public Iterable<IChemObject> toChemObjects() {
455489
* }
456490
* </pre></blockquote>
457491
*
458-
* @return lazy iterable of molecules
492+
* @return non-lazy iterable of molecules
459493
*/
460494
public Iterable<IAtomContainer> toSubstructures() {
461-
return FluentIterable.from(map(new ToAtomBondMap(query, target)))
462-
.transform(map -> {
463-
final IAtomContainer submol = target.getBuilder()
464-
.newInstance(IAtomContainer.class,
465-
query.getAtomCount(), target.getBondCount(), 0, 0);
466-
for (IAtom atom : query.atoms())
467-
submol.addAtom((IAtom)map.get(atom));
468-
for (IBond bond : query.bonds())
469-
submol.addBond((IBond)map.get(bond));
470-
return submol;
471-
});
495+
return toSubstructuresStream().collect(Collectors.toList());
472496
}
473497

474498
/**

‎base/isomorphism/src/test/java/org/openscience/cdk/isomorphism/UllmannTest.java

Lines changed: 4 additions & 7 deletions
Original file line numberDiff line numberDiff line change
@@ -24,7 +24,6 @@
2424

2525
package org.openscience.cdk.isomorphism;
2626

27-
import com.google.common.collect.FluentIterable;
2827
import org.junit.Test;
2928
import org.openscience.cdk.templates.TestMoleculeFactory;
3029

@@ -44,9 +43,8 @@ public void benzeneSubsearch() throws Exception {
4443
int[] match = Ullmann.findSubstructure(TestMoleculeFactory.makeBenzene()).match(
4544
TestMoleculeFactory.makeNaphthalene());
4645
assertThat(match, is(new int[]{2, 7, 6, 5, 4, 3}));
47-
int count = FluentIterable.from(
48-
Ullmann.findSubstructure(TestMoleculeFactory.makeBenzene()).matchAll(
49-
TestMoleculeFactory.makeNaphthalene())).size();
46+
int count = Ullmann.findSubstructure(TestMoleculeFactory.makeBenzene())
47+
.matchAll(TestMoleculeFactory.makeNaphthalene()).count();
5048
assertThat(count, is(6)); // note: aromatic one would be 24
5149
}
5250

@@ -55,9 +53,8 @@ public void napthaleneSubsearch() throws Exception {
5553
int[] match = Ullmann.findSubstructure(TestMoleculeFactory.makeNaphthalene()).match(
5654
TestMoleculeFactory.makeBenzene());
5755
assertThat(match, is(new int[0]));
58-
int count = FluentIterable.from(
59-
Ullmann.findSubstructure(TestMoleculeFactory.makeNaphthalene()).matchAll(
60-
TestMoleculeFactory.makeBenzene())).size();
56+
int count = Ullmann.findSubstructure(TestMoleculeFactory.makeNaphthalene())
57+
.matchAll(TestMoleculeFactory.makeBenzene()).count();
6158
assertThat(count, is(0));
6259
}
6360
}

‎base/isomorphism/src/test/java/org/openscience/cdk/isomorphism/VentoFoggiaTest.java

Lines changed: 11 additions & 13 deletions
Original file line numberDiff line numberDiff line change
@@ -24,7 +24,6 @@
2424

2525
package org.openscience.cdk.isomorphism;
2626

27-
import com.google.common.collect.FluentIterable;
2827
import org.junit.Test;
2928
import org.openscience.cdk.templates.TestMoleculeFactory;
3029

@@ -44,9 +43,9 @@ public void benzeneIdentical() throws Exception {
4443
int[] match = VentoFoggia.findIdentical(TestMoleculeFactory.makeBenzene()).match(
4544
TestMoleculeFactory.makeBenzene());
4645
assertThat(match, is(new int[]{0, 1, 2, 3, 4, 5}));
47-
int count = FluentIterable.from(
48-
VentoFoggia.findIdentical(TestMoleculeFactory.makeBenzene())
49-
.matchAll(TestMoleculeFactory.makeBenzene())).size();
46+
int count = VentoFoggia.findIdentical(TestMoleculeFactory.makeBenzene())
47+
.matchAll(TestMoleculeFactory.makeBenzene())
48+
.count();
5049
assertThat(count, is(6)); // note: aromatic one would be 12
5150
}
5251

@@ -55,9 +54,9 @@ public void benzeneNonIdentical() throws Exception {
5554
int[] match = VentoFoggia.findIdentical(TestMoleculeFactory.makeBenzene()).match(
5655
TestMoleculeFactory.makeNaphthalene());
5756
assertThat(match, is(new int[0]));
58-
int count = FluentIterable.from(
59-
VentoFoggia.findIdentical(TestMoleculeFactory.makeBenzene()).matchAll(
60-
TestMoleculeFactory.makeNaphthalene())).size();
57+
int count = VentoFoggia.findIdentical(TestMoleculeFactory.makeBenzene())
58+
.matchAll(TestMoleculeFactory.makeNaphthalene())
59+
.count();
6160
assertThat(count, is(0));
6261
}
6362

@@ -66,9 +65,9 @@ public void benzeneSubsearch() throws Exception {
6665
int[] match = VentoFoggia.findSubstructure(TestMoleculeFactory.makeBenzene()).match(
6766
TestMoleculeFactory.makeNaphthalene());
6867
assertThat(match, is(new int[]{2, 7, 6, 5, 4, 3}));
69-
int count = FluentIterable.from(
70-
VentoFoggia.findSubstructure(TestMoleculeFactory.makeBenzene()).matchAll(
71-
TestMoleculeFactory.makeNaphthalene())).size();
68+
int count = VentoFoggia.findSubstructure(TestMoleculeFactory.makeBenzene())
69+
.matchAll(TestMoleculeFactory.makeNaphthalene())
70+
.count();
7271
assertThat(count, is(6)); // note: aromatic one would be 24
7372
}
7473

@@ -77,9 +76,8 @@ public void napthaleneSubsearch() throws Exception {
7776
int[] match = VentoFoggia.findSubstructure(TestMoleculeFactory.makeNaphthalene()).match(
7877
TestMoleculeFactory.makeBenzene());
7978
assertThat(match, is(new int[0]));
80-
int count = FluentIterable.from(
81-
VentoFoggia.findSubstructure(TestMoleculeFactory.makeNaphthalene()).matchAll(
82-
TestMoleculeFactory.makeBenzene())).size();
79+
int count = VentoFoggia.findSubstructure(TestMoleculeFactory.makeNaphthalene())
80+
.matchAll(TestMoleculeFactory.makeBenzene()).count();
8381
assertThat(count, is(0));
8482
}
8583
}

‎legacy/src/main/java/org/openscience/cdk/smiles/smarts/SMARTSQueryTool.java

Lines changed: 5 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -18,7 +18,6 @@
1818
*/
1919
package org.openscience.cdk.smiles.smarts;
2020

21-
import com.google.common.collect.FluentIterable;
2221
import org.openscience.cdk.aromaticity.Aromaticity;
2322
import org.openscience.cdk.aromaticity.ElectronDonation;
2423
import org.openscience.cdk.exception.CDKException;
@@ -50,6 +49,7 @@
5049
import java.util.TreeSet;
5150
import java.util.stream.Collectors;
5251
import java.util.stream.IntStream;
52+
import java.util.stream.StreamSupport;
5353

5454

5555
/**
@@ -365,10 +365,10 @@ public boolean matches(IAtomContainer atomContainer, boolean forceInitialization
365365
}
366366
}
367367
} else {
368-
mappings = FluentIterable.from(VentoFoggia.findSubstructure(query)
369-
.matchAll(atomContainer)
370-
.filter(new SmartsStereoMatch(query, atomContainer)))
371-
.toList();
368+
mappings = StreamSupport.stream(VentoFoggia.findSubstructure(query)
369+
.matchAll(atomContainer)
370+
.filter(new SmartsStereoMatch(query, atomContainer)).spliterator(), false)
371+
.collect(Collectors.toList());
372372
}
373373

374374
return !mappings.isEmpty();

0 commit comments

Comments
 (0)