Skip to content

Commit d29b8f3

Browse files
sblivensbliven
committed
Automatically adding missing @OverRide 
1 parent 2417c23 commit d29b8f3

File tree

45 files changed

+236
-2
lines changed

Some content is hidden

Large Commits have some content hidden by default. Use the searchbox below for content that may be hidden.

45 files changed

+236
-2
lines changed

‎biojava-core/src/main/java/org/biojava/nbio/core/search/io/blast/BlastXMLParser.java‎

Lines changed: 3 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -62,6 +62,7 @@ public class BlastXMLParser implements ResultFactory {
6262
public BlastXMLParser() {
6363

6464
}
65+
@Override
6566
public void setFile(File f){
6667
targetFile = f;
6768
}
@@ -80,6 +81,7 @@ private void readFile(String blastFile) throws IOException, ParseException{
8081
logger.info("Read finished");
8182
}
8283

84+
@Override
8385
public List<Result> createObjects(double maxEScore) throws IOException, ParseException {
8486
if (targetFile == null) throw new IllegalStateException("File to be parsed not specified.");
8587

@@ -191,6 +193,7 @@ public List<Result> createObjects(double maxEScore) throws IOException, ParseExc
191193
return resultsCollection;
192194
}
193195

196+
@Override
194197
public List<String> getFileExtensions(){
195198
ArrayList<String> extensions = new ArrayList<String>(1);
196199
extensions.add("blastxml");

‎biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/StructurePairAlignerTest.java‎

Lines changed: 1 addition & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -36,6 +36,7 @@ public class StructurePairAlignerTest extends TestCase {
3636
Structure structure1;
3737
Structure structure2;
3838

39+
@Override
3940
protected void setUp()
4041
{
4142
InputStream inStream = this.getClass().getResourceAsStream("/5pti.pdb");

‎biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/align/ce/OptimalCECPMainTest.java‎

Lines changed: 1 addition & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -49,6 +49,7 @@ public class OptimalCECPMainTest extends TestCase {
4949
/* (non-Javadoc)
5050
* @see junit.framework.TestCase#setUp()
5151
*/
52+
@Override
5253
protected void setUp() throws Exception {
5354
super.setUp();
5455
}

‎biojava-ontology/src/main/java/org/biojava/nbio/ontology/AbstractTerm.java‎

Lines changed: 1 addition & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -38,6 +38,7 @@ public abstract class AbstractTerm implements Term {
3838

3939
protected String description;
4040

41+
@Override
4142
public void setDescription(String description){
4243
this.description = description;
4344
}

‎biojava-ontology/src/main/java/org/biojava/nbio/ontology/IntegerOntology.java‎

Lines changed: 32 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -41,39 +41,49 @@ public class IntegerOntology
4141
termCache = new WeakValueHashMap();
4242
}
4343

44+
@Override
4445
public String getName() {
4546
return "core.integer";
4647
}
4748

49+
@Override
4850
public String getDescription() {
4951
return "Ontology containing all integers";
5052
}
5153

54+
@Override
5255
public void setDescription(String description){
5356
}
5457

58+
@Override
5559
public Set getTerms() {
5660
return new AbstractSet() {
61+
@Override
5762
public boolean contains(Object o) {
5863
return o instanceof IntTerm;
5964
}
6065

66+
@Override
6167
public int size() {
6268
return Integer.MAX_VALUE;
6369
}
6470

71+
@Override
6572
public Iterator iterator() {
6673
return new Iterator() {
6774
int i = 0;
6875

76+
@Override
6977
public boolean hasNext() {
7078
return i > 0;
7179
}
7280

81+
@Override
7382
public Object next() {
7483
return resolveInt(i++);
7584
}
7685

86+
@Override
7787
public void remove() {
7888
throw new UnsupportedOperationException();
7989
}
@@ -82,27 +92,33 @@ public void remove() {
8292
};
8393
}
8494

95+
@Override
8596
public Term getTerm(String s) throws NoSuchElementException {
8697
int val = Integer.parseInt(s);
8798
return resolveInt(val);
8899
}
89100

101+
@Override
90102
public Set getTriples(Term subject, Term object, Term predicate) {
91103
return Collections.EMPTY_SET;
92104
}
93105

106+
@Override
94107
public OntologyOps getOps() {
95108
return new DefaultOps() {
109+
@Override
96110
public Set getRemoteTerms() {
97111
return Collections.EMPTY_SET;
98112
}
99113
};
100114
}
101115

116+
@Override
102117
public Term createTerm(String name) throws AlreadyExistsException, IllegalArgumentException {
103118
throw new IllegalArgumentException(getName() + " is immutable");
104119
}
105120

121+
@Override
106122
public Term createTerm(String name, String description)
107123
throws
108124
AlreadyExistsException,
@@ -112,6 +128,7 @@ public Term createTerm(String name, String description)
112128
throw new IllegalArgumentException(getName() + " is immutable");
113129
}
114130

131+
@Override
115132
public Term createTerm(String name, String description, Object[] synonyms)
116133
throws
117134
AlreadyExistsException,
@@ -121,6 +138,7 @@ public Term createTerm(String name, String description, Object[] synonyms)
121138
throw new IllegalArgumentException(getName() + " is immutable");
122139
}
123140

141+
@Override
124142
public Variable createVariable(String name, String description)
125143
throws
126144
AlreadyExistsException,
@@ -130,28 +148,33 @@ public Variable createVariable(String name, String description)
130148
throw new IllegalArgumentException(getName() + " is immutable");
131149
}
132150

151+
@Override
133152
public Term importTerm(Term t, String name)
134153

135154

136155
{
137156
throw new IllegalArgumentException(getName() + " is immutable");
138157
}
139158

159+
@Override
140160
public Triple createTriple(Term subject, Term object, Term predicate, String name, String description)
141161
throws
142162
AlreadyExistsException
143163
{
144164
throw new IllegalArgumentException(getName() + " is immutable");
145165
}
146166

167+
@Override
147168
public boolean containsTriple(Term subject, Term object, Term predicate) {
148169
return false;
149170
}
150171

172+
@Override
151173
public void deleteTerm(Term t) {
152174
throw new RuntimeException(getName() + " is immutable");
153175
}
154176

177+
@Override
155178
public boolean containsTerm(String name) {
156179
// uglee hack - perhaps we should use a regex?
157180
try {
@@ -192,14 +215,17 @@ public IntTerm(int val, Object[] synonyms) {
192215
if (synonyms!=null) this.synonyms.addAll(Arrays.asList(synonyms));
193216
}
194217

218+
@Override
195219
public void addSynonym(Object synonym) {
196220
this.synonyms.add(synonym);
197221
}
198222

223+
@Override
199224
public void removeSynonym(Object synonym) {
200225
this.synonyms.remove(synonym);
201226
}
202227

228+
@Override
203229
public Object[] getSynonyms() {
204230
return this.synonyms.toArray();
205231
}
@@ -208,27 +234,33 @@ public int intValue() {
208234
return val;
209235
}
210236

237+
@Override
211238
public String getName() {
212239
return String.valueOf(val);
213240
}
214241

242+
@Override
215243
public String getDescription() {
216244
return "The integer " + getName();
217245
}
218246

247+
@Override
219248
public void setDescription(String description){
220249

221250
}
222251

252+
@Override
223253
public Ontology getOntology() {
224254
return IntegerOntology.this;
225255
}
226256

257+
@Override
227258
public Annotation getAnnotation() {
228259
return Annotation.EMPTY_ANNOTATION;
229260
}
230261
}
231262

263+
@Override
232264
public void setName(String name) {
233265
//ignore
234266

‎biojava-ontology/src/main/java/org/biojava/nbio/ontology/OntoTools.java‎

Lines changed: 1 addition & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -74,6 +74,7 @@ public final class OntoTools {
7474

7575
static {
7676
DEFAULT_FACTORY = new OntologyFactory() {
77+
@Override
7778
public Ontology createOntology(String name, String desc)
7879
throws OntologyException {
7980
return new Ontology.Impl(name, desc);

‎biojava-ontology/src/main/java/org/biojava/nbio/ontology/Ontology.java‎

Lines changed: 19 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -312,29 +312,35 @@ public Impl(String name, String description) {
312312
*/
313313
private static final long serialVersionUID = -2135777733685713181L;
314314

315+
@Override
315316
public Set<Term> getRemoteTerms() {
316317
return localRemoteTerms;
317318
}
318319
};
319320
}
320321

322+
@Override
321323
public String getName() {
322324
return name;
323325
}
324326

327+
@Override
325328
public String getDescription() {
326329
return description;
327330
}
328331

329332

333+
@Override
330334
public void setDescription(String description){
331335
this.description = description;
332336
}
333337

338+
@Override
334339
public Set<Term> getTerms() {
335340
return new HashSet<Term>(terms.values());
336341
}
337342

343+
@Override
338344
public Term getTerm(String name)
339345
throws NoSuchElementException
340346
{
@@ -346,6 +352,7 @@ public Term getTerm(String name)
346352
}
347353
}
348354

355+
@Override
349356
public Set<Triple> getTriples(Term subject, Term object, Term predicate) {
350357
if(subject != null && subject.getOntology() != this) {
351358
throw new IllegalArgumentException("Subject is not in this ontology: " + subject + " " + this);
@@ -406,6 +413,7 @@ private void addTerm(Term t)
406413

407414
}
408415

416+
@Override
409417
public Term createTerm(String name)
410418
throws AlreadyExistsException, IllegalArgumentException
411419
{
@@ -414,6 +422,7 @@ public Term createTerm(String name)
414422
return t;
415423
}
416424

425+
@Override
417426
public Term createTerm(String name, String description)
418427
throws AlreadyExistsException, IllegalArgumentException
419428
{
@@ -422,6 +431,7 @@ public Term createTerm(String name, String description)
422431
return t;
423432
}
424433

434+
@Override
425435
public Term createTerm(String name, String description, Object[] synonyms)
426436
throws AlreadyExistsException, IllegalArgumentException
427437
{
@@ -430,6 +440,7 @@ public Term createTerm(String name, String description, Object[] synonyms)
430440
return t;
431441
}
432442

443+
@Override
433444
public Variable createVariable(String name, String description)
434445
throws
435446
AlreadyExistsException,
@@ -449,6 +460,7 @@ public OntologyTerm createOntologyTerm(Ontology o)
449460
}
450461

451462

463+
@Override
452464
public Term importTerm(Term t, String name)
453465
throws IllegalArgumentException
454466
{
@@ -477,6 +489,7 @@ public Term importTerm(Term t, String name)
477489
return rt;
478490
}
479491

492+
@Override
480493
public void deleteTerm(Term t)
481494

482495
{
@@ -492,6 +505,7 @@ public void deleteTerm(Term t)
492505

493506
}
494507

508+
@Override
495509
public boolean containsTerm(String name) {
496510
return terms.containsKey(name);
497511
}
@@ -500,6 +514,7 @@ private boolean containsTerm(Term t) {
500514
return (terms.get(t.getName()) == t);
501515
}
502516

517+
@Override
503518
public boolean containsTriple(Term subject, Term object, Term predicate) {
504519
if(!(subject.getOntology() == this)) return false;
505520
if(!(object.getOntology() == this)) return false;
@@ -508,6 +523,7 @@ public boolean containsTriple(Term subject, Term object, Term predicate) {
508523
return triples.contains(new Triple.Impl(subject, object, predicate));
509524
}
510525

526+
@Override
511527
public Triple createTriple(Term subject,
512528
Term object,
513529
Term predicate,
@@ -570,14 +586,17 @@ private void pullTriple(Map<Term, Set<Triple>> subjectTriples2, Term key, Triple
570586
}
571587
}
572588

589+
@Override
573590
public OntologyOps getOps() {
574591
return ops;
575592
}
576593

594+
@Override
577595
public String toString() {
578596
return "ontology: " + getName();
579597
}
580598

599+
@Override
581600
public void setName(String name) {
582601
this.name=name;
583602

0 commit comments

Comments
 (0)