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Merged
josemduarte merged 1 commit into from
Jun 30, 2023
Merged

Fix Sonar S2129 Constructors should not be used to instantiate 'String', … #1067

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5 changes: 2 additions & 3 deletions biojava-alignment/src/main/java/org/biojava/nbio/alignment/io/StockholmStructure.java
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Expand Up @@ -256,9 +256,8 @@ else if (forcedSequenceType.equals(PFAM))
}
String[] seqDetails = splitSeqName(sequencename);
seq.setDescription(seqDetails[0]);
seq.setBioBegin((seqDetails[1] == null || seqDetails[1].trim().equals("") ? null : new Integer(
seqDetails[1])));
seq.setBioEnd((seqDetails[2] == null || seqDetails[2].trim().equals("") ? null : new Integer(seqDetails[2])));
seq.setBioBegin((seqDetails[1] == null || seqDetails[1].trim().equals("") ? null : Integer.valueOf(seqDetails[1])));
seq.setBioEnd((seqDetails[2] == null || seqDetails[2].trim().equals("") ? null : Integer.valueOf(seqDetails[2])));

seqs.add(seq);
}
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22 changes: 11 additions & 11 deletions biojava-core/src/main/java/org/biojava/nbio/core/search/io/blast/BlastTabularParser.java
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Expand Up @@ -136,23 +136,23 @@ public List<Result> createObjects(double maxEScore) throws IOException, ParseExc

String currentSubjectId=subjectId;
while (currentSubjectId.equals(subjectId) && lineNumber < fileLinesCount){
if (new Double(evalue) > maxEScore) {
if (Double.valueOf(evalue) > maxEScore) {
line = fetchData(scanner);
lineNumber++;
continue;
}
BlastHspBuilder hspBuilder = new BlastHspBuilder();
hspBuilder
.setHspAlignLen(new Integer(alnLength))
.setHspGaps(new Integer(gapOpenCount))
.setHspQueryFrom(new Integer(queryStart))
.setHspQueryTo(new Integer(queryEnd))
.setHspHitFrom(new Integer(subjectStart))
.setHspHitTo(new Integer(subjectEnd))
.setHspEvalue(new Double(evalue))
.setHspBitScore(new Double(bitScore))
.setPercentageIdentity(new Double(percIdentity)/100)
.setMismatchCount(new Integer(mismatchCount));
.setHspAlignLen(Integer.valueOf(alnLength))
.setHspGaps(Integer.valueOf(gapOpenCount))
.setHspQueryFrom(Integer.valueOf(queryStart))
.setHspQueryTo(Integer.valueOf(queryEnd))
.setHspHitFrom(Integer.valueOf(subjectStart))
.setHspHitTo(Integer.valueOf(subjectEnd))
.setHspEvalue(Double.valueOf(evalue))
.setHspBitScore(Double.valueOf(bitScore))
.setPercentageIdentity(Double.valueOf(percIdentity)/100)
.setMismatchCount(Integer.valueOf(mismatchCount));
hsps.add(hspBuilder.createBlastHsp());
if (scanner.hasNext()) line = fetchData(scanner);
lineNumber++;
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36 changes: 18 additions & 18 deletions biojava-core/src/main/java/org/biojava/nbio/core/search/io/blast/BlastXMLParser.java
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Expand Up @@ -117,10 +117,10 @@ public List<Result> createObjects(double maxEScore) throws IOException, ParseExc

// Iteration* section keys:
resultBuilder
.setIterationNumber(new Integer(XMLHelper.selectSingleElement(element,"Iteration_iter-num").getTextContent()))
.setIterationNumber(Integer.valueOf(XMLHelper.selectSingleElement(element,"Iteration_iter-num").getTextContent()))
.setQueryID(XMLHelper.selectSingleElement(element,"Iteration_query-ID").getTextContent())
.setQueryDef(XMLHelper.selectSingleElement(element, "Iteration_query-def").getTextContent())
.setQueryLength(new Integer(XMLHelper.selectSingleElement(element,"Iteration_query-len").getTextContent()));
.setQueryLength(Integer.valueOf(XMLHelper.selectSingleElement(element,"Iteration_query-len").getTextContent()));

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

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

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

// add the new hsp only if it pass the specified threshold. It can save lot of memory and some parsing time
if (evalue <= maxEScore) {
BlastHspBuilder blastHspBuilder = new BlastHspBuilder();
blastHspBuilder
.setHspNum(new Integer(XMLHelper.selectSingleElement(hspElement, "Hsp_num").getTextContent()))
.setHspBitScore(new Double(XMLHelper.selectSingleElement(hspElement, "Hsp_bit-score").getTextContent()))
.setHspScore(new Integer(XMLHelper.selectSingleElement(hspElement, "Hsp_score").getTextContent()))
.setHspNum(Integer.valueOf(XMLHelper.selectSingleElement(hspElement, "Hsp_num").getTextContent()))
.setHspBitScore(Double.valueOf(XMLHelper.selectSingleElement(hspElement, "Hsp_bit-score").getTextContent()))
.setHspScore(Integer.valueOf(XMLHelper.selectSingleElement(hspElement, "Hsp_score").getTextContent()))
.setHspEvalue(evalue)
.setHspQueryFrom(new Integer(XMLHelper.selectSingleElement(hspElement, "Hsp_query-from").getTextContent()))
.setHspQueryTo(new Integer(XMLHelper.selectSingleElement(hspElement, "Hsp_query-to").getTextContent()))
.setHspHitFrom(new Integer(XMLHelper.selectSingleElement(hspElement, "Hsp_hit-from").getTextContent()))
.setHspHitTo(new Integer(XMLHelper.selectSingleElement(hspElement, "Hsp_hit-to").getTextContent()))
.setHspQueryFrame(new Integer(XMLHelper.selectSingleElement(hspElement, "Hsp_query-frame").getTextContent()))
.setHspHitFrame(new Integer(XMLHelper.selectSingleElement(hspElement, "Hsp_hit-frame").getTextContent()))
.setHspIdentity(new Integer(XMLHelper.selectSingleElement(hspElement, "Hsp_identity").getTextContent()))
.setHspPositive(new Integer(XMLHelper.selectSingleElement(hspElement, "Hsp_positive").getTextContent()))
.setHspGaps(new Integer(XMLHelper.selectSingleElement(hspElement, "Hsp_gaps").getTextContent()))
.setHspAlignLen(new Integer(XMLHelper.selectSingleElement(hspElement, "Hsp_align-len").getTextContent()))
.setHspQueryFrom(Integer.valueOf(XMLHelper.selectSingleElement(hspElement, "Hsp_query-from").getTextContent()))
.setHspQueryTo(Integer.valueOf(XMLHelper.selectSingleElement(hspElement, "Hsp_query-to").getTextContent()))
.setHspHitFrom(Integer.valueOf(XMLHelper.selectSingleElement(hspElement, "Hsp_hit-from").getTextContent()))
.setHspHitTo(Integer.valueOf(XMLHelper.selectSingleElement(hspElement, "Hsp_hit-to").getTextContent()))
.setHspQueryFrame(Integer.valueOf(XMLHelper.selectSingleElement(hspElement, "Hsp_query-frame").getTextContent()))
.setHspHitFrame(Integer.valueOf(XMLHelper.selectSingleElement(hspElement, "Hsp_hit-frame").getTextContent()))
.setHspIdentity(Integer.valueOf(XMLHelper.selectSingleElement(hspElement, "Hsp_identity").getTextContent()))
.setHspPositive(Integer.valueOf(XMLHelper.selectSingleElement(hspElement, "Hsp_positive").getTextContent()))
.setHspGaps(Integer.valueOf(XMLHelper.selectSingleElement(hspElement, "Hsp_gaps").getTextContent()))
.setHspAlignLen(Integer.valueOf(XMLHelper.selectSingleElement(hspElement, "Hsp_align-len").getTextContent()))
.setHspQseq(XMLHelper.selectSingleElement(hspElement, "Hsp_qseq").getTextContent())
.setHspHseq(XMLHelper.selectSingleElement(hspElement, "Hsp_hseq").getTextContent())
.setHspIdentityString(XMLHelper.selectSingleElement(hspElement, "Hsp_midline").getTextContent());
Expand Down
2 changes: 1 addition & 1 deletion biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/ABITrace.java
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Expand Up @@ -434,7 +434,7 @@ private void setSeq() {
for (int x = 0; x <= seqLength - 1; ++x) {
tempseq[x] = (char) traceData[PBAS2 + x];
}
sequence = new String(tempseq);
sequence = String.valueOf(tempseq);
}

/**
Expand Down
4 changes: 2 additions & 2 deletions biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/GeneIDGFF2Reader.java
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Expand Up @@ -147,9 +147,9 @@ private static Feature parseLine(String s) {
end = s.indexOf('#', start);
String attributes = null;
if (end < 0) {
attributes = new String(s.substring(start));
attributes = s.substring(start);
} else {
attributes = new String(s.substring(start, end));
attributes = s.substring(start, end);
}
//need to add in attribute assignment for geneid where it just provides a gene name and will make it gtf like
attributes = "gene_id " + '"' + attributes + '"' + ";";
Expand Down
4 changes: 2 additions & 2 deletions biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/GeneMarkGTFReader.java
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Expand Up @@ -147,9 +147,9 @@ private static Feature parseLine(String s) {
end = s.indexOf('#', start);
String attributes = null;
if (end < 0) {
attributes = new String(s.substring(start));
attributes = s.substring(start);
} else {
attributes = new String(s.substring(start, end));
attributes = s.substring(start, end);
}

return new Feature(seqname, source, type, location, score, frame, attributes);
Expand Down
2 changes: 1 addition & 1 deletion biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/Location.java
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Expand Up @@ -843,7 +843,7 @@ public boolean isSameStrand( Location other )
@Override
public String toString()
{
return new String( "[L=" + (mEnd - mStart) + "; S=" + mStart + "; E=" + mEnd +"]" );
return "[L=" + (mEnd - mStart) + "; S=" + mStart + "; E=" + mEnd +"]";
}

/* (non-Javadoc)
Expand Down
2 changes: 1 addition & 1 deletion biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/twobit/TwoBitParser.java
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Expand Up @@ -91,7 +91,7 @@ else if(sign==0x4327411A) {
int name_len = raf.read();
char[] chars = new char[name_len];
for(int j=0;j<name_len;j++) chars[j] = (char)raf.read();
seq_names[i] = new String(chars);
seq_names[i] = String.valueOf(chars);
long pos = readFourBytes();
seq2pos.put(seq_names[i],pos);
logger.debug("2bit: Sequence name=[{}], pos={}", seq_names[i], pos);
Expand Down
2 changes: 1 addition & 1 deletion biojava-ontology/src/main/java/org/biojava/nbio/ontology/IntegerOntology.java
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Expand Up @@ -190,7 +190,7 @@ public boolean containsTerm(String name) {
}

public IntTerm resolveInt(int val) {
Integer i = new Integer(val);
Integer i = val;
IntTerm term = (IntTerm) termCache.get(i);

if(term == null) {
Expand Down
34 changes: 17 additions & 17 deletions biojava-ontology/src/main/java/org/biojava/nbio/ontology/obo/OboFileParser.java
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Expand Up @@ -67,21 +67,21 @@ public class OboFileParser {
new HashMap<Character, Character>();

static {
escapeChars.put(new Character('n'), new Character('\n'));
escapeChars.put(new Character('W'), new Character(' '));
escapeChars.put(new Character('t'), new Character('\t'));
escapeChars.put(new Character(':'), new Character(':'));
escapeChars.put(new Character(','), new Character(','));
escapeChars.put(new Character('"'), new Character('"'));
escapeChars.put(new Character('\''), new Character('\''));
escapeChars.put(new Character('\\'), new Character('\\'));
escapeChars.put(new Character('{'), new Character('{'));
escapeChars.put(new Character('}'), new Character('}'));
escapeChars.put(new Character('('), new Character('('));
escapeChars.put(new Character(')'), new Character(')'));
escapeChars.put(new Character('['), new Character('['));
escapeChars.put(new Character(']'), new Character(']'));
escapeChars.put(new Character('!'), new Character('!'));
escapeChars.put('n', '\n');
escapeChars.put('W', ' ');
escapeChars.put('t', '\t');
escapeChars.put(':', ':');
escapeChars.put(',', ',');
escapeChars.put('"', '"');
escapeChars.put('\'', '\'');
escapeChars.put('\\', '\\');
escapeChars.put('{', '{');
escapeChars.put('}', '}');
escapeChars.put('(', '(');
escapeChars.put(')', ')');
escapeChars.put('[', '[');
escapeChars.put(']', ']');
escapeChars.put('!', '!');
Iterator <Character> it = escapeChars.keySet().iterator();
while (it.hasNext()) {
Character key = it.next();
Expand Down Expand Up @@ -417,7 +417,7 @@ public static String escape(String str, boolean escapespaces) {
StringBuffer out = new StringBuffer();
for (int i = 0; i < str.length(); i++) {
char c = str.charAt(i);
Object o = unescapeChars.get(new Character(c));
Object o = unescapeChars.get(c);
if (o == null)
out.append(c);
else {
Expand Down Expand Up @@ -449,7 +449,7 @@ public SOPair unescape(String str, char toChar, int startindex,
i++;
c = str.charAt(i);
Character mapchar = escapeChars
.get(new Character(c));
.get(c);
if (mapchar == null)
throw new IOException("Unrecognized escape"
+ " character " + c + " found.");
Expand Down
12 changes: 6 additions & 6 deletions ...e-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/StructureAlignmentJmol.java
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Expand Up @@ -257,12 +257,12 @@ public void itemStateChanged(ItemEvent e) {
zoomSlider.setPaintTicks(true);

Hashtable<Integer, JLabel> labelTable = new Hashtable<Integer, JLabel>();
labelTable.put(new Integer(0),new JLabel("0%"));
labelTable.put(new Integer(100),new JLabel("100%"));
labelTable.put(new Integer(200),new JLabel("200%"));
labelTable.put(new Integer(300),new JLabel("300%"));
labelTable.put(new Integer(400),new JLabel("400%"));
labelTable.put(new Integer(500),new JLabel("500%"));
labelTable.put(0,new JLabel("0%"));
labelTable.put(100,new JLabel("100%"));
labelTable.put(200,new JLabel("200%"));
labelTable.put(300,new JLabel("300%"));
labelTable.put(400,new JLabel("400%"));
labelTable.put(500,new JLabel("500%"));

zoomSlider.setLabelTable(labelTable);
zoomSlider.setPaintLabels(true);
Expand Down
12 changes: 6 additions & 6 deletions ...ture-gui/src/main/java/org/biojava/nbio/structure/gui/util/AlternativeAlignmentFrame.java
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Expand Up @@ -126,12 +126,12 @@ private Object[][] getDataFromAligs(AlternativeAlignment[] aligs){
for ( int i=0;i< aligs.length;i++){
AlternativeAlignment alig = aligs[i];

data[i][0] = new Integer(i+1);
data[i][1] = new Integer(alig.getEqr());
data[i][2] = new Double(alig.getScore());
data[i][3] = new Double(alig.getRmsd());
data[i][4] = new Integer(alig.getGaps());
data[i][5] = new Integer(alig.getCluster());
data[i][0] = Integer.valueOf(i+1);
data[i][1] = Integer.valueOf(alig.getEqr());
data[i][2] = Double.valueOf(alig.getScore());
data[i][3] = Double.valueOf(alig.getRmsd());
data[i][4] = Integer.valueOf(alig.getGaps());
data[i][5] = Integer.valueOf(alig.getCluster());
JButton maxb = new JButton("Distance Matrix");
maxb.addMouseListener(new MatrixMouseListener(this,i));

Expand Down
20 changes: 10 additions & 10 deletions biojava-structure/src/main/java/org/biojava/nbio/structure/align/StrucAligParameters.java
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Expand Up @@ -125,16 +125,16 @@ public String toString() {
StringBuffer buf = new StringBuffer();
String t = " ";

Object[] params = new Object[]{new Integer(initialK) ,new Integer(seedFragmentLength),
new Float(seedRmsdCutoff),
new Integer(fragmentLength),
new Integer(diagonalDistance), new Integer(diagonalDistance2), new Float(fragmentMiniDistance),
new Integer(angleDiff),
new Float(fragCompat), new Integer(maxrefine),
new Boolean(reduceInitialFragments), new Double(joinRMSCutoff), new Boolean(joinPlo),
new Boolean(doAngleCheck), new Boolean(doDistanceCheck), new Boolean(doRMSCheck),
new Boolean(doDensityCheck), new Float(densityCutoff), new Float(create_co), new Integer(maxIter),
new Float(gapOpen), new Float(gapExtension), new Integer(permutationSize), new Float(evalCutoff)};
Object[] params = new Object[]{Integer.valueOf(initialK) ,Integer.valueOf(seedFragmentLength),
Float.valueOf(seedRmsdCutoff),
Integer.valueOf(fragmentLength),
Integer.valueOf(diagonalDistance), Integer.valueOf(diagonalDistance2), Float.valueOf(fragmentMiniDistance),
Integer.valueOf(angleDiff),
Float.valueOf(fragCompat), Integer.valueOf(maxrefine),
Boolean.valueOf(reduceInitialFragments), Double.valueOf(joinRMSCutoff), Boolean.valueOf(joinPlo),
Boolean.valueOf(doAngleCheck), Boolean.valueOf(doDistanceCheck), Boolean.valueOf(doRMSCheck),
Boolean.valueOf(doDensityCheck), Float.valueOf(densityCutoff), Float.valueOf(create_co), Integer.valueOf(maxIter),
Float.valueOf(gapOpen), Float.valueOf(gapExtension), Integer.valueOf(permutationSize), Float.valueOf(evalCutoff)};

for (int i=0 ; i< params.length ; i++){
buf.append(params[i]);
Expand Down
4 changes: 2 additions & 2 deletions biojava-structure/src/main/java/org/biojava/nbio/structure/align/model/AFPChain.java
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Expand Up @@ -447,8 +447,8 @@ private void init(){
afpChainTwiNum = 0;
alignScore = 0;
alignScoreUpdate = 0;
conn = new Double(0);
dvar = new Double(0);
conn = Double.valueOf(0);
dvar = Double.valueOf(0);
calculationTime = 0;

similarity = -1;
Expand Down
10 changes: 5 additions & 5 deletions biojava-structure/src/main/java/org/biojava/nbio/structure/align/model/AfpChainWriter.java
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Expand Up @@ -263,9 +263,9 @@ public static String toFatCatCore(


//System.err.println("t,len:"+t+":"+len);
String lseq1 = new String(alnseq1).substring(t,t+len);
String lseq2 = new String(alnseq2).substring(t,t+len);
String lsymb = new String(alnsymb).substring(t,t+len);
String lseq1 = String.valueOf(alnseq1).substring(t,t+len);
String lseq2 = String.valueOf(alnseq2).substring(t,t+len);
String lsymb = String.valueOf(alnsymb).substring(t,t+len);

//System.err.println("B:" + b);

Expand Down Expand Up @@ -1197,8 +1197,8 @@ public static String toCE(AFPChain afpChain, Atom[] ca1, Atom[] ca2)


//System.err.println("t,len:"+t+":"+len);
a = new String(alnseq1).substring(t,t+len);
b = new String(alnseq2).substring(t,t+len);
a = String.valueOf(alnseq1).substring(t,t+len);
b = String.valueOf(alnseq2).substring(t,t+len);

//System.err.println("B:" + b);

Expand Down
4 changes: 2 additions & 2 deletions biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/CliTools.java
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Expand Up @@ -153,13 +153,13 @@ public static String[] configureBean(Object bean, String[] args)

if (propType == Integer.TYPE) {
try {
propVal = new Integer(args[++i]);
propVal = Integer.valueOf(args[++i]);
} catch (Exception ex) {
throw new ConfigurationException("Option " + arg + " requires an integer parameter");
}
} else if (propType == Double.TYPE || propType == Double.class ) {
try {
propVal = new Double(args[++i]);
propVal = Double.valueOf(args[++i]);
} catch (Exception ex) {
throw new ConfigurationException("Option " + arg + " requires a numerical parameter");
}
Expand Down
10 changes: 5 additions & 5 deletions ...ucture/src/main/java/org/biojava/nbio/structure/align/xml/MultipleAlignmentXMLParser.java
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Expand Up @@ -202,7 +202,7 @@ private static Block parseBlock(Node root, BlockSet blockSet) {
if (residue.equals("null")){
alignRes.get(str-1).add(null);
} else {
alignRes.get(str-1).add(new Integer(residue));
alignRes.get(str-1).add(Integer.valueOf(residue));
}

str++;
Expand All @@ -225,7 +225,7 @@ private static Matrix4d parseMatrix4d(Node node) {
for (int y=0; y<4; y++){
String key = "mat"+(x+1)+(y+1);
String value = atts.getNamedItem(key).getTextContent();
m.setElement(x, y, new Double(value));
m.setElement(x, y, Double.valueOf(value));
}
}
return m;
Expand All @@ -241,7 +241,7 @@ private static void parseScoresCache(Node root, ScoresCache cache) {
NamedNodeMap atts = child.getAttributes();
if (atts != null) {
Node score = atts.getNamedItem("value");
Double value = new Double(score.getTextContent());
Double value = Double.valueOf(score.getTextContent());
cache.putScore(child.getNodeName(), value);
}
}
Expand All @@ -264,12 +264,12 @@ private static void parseHeader(Node node,

String ioTime = atts.getNamedItem("IOTime").getTextContent();
if (!ioTime.equals("null")){
ensemble.setIoTime(new Long(ioTime));
ensemble.setIoTime(Long.valueOf(ioTime));
}

String time = atts.getNamedItem("CalculationTime").getTextContent();
if (!time.equals("null")){
ensemble.setCalculationTime(new Long(time));
ensemble.setCalculationTime(Long.valueOf(time));
}
}

Expand Down
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