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andreasprlicandreasprlic
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changing equals(Sequence) method signature to equals(Object)
1 parent f4c9b69 commit 7587b03

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10 files changed

+70
-38
lines changed

10 files changed

+70
-38
lines changed

‎biojava-core/src/main/java/org/biojava/nbio/core/alignment/SimpleAlignedSequence.java‎

Lines changed: 10 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -31,6 +31,7 @@
3131
import org.biojava.nbio.core.sequence.location.template.Location;
3232
import org.biojava.nbio.core.sequence.location.template.Point;
3333
import org.biojava.nbio.core.sequence.template.*;
34+
import org.biojava.nbio.core.util.Equals;
3435

3536
import java.io.Serializable;
3637
import java.util.ArrayList;
@@ -269,8 +270,15 @@ public List<C> getAsList() {
269270
return compounds;
270271
}
271272

272-
@Override
273-
public boolean equals(Sequence<C>other){
273+
274+
public boolean equals(Object o){
275+
276+
if(! Equals.classEqual(this, o)) {
277+
return false;
278+
}
279+
280+
Sequence<C> other = (Sequence<C>)o;
281+
274282
if ( original.getAsList().size() != other.getAsList().size())
275283
return false;
276284

‎biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/SequenceFileProxyLoader.java‎

Lines changed: 9 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -31,6 +31,7 @@
3131
import org.biojava.nbio.core.sequence.io.template.SequenceParserInterface;
3232
import org.biojava.nbio.core.sequence.storage.SequenceAsStringHelper;
3333
import org.biojava.nbio.core.sequence.template.*;
34+
import org.biojava.nbio.core.util.Equals;
3435

3536
import java.io.BufferedReader;
3637
import java.io.File;
@@ -219,7 +220,14 @@ public List<C> getAsList() {
219220
}
220221

221222
@Override
222-
public boolean equals(Sequence<C> other) {
223+
public boolean equals(Object o) {
224+
225+
if(! Equals.classEqual(this, o)) {
226+
return false;
227+
}
228+
229+
Sequence<C> other = (Sequence<C>)o;
230+
223231

224232
if ( other.getCompoundSet() != getCompoundSet())
225233
return false;

‎biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/StringProxySequenceReader.java‎

Lines changed: 10 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -30,6 +30,7 @@
3030
import org.biojava.nbio.core.sequence.Strand;
3131
import org.biojava.nbio.core.sequence.storage.SequenceAsStringHelper;
3232
import org.biojava.nbio.core.sequence.template.*;
33+
import org.biojava.nbio.core.util.Equals;
3334

3435
import java.util.ArrayList;
3536
import java.util.Iterator;
@@ -161,8 +162,15 @@ public SequenceView<C> getInverse() {
161162
return SequenceMixin.inverse(this);
162163
}
163164

164-
@Override
165-
public boolean equals(Sequence<C> other){
165+
166+
public boolean equals(Object o){
167+
168+
if(! Equals.classEqual(this, o)) {
169+
return false;
170+
}
171+
172+
Sequence<C> other = (Sequence<C>)o;
173+
166174
if ( other.getCompoundSet() != getCompoundSet())
167175
return false;
168176

‎biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/UniprotProxySequenceReader.java‎

Lines changed: 10 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -36,6 +36,7 @@
3636
import org.biojava.nbio.core.sequence.features.FeaturesKeyWordInterface;
3737
import org.biojava.nbio.core.sequence.storage.SequenceAsStringHelper;
3838
import org.biojava.nbio.core.sequence.template.*;
39+
import org.biojava.nbio.core.util.Equals;
3940
import org.biojava.nbio.core.util.XMLHelper;
4041
import org.slf4j.Logger;
4142
import org.slf4j.LoggerFactory;
@@ -230,8 +231,15 @@ public List<C> getAsList() {
230231
return this.parsedCompounds;
231232
}
232233

233-
@Override
234-
public boolean equals(Sequence<C> other){
234+
235+
public boolean equals(Object o){
236+
237+
if(! Equals.classEqual(this, o)) {
238+
return false;
239+
}
240+
241+
Sequence<C> other = (Sequence<C>)o;
242+
235243
if ( other.getCompoundSet() != getCompoundSet())
236244
return false;
237245

‎biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/ArrayListSequenceReader.java‎

Lines changed: 0 additions & 11 deletions
Original file line numberDiff line numberDiff line change
@@ -85,17 +85,6 @@ public String getSequenceAsString() {
8585
return getSequenceAsString(1, getLength(), Strand.POSITIVE);
8686
}
8787

88-
public boolean equals(Sequence<C>other){
89-
if ( parsedCompounds.size() != other.getAsList().size())
90-
return false;
91-
92-
for ( int i = 0 ; i< parsedCompounds.size() ; i++){
93-
if ( ! parsedCompounds.get(i).equalsIgnoreCase(other.getAsList().get(i)))
94-
return false;
95-
}
96-
97-
return true;
98-
}
9988

10089
/**
10190
*

‎biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/BitSequenceReader.java‎

Lines changed: 0 additions & 11 deletions
Original file line numberDiff line numberDiff line change
@@ -199,17 +199,6 @@ public boolean equals(Object o) {
199199
return false;
200200
}
201201

202-
public boolean equals(Sequence<C> o){
203-
204-
if(Equals.classEqual(this, o)) {
205-
@SuppressWarnings("unchecked")
206-
BitSequenceReader<C> that = (BitSequenceReader<C>)o;
207-
return Equals.equal(this.accession, that.accession) &&
208-
Equals.equal(this.worker, that.worker);
209-
}
210-
return false;
211-
212-
}
213202

214203
/**
215204
* The logic of working with a bit has been separated out into this class

‎biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/JoiningSequenceReader.java‎

Lines changed: 11 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -23,6 +23,7 @@
2323
import org.biojava.nbio.core.exceptions.CompoundNotFoundException;
2424
import org.biojava.nbio.core.sequence.AccessionID;
2525
import org.biojava.nbio.core.sequence.template.*;
26+
import org.biojava.nbio.core.util.Equals;
2627

2728
import java.util.*;
2829

@@ -298,8 +299,16 @@ public List<C> getAsList() {
298299
return SequenceMixin.toList(this);
299300
}
300301

301-
@Override
302-
public boolean equals(Sequence<C> other) {
302+
303+
public boolean equals(Sequence<C> o) {
304+
305+
306+
if(! Equals.classEqual(this, o)) {
307+
return false;
308+
}
309+
310+
Sequence<C> other = (Sequence<C>)o;
311+
303312

304313
if ( other.getCompoundSet() != getCompoundSet())
305314
return false;

‎biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/AbstractSequence.java‎

Lines changed: 9 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -37,6 +37,7 @@
3737
import org.biojava.nbio.core.sequence.location.SimpleLocation;
3838
import org.biojava.nbio.core.sequence.location.template.Location;
3939
import org.biojava.nbio.core.sequence.storage.ArrayListSequenceReader;
40+
import org.biojava.nbio.core.util.Equals;
4041
import org.slf4j.Logger;
4142
import org.slf4j.LoggerFactory;
4243

@@ -520,7 +521,14 @@ public void setCompoundSet(CompoundSet<C> compoundSet) {
520521
}
521522

522523

523-
public boolean equals(Sequence<C> other){
524+
public boolean equals(Object o){
525+
526+
if(! Equals.classEqual(this, o)) {
527+
return false;
528+
}
529+
530+
Sequence<C> other = (Sequence<C>)o;
531+
524532
if ( other.getCompoundSet() != getCompoundSet())
525533
return false;
526534

‎biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/Sequence.java‎

Lines changed: 0 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -79,10 +79,6 @@ public interface Sequence<C extends Compound> extends Iterable<C>, Accessioned {
7979
*/
8080
public List<C> getAsList();
8181

82-
public boolean equals(Sequence<C> other);
83-
84-
public int hashCode();
85-
8682
/**
8783
* Returns a portion of the sequence from the different positions. This is
8884
* indexed from 1

‎biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/SequenceProxyView.java‎

Lines changed: 11 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -26,6 +26,7 @@
2626
package org.biojava.nbio.core.sequence.template;
2727

2828
import org.biojava.nbio.core.sequence.AccessionID;
29+
import org.biojava.nbio.core.util.Equals;
2930

3031
import java.util.Iterator;
3132
import java.util.List;
@@ -71,8 +72,16 @@ public List<C> getAsList() {
7172
return SequenceMixin.toList(this);
7273
}
7374

74-
@Override
75-
public boolean equals(Sequence<C> other) {
75+
76+
public boolean equals(Object o) {
77+
78+
if(! Equals.classEqual(this, o)) {
79+
return false;
80+
}
81+
82+
Sequence<C> other = (Sequence<C>)o;
83+
84+
7685
return sequence.equals(other);
7786
}
7887

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