MATH-1569: Manual array copy. (#219)

commons-math-legacy-core/src/main/java/org/apache/commons/math4/legacy/core/dfp/Dfp.java

@@ -663,8 +663,8 @@ public class Dfp implements RealFieldElement<Dfp> {
     /** Shift the mantissa left, and adjust the exponent to compensate.
      */
     protected void shiftLeft() {
-        for (int i = mant.length - 1; i > 0; i--) {
+        if (mant.length - 1 > 0) {
-            mant[i] = mant[i - 1];
+            System.arraycopy(mant, 0, mant, 1, mant.length - 1);
         }
         mant[0] = 0;
         exp--;
@@ -675,8 +675,8 @@ public class Dfp implements RealFieldElement<Dfp> {
     /** Shift the mantissa right, and adjust the exponent to compensate.
      */
     protected void shiftRight() {
-        for (int i = 0; i < mant.length - 1; i++) {
+        if (mant.length - 1 > 0) {
-            mant[i] = mant[i + 1];
+            System.arraycopy(mant, 1, mant, 0, mant.length - 1);
         }
         mant[mant.length - 1] = 0;
         exp++;
@@ -1849,9 +1849,7 @@ public class Dfp implements RealFieldElement<Dfp> {
 
             /* move the remainder into the dividend while left shifting */
             dividend[0] = 0;
-            for (int i = 0; i < mant.length; i++) {
+            System.arraycopy(remainder, 0, dividend, 1, mant.length);
-                dividend[i + 1] = remainder[i];
-            }
         }
 
         /* Find the most sig digit */

commons-math-legacy/src/main/java/org/apache/commons/math4/legacy/analysis/solvers/LaguerreSolver.java

@@ -273,10 +273,7 @@ public class LaguerreSolver extends AbstractPolynomialSolver {
                 throw new NoDataException(LocalizedFormats.POLYNOMIAL);
             }
             // Coefficients for deflated polynomial.
-            final Complex[] c = new Complex[n + 1];
+            final Complex[] c = coefficients.clone();
-            for (int i = 0; i <= n; i++) {
-                c[i] = coefficients[i];
-            }
 
             // Solve individual roots successively.
             final Complex[] root = new Complex[n];

commons-math-legacy/src/main/java/org/apache/commons/math4/legacy/fitting/leastsquares/LevenbergMarquardtOptimizer.java

@@ -349,9 +349,7 @@ public class LevenbergMarquardtOptimizer implements LeastSquaresOptimizer {
 
             //residuals already have weights applied
             double[] weightedResidual = currentResiduals;
-            for (int i = 0; i < nR; i++) {
+            System.arraycopy(weightedResidual, 0, qtf, 0, nR);
-                qtf[i] = weightedResidual[i];
-            }
 
             // compute Qt.res
             qTy(qtf, internalData);

commons-math-legacy/src/main/java/org/apache/commons/math4/legacy/linear/HessenbergTransformer.java

@@ -150,9 +150,7 @@ class HessenbergTransformer {
                 }
 
                 // copy upper triangular part of the matrix
-                for (int j = i; j < m; ++j) {
+                System.arraycopy(householderVectors[i], i, h[i], i, m - i);
-                    h[i][j] = householderVectors[i][j];
-                }
             }
             cachedH = MatrixUtils.createRealMatrix(h);
         }

commons-math-legacy/src/main/java/org/apache/commons/math4/legacy/ode/nonstiff/AdamsNordsieckFieldTransformer.java

@@ -170,9 +170,9 @@ public final class AdamsNordsieckFieldTransformer<T extends RealFieldElement<T>>
         // Nordsieck to multistep, then shifting rows to represent step advance
         // then applying inverse transform
         T[][] shiftedP = bigP.getData();
-        for (int i = shiftedP.length - 1; i > 0; --i) {
+        // shift rows
-            // shift rows
+        if (shiftedP.length - 1 > 0){
-            shiftedP[i] = shiftedP[i - 1];
+            System.arraycopy(shiftedP, 0, shiftedP, 1, shiftedP.length - 1);
         }
         shiftedP[0] = MathArrays.buildArray(field, rows);
         Arrays.fill(shiftedP[0], field.getZero());

commons-math-legacy/src/main/java/org/apache/commons/math4/legacy/optim/nonlinear/scalar/noderiv/CMAESOptimizer.java

@@ -752,8 +752,8 @@ public class CMAESOptimizer
      * @param val Current best fitness value.
      */
     private static void push(double[] vals, double val) {
-        for (int i = vals.length-1; i > 0; i--) {
+        if (vals.length - 1 > 0) {
-            vals[i] = vals[i-1];
+            System.arraycopy(vals, 0, vals, 1, vals.length - 1);
         }
         vals[0] = val;
     }

commons-math-neuralnet/src/main/java/org/apache/commons/math4/neuralnet/twod/NeuronSquareMesh2D.java

@@ -235,9 +235,7 @@ public class NeuronSquareMesh2D
     public synchronized NeuronSquareMesh2D copy() {
         final long[][] idGrid = new long[numberOfRows][numberOfColumns];
         for (int r = 0; r < numberOfRows; r++) {
-            for (int c = 0; c < numberOfColumns; c++) {
+            System.arraycopy(identifiers[r], 0, idGrid[r], 0, numberOfColumns);
-                idGrid[r][c] = identifiers[r][c];
-            }
         }
 
         return new NeuronSquareMesh2D(wrapRows,

src/main/resources/checkstyle/checkstyle-suppressions-legacy.xml

@@ -44,7 +44,7 @@
   <suppress checks="UnnecessaryParentheses" files=".*[/\\]SparseGradient\.java$" lines="385,396" />
   <suppress checks="UnnecessaryParentheses" files=".*[/\\]DerivativeStructure\.java$" lines="468,481" />
   <suppress checks="UnnecessaryParentheses" files=".*[/\\]SimpleCurveFitter\.java$" lines="321-322" />
-  <suppress checks="UnnecessaryParentheses" files=".*[/\\]LevenbergMarquardtOptimizer\.java$" lines="527,741" />
+  <suppress checks="UnnecessaryParentheses" files=".*[/\\]LevenbergMarquardtOptimizer\.java$" lines="525,739" />
   <suppress checks="UnnecessaryParentheses" files=".*[/\\]EnumeratedDistribution\.java$" lines="128-129" />
   <suppress checks="UnnecessaryParentheses" files=".*[/\\]SimpleRegression\.java$" lines="823" />
   <suppress checks="UnnecessaryParentheses" files=".*[/\\]MillerUpdatingRegression\.java$" lines="172-173" />