--- src/javajs/util/JSJSONParser.java.orig 2023-10-01 13:39:25.000000000 -0600
+++ src/javajs/util/JSJSONParser.java 2023-10-23 10:37:22.675088352 -0600
@@ -167,7 +167,7 @@ public class JSJSONParser {
try {
if (string.indexOf('.') < 0 && string.indexOf('e') < 0
&& string.indexOf('E') < 0)
- return new Integer(string);
+ return Integer.valueOf(string);
// not allowing infinity or NaN
// using float here because Jmol does not use Double
Float d = Float.valueOf(string);
--- src/jme/JMEmol.java.orig 2023-10-01 13:39:25.000000000 -0600
+++ src/jme/JMEmol.java 2023-10-23 10:46:02.331981547 -0600
@@ -3721,7 +3721,7 @@ public class JMEmol {
smilesAddBond(con1[j], con2[j], smiles, slashBond, queryMode);
if (j > 9)
smiles.append("%");
- smiles.append(new Integer(j).toString());
+ smiles.append(Integer.valueOf(j).toString());
}
}
@@ -4943,14 +4943,14 @@ public class JMEmol {
if (atag[i] == null || atag[i].length() == 0)
continue;
if (atag[i].equals("abs"))
- abs.add(new Integer(i));
+ abs.add(Integer.valueOf(i));
else if (atag[i].startsWith("mix")) {
int n = Integer.parseInt(atag[i].substring(3));
ArrayList<Integer> o = null;
if (mixlists.size() > n)
o = mixlists.get(n);
ArrayList<Integer> l = (o == null ? new ArrayList<Integer>() : o);
- l.add(new Integer(i));
+ l.add(Integer.valueOf(i));
mixlists.set(n, l);
} else if (atag[i].startsWith("or")) {
int n = Integer.parseInt(atag[i].substring(2));
@@ -4958,7 +4958,7 @@ public class JMEmol {
if (orlists.size() > n)
o = orlists.get(n);
ArrayList<Integer> l = (o == null ? new ArrayList<Integer>() : o);
- l.add(new Integer(i));
+ l.add(Integer.valueOf(i));
orlists.set(n, l);
}
}
@@ -5001,7 +5001,7 @@ public class JMEmol {
// ----------------------------------------------------------------------------
static String iformat(int number, int len) {
- Integer n = new Integer(number);
+ Integer n = Integer.valueOf(number);
String s = n.toString();
if (s.length() > len)
s = "?";
@@ -5021,7 +5021,7 @@ public class JMEmol {
number = 0.; // 2012 fix 1.0E-4
number = (int) Math.round(number * Math.pow(10., dec))
/ (Math.pow(10., dec));
- String s = new Double(number).toString(); // this sometimes return 1.0E-4
+ String s = Double.valueOf(number).toString(); // this sometimes return 1.0E-4
int dotpos = s.indexOf('.');
if (dotpos < 0) {
s += ".";
--- src/jme/JMEUtil.java.orig 2023-10-01 13:39:25.000000000 -0600
+++ src/jme/JMEUtil.java 2023-10-23 10:46:19.107751456 -0600
@@ -585,7 +585,7 @@ public abstract class JMEUtil {
number = 0.; // 2012 fix 1.0E-4
double m = Math.pow(10, dec);
number = (int) Math.round(number * m) / m;
- String s = new Double(number).toString(); // this sometimes return 1.0E-4
+ String s = Double.valueOf(number).toString(); // this sometimes return 1.0E-4
int dotpos = s.indexOf('.');
if (dotpos < 0) {
s += ".";
--- src/jspecview/common/PanelData.java.orig 2023-10-01 13:39:26.000000000 -0600
+++ src/jspecview/common/PanelData.java 2023-10-23 10:37:22.676088338 -0600
@@ -1314,7 +1314,7 @@ public class PanelData implements EventM
if (useFileName)
title = JSVFileManager.getTagName(spectrum.getFilePath()) + " - " + title;
GenericColor plotColor = getCurrentPlotColor(index);
- cols[0] = new Integer(index + 1);
+ cols[0] = Integer.valueOf(index + 1);
cols[1] = plotColor;
cols[2] = " " + title;
data[index] = cols;
--- src/jspecview/export/FormContext.java.orig 2023-10-01 13:39:26.000000000 -0600
+++ src/jspecview/export/FormContext.java 2023-10-23 10:37:22.676088338 -0600
@@ -110,10 +110,10 @@ class FormContext {
commandLevel++;
if (token.indexOf("#if") == firstChar) {
cmdType = VT_IF;
- cmds.add(0, new Integer(ptr));
+ cmds.add(0, Integer.valueOf(ptr));
} else if (token.indexOf("#foreach") == firstChar) {
cmdType = VT_FOREACH;
- cmds.add(0, new Integer(ptr));
+ cmds.add(0, Integer.valueOf(ptr));
cmdPtr = ptr;
if (token.indexOf("#end") > 0) {
int pt = token.indexOf(")") + 1;
@@ -133,7 +133,7 @@ class FormContext {
FormToken vt = formTokens.get(cmdPtr);
checkIf = true;
vt.endPtr = ptr;
- cmds.add(0, new Integer(ptr));
+ cmds.add(0, Integer.valueOf(ptr));
} else if (token.indexOf("#else") == firstChar) {
if (cmds.size() == 0) {
strError = "misplaced #else";
@@ -143,7 +143,7 @@ class FormContext {
checkIf = true;
cmdPtr = cmds.removeItemAt(0).intValue();
formTokens.get(cmdPtr).endPtr = ptr;
- cmds.add(0, new Integer(ptr));
+ cmds.add(0, Integer.valueOf(ptr));
} else {
Logger.warn("??? " + token);
}
@@ -251,9 +251,9 @@ class FormContext {
Object varData = vt.vc.get(vt.pointCount);
if (varData instanceof Coordinate) {
Coordinate c = (Coordinate) varData;
- context.put("pointCount", new Integer(vt.pointCount));
- context.put(vt.var + ".xVal", new Double(c.getXVal()));
- context.put(vt.var + ".yVal", new Double(c.getYVal()));
+ context.put("pointCount", Integer.valueOf(vt.pointCount));
+ context.put(vt.var + ".xVal", Double.valueOf(c.getXVal()));
+ context.put(vt.var + ".yVal", Double.valueOf(c.getYVal()));
context.put(vt.var + ".getXString()", getXString(c));
context.put(vt.var + ".getYString()", getYString(c));
} else if (varData instanceof Map<?, ?>) {
--- src/jspecview/export/SVGExporter.java.orig 2023-10-01 13:39:26.000000000 -0600
+++ src/jspecview/export/SVGExporter.java 2023-10-23 10:37:22.676088338 -0600
@@ -126,7 +126,7 @@ public class SVGExporter extends FormExp
int topPlotArea = topInset;
int bottomPlotArea = topInset + plotAreaHeight;
int titlePosition = bottomPlotArea + 60;
- context.put("titlePosition", new Integer(titlePosition));
+ context.put("titlePosition", Integer.valueOf(titlePosition));
double xPt, yPt;
String xStr, yStr;
@@ -239,25 +239,25 @@ public class SVGExporter extends FormExp
context.put("scaleColor", toRGBHexString(scaleColor));
context.put("unitsColor", toRGBHexString(unitsColor));
- context.put("svgHeight", new Integer(svgHeight));
- context.put("svgWidth", new Integer(svgWidth));
- context.put("leftPlotArea", new Integer(leftPlotArea));
- context.put("rightPlotArea", new Integer(rightPlotArea));
- context.put("topPlotArea", new Integer(topPlotArea));
- context.put("bottomPlotArea", new Integer(bottomPlotArea));
- context.put("plotAreaHeight", new Integer(plotAreaHeight));
- context.put("plotAreaWidth", new Integer(plotAreaWidth));
+ context.put("svgHeight", Integer.valueOf(svgHeight));
+ context.put("svgWidth", Integer.valueOf(svgWidth));
+ context.put("leftPlotArea", Integer.valueOf(leftPlotArea));
+ context.put("rightPlotArea", Integer.valueOf(rightPlotArea));
+ context.put("topPlotArea", Integer.valueOf(topPlotArea));
+ context.put("bottomPlotArea", Integer.valueOf(bottomPlotArea));
+ context.put("plotAreaHeight", Integer.valueOf(plotAreaHeight));
+ context.put("plotAreaWidth", Integer.valueOf(plotAreaWidth));
- context.put("minXOnScale", new Double(minXOnScale));
- context.put("maxXOnScale", new Double(maxXOnScale));
- context.put("minYOnScale", new Double(minYOnScale));
- context.put("maxYOnScale", new Double(maxYOnScale));
- context.put("yTickA", new Double(yTickA));
- context.put("yTickB", new Double(yTickB));
- context.put("xScaleFactor", new Double(xScaleFactor));
- context.put("yScaleFactor", new Double(yScaleFactor));
+ context.put("minXOnScale", Double.valueOf(minXOnScale));
+ context.put("maxXOnScale", Double.valueOf(maxXOnScale));
+ context.put("minYOnScale", Double.valueOf(minYOnScale));
+ context.put("maxYOnScale", Double.valueOf(maxYOnScale));
+ context.put("yTickA", Double.valueOf(yTickA));
+ context.put("yTickB", Double.valueOf(yTickB));
+ context.put("xScaleFactor", Double.valueOf(xScaleFactor));
+ context.put("yScaleFactor", Double.valueOf(yScaleFactor));
- context.put("increasing", new Boolean(increasing));
+ context.put("increasing", Boolean.valueOf(increasing));
context.put("verticalGridCoords", vertGridCoords);
context.put("horizontalGridCoords", horizGridCoords);
@@ -274,13 +274,13 @@ public class SVGExporter extends FormExp
System.out.println("SVG " + spec.isXIncreasing() + " " + spec.shouldDisplayXAxisIncreasing() + " " + firstX + " "+ lastX + " " + startIndex + " " + endIndex + " " + newXYCoords.get(0).toString() + " " + increasing);
context.put("title", spec.getTitle());
context.put("xyCoords", newXYCoords);
- context.put("continuous", new Boolean(spec.isContinuous()));
- context.put("firstTranslateX", new Double(firstTranslateX));
- context.put("firstTranslateY", new Double(firstTranslateY));
- context.put("scaleX", new Double(scaleX));
- context.put("scaleY", new Double(scaleY));
- context.put("secondTranslateX", new Double(secondTranslateX));
- context.put("secondTranslateY", new Double(secondTranslateY));
+ context.put("continuous", Boolean.valueOf(spec.isContinuous()));
+ context.put("firstTranslateX", Double.valueOf(firstTranslateX));
+ context.put("firstTranslateY", Double.valueOf(firstTranslateY));
+ context.put("scaleX", Double.valueOf(scaleX));
+ context.put("scaleY", Double.valueOf(scaleY));
+ context.put("secondTranslateX", Double.valueOf(secondTranslateX));
+ context.put("secondTranslateY", Double.valueOf(secondTranslateY));
context.put("plotStrokeWidth", getPlotStrokeWidth(scaleX, scaleY));
if (increasing) {
@@ -310,9 +310,9 @@ public class SVGExporter extends FormExp
context.put("yUnitLabelX", "" + yUnitLabelX);
context.put("yUnitLabelY", "" + yUnitLabelY);
- context.put("numDecimalPlacesX", new Integer(Math
+ context.put("numDecimalPlacesX", Integer.valueOf(Math
.abs(scaleData.exportPrecision[0])));
- context.put("numDecimalPlacesY", new Integer(Math
+ context.put("numDecimalPlacesY", Integer.valueOf(Math
.abs(scaleData.exportPrecision[1])));
String vm = (mode == ExportType.SVGI ? "plot_ink.vm" : "plot.vm");
--- src/jspecview/export/XMLExporter.java.orig 2023-10-01 13:39:26.000000000 -0600
+++ src/jspecview/export/XMLExporter.java 2023-10-23 10:37:22.677088325 -0600
@@ -255,8 +255,8 @@ abstract class XMLExporter extends FormE
context.put("title", title);
context.put("ident", ident);
context.put("state", state);
- context.put("firstX", new Double(firstX));
- context.put("lastX", new Double(lastX));
+ context.put("firstX", Double.valueOf(firstX));
+ context.put("lastX", Double.valueOf(lastX));
context.put("xyCoords", newXYCoords);
context.put("xdata_type", "Float32");
context.put("ydata_type", "Float32");
@@ -268,7 +268,7 @@ abstract class XMLExporter extends FormE
context.put("xUnitLabel", xUnitLabel);
context.put("yUnitLabel", yUnitLabel);
context.put("specinits", spectypeInitials);
- context.put("deltaX", new Double(deltaX));
+ context.put("deltaX", Double.valueOf(deltaX));
context.put("owner", owner);
context.put("origin", origin);
context.put("timestamp", longdate);
@@ -281,7 +281,7 @@ abstract class XMLExporter extends FormE
context.put("CASn", casName);
context.put("mp", mp);
context.put("bp", bp);
- context.put("ObFreq", new Double(obFreq));
+ context.put("ObFreq", Double.valueOf(obFreq));
context.put("ObNucleus", obNucleus);
context.put("SolvName", solvName);
context.put("SolvRef", solvRef);
--- src/jspecview/java/AwtFile.java.orig 2023-10-01 13:39:26.000000000 -0600
+++ src/jspecview/java/AwtFile.java 2023-10-23 10:37:22.677088325 -0600
@@ -7,7 +7,6 @@ import java.io.IOException;
import java.io.OutputStreamWriter;
import java.net.URL;
import java.net.URLConnection;
-import java.security.AccessControlException;
import org.jmol.api.GenericFileInterface;
@@ -33,7 +32,7 @@ class AwtFile extends File implements Ge
try {
File file = getParentFile();
f = new AwtFile(file.getAbsolutePath());
- } catch (AccessControlException e) {
+ } catch (SecurityException e) {
//
}
return f;
--- src/org/jmol/awt/AwtFile.java.orig 2023-10-01 13:39:26.000000000 -0600
+++ src/org/jmol/awt/AwtFile.java 2023-10-23 10:37:22.677088325 -0600
@@ -7,7 +7,6 @@ import java.io.IOException;
import java.io.OutputStreamWriter;
import java.net.URL;
import java.net.URLConnection;
-import java.security.AccessControlException;
import org.jmol.api.GenericFileInterface;
import org.jmol.viewer.Viewer;
@@ -34,7 +33,7 @@ class AwtFile extends File implements Ge
try {
File file = getParentFile();
f = new AwtFile(file.getAbsolutePath());
- } catch (AccessControlException e) {
+ } catch (SecurityException e) {
//
}
return f;
--- src/org/jmol/quantum/NMRCalculation.java.orig 2023-10-23 09:53:38.494843230 -0600
+++ src/org/jmol/quantum/NMRCalculation.java 2023-10-23 10:37:22.677088325 -0600
@@ -539,15 +539,15 @@ public class NMRCalculation implements J
// Values taken from www.spectroscopynow.com/Spy/tools/proton-proton.html website. Need to find original source
// 2.20 is eneg of H
double enegH = 2.20;
- deltaElectro.put("C", new Double(2.60 - enegH));
- deltaElectro.put("O", new Double(3.50 - enegH));
- deltaElectro.put("N", new Double(3.05 - enegH));
- deltaElectro.put("F", new Double(3.90 - enegH));
- deltaElectro.put("Cl", new Double(3.15 - enegH));
- deltaElectro.put("Br", new Double(2.95 - enegH));
- deltaElectro.put("I", new Double(2.65 - enegH));
- deltaElectro.put("S", new Double(2.58 - enegH));// Pauling
- deltaElectro.put("Si", new Double(1.90 - enegH));// Pauling
+ deltaElectro.put("C", Double.valueOf(2.60 - enegH));
+ deltaElectro.put("O", Double.valueOf(3.50 - enegH));
+ deltaElectro.put("N", Double.valueOf(3.05 - enegH));
+ deltaElectro.put("F", Double.valueOf(3.90 - enegH));
+ deltaElectro.put("Cl", Double.valueOf(3.15 - enegH));
+ deltaElectro.put("Br", Double.valueOf(2.95 - enegH));
+ deltaElectro.put("I", Double.valueOf(2.65 - enegH));
+ deltaElectro.put("S", Double.valueOf(2.58 - enegH));// Pauling
+ deltaElectro.put("Si", Double.valueOf(1.90 - enegH));// Pauling
}
static double[][] pAltona = new double[5][8];
--- src/org/openscience/jmol/app/janocchio/LoadMeasureThread.java.orig 2023-10-01 13:39:27.000000000 -0600
+++ src/org/openscience/jmol/app/janocchio/LoadMeasureThread.java 2023-10-23 10:37:30.458982298 -0600
@@ -89,10 +89,10 @@ public class LoadMeasureThread extends T
if (line.trim().length() == 0)
break;
String[] l = line.split("\\s+");
- int ia = (new Integer(l[0])).intValue();
- int ib = (new Integer(l[1])).intValue();
- int ic = (new Integer(l[2])).intValue();
- int id = (new Integer(l[3])).intValue();
+ int ia = (Integer.valueOf(l[0])).intValue();
+ int ib = (Integer.valueOf(l[1])).intValue();
+ int ic = (Integer.valueOf(l[2])).intValue();
+ int id = (Integer.valueOf(l[3])).intValue();
addCouple(ia, ib, ic, id, l[4]);
}
}
@@ -117,8 +117,8 @@ public class LoadMeasureThread extends T
// ia ib one-word-label
while ((line = inp.readLine()).trim().length() != 0) {
String[] l = line.split("\\s+");
- int ia = (new Integer(l[0])).intValue();
- int ib = (new Integer(l[1])).intValue();
+ int ia = (Integer.valueOf(l[0])).intValue();
+ int ib = (Integer.valueOf(l[1])).intValue();
addNOE(ia, ib, l[2], null);
}
}
@@ -141,7 +141,7 @@ public class LoadMeasureThread extends T
String line;
while ((line = inp.readLine()).trim().length() != 0) {
String[] l = line.split("\\s+");
- int i = (new Integer(l[0])).intValue();
+ int i = (Integer.valueOf(l[0])).intValue();
command += ";" + nmrPanel.labelSetter.setLabel(i - 1, l[1]);
}
return true;
--- src/org/openscience/jmol/app/janocchio/LoadMeasureThreadJSON.java.orig 2023-10-01 13:39:27.000000000 -0600
+++ src/org/openscience/jmol/app/janocchio/LoadMeasureThreadJSON.java 2023-10-23 10:37:30.458982298 -0600
@@ -264,8 +264,8 @@ public class LoadMeasureThreadJSON exten
if (noe.containsKey("expd")) {
String exp = (String) noe.get("expd");
if (exp != null) {
- int j = (new Integer(a)).intValue() - 1;
- int k = (new Integer(b)).intValue() - 1;
+ int j = (Integer.valueOf(a)).intValue() - 1;
+ int k = (Integer.valueOf(b)).intValue() - 1;
props.addJmolDistance(j + base, k + base);
}
}
@@ -280,10 +280,10 @@ public class LoadMeasureThreadJSON exten
if (couple.containsKey("exp")) {
String exp = (String) couple.get("exp");
if (exp != null) {
- int j = (new Integer(a)).intValue() - 1;
- int k = (new Integer(b)).intValue() - 1;
- int l = (new Integer(c)).intValue() - 1;
- int m = (new Integer(d)).intValue() - 1;
+ int j = (Integer.valueOf(a)).intValue() - 1;
+ int k = (Integer.valueOf(b)).intValue() - 1;
+ int l = (Integer.valueOf(c)).intValue() - 1;
+ int m = (Integer.valueOf(d)).intValue() - 1;
props.addJmolCouple(j + base, k + base, l + base, m + base);
}
}
@@ -291,11 +291,11 @@ public class LoadMeasureThreadJSON exten
// NAMFIS has problems on some systems if there are zero noes or couplings
// Always add dummy variable
Vector<Double> vec = props.getDistances();
- vec.add(new Double(1.0));
+ vec.add(Double.valueOf(1.0));
writeVector(vec, out1);
vec = props.getCouples();
- vec.add(new Double(1.0));
+ vec.add(Double.valueOf(1.0));
writeVector(vec, out1);
}
@@ -523,8 +523,8 @@ public class LoadMeasureThreadJSON exten
int[] noeNPrefIndices = noeTable.getnoeNPrefIndices();
Map<String, Object> refNOE = new Hashtable<String, Object>();
- refNOE.put("a", new Integer(noeNPrefIndices[0]));
- refNOE.put("b", new Integer(noeNPrefIndices[1]));
+ refNOE.put("a", Integer.valueOf(noeNPrefIndices[0]));
+ refNOE.put("b", Integer.valueOf(noeNPrefIndices[1]));
data.put("RefNOE", refNOE);
double noeExprefValue = noeTable.getNoeExprefValue();
@@ -594,8 +594,8 @@ public class LoadMeasureThreadJSON exten
if (noe.containsKey("expd")) {
String exp = (String) noe.get("expd");
if (exp != null) {
- int j = (new Integer(a)).intValue() - 1;
- int k = (new Integer(b)).intValue() - 1;
+ int j = (Integer.valueOf(a)).intValue() - 1;
+ int k = (Integer.valueOf(b)).intValue() - 1;
double cDist = props.getJmolDistance(j + base, k + base);
MeasureDist measure = new MeasureDist(exp, cDist);
diffDist += measure.getDiff();
@@ -604,8 +604,8 @@ public class LoadMeasureThreadJSON exten
if (noe.containsKey("exp")) {
String exp = (String) noe.get("exp");
if (exp != null) {
- int j = (new Integer(a)).intValue() - 1;
- int k = (new Integer(b)).intValue() - 1;
+ int j = (Integer.valueOf(a)).intValue() - 1;
+ int k = (Integer.valueOf(b)).intValue() - 1;
double cNoe = props.getJmolNoe(j + base, k + base);
MeasureNoe measure = new MeasureNoe(exp, cNoe);
diffNoe += measure.getDiff();
@@ -622,10 +622,10 @@ public class LoadMeasureThreadJSON exten
if (couple.containsKey("exp")) {
String exp = (String) couple.get("exp");
if (exp != null) {
- int j = (new Integer(a)).intValue() - 1;
- int k = (new Integer(b)).intValue() - 1;
- int l = (new Integer(c)).intValue() - 1;
- int m = (new Integer(d)).intValue() - 1;
+ int j = (Integer.valueOf(a)).intValue() - 1;
+ int k = (Integer.valueOf(b)).intValue() - 1;
+ int l = (Integer.valueOf(c)).intValue() - 1;
+ int m = (Integer.valueOf(d)).intValue() - 1;
double[] cCouple = props.calcJmolCouple(j + base, k + base, l + base, m + base);
MeasureCouple measure = new MeasureCouple(exp, cCouple[1]);
diffCouple += measure.getDiff();
--- src/org/openscience/jmol/app/janocchio/NMR_JmolPanel.java.orig 2023-10-01 13:39:27.000000000 -0600
+++ src/org/openscience/jmol/app/janocchio/NMR_JmolPanel.java 2023-10-23 10:37:30.458982298 -0600
@@ -754,8 +754,8 @@ public class NMR_JmolPanel extends JmolP
while ((line = inp.readLine()).trim().length() != 0) {
String[] l = line.split("[()=\\s]+");
- int i = (new Integer(l[1])).intValue();
- double p = (new Double(l[2])).doubleValue();
+ int i = (Integer.valueOf(l[1])).intValue();
+ double p = (Double.valueOf(l[2])).doubleValue();
population[i] = p;
}
--- src/org/openscience/jmol/app/janocchio/NmrMolecule.java.orig 2023-10-01 13:39:27.000000000 -0600
+++ src/org/openscience/jmol/app/janocchio/NmrMolecule.java 2023-10-23 10:37:30.459982284 -0600
@@ -114,7 +114,7 @@ public class NmrMolecule {
double jvalue = dihe.getJvalue();
if (Double.isNaN(jvalue))
return;
- couples.add(new Double(jvalue));
+ couples.add(Double.valueOf(jvalue));
couplesWhole.add(dihe);
}
@@ -197,7 +197,7 @@ public class NmrMolecule {
*/
public void addJmolDistance(int a, int b) {
- distances.add(new Double(noeMatrix.getJmolDistance(a, b)));
+ distances.add(Double.valueOf(noeMatrix.getJmolDistance(a, b)));
}
--- src/org/openscience/jmol/app/janocchio/NmrReaderThread.java.orig 2023-10-01 13:39:27.000000000 -0600
+++ src/org/openscience/jmol/app/janocchio/NmrReaderThread.java 2023-10-23 10:37:30.459982284 -0600
@@ -88,7 +88,7 @@ class NmrReaderThread extends Thread {
//labels
while ((line = inp.readLine()).trim().length() != 0) {
String[] l = line.split("\\s+");
- int i = (new Integer(l[0])).intValue();
+ int i = (Integer.valueOf(l[0])).intValue();
String com = nmr.labelSetter.setLabel(i - 1, l[1]);
command = command + ";" + com;
}
@@ -102,8 +102,8 @@ class NmrReaderThread extends Thread {
command = command + ";measure " + l[0] + " " + l[1];
if (l[2] != null) {
if (!l[2].equals("null")) {
- int i = (new Integer(l[0])).intValue();
- int j = (new Integer(l[1])).intValue();
+ int i = (Integer.valueOf(l[0])).intValue();
+ int j = (Integer.valueOf(l[1])).intValue();
nmr.noeTable.setExpNoe(l[2], i - 1, j - 1);
}
}
@@ -118,8 +118,8 @@ class NmrReaderThread extends Thread {
+ l[3];
if (l[4] != null) {
if (!l[4].equals("null")) {
- int i = (new Integer(l[0])).intValue();
- int j = (new Integer(l[3])).intValue();
+ int i = (Integer.valueOf(l[0])).intValue();
+ int j = (Integer.valueOf(l[3])).intValue();
nmr.coupleTable.setExpCouple(l[4], i - 1, j - 1);
}
}
--- src/org/openscience/jmol/app/JmolApp.java.orig 2023-10-01 13:39:27.000000000 -0600
+++ src/org/openscience/jmol/app/JmolApp.java 2023-10-23 10:37:30.459982284 -0600
@@ -97,12 +97,6 @@ public class JmolApp implements JmolAppA
*/
public JmolApp(String[] args) {
- if (System.getProperty("javawebstart.version") != null) {
-
- // If the property is found, Jmol is running with Java Web Start. To fix
- // bug 4621090, the security manager is set to null.
- System.setSecurityManager(null);
- }
if (System.getProperty("user.home") == null) {
System.err.println(GT
.$("Error starting Jmol: the property 'user.home' is not defined."));