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josemduartejosemduarte
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Merge pull request #1067 from jlerbsc/master
Fix Sonar S2129 Constructors should not be used to instantiate 'String', …
2 parents d5de4b1 + 4a1863d commit 6d07ffe

19 files changed

Lines changed: 100 additions & 101 deletions

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‎biojava-alignment/src/main/java/org/biojava/nbio/alignment/io/StockholmStructure.java‎

Lines changed: 2 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -256,9 +256,8 @@ else if (forcedSequenceType.equals(PFAM))
256256
}
257257
String[] seqDetails = splitSeqName(sequencename);
258258
seq.setDescription(seqDetails[0]);
259-
seq.setBioBegin((seqDetails[1] == null || seqDetails[1].trim().equals("") ? null : new Integer(
260-
seqDetails[1])));
261-
seq.setBioEnd((seqDetails[2] == null || seqDetails[2].trim().equals("") ? null : new Integer(seqDetails[2])));
259+
seq.setBioBegin((seqDetails[1] == null || seqDetails[1].trim().equals("") ? null : Integer.valueOf(seqDetails[1])));
260+
seq.setBioEnd((seqDetails[2] == null || seqDetails[2].trim().equals("") ? null : Integer.valueOf(seqDetails[2])));
262261

263262
seqs.add(seq);
264263
}

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

Lines changed: 11 additions & 11 deletions
Original file line numberDiff line numberDiff line change
@@ -136,23 +136,23 @@ public List<Result> createObjects(double maxEScore) throws IOException, ParseExc
136136

137137
String currentSubjectId=subjectId;
138138
while (currentSubjectId.equals(subjectId) && lineNumber < fileLinesCount){
139-
if (new Double(evalue) > maxEScore) {
139+
if (Double.valueOf(evalue) > maxEScore) {
140140
line = fetchData(scanner);
141141
lineNumber++;
142142
continue;
143143
}
144144
BlastHspBuilder hspBuilder = new BlastHspBuilder();
145145
hspBuilder
146-
.setHspAlignLen(new Integer(alnLength))
147-
.setHspGaps(new Integer(gapOpenCount))
148-
.setHspQueryFrom(new Integer(queryStart))
149-
.setHspQueryTo(new Integer(queryEnd))
150-
.setHspHitFrom(new Integer(subjectStart))
151-
.setHspHitTo(new Integer(subjectEnd))
152-
.setHspEvalue(new Double(evalue))
153-
.setHspBitScore(new Double(bitScore))
154-
.setPercentageIdentity(new Double(percIdentity)/100)
155-
.setMismatchCount(new Integer(mismatchCount));
146+
.setHspAlignLen(Integer.valueOf(alnLength))
147+
.setHspGaps(Integer.valueOf(gapOpenCount))
148+
.setHspQueryFrom(Integer.valueOf(queryStart))
149+
.setHspQueryTo(Integer.valueOf(queryEnd))
150+
.setHspHitFrom(Integer.valueOf(subjectStart))
151+
.setHspHitTo(Integer.valueOf(subjectEnd))
152+
.setHspEvalue(Double.valueOf(evalue))
153+
.setHspBitScore(Double.valueOf(bitScore))
154+
.setPercentageIdentity(Double.valueOf(percIdentity)/100)
155+
.setMismatchCount(Integer.valueOf(mismatchCount));
156156
hsps.add(hspBuilder.createBlastHsp());
157157
if (scanner.hasNext()) line = fetchData(scanner);
158158
lineNumber++;

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

Lines changed: 18 additions & 18 deletions
Original file line numberDiff line numberDiff line change
@@ -117,10 +117,10 @@ public List<Result> createObjects(double maxEScore) throws IOException, ParseExc
117117

118118
// Iteration* section keys:
119119
resultBuilder
120-
.setIterationNumber(new Integer(XMLHelper.selectSingleElement(element,"Iteration_iter-num").getTextContent()))
120+
.setIterationNumber(Integer.valueOf(XMLHelper.selectSingleElement(element,"Iteration_iter-num").getTextContent()))
121121
.setQueryID(XMLHelper.selectSingleElement(element,"Iteration_query-ID").getTextContent())
122122
.setQueryDef(XMLHelper.selectSingleElement(element, "Iteration_query-def").getTextContent())
123-
.setQueryLength(new Integer(XMLHelper.selectSingleElement(element,"Iteration_query-len").getTextContent()));
123+
.setQueryLength(Integer.valueOf(XMLHelper.selectSingleElement(element,"Iteration_query-len").getTextContent()));
124124

125125
if (queryReferences != null) resultBuilder.setQuerySequence(queryReferencesMap.get(
126126
XMLHelper.selectSingleElement(element,"Iteration_query-ID").getTextContent()
@@ -135,11 +135,11 @@ public List<Result> createObjects(double maxEScore) throws IOException, ParseExc
135135
for (Element hitElement : hitList) {
136136
BlastHitBuilder blastHitBuilder = new BlastHitBuilder();
137137
blastHitBuilder
138-
.setHitNum(new Integer(XMLHelper.selectSingleElement(hitElement, "Hit_num").getTextContent()))
138+
.setHitNum(Integer.valueOf(XMLHelper.selectSingleElement(hitElement, "Hit_num").getTextContent()))
139139
.setHitId(XMLHelper.selectSingleElement(hitElement, "Hit_id").getTextContent())
140140
.setHitDef(XMLHelper.selectSingleElement(hitElement, "Hit_def").getTextContent())
141141
.setHitAccession(XMLHelper.selectSingleElement(hitElement, "Hit_accession").getTextContent())
142-
.setHitLen(new Integer(XMLHelper.selectSingleElement(hitElement, "Hit_len").getTextContent()));
142+
.setHitLen(Integer.valueOf(XMLHelper.selectSingleElement(hitElement, "Hit_len").getTextContent()));
143143

144144
if (databaseReferences != null) blastHitBuilder.setHitSequence(databaseReferencesMap.get(
145145
XMLHelper.selectSingleElement(hitElement, "Hit_id").getTextContent()
@@ -150,26 +150,26 @@ public List<Result> createObjects(double maxEScore) throws IOException, ParseExc
150150

151151
hspsCollection = new ArrayList<Hsp>();
152152
for (Element hspElement : hspList) {
153-
Double evalue = new Double(XMLHelper.selectSingleElement(hspElement, "Hsp_evalue").getTextContent());
153+
Double evalue = Double.valueOf(XMLHelper.selectSingleElement(hspElement, "Hsp_evalue").getTextContent());
154154

155155
// add the new hsp only if it pass the specified threshold. It can save lot of memory and some parsing time
156156
if (evalue <= maxEScore) {
157157
BlastHspBuilder blastHspBuilder = new BlastHspBuilder();
158158
blastHspBuilder
159-
.setHspNum(new Integer(XMLHelper.selectSingleElement(hspElement, "Hsp_num").getTextContent()))
160-
.setHspBitScore(new Double(XMLHelper.selectSingleElement(hspElement, "Hsp_bit-score").getTextContent()))
161-
.setHspScore(new Integer(XMLHelper.selectSingleElement(hspElement, "Hsp_score").getTextContent()))
159+
.setHspNum(Integer.valueOf(XMLHelper.selectSingleElement(hspElement, "Hsp_num").getTextContent()))
160+
.setHspBitScore(Double.valueOf(XMLHelper.selectSingleElement(hspElement, "Hsp_bit-score").getTextContent()))
161+
.setHspScore(Integer.valueOf(XMLHelper.selectSingleElement(hspElement, "Hsp_score").getTextContent()))
162162
.setHspEvalue(evalue)
163-
.setHspQueryFrom(new Integer(XMLHelper.selectSingleElement(hspElement, "Hsp_query-from").getTextContent()))
164-
.setHspQueryTo(new Integer(XMLHelper.selectSingleElement(hspElement, "Hsp_query-to").getTextContent()))
165-
.setHspHitFrom(new Integer(XMLHelper.selectSingleElement(hspElement, "Hsp_hit-from").getTextContent()))
166-
.setHspHitTo(new Integer(XMLHelper.selectSingleElement(hspElement, "Hsp_hit-to").getTextContent()))
167-
.setHspQueryFrame(new Integer(XMLHelper.selectSingleElement(hspElement, "Hsp_query-frame").getTextContent()))
168-
.setHspHitFrame(new Integer(XMLHelper.selectSingleElement(hspElement, "Hsp_hit-frame").getTextContent()))
169-
.setHspIdentity(new Integer(XMLHelper.selectSingleElement(hspElement, "Hsp_identity").getTextContent()))
170-
.setHspPositive(new Integer(XMLHelper.selectSingleElement(hspElement, "Hsp_positive").getTextContent()))
171-
.setHspGaps(new Integer(XMLHelper.selectSingleElement(hspElement, "Hsp_gaps").getTextContent()))
172-
.setHspAlignLen(new Integer(XMLHelper.selectSingleElement(hspElement, "Hsp_align-len").getTextContent()))
163+
.setHspQueryFrom(Integer.valueOf(XMLHelper.selectSingleElement(hspElement, "Hsp_query-from").getTextContent()))
164+
.setHspQueryTo(Integer.valueOf(XMLHelper.selectSingleElement(hspElement, "Hsp_query-to").getTextContent()))
165+
.setHspHitFrom(Integer.valueOf(XMLHelper.selectSingleElement(hspElement, "Hsp_hit-from").getTextContent()))
166+
.setHspHitTo(Integer.valueOf(XMLHelper.selectSingleElement(hspElement, "Hsp_hit-to").getTextContent()))
167+
.setHspQueryFrame(Integer.valueOf(XMLHelper.selectSingleElement(hspElement, "Hsp_query-frame").getTextContent()))
168+
.setHspHitFrame(Integer.valueOf(XMLHelper.selectSingleElement(hspElement, "Hsp_hit-frame").getTextContent()))
169+
.setHspIdentity(Integer.valueOf(XMLHelper.selectSingleElement(hspElement, "Hsp_identity").getTextContent()))
170+
.setHspPositive(Integer.valueOf(XMLHelper.selectSingleElement(hspElement, "Hsp_positive").getTextContent()))
171+
.setHspGaps(Integer.valueOf(XMLHelper.selectSingleElement(hspElement, "Hsp_gaps").getTextContent()))
172+
.setHspAlignLen(Integer.valueOf(XMLHelper.selectSingleElement(hspElement, "Hsp_align-len").getTextContent()))
173173
.setHspQseq(XMLHelper.selectSingleElement(hspElement, "Hsp_qseq").getTextContent())
174174
.setHspHseq(XMLHelper.selectSingleElement(hspElement, "Hsp_hseq").getTextContent())
175175
.setHspIdentityString(XMLHelper.selectSingleElement(hspElement, "Hsp_midline").getTextContent());

‎biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/ABITrace.java‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -434,7 +434,7 @@ private void setSeq() {
434434
for (int x = 0; x <= seqLength - 1; ++x) {
435435
tempseq[x] = (char) traceData[PBAS2 + x];
436436
}
437-
sequence = new String(tempseq);
437+
sequence = String.valueOf(tempseq);
438438
}
439439

440440
/**

‎biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/GeneIDGFF2Reader.java‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -147,9 +147,9 @@ private static Feature parseLine(String s) {
147147
end = s.indexOf('#', start);
148148
String attributes = null;
149149
if (end < 0) {
150-
attributes = new String(s.substring(start));
150+
attributes = s.substring(start);
151151
} else {
152-
attributes = new String(s.substring(start, end));
152+
attributes = s.substring(start, end);
153153
}
154154
//need to add in attribute assignment for geneid where it just provides a gene name and will make it gtf like
155155
attributes = "gene_id " + '"' + attributes + '"' + ";";

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

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -147,9 +147,9 @@ private static Feature parseLine(String s) {
147147
end = s.indexOf('#', start);
148148
String attributes = null;
149149
if (end < 0) {
150-
attributes = new String(s.substring(start));
150+
attributes = s.substring(start);
151151
} else {
152-
attributes = new String(s.substring(start, end));
152+
attributes = s.substring(start, end);
153153
}
154154

155155
return new Feature(seqname, source, type, location, score, frame, attributes);

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

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -843,7 +843,7 @@ public boolean isSameStrand( Location other )
843843
@Override
844844
public String toString()
845845
{
846-
return new String( "[L=" + (mEnd - mStart) + "; S=" + mStart + "; E=" + mEnd +"]" );
846+
return "[L=" + (mEnd - mStart) + "; S=" + mStart + "; E=" + mEnd +"]";
847847
}
848848

849849
/* (non-Javadoc)

‎biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/twobit/TwoBitParser.java‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -91,7 +91,7 @@ else if(sign==0x4327411A) {
9191
int name_len = raf.read();
9292
char[] chars = new char[name_len];
9393
for(int j=0;j<name_len;j++) chars[j] = (char)raf.read();
94-
seq_names[i] = new String(chars);
94+
seq_names[i] = String.valueOf(chars);
9595
long pos = readFourBytes();
9696
seq2pos.put(seq_names[i],pos);
9797
logger.debug("2bit: Sequence name=[{}], pos={}", seq_names[i], pos);

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

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -190,7 +190,7 @@ public boolean containsTerm(String name) {
190190
}
191191

192192
public IntTerm resolveInt(int val) {
193-
Integer i = new Integer(val);
193+
Integer i = val;
194194
IntTerm term = (IntTerm) termCache.get(i);
195195

196196
if(term == null) {

‎biojava-ontology/src/main/java/org/biojava/nbio/ontology/obo/OboFileParser.java‎

Lines changed: 17 additions & 17 deletions
Original file line numberDiff line numberDiff line change
@@ -67,21 +67,21 @@ public class OboFileParser {
6767
new HashMap<Character, Character>();
6868

6969
static {
70-
escapeChars.put(new Character('n'), new Character('\n'));
71-
escapeChars.put(new Character('W'), new Character(' '));
72-
escapeChars.put(new Character('t'), new Character('\t'));
73-
escapeChars.put(new Character(':'), new Character(':'));
74-
escapeChars.put(new Character(','), new Character(','));
75-
escapeChars.put(new Character('"'), new Character('"'));
76-
escapeChars.put(new Character('\''), new Character('\''));
77-
escapeChars.put(new Character('\\'), new Character('\\'));
78-
escapeChars.put(new Character('{'), new Character('{'));
79-
escapeChars.put(new Character('}'), new Character('}'));
80-
escapeChars.put(new Character('('), new Character('('));
81-
escapeChars.put(new Character(')'), new Character(')'));
82-
escapeChars.put(new Character('['), new Character('['));
83-
escapeChars.put(new Character(']'), new Character(']'));
84-
escapeChars.put(new Character('!'), new Character('!'));
70+
escapeChars.put('n', '\n');
71+
escapeChars.put('W', ' ');
72+
escapeChars.put('t', '\t');
73+
escapeChars.put(':', ':');
74+
escapeChars.put(',', ',');
75+
escapeChars.put('"', '"');
76+
escapeChars.put('\'', '\'');
77+
escapeChars.put('\\', '\\');
78+
escapeChars.put('{', '{');
79+
escapeChars.put('}', '}');
80+
escapeChars.put('(', '(');
81+
escapeChars.put(')', ')');
82+
escapeChars.put('[', '[');
83+
escapeChars.put(']', ']');
84+
escapeChars.put('!', '!');
8585
Iterator <Character> it = escapeChars.keySet().iterator();
8686
while (it.hasNext()) {
8787
Character key = it.next();
@@ -417,7 +417,7 @@ public static String escape(String str, boolean escapespaces) {
417417
StringBuffer out = new StringBuffer();
418418
for (int i = 0; i < str.length(); i++) {
419419
char c = str.charAt(i);
420-
Object o = unescapeChars.get(new Character(c));
420+
Object o = unescapeChars.get(c);
421421
if (o == null)
422422
out.append(c);
423423
else {
@@ -449,7 +449,7 @@ public SOPair unescape(String str, char toChar, int startindex,
449449
i++;
450450
c = str.charAt(i);
451451
Character mapchar = escapeChars
452-
.get(new Character(c));
452+
.get(c);
453453
if (mapchar == null)
454454
throw new IOException("Unrecognized escape"
455455
+ " character " + c + " found.");

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