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author
Mohamed Ezzat
committed
squid:S1125 - Literal boolean values should not be used in condition expressions
1 parent 57f456b commit 2c1793e

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7 files changed

+25
-25
lines changed

7 files changed

+25
-25
lines changed

‎biojava-core/src/main/java/org/biojava/nbio/core/sequence/transcription/RNAToAminoAcidTranslator.java‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -215,7 +215,7 @@ public List<Sequence<AminoAcidCompound>> createSequences(
215215
target = quickLookup.get(triplet);
216216

217217
// Check for a start
218-
if (doTranslate == false && target.isStart()) {
218+
if (!doTranslate && target.isStart()) {
219219
doTranslate = true;
220220
}
221221

‎biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/jmolScript/JmolSymmetryScriptGeneratorPointGroup.java‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -757,7 +757,7 @@ private String getSymmetryAxis(int i, int j, String pointGroup, int n, Vector3d
757757
p2 = new Point3d(axis);
758758
p2.scaleAdd(1.01*radius, center);
759759

760-
if (drawPolygon == true) {
760+
if (drawPolygon) {
761761
double polygonRadius = getMeanExtension() * 0.06;
762762
if (n == 2) {
763763
referenceAxis = getAligmentVector(p1, axis);

‎biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AtomCache.java‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -930,7 +930,7 @@ public void setUseMmCif(boolean useMmCif) {
930930
*/
931931
public void setUseMmtf(boolean useMmtf) {
932932
this.useMmtf = useMmtf;
933-
if(useMmtf==true){
933+
if(useMmtf){
934934
useMmCif=false;
935935
}
936936

‎biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxR.java‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -519,7 +519,7 @@ public CoxInfo process(ArrayList<String> variables, ArrayList<SurvivalInfo> data
519519
/*
520520
** here is the main loop
521521
*/
522-
if (gotofinish == false) {
522+
if (!gotofinish) {
523523
halving = 0; /* =1 when in the midst of "step halving" */
524524
for (iter = 1; iter <= maxiter; iter++) {
525525
newlk = 0;
@@ -675,7 +675,7 @@ public CoxInfo process(ArrayList<String> variables, ArrayList<SurvivalInfo> data
675675
} /* return for another iteration */
676676
}
677677

678-
if (gotofinish == false) {
678+
if (!gotofinish) {
679679
/*
680680
** We end up here only if we ran out of iterations
681681
*/

‎biojava-survival/src/main/java/org/biojava/nbio/survival/cox/SurvivalInfoHelper.java‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -194,7 +194,7 @@ public static void groupByRange(double[] range, String variable, String groupNam
194194
}
195195
int rangeIndex = getRangeIndex(range, value);
196196
String label = labels.get(rangeIndex);
197-
if (validLabels.contains(groupName + "_" + label) == false) {
197+
if (!validLabels.contains(groupName + "_" + label)) {
198198
validLabels.add(groupName + "_" + label);
199199
}
200200
}

‎biojava-survival/src/main/java/org/biojava/nbio/survival/data/WorkSheet.java‎

Lines changed: 18 additions & 18 deletions
Original file line numberDiff line numberDiff line change
@@ -243,7 +243,7 @@ public ArrayList<String> getMetaDataColumns() {
243243
ArrayList<String> metaColumns = new ArrayList<String>();
244244
for (String key : metaDataColumnsHashMap.keySet()) {
245245
HeaderInfo hi = columnLookup.get(key);
246-
if (hi.isHide() == false) {
246+
if (!hi.isHide()) {
247247
metaColumns.add(key);
248248
}
249249
}
@@ -258,7 +258,7 @@ public ArrayList<String> getMetaDataRows() {
258258
ArrayList<String> metaRows = new ArrayList<String>();
259259
for (String key : metaDataRowsHashMap.keySet()) {
260260
HeaderInfo hi = rowLookup.get(key);
261-
if (hi.isHide() == false) {
261+
if (!hi.isHide()) {
262262
metaRows.add(key);
263263
}
264264
}
@@ -273,7 +273,7 @@ public ArrayList<String> getDataColumns() {
273273
ArrayList<String> dataColumns = new ArrayList<String>();
274274
ArrayList<String> columns = this.getColumns();
275275
for (String column : columns) {
276-
if (metaDataColumnsHashMap.containsKey(column) == false) {
276+
if (!metaDataColumnsHashMap.containsKey(column)) {
277277
dataColumns.add(column);
278278
}
279279
}
@@ -439,7 +439,7 @@ public void setMetaDataRowsAfterRow(String row) {
439439
ArrayList<String> rows = this.getRows();
440440
boolean metarow = false;
441441
for (String r : rows) {
442-
if (r.equals(row) && metarow == false) {
442+
if (r.equals(row) && !metarow) {
443443
metarow = true;
444444
}
445445
if (metarow) {
@@ -456,7 +456,7 @@ public void setMetaDataColumnsAfterColumn(String column) {
456456
ArrayList<String> cols = this.getColumns();
457457
boolean metacolumns = false;
458458
for (String col : cols) {
459-
if (col.equals(column) && metacolumns == false) {
459+
if (col.equals(column) && !metacolumns) {
460460
metacolumns = true;
461461
}
462462
if (metacolumns) {
@@ -1067,7 +1067,7 @@ public ArrayList<String> getColumns() {
10671067
ArrayList<String> columns = new ArrayList<String>();
10681068
for (String col : columnLookup.keySet()) {
10691069
HeaderInfo hi = columnLookup.get(col);
1070-
if (hi.isHide() == false) {
1070+
if (!hi.isHide()) {
10711071
columns.add(col);
10721072
}
10731073
}
@@ -1087,7 +1087,7 @@ public ArrayList<String> getDiscreteColumnValues(String column) throws Exception
10871087
ArrayList<String> rows = getDataRows();
10881088
for (String row : rows) {
10891089
String value = getCell(row, column);
1090-
if (hashMapValues.containsKey(value) == false) {
1090+
if (!hashMapValues.containsKey(value)) {
10911091
hashMapValues.put(value, value);
10921092
values.add(value);
10931093
}
@@ -1107,7 +1107,7 @@ public ArrayList<String> getDiscreteRowValues(String row) throws Exception {
11071107
ArrayList<String> values = new ArrayList<String>();
11081108
for (String column : getColumns()) {
11091109
String value = getCell(row, column);
1110-
if (hashMapValues.containsKey(value) == false) {
1110+
if (!hashMapValues.containsKey(value)) {
11111111
hashMapValues.put(value, value);
11121112
values.add(value);
11131113
}
@@ -1138,7 +1138,7 @@ public ArrayList<String> getRows() {
11381138
ArrayList<String> rows = new ArrayList<String>();
11391139
for (String row : rowLookup.keySet()) {
11401140
HeaderInfo hi = rowLookup.get(row);
1141-
if (hi.isHide() == false) {
1141+
if (!hi.isHide()) {
11421142
rows.add(row);
11431143
}
11441144
}
@@ -1157,7 +1157,7 @@ public ArrayList<String> getDataRows() {
11571157
continue;
11581158
}
11591159
HeaderInfo hi = rowLookup.get(row);
1160-
if (hi.isHide() == false) {
1160+
if (!hi.isHide()) {
11611161
rows.add(row);
11621162
}
11631163
}
@@ -1383,24 +1383,24 @@ static public WorkSheet unionWorkSheetsRowJoin(WorkSheet w1, WorkSheet w2, boole
13831383

13841384

13851385
if (secondSheetMetaData) {
1386-
if (w1.getColumns().contains("META_DATA") == false) {
1386+
if (!w1.getColumns().contains("META_DATA")) {
13871387
w1DataColumns.add("META_DATA");
13881388
}
13891389
}
13901390

13911391
ArrayList<String> joinedColumns = new ArrayList<String>();
13921392
joinedColumns.addAll(w1DataColumns);
13931393
joinedColumns.addAll(w2DataColumns);
1394-
if (joinedColumns.contains("META_DATA") == false && (w1MetaDataColumns.size() > 0 || w2MetaDataColumns.size() > 0)) {
1394+
if (!joinedColumns.contains("META_DATA") && (w1MetaDataColumns.size() > 0 || w2MetaDataColumns.size() > 0)) {
13951395
joinedColumns.add("META_DATA");
13961396
}
13971397
for (String column : w1MetaDataColumns) {
1398-
if (joinedColumns.contains(column) == false) {
1398+
if (!joinedColumns.contains(column)) {
13991399
joinedColumns.add(column);
14001400
}
14011401
}
14021402
for (String column : w2MetaDataColumns) {
1403-
if (joinedColumns.contains(column) == false) {
1403+
if (!joinedColumns.contains(column)) {
14041404
joinedColumns.add(column);
14051405
}
14061406
}
@@ -1489,7 +1489,7 @@ static public WorkSheet readCSV(InputStream is, char delimiter) throws Exception
14891489
public void saveCSV(String fileName) throws Exception {
14901490
File f = new File(fileName);
14911491
File parentFile = f.getParentFile();
1492-
if (parentFile.isDirectory() == false) {
1492+
if (!parentFile.isDirectory()) {
14931493
parentFile.mkdirs();
14941494
}
14951495
FileOutputStream file = new FileOutputStream(fileName);
@@ -1507,7 +1507,7 @@ public void saveCSV(String fileName) throws Exception {
15071507
public void saveTXT(String fileName) throws Exception {
15081508
File f = new File(fileName);
15091509
File parentFile = f.getParentFile();
1510-
if (parentFile.isDirectory() == false) {
1510+
if (!parentFile.isDirectory()) {
15111511
parentFile.mkdirs();
15121512
}
15131513
FileOutputStream file = new FileOutputStream(fileName);
@@ -1570,7 +1570,7 @@ public void appendWorkSheetRows(WorkSheet worksheet) throws Exception {
15701570

15711571
this.addRows(newRows, "");
15721572
for (String col : this.getColumns()) {
1573-
if (worksheet.isValidColumn(col) == false) {
1573+
if (!worksheet.isValidColumn(col)) {
15741574
continue;
15751575
}
15761576
for (String row : newRows) {
@@ -1618,7 +1618,7 @@ public void save(OutputStream outputStream, char delimitter, boolean quoteit) th
16181618
// try{
16191619
String value = getCell(row, col);
16201620
outputStream.write(delimitter);
1621-
if (this.isMetaDataColumn(col) == false && this.isMetaDataRow(row) == false) {
1621+
if (!this.isMetaDataColumn(col) && !this.isMetaDataRow(row)) {
16221622
if (value == null || value.length() == 0 || value.equalsIgnoreCase("null")) {
16231623
value = "NaN";
16241624
}

‎biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/figure/SurvFitKM.java‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -397,7 +397,7 @@ public LinkedHashMap<String, StrataInfo> processStrataInfo(String variable, Arr
397397
}
398398
ArrayList<Integer> zz = new ArrayList<Integer>();
399399
for (int i = 0; i < events.size(); i++) {
400-
if (events.get(i) == true) {
400+
if (events.get(i)) {
401401
zz.add(i + 1);
402402
}
403403
}

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