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Commit c0240dd

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Pasjonat90DPasjonat90D
committed
Refactor: fix SonarQube S1155 issues (#1079)
1 parent 51f48cd commit c0240dd

39 files changed

Lines changed: 80 additions & 82 deletions

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‎biojava-core/src/test/java/org/biojava/nbio/core/sequence/loader/GenbankProxySequenceReaderTest.java‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -162,7 +162,7 @@ so it should be done here (manualy).
162162
logger.info("taxonomy name '{}'", taxonName);
163163
Assert.assertNotNull(taxonName);
164164

165-
if (seq.getFeaturesByType("CDS").size() > 0) {
165+
if (!seq.getFeaturesByType("CDS").isEmpty()) {
166166
FeatureInterface<AbstractSequence<AminoAcidCompound>, AminoAcidCompound> CDS = seq.getFeaturesByType("CDS").get(0);
167167
logger.info("CDS: {}", CDS);
168168
String codedBy = CDS.getQualifiers().get("coded_by").get(0).getValue();

‎biojava-genome/src/main/java/org/biojava/nbio/genome/GeneFeatureHelper.java‎

Lines changed: 7 additions & 7 deletions
Original file line numberDiff line numberDiff line change
@@ -36,7 +36,7 @@
3636

3737
/**
3838
*
39-
* @author Scooter Willis
39+
* @author Scooter Willis
4040
*/
4141
public class GeneFeatureHelper {
4242

@@ -418,7 +418,7 @@ static public void addGmodGFF3GeneFeatures(Map<String, ChromosomeSequence> chrom
418418
String startCodonName = "";
419419
String stopCodonName = "";
420420
FeatureList startCodonList = mRNAChildren.selectByType("five_prime_UTR");
421-
if (startCodonList != null && startCodonList.size() > 0) {
421+
if (startCodonList != null && !startCodonList.isEmpty()) {
422422
startCodon = startCodonList.get(0);
423423
if (strand == Strand.NEGATIVE) {
424424
startCodonBegin = startCodon.location().bioEnd();
@@ -430,7 +430,7 @@ static public void addGmodGFF3GeneFeatures(Map<String, ChromosomeSequence> chrom
430430

431431
FeatureList stopCodonList = mRNAChildren.selectByType("three_prime_UTR");
432432

433-
if (stopCodonList != null && stopCodonList.size() > 0) {
433+
if (stopCodonList != null && !stopCodonList.isEmpty()) {
434434
stopCodon = stopCodonList.get(0);
435435
if (strand == Strand.NEGATIVE) {
436436
stopCodonEnd = stopCodon.location().bioStart();
@@ -577,7 +577,7 @@ static public void addGlimmerGFF3GeneFeatures(Map<String, ChromosomeSequence> ch
577577
String startCodonName = "";
578578
String stopCodonName = "";
579579
FeatureList startCodonList = gene.selectByAttribute("Note", "initial-exon");
580-
if (startCodonList != null && startCodonList.size() > 0) {
580+
if (startCodonList != null && !startCodonList.isEmpty()) {
581581
startCodon = startCodonList.get(0);
582582
if (strand == Strand.NEGATIVE) {
583583
startCodonBegin = startCodon.location().bioEnd();
@@ -589,7 +589,7 @@ static public void addGlimmerGFF3GeneFeatures(Map<String, ChromosomeSequence> ch
589589

590590
FeatureList stopCodonList = gene.selectByAttribute("Note", "final-exon");
591591

592-
if (stopCodonList != null && stopCodonList.size() > 0) {
592+
if (stopCodonList != null && !stopCodonList.isEmpty()) {
593593
stopCodon = stopCodonList.get(0);
594594
if (strand == Strand.NEGATIVE) {
595595
stopCodonEnd = stopCodon.location().bioStart();
@@ -723,7 +723,7 @@ static public void addGeneMarkGTFGeneFeatures(Map<String, ChromosomeSequence> ch
723723
String startCodonName = "";
724724
String stopCodonName = "";
725725
FeatureList startCodonList = transcriptFeature.selectByType("start_codon");
726-
if (startCodonList != null && startCodonList.size() > 0) {
726+
if (startCodonList != null && !startCodonList.isEmpty()) {
727727
startCodon = startCodonList.get(0);
728728
if (strand == Strand.POSITIVE) {
729729
startCodonBegin = startCodon.location().bioStart();
@@ -735,7 +735,7 @@ static public void addGeneMarkGTFGeneFeatures(Map<String, ChromosomeSequence> ch
735735

736736
FeatureList stopCodonList = transcriptFeature.selectByType("stop_codon");
737737

738-
if (stopCodonList != null && stopCodonList.size() > 0) {
738+
if (stopCodonList != null && !stopCodonList.isEmpty()) {
739739
stopCodon = stopCodonList.get(0);
740740
if (strand == Strand.POSITIVE) {
741741
stopCodonEnd = stopCodon.location().bioEnd();

‎biojava-genome/src/main/java/org/biojava/nbio/genome/homology/GFF3FromUniprotBlastHits.java‎

Lines changed: 7 additions & 7 deletions
Original file line numberDiff line numberDiff line change
@@ -46,7 +46,7 @@
4646

4747
/**
4848
*
49-
* @author Scooter Willis
49+
* @author Scooter Willis
5050
* @author Mark Chapman
5151
*/
5252
public class GFF3FromUniprotBlastHits {
@@ -163,7 +163,7 @@ PairwiseSequenceAlignerType.LOCAL, new SimpleGapPenalty(),
163163
String notes = "";
164164
if (featureKeyWords != null) {
165165
List<String> keyWords = featureKeyWords.getKeyWords();
166-
if (keyWords.size() > 0) {
166+
if (!keyWords.isEmpty()) {
167167
notes = ";Note=";
168168
for (String note : keyWords) {
169169
if ("Complete proteome".equals(note)) {
@@ -187,7 +187,7 @@ PairwiseSequenceAlignerType.LOCAL, new SimpleGapPenalty(),
187187
List<DBReferenceInfo> cazyList = databaseReferenceHashMap.get("CAZy");
188188
List<DBReferenceInfo> goList = databaseReferenceHashMap.get("GO");
189189
List<DBReferenceInfo> eccList = databaseReferenceHashMap.get("BRENDA");
190-
if (pfamList != null && pfamList.size() > 0) {
190+
if (pfamList != null && !pfamList.isEmpty()) {
191191
if (notes.length() == 0) {
192192
notes = ";Note=";
193193
}
@@ -197,7 +197,7 @@ PairwiseSequenceAlignerType.LOCAL, new SimpleGapPenalty(),
197197
}
198198
}
199199

200-
if (cazyList != null && cazyList.size() > 0) {
200+
if (cazyList != null && !cazyList.isEmpty()) {
201201
if (notes.length() == 0) {
202202
notes = ";Note=";
203203
}
@@ -208,7 +208,7 @@ PairwiseSequenceAlignerType.LOCAL, new SimpleGapPenalty(),
208208
}
209209
}
210210

211-
if (eccList != null && eccList.size() > 0) {
211+
if (eccList != null && !eccList.isEmpty()) {
212212
if (notes.length() == 0) {
213213
notes = ";Note=";
214214
}
@@ -221,8 +221,8 @@ PairwiseSequenceAlignerType.LOCAL, new SimpleGapPenalty(),
221221
}
222222
}
223223

224-
if (goList != null && goList.size() > 0) {
225-
if (notes.length() == 0) {
224+
if (goList != null && !goList.isEmpty()) {
225+
if (notes.isEmpty()) {
226226
notes = ";Note=";
227227
}
228228
for (DBReferenceInfo note : goList) {

‎biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/GFF3Writer.java‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -31,7 +31,7 @@
3131

3232
/**
3333
*
34-
* @author Scooter Willis
34+
* @author Scooter Willis
3535
*/
3636
public class GFF3Writer {
3737

@@ -122,7 +122,7 @@ public void write(OutputStream outputStream, Map<String, ChromosomeSequence> chr
122122
private String getGFF3Note(List<String> notesList) {
123123
String notes = "";
124124

125-
if (notesList.size() > 0) {
125+
if (!notesList.isEmpty()) {
126126
notes = ";Note=";
127127
int noteindex = 1;
128128
for (String note : notesList) {

‎biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/io/TestSeqResParsing.java‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -53,7 +53,7 @@ public void test11GS() throws IOException, StructureException{
5353

5454
s = StructureIO.getStructure(pdbID);
5555
assertNotNull(s);
56-
assertTrue(s.getChains().size() > 0);
56+
assertFalse(s.getChains().isEmpty());
5757
Chain c = s.getChainByIndex(0);
5858

5959
assertTrue(c.getSeqResGroups().size() > 2);

‎biojava-modfinder/src/main/java/org/biojava/nbio/protmod/io/ModifiedCompoundXMLConverter.java‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -69,7 +69,7 @@ public static String toXML(ModifiedCompound mc) throws IOException{
6969

7070

7171
Set<StructureAtomLinkage > linkages = mc.getAtomLinkages();
72-
if ( linkages.size() > 0 ) {
72+
if (!linkages.isEmpty()) {
7373
int pos = -1;
7474
for ( StructureAtomLinkage link: linkages){
7575
pos ++;

‎biojava-modfinder/src/main/java/org/biojava/nbio/protmod/structure/ProteinModificationIdentifier.java‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -285,7 +285,7 @@ public void identify(final List<Chain> chains,
285285

286286
if (residues.isEmpty()) {
287287
String pdbId = "?";
288-
if ( chains.size() > 0) {
288+
if (!chains.isEmpty()) {
289289
Structure struc = chains.get(0).getStructure();
290290
if ( struc != null)
291291
pdbId = struc.getPDBCode();

‎biojava-modfinder/src/test/java/org/biojava/nbio/protmod/phosphosite/TestAcetylation.java‎

Lines changed: 4 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -32,7 +32,8 @@
3232
import java.net.URL;
3333
import java.util.List;
3434

35-
import static org.junit.Assert.assertTrue;
35+
import static org.junit.Assert.assertFalse;
36+
import static org.junit.Assert.assertNotNull;
3637
import static org.junit.Assert.fail;
3738

3839

@@ -100,11 +101,11 @@ public void testAcetylation() throws IOException {
100101

101102
List<Site> sites = Site.parseSites(localFile);
102103

103-
assertTrue(sites.size() > 0);
104+
assertFalse(sites.isEmpty());
104105

105106
for (Site s : sites) {
106107

107-
assertTrue(s.getResidue() != null);
108+
assertNotNull(s.getResidue());
108109

109110
}
110111

‎biojava-ontology/src/main/java/org/biojava/nbio/ontology/utils/WeakValueHashMap.java‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -58,12 +58,12 @@ public WeakValueHashMap() {
5858
private void diddleReferenceQueue() {
5959
// Avoid making behind-the-scenes modifications while iterators exist.
6060

61-
if (iteratorRefs.size() > 0) {
61+
if (!iteratorRefs.isEmpty()) {
6262
Reference ref;
6363
while ((ref = iteratorRefQueue.poll()) != null) {
6464
iteratorRefs.remove(ref);
6565
}
66-
if (iteratorRefs.size() > 0) {
66+
if (!iteratorRefs.isEmpty()) {
6767
return;
6868
}
6969
}

‎biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/autosuggest/JAutoSuggest.java‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -229,7 +229,7 @@ public void keyReleased(KeyEvent e) {
229229
list.ensureIndexIsVisible(list.getSelectedIndex() - 1);
230230
return;
231231
} else if (e.getKeyCode() == KeyEvent.VK_ENTER
232-
&& list.getSelectedIndex() != -1 && suggestions.size() > 0) {
232+
&& list.getSelectedIndex() != -1 && !suggestions.isEmpty()) {
233233
setText((String) list.getSelectedValue());
234234

235235

@@ -365,7 +365,7 @@ public String doInBackground() {
365365

366366
setFont(regular);
367367

368-
if (suggestions.size() > 0) {
368+
if (!suggestions.isEmpty()) {
369369
list.setListData(suggestions);
370370
list.setSelectedIndex(0);
371371
list.ensureIndexIsVisible(0);

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