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andreasprlicandreasprlic
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Merge pull request biojava#499 from DevFactory/release--primitives-should-not-be-boxed-just-for-String-conversion-fix-1
squid:S2131 - Primitives should not be boxed just for String conversion
2 parents 253da8d + fa52fd8 commit 1d874f1

30 files changed

Lines changed: 57 additions & 58 deletions

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‎biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/PeptideProperties.java‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -460,7 +460,7 @@ public static final double getEnrichment(String sequence, SingleLetterAACode ami
460460
* @return the composition of specified amino acid in the sequence
461461
*/
462462
public static final double getEnrichment(String sequence, char aminoAcidCode){
463-
return getEnrichment(sequence, aminoAcidCode + "");
463+
return getEnrichment(sequence, aminoAcidCode);
464464
}
465465

466466
/**

‎biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/PeptidePropertiesImpl.java‎

Lines changed: 6 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -75,7 +75,7 @@ public double getMolecularWeight(ProteinSequence sequence) {
7575
AminoAcidCompoundSet aaSet = new AminoAcidCompoundSet();
7676
char[] seq = getSequence(sequence.toString(), true);//ignore case
7777
for(char aa:seq){
78-
AminoAcidCompound c = aaSet.getCompoundForString(aa + "");
78+
AminoAcidCompound c = aaSet.getCompoundForString(String.valueOf(aa));
7979
if(Constraints.aa2MolecularWeight.containsKey(c)){
8080
value += Constraints.aa2MolecularWeight.get(c);
8181
}
@@ -263,7 +263,7 @@ public double getAvgHydropathy(ProteinSequence sequence) {
263263
AminoAcidCompoundSet aaSet = new AminoAcidCompoundSet();
264264
char[] seq = this.getSequence(sequence.toString(), true);
265265
for(char aa:seq){
266-
AminoAcidCompound c = aaSet.getCompoundForString(aa + "");
266+
AminoAcidCompound c = aaSet.getCompoundForString(String.valueOf(aa));
267267
if(Constraints.aa2Hydrophathicity.containsKey(c)){
268268
total += Constraints.aa2Hydrophathicity.get(c);
269269
validLength++;
@@ -477,13 +477,13 @@ private double getNetChargeInnovagen(Map<AminoAcidCompound, Integer> chargedAA2C
477477
AminoAcidCompoundSet aaSet = new AminoAcidCompoundSet();
478478

479479
double nTerminalCharge = 0.0;
480-
AminoAcidCompound nTermCompound = aaSet.getCompoundForString(nTerminalChar + "");
480+
AminoAcidCompound nTermCompound = aaSet.getCompoundForString(String.valueOf(nTerminalChar));
481481
if(Constraints.aa2NTerminalPka.containsKey(nTermCompound)){
482482
nTerminalCharge = this.getPosCharge(Constraints.aa2NTerminalPka.get(nTermCompound), ph);
483483
}
484484

485485
double cTerminalCharge = 0.0;
486-
AminoAcidCompound cTermCompound = aaSet.getCompoundForString(cTerminalChar + "");
486+
AminoAcidCompound cTermCompound = aaSet.getCompoundForString(String.valueOf(cTerminalChar));
487487
if(Constraints.aa2CTerminalPka.containsKey(cTermCompound)){
488488
cTerminalCharge = this.getNegCharge(Constraints.aa2CTerminalPka.get(cTermCompound), ph);
489489
}
@@ -548,7 +548,7 @@ public double getEnrichment(ProteinSequence sequence, AminoAcidCompound aminoAci
548548
double counter = 0.0;
549549
char[] seq = this.getSequence(sequence.getSequenceAsString(), true);
550550
for(char aa:seq){
551-
if(aminoAcidCode.getShortName().equals(aa + "")){
551+
if(aminoAcidCode.getShortName().equals(String.valueOf(aa))){
552552
counter++;
553553
}
554554
}
@@ -566,7 +566,7 @@ public Map<AminoAcidCompound, Double> getAAComposition(ProteinSequence sequence)
566566
char[] seq = this.getSequence(sequence.toString(), true);
567567
for(char aa:seq){
568568
if(PeptideProperties.standardAASet.contains(aa)){
569-
AminoAcidCompound compound = aaSet.getCompoundForString(aa + "");
569+
AminoAcidCompound compound = aaSet.getCompoundForString(String.valueOf(aa));
570570
aa2Composition.put(compound, aa2Composition.get(compound) + 1.0);
571571
validLength++;
572572
}

‎biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/convertor/Convertor.java‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -81,7 +81,7 @@ public String convert(ProteinSequence sequence){
8181
String convertedSequence = "";
8282
String uppercaseSequence = sequence.getSequenceAsString().toUpperCase();
8383
for(int x = 0; x < uppercaseSequence.length(); x++){
84-
convertedSequence += convert(uppercaseSequence.charAt(x));
84+
convertedSequence += String.valueOf(convert(uppercaseSequence.charAt(x)));
8585
}
8686
return convertedSequence;
8787
}

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

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -567,8 +567,8 @@ private void printConservation(StringBuilder s, String idFormat, int seqIndexPad
567567
private boolean isSimilar(char c1, char c2) {
568568
AminoAcidCompoundSet set = AminoAcidCompoundSet.getAminoAcidCompoundSet();
569569

570-
AminoAcidCompound aa1 = set.getCompoundForString(""+c1);
571-
AminoAcidCompound aa2 = set.getCompoundForString(""+c2);
570+
AminoAcidCompound aa1 = set.getCompoundForString(String.valueOf(c1));
571+
AminoAcidCompound aa2 = set.getCompoundForString(String.valueOf(c2));
572572

573573
short val = matrix.getValue(aa1,aa2);
574574
return val > 0;

‎biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/AAIndexFileParser.java‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -185,14 +185,14 @@ private void initMatrix(String line) {
185185
AminoAcidCompoundSet compoundSet = AminoAcidCompoundSet.getAminoAcidCompoundSet();
186186
for ( int i = 0 ; i < currentRows.length() ; i ++){
187187
char c = currentRows.charAt(i);
188-
AminoAcidCompound aa = compoundSet.getCompoundForString(c+"");
188+
AminoAcidCompound aa = compoundSet.getCompoundForString(String.valueOf(c));
189189

190190
rows.add(aa);
191191
}
192192

193193
for ( int i = 0 ; i < currentCols.length() ; i ++){
194194
char c = currentRows.charAt(i);
195-
AminoAcidCompound aa = compoundSet.getCompoundForString(c+"");
195+
AminoAcidCompound aa = compoundSet.getCompoundForString(String.valueOf(c));
196196

197197
cols.add(aa);
198198
}

‎biojava-core/src/main/java/org/biojava/nbio/core/sequence/CDSSequence.java‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -94,7 +94,7 @@ public String getCodingSequence() {
9494
StringBuilder b = new StringBuilder(getLength());
9595
CompoundSet<NucleotideCompound> compoundSet = this.getCompoundSet();
9696
for (int i = 0; i < sequence.length(); i++) {
97-
String nucleotide = sequence.charAt(i) + "";
97+
String nucleotide = String.valueOf(sequence.charAt(i));
9898
NucleotideCompound nucleotideCompound = compoundSet.getCompoundForString(nucleotide);
9999
b.append(nucleotideCompound.getComplement().getShortName());
100100
}

‎biojava-core/src/main/java/org/biojava/nbio/core/sequence/GeneSequence.java‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -298,7 +298,7 @@ public DNASequence getSequence5PrimeTo3Prime() {
298298
StringBuilder b = new StringBuilder(getLength());
299299
CompoundSet<NucleotideCompound> compoundSet = this.getCompoundSet();
300300
for (int i = 0; i < sequence.length(); i++) {
301-
String nucleotide = sequence.charAt(i) + "";
301+
String nucleotide = String.valueOf(sequence.charAt(i));
302302
NucleotideCompound nucleotideCompound = compoundSet.getCompoundForString(nucleotide);
303303
b.append(nucleotideCompound.getComplement().getShortName());
304304
}

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

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -110,7 +110,7 @@ public void process() throws Exception {
110110
for (int i = featureBioBegin; i <= featureBioEnd; i++) {
111111
char ch = sb.charAt(i);
112112
//probably not the fastest but the safest way if language is not standard ASCII
113-
String temp = ch + "";
113+
String temp = String.valueOf(ch);
114114
ch = temp.toUpperCase().charAt(0);
115115
sb.setCharAt(i, ch);
116116
}

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

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -276,7 +276,7 @@ public static <S extends Sequence<C>, C extends Compound> String getIDFormat(Lis
276276
* @return formatted String
277277
*/
278278
public static String getPDBCharacter(boolean web, char c1, char c2, boolean similar, char c) {
279-
String s = c + "";
279+
String s = String.valueOf(c);
280280
return getPDBString(web, c1, c2, similar, s, s, s, s);
281281
}
282282

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

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -212,7 +212,7 @@ private void initAttributeHashMap(){
212212
String[] data = attribute.split(splitData);
213213
String value = "";
214214
if(data.length >= 2 && data[1].indexOf('"') != -1){ // an attibute field could be empty
215-
value = data[1].replaceAll('"' + "","").trim();
215+
value = data[1].replaceAll("\"","").trim();
216216
}else if(data.length >= 2){
217217
value = data[1].trim();
218218
}

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