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Use Interger.parseInt when we need an int and not an Integer
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@johnmay
johnmay committed Feb 10, 2022
1 parent dfaa593 commit 8948015
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Showing 15 changed files with 58 additions and 58 deletions.
18 changes: 9 additions & 9 deletions base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/matchers/RGroupList.java
View file
Expand Up @@ -205,21 +205,21 @@ public static boolean isValidOccurrenceSyntax(String occ) {
do {
//Number: "n"
if (match("^\\d+$", cond)) {
if (Integer.valueOf(cond) < 0) // not allowed
if (Integer.parseInt(cond) < 0) // not allowed
return false;
break;
}
//Range: "n-m"
if (match("^\\d+-\\d+$", cond)) {
int from = Integer.valueOf(cond.substring(0, cond.indexOf('-')));
int to = Integer.valueOf(cond.substring(cond.indexOf('-') + 1, cond.length()));
int from = Integer.parseInt(cond.substring(0, cond.indexOf('-')));
int to = Integer.parseInt(cond.substring(cond.indexOf('-') + 1, cond.length()));
if (from < 0 || to < 0 || to < from) // not allowed
return false;
break;
}
//Smaller than: "<n"
if (match("^<\\d+$", cond)) {
int n = Integer.valueOf(cond.substring(cond.indexOf('<') + 1, cond.length()));
int n = Integer.parseInt(cond.substring(cond.indexOf('<') + 1, cond.length()));
if (n == 0) // not allowed
return false;
break;
Expand Down Expand Up @@ -276,23 +276,23 @@ public List<Integer> matchOccurence(int maxAttachments) {
while (st.hasMoreTokens() && !addVal) {
String cond = st.nextToken().trim().replaceAll(" ", "");
if (match("^\\d+$", cond)) { // n
if (Integer.valueOf(cond) == val) addVal = true;
if (Integer.parseInt(cond) == val) addVal = true;
}
if (match("^\\d+-\\d+$", cond)) { // n-m
int from = Integer.valueOf(cond.substring(0, cond.indexOf('-')));
int to = Integer.valueOf(cond.substring(cond.indexOf('-') + 1, cond.length()));
int from = Integer.parseInt(cond.substring(0, cond.indexOf('-')));
int to = Integer.parseInt(cond.substring(cond.indexOf('-') + 1, cond.length()));
if (val >= from && val <= to) {
addVal = true;
}
}
if (match("^>\\d+$", cond)) { // <n
int n = Integer.valueOf(cond.substring(cond.indexOf('>') + 1, cond.length()));
int n = Integer.parseInt(cond.substring(cond.indexOf('>') + 1, cond.length()));
if (val > n) {
addVal = true;
}
}
if (match("^<\\d+$", cond)) { // >n
int n = Integer.valueOf(cond.substring(cond.indexOf('<') + 1, cond.length()));
int n = Integer.parseInt(cond.substring(cond.indexOf('<') + 1, cond.length()));
if (val < n) {
addVal = true;
}
Expand Down
6 changes: 3 additions & 3 deletions base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/matchers/RGroupQuery.java
View file
Expand Up @@ -145,7 +145,7 @@ public List<IAtom> getAllRgroupQueryAtoms() {
public static boolean isValidRgroupQueryLabel(String Rxx) {
Matcher matcher = validLabelPattern.matcher(Rxx);
if (matcher.find()) {
int groupNumber = Integer.valueOf(Rxx.substring(1));
int groupNumber = Integer.parseInt(Rxx.substring(1));
if (groupNumber >= 1 && groupNumber <= 32) {
return true;
}
Expand All @@ -160,7 +160,7 @@ public boolean areSubstituentsDefined() {

for (IAtom rgp : allRgroupAtoms) {
if (RGroupQuery.isValidRgroupQueryLabel(((IPseudoAtom) rgp).getLabel())) {
int groupNum = Integer.valueOf(((IPseudoAtom) rgp).getLabel().substring(1));
int groupNum = Integer.parseInt(((IPseudoAtom) rgp).getLabel().substring(1));
if (rGroupDefinitions == null || rGroupDefinitions.get(groupNum) == null
|| rGroupDefinitions.get(groupNum).getRGroups() == null
|| rGroupDefinitions.get(groupNum).getRGroups().size() == 0) {
Expand All @@ -179,7 +179,7 @@ public boolean areRootAtomsDefined() {
if (rootAtom instanceof IPseudoAtom && rootAtom.getSymbol().startsWith("R")) {
IPseudoAtom pseudo = (IPseudoAtom) rootAtom;
if (pseudo.getLabel().length() > 1) {
int rootAtomRgrpNumber = Integer.valueOf(pseudo.getLabel().substring(1));
int rootAtomRgrpNumber = Integer.parseInt(pseudo.getLabel().substring(1));
if (rootAtomRgrpNumber == rgpNum) {
represented = true;
break rootLoop;
Expand Down
12 changes: 6 additions & 6 deletions misc/extra/src/main/java/org/openscience/cdk/io/ZMatrixReader.java
View file
Expand Up @@ -187,23 +187,23 @@ private IChemFile readChemFile(IChemFile file) {
i++;
} else if (i == 1) {
types[i] = tokenizer.nextToken();
d_atom[i] = Integer.valueOf(tokenizer.nextToken()) - 1;
d_atom[i] = Integer.parseInt(tokenizer.nextToken()) - 1;
d[i] = Double.valueOf(tokenizer.nextToken());
i++;
} else if (i == 2) {
types[i] = tokenizer.nextToken();
d_atom[i] = Integer.valueOf(tokenizer.nextToken()) - 1;
d_atom[i] = Integer.parseInt(tokenizer.nextToken()) - 1;
d[i] = Double.valueOf(tokenizer.nextToken());
a_atom[i] = Integer.valueOf(tokenizer.nextToken()) - 1;
a_atom[i] = Integer.parseInt(tokenizer.nextToken()) - 1;
a[i] = Double.valueOf(tokenizer.nextToken());
i++;
} else {
types[i] = tokenizer.nextToken();
d_atom[i] = Integer.valueOf(tokenizer.nextToken()) - 1;
d_atom[i] = Integer.parseInt(tokenizer.nextToken()) - 1;
d[i] = Double.valueOf(tokenizer.nextToken());
a_atom[i] = Integer.valueOf(tokenizer.nextToken()) - 1;
a_atom[i] = Integer.parseInt(tokenizer.nextToken()) - 1;
a[i] = Double.valueOf(tokenizer.nextToken());
da_atom[i] = Integer.valueOf(tokenizer.nextToken()) - 1;
da_atom[i] = Integer.parseInt(tokenizer.nextToken()) - 1;
da[i] = Double.valueOf(tokenizer.nextToken());
i++;
}
Expand Down
6 changes: 3 additions & 3 deletions storage/ctab/src/main/java/org/openscience/cdk/io/MDLRXNV2000Reader.java
View file
Expand Up @@ -209,11 +209,11 @@ private IReaction readReaction(IChemObjectBuilder builder) throws CDKException {
* this line contains the number of reactants and products
*/
StringTokenizer tokenizer = new StringTokenizer(countsLine);
numReactans = Integer.valueOf(tokenizer.nextToken());
numReactans = Integer.parseInt(tokenizer.nextToken());
logger.info("Expecting " + numReactans + " reactants in file");
numProducts = Integer.valueOf(tokenizer.nextToken());
numProducts = Integer.parseInt(tokenizer.nextToken());
if (tokenizer.hasMoreTokens()) {
agentCount = Integer.valueOf(tokenizer.nextToken());
agentCount = Integer.parseInt(tokenizer.nextToken());
// ChemAxon extension, technically BIOVIA now support this but
// not documented yet
if (mode == Mode.STRICT && agentCount > 0)
Expand Down
6 changes: 3 additions & 3 deletions storage/ctab/src/main/java/org/openscience/cdk/io/MDLRXNV3000Reader.java
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Expand Up @@ -187,12 +187,12 @@ private IReaction readReaction(IChemObjectBuilder builder) throws CDKException {
StringTokenizer tokenizer = new StringTokenizer(command);
try {
tokenizer.nextToken();
reactantCount = Integer.valueOf(tokenizer.nextToken());
reactantCount = Integer.parseInt(tokenizer.nextToken());
logger.info("Expecting " + reactantCount + " reactants in file");
productCount = Integer.valueOf(tokenizer.nextToken());
productCount = Integer.parseInt(tokenizer.nextToken());
logger.info("Expecting " + productCount + " products in file");
if (tokenizer.hasMoreTokens()) {
agentCount = Integer.valueOf(tokenizer.nextToken());
agentCount = Integer.parseInt(tokenizer.nextToken());
logger.info("Expecting " + agentCount + " products in file");
if (mode == Mode.STRICT && agentCount > 0)
throw new CDKException("RXN files uses agent count extension");
Expand Down
12 changes: 6 additions & 6 deletions storage/ctab/src/main/java/org/openscience/cdk/io/MDLReader.java
View file
Expand Up @@ -370,9 +370,9 @@ private IAtomContainer readMolecule(IAtomContainer molecule) throws CDKException
throw new CDKException("This file must be read with the MDLV3000Reader.");
}
}
atoms = Integer.valueOf(line.substring(0, 3).trim());
atoms = Integer.parseInt(line.substring(0, 3).trim());
logger.debug("Atomcount: " + atoms);
bonds = Integer.valueOf(line.substring(3, 6).trim());
bonds = Integer.parseInt(line.substring(3, 6).trim());
logger.debug("Bondcount: " + bonds);

// read ATOM block
Expand Down Expand Up @@ -532,11 +532,11 @@ private IAtomContainer readMolecule(IAtomContainer molecule) throws CDKException
for (int f = 0; f < bonds; f++) {
line = input.readLine();
linecount++;
atom1 = Integer.valueOf(line.substring(0, 3).trim());
atom2 = Integer.valueOf(line.substring(3, 6).trim());
order = Integer.valueOf(line.substring(6, 9).trim());
atom1 = Integer.parseInt(line.substring(0, 3).trim());
atom2 = Integer.parseInt(line.substring(3, 6).trim());
order = Integer.parseInt(line.substring(6, 9).trim());
if (line.length() > 12) {
int mdlStereo = Integer.valueOf(line.substring(9, 12).trim());
int mdlStereo = Integer.parseInt(line.substring(9, 12).trim());
if (mdlStereo == 1) {
// MDL up bond
stereo = IBond.Stereo.UP;
Expand Down
2 changes: 1 addition & 1 deletion storage/ctab/src/main/java/org/openscience/cdk/io/MDLV2000Reader.java
View file
Expand Up @@ -2212,7 +2212,7 @@ private void readPropertiesSlow(BufferedReader input, IAtomContainer container,
//Process the R group numbers as defined in RGP line.
while (st.hasMoreTokens()) {
Integer position = Integer.valueOf(st.nextToken());
int rNumber = Integer.valueOf(st.nextToken());
int rNumber = Integer.parseInt(st.nextToken());
// the container may have already had atoms before the new atoms were read
int index = container.getAtomCount() - nAtoms + position - 1;
IPseudoAtom pseudoAtom = (IPseudoAtom) container.getAtom(index);
Expand Down
2 changes: 1 addition & 1 deletion storage/ctab/src/main/java/org/openscience/cdk/io/MDLV3000Reader.java
View file
Expand Up @@ -503,7 +503,7 @@ public void readAtomBlock(ReadState state) throws CDKException {
rGroup = element.split("^R");
if (rGroup.length > 1) {
try {
Rnumber = Integer.valueOf(rGroup[(rGroup.length - 1)]);
Rnumber = Integer.parseInt(rGroup[(rGroup.length - 1)]);
RGroupCounter = Rnumber;
} catch (Exception ex) {
Rnumber = RGroupCounter;
Expand Down
18 changes: 9 additions & 9 deletions storage/ctab/src/main/java/org/openscience/cdk/io/RGroupQueryReader.java
View file
Expand Up @@ -230,9 +230,9 @@ private RGroupQuery parseRGFile(RGroupQuery rGroupQuery) throws CDKException {
RGroupLogic log;

log = new RGroupLogic();
int rgroupNumber = Integer.valueOf(strTk.nextToken());
int rgroupNumber = Integer.parseInt(strTk.nextToken());
String tok = strTk.nextToken();
log.rgoupNumberRequired = tok.equals("0") ? 0 : Integer.valueOf(tok);
log.rgoupNumberRequired = tok.equals("0") ? 0 : Integer.parseInt(tok);
log.restH = strTk.nextToken().equals("1") ? true : false;
tok = "";
while (strTk.hasMoreTokens()) {
Expand Down Expand Up @@ -260,15 +260,15 @@ private RGroupQuery parseRGFile(RGroupQuery rGroupQuery) throws CDKException {
StringTokenizer stAAL = new StringTokenizer(line);
stAAL.nextToken();
stAAL.nextToken();
int pos = Integer.valueOf(stAAL.nextToken());
int pos = Integer.parseInt(stAAL.nextToken());
IAtom rGroup = root.getAtom(pos - 1);
stAAL.nextToken();
Map<Integer, IBond> bondMap = new HashMap<>();
while (stAAL.hasMoreTokens()) {
pos = Integer.valueOf(stAAL.nextToken());
pos = Integer.parseInt(stAAL.nextToken());
IAtom partner = root.getAtom(pos - 1);
IBond bond = root.getBond(rGroup, partner);
int order = Integer.valueOf(stAAL.nextToken());
int order = Integer.parseInt(stAAL.nextToken());
bondMap.put(order, bond);
logger.info("AAL " + order + " " + ((IPseudoAtom) rGroup).getLabel() + "-"
+ partner.getSymbol());
Expand Down Expand Up @@ -319,7 +319,7 @@ private RGroupQuery parseRGFile(RGroupQuery rGroupQuery) throws CDKException {
if (atom instanceof IPseudoAtom) {
IPseudoAtom rGroup = (IPseudoAtom) atom;
if (RGroupQuery.isValidRgroupQueryLabel(rGroup.getLabel())) {
int rgroupNum = Integer.valueOf(rGroup.getLabel().substring(1));
int rgroupNum = Integer.parseInt(rGroup.getLabel().substring(1));
RGroupList rgroupList = new RGroupList(rgroupNum);
if (!rGroupDefinitions.containsKey(rgroupNum)) {
logger.info("Define Rgroup R" + rgroupNum);
Expand Down Expand Up @@ -350,7 +350,7 @@ private RGroupQuery parseRGFile(RGroupQuery rGroupQuery) throws CDKException {
line = input.readLine();
++lineCount;
logger.info("line for num is " + line);
int rgroupNum = Integer.valueOf(line.trim());
int rgroupNum = Integer.parseInt(line.trim());
line = input.readLine();
++lineCount;

Expand Down Expand Up @@ -381,8 +381,8 @@ private RGroupQuery parseRGFile(RGroupQuery rGroupQuery) throws CDKException {
stAPO.nextToken();
stAPO.nextToken();
while (stAPO.hasMoreTokens()) {
int pos = Integer.valueOf(stAPO.nextToken());
int apo = Integer.valueOf(stAPO.nextToken());
int pos = Integer.parseInt(stAPO.nextToken());
int apo = Integer.parseInt(stAPO.nextToken());
IAtom at = group.getAtom(pos - 1);
switch (apo) {
case 1:
Expand Down
2 changes: 1 addition & 1 deletion storage/inchi/src/main/java/org/openscience/cdk/graph/invariant/InChINumbersTools.java
View file
Expand Up @@ -64,7 +64,7 @@ public static void parseAuxInfo(String aux, long[] numbers) {
String numberStringAux = aux.substring(0, aux.indexOf('/'));
int i = 1;
for (String numberString : numberStringAux.split("[,;]"))
numbers[Integer.valueOf(numberString) - 1] = i++;
numbers[Integer.parseInt(numberString) - 1] = i++;
}

/**
Expand Down
8 changes: 4 additions & 4 deletions ...mula/src/main/java/org/openscience/cdk/tools/manipulator/MolecularFormulaManipulator.java
View file
Expand Up @@ -1367,12 +1367,12 @@ public static String simplifyMolecularFormula(String formula) {
if (f == thisFormula.length() - 1
|| (thisFormula.charAt(f + 1) >= 'A' && thisFormula.charAt(f + 1) <= 'Z')) {
int posit = eleSymb.indexOf(recentElementSymbol);
int count = Integer.valueOf(recentElementCountString);
int count = Integer.parseInt(recentElementCountString);
if (posit == -1) {
eleSymb.add(recentElementSymbol);
eleCount.add(count);
} else {
int countP = Integer.valueOf(recentElementCountString);
int countP = Integer.parseInt(recentElementCountString);
if (countP == 0) countP = 1;
int countA = eleCount.get(posit);
if (countA == 0) countA = 1;
Expand Down Expand Up @@ -1434,7 +1434,7 @@ private static String breakExtractor(String formula) {
multipliedformula += thisChar;
}
}
finalformula += muliplier(multipliedformula, multiple.isEmpty() ? 1:Integer.valueOf(multiple)) + formulaEnd;
finalformula += muliplier(multipliedformula, multiple.isEmpty() ? 1:Integer.parseInt(multiple)) + formulaEnd;

if (finalformula.contains("("))
return breakExtractor(finalformula);
Expand Down Expand Up @@ -1467,7 +1467,7 @@ private static String multipleExtractor(String formula) {
recentCompound += thisChar;
}
}
return muliplier(recentCompound, Integer.valueOf(recentCompoundCount));
return muliplier(recentCompound, Integer.parseInt(recentCompoundCount));
}

/**
Expand Down
8 changes: 4 additions & 4 deletions tool/model/src/main/java/org/openscience/cdk/fingerprint/model/Bayesian.java
View file
Expand Up @@ -564,7 +564,7 @@ public static Bayesian deserialise(BufferedReader rdr) throws IOException {
.equals("FCFP6") ? CircularFingerprinter.CLASS_FCFP6 : 0;
if (classType == 0) throw new IOException("Unknown fingerprint type: " + bits[0]);

int folding = Integer.valueOf(bits[1]);
int folding = Integer.parseInt(bits[1]);
if (folding > 0) for (int f = folding; f > 0; f = f >> 1)
if ((f & 1) == 1 && f != 1) {
folding = -1;
Expand All @@ -586,18 +586,18 @@ public static Bayesian deserialise(BufferedReader rdr) throws IOException {

Matcher m = PTN_HASHLINE.matcher(line);
if (m.find()) {
int hash = Integer.valueOf(m.group(1));
int hash = Integer.parseInt(m.group(1));
double c = Double.valueOf(m.group(2));
model.contribs.put(hash, c);
} else if (line.startsWith("training:size=")) {
try {
model.trainingSize = Integer.valueOf(line.substring(14));
model.trainingSize = Integer.parseInt(line.substring(14));
} catch (NumberFormatException ex) {
throw new IOException("Invalid training info line: " + line);
}
} else if (line.startsWith("training:actives=")) {
try {
model.trainingActives = Integer.valueOf(line.substring(17));
model.trainingActives = Integer.parseInt(line.substring(17));
} catch (NumberFormatException ex) {
throw new IOException("Invalid training info line: " + line);
}
Expand Down
2 changes: 1 addition & 1 deletion tool/model/src/test/java/org/openscience/cdk/fingerprint/model/BayesianTest.java
View file
Expand Up @@ -392,7 +392,7 @@ private void runTest(String sdfile, String actvField, int classType, int folding
row++;

String stractv = (String) mol.getProperties().get(actvField);
int active = stractv.equals("true") ? 1 : stractv.equals("false") ? 0 : Integer.valueOf(stractv);
int active = stractv.equals("true") ? 1 : stractv.equals("false") ? 0 : Integer.parseInt(stractv);
if (active != 0 && active != 1) throw new CDKException("Activity field not found or invalid");

model.addMolecule(mol, active == 1);
Expand Down

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