http://git-wip-us.apache.org/repos/asf/incubator-samoa/blob/9b178f63/samoa-api/src/main/java/com/yahoo/labs/samoa/moa/core/MiscUtils.java ---------------------------------------------------------------------- diff --git a/samoa-api/src/main/java/com/yahoo/labs/samoa/moa/core/MiscUtils.java b/samoa-api/src/main/java/com/yahoo/labs/samoa/moa/core/MiscUtils.java deleted file mode 100644 index b3bdcc5..0000000 --- a/samoa-api/src/main/java/com/yahoo/labs/samoa/moa/core/MiscUtils.java +++ /dev/null @@ -1,96 +0,0 @@ -package com.yahoo.labs.samoa.moa.core; - -/* - * #%L - * SAMOA - * %% - * Copyright (C) 2014 - 2015 Apache Software Foundation - * %% - * Licensed under the Apache License, Version 2.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.apache.org/licenses/LICENSE-2.0 - * - * Unless required by applicable law or agreed to in writing, software - * distributed under the License is distributed on an "AS IS" BASIS, - * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - * See the License for the specific language governing permissions and - * limitations under the License. - * #L% - */ - -import java.io.PrintWriter; -import java.io.StringWriter; -import java.util.Random; - -/** - * Class implementing some utility methods. - * - * @author Richard Kirkby ([email protected]) - * @author Bernhard Pfahringer ([email protected]) - * @version $Revision: 7 $ - */ -public class MiscUtils { - - public static int chooseRandomIndexBasedOnWeights(double[] weights, - Random random) { - double probSum = Utils.sum(weights); - double val = random.nextDouble() * probSum; - int index = 0; - double sum = 0.0; - while ((sum <= val) && (index < weights.length)) { - sum += weights[index++]; - } - return index - 1; - } - - public static int poisson(double lambda, Random r) { - if (lambda < 100.0) { - double product = 1.0; - double sum = 1.0; - double threshold = r.nextDouble() * Math.exp(lambda); - int i = 1; - int max = Math.max(100, 10 * (int) Math.ceil(lambda)); - while ((i < max) && (sum <= threshold)) { - product *= (lambda / i); - sum += product; - i++; - } - return i - 1; - } - double x = lambda + Math.sqrt(lambda) * r.nextGaussian(); - if (x < 0.0) { - return 0; - } - return (int) Math.floor(x); - } - - public static String getStackTraceString(Exception ex) { - StringWriter stackTraceWriter = new StringWriter(); - ex.printStackTrace(new PrintWriter(stackTraceWriter)); - return "*** STACK TRACE ***\n" + stackTraceWriter.toString(); - } - - /** - * Returns index of maximum element in a given array of doubles. First maximum is returned. - * - * @param doubles - * the array of doubles - * @return the index of the maximum element - */ - public static/* @pure@ */int maxIndex(double[] doubles) { - - double maximum = 0; - int maxIndex = 0; - - for (int i = 0; i < doubles.length; i++) { - if ((i == 0) || (doubles[i] > maximum)) { - maxIndex = i; - maximum = doubles[i]; - } - } - - return maxIndex; - } -}
http://git-wip-us.apache.org/repos/asf/incubator-samoa/blob/9b178f63/samoa-api/src/main/java/com/yahoo/labs/samoa/moa/core/ObjectRepository.java ---------------------------------------------------------------------- diff --git a/samoa-api/src/main/java/com/yahoo/labs/samoa/moa/core/ObjectRepository.java b/samoa-api/src/main/java/com/yahoo/labs/samoa/moa/core/ObjectRepository.java deleted file mode 100644 index 156ed85..0000000 --- a/samoa-api/src/main/java/com/yahoo/labs/samoa/moa/core/ObjectRepository.java +++ /dev/null @@ -1,32 +0,0 @@ -package com.yahoo.labs.samoa.moa.core; - -/* - * #%L - * SAMOA - * %% - * Copyright (C) 2014 - 2015 Apache Software Foundation - * %% - * Licensed under the Apache License, Version 2.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.apache.org/licenses/LICENSE-2.0 - * - * Unless required by applicable law or agreed to in writing, software - * distributed under the License is distributed on an "AS IS" BASIS, - * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - * See the License for the specific language governing permissions and - * limitations under the License. - * #L% - */ - -/** - * Interface for object repositories. - * - * @author Richard Kirkby ([email protected]) - * @version $Revision: 7 $ - */ -public interface ObjectRepository { - - Object getObjectNamed(String string); -} http://git-wip-us.apache.org/repos/asf/incubator-samoa/blob/9b178f63/samoa-api/src/main/java/com/yahoo/labs/samoa/moa/core/SerializeUtils.java ---------------------------------------------------------------------- diff --git a/samoa-api/src/main/java/com/yahoo/labs/samoa/moa/core/SerializeUtils.java b/samoa-api/src/main/java/com/yahoo/labs/samoa/moa/core/SerializeUtils.java deleted file mode 100644 index fc71330..0000000 --- a/samoa-api/src/main/java/com/yahoo/labs/samoa/moa/core/SerializeUtils.java +++ /dev/null @@ -1,112 +0,0 @@ -package com.yahoo.labs.samoa.moa.core; - -/* - * #%L - * SAMOA - * %% - * Copyright (C) 2014 - 2015 Apache Software Foundation - * %% - * Licensed under the Apache License, Version 2.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.apache.org/licenses/LICENSE-2.0 - * - * Unless required by applicable law or agreed to in writing, software - * distributed under the License is distributed on an "AS IS" BASIS, - * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - * See the License for the specific language governing permissions and - * limitations under the License. - * #L% - */ - -import java.io.BufferedInputStream; -import java.io.BufferedOutputStream; -import java.io.ByteArrayInputStream; -import java.io.ByteArrayOutputStream; -import java.io.File; -import java.io.FileInputStream; -import java.io.FileOutputStream; -import java.io.IOException; -import java.io.ObjectInputStream; -import java.io.ObjectOutputStream; -import java.io.OutputStream; -import java.io.Serializable; -import java.util.zip.GZIPInputStream; -import java.util.zip.GZIPOutputStream; - -/** - * Class implementing some serialize utility methods. - * - * @author Richard Kirkby ([email protected]) - * @version $Revision: 7 $ - */ -public class SerializeUtils { - - public static class ByteCountingOutputStream extends OutputStream { - - protected int numBytesWritten = 0; - - public int getNumBytesWritten() { - return this.numBytesWritten; - } - - @Override - public void write(int b) throws IOException { - this.numBytesWritten++; - } - - @Override - public void write(byte[] b, int off, int len) throws IOException { - this.numBytesWritten += len; - } - - @Override - public void write(byte[] b) throws IOException { - this.numBytesWritten += b.length; - } - } - - public static void writeToFile(File file, Serializable obj) - throws IOException { - ObjectOutputStream out = new ObjectOutputStream(new GZIPOutputStream( - new BufferedOutputStream(new FileOutputStream(file)))); - out.writeObject(obj); - out.flush(); - out.close(); - } - - public static Object readFromFile(File file) throws IOException, - ClassNotFoundException { - ObjectInputStream in = new ObjectInputStream(new GZIPInputStream( - new BufferedInputStream(new FileInputStream(file)))); - Object obj = in.readObject(); - in.close(); - return obj; - } - - public static Object copyObject(Serializable obj) throws Exception { - ByteArrayOutputStream baoStream = new ByteArrayOutputStream(); - ObjectOutputStream out = new ObjectOutputStream( - new BufferedOutputStream(baoStream)); - out.writeObject(obj); - out.flush(); - out.close(); - byte[] byteArray = baoStream.toByteArray(); - ObjectInputStream in = new ObjectInputStream(new BufferedInputStream( - new ByteArrayInputStream(byteArray))); - Object copy = in.readObject(); - in.close(); - return copy; - } - - public static int measureObjectByteSize(Serializable obj) throws Exception { - ByteCountingOutputStream bcoStream = new ByteCountingOutputStream(); - ObjectOutputStream out = new ObjectOutputStream( - new BufferedOutputStream(bcoStream)); - out.writeObject(obj); - out.flush(); - out.close(); - return bcoStream.getNumBytesWritten(); - } -} http://git-wip-us.apache.org/repos/asf/incubator-samoa/blob/9b178f63/samoa-api/src/main/java/com/yahoo/labs/samoa/moa/core/Statistics.java ---------------------------------------------------------------------- diff --git a/samoa-api/src/main/java/com/yahoo/labs/samoa/moa/core/Statistics.java b/samoa-api/src/main/java/com/yahoo/labs/samoa/moa/core/Statistics.java deleted file mode 100644 index 868b905..0000000 --- a/samoa-api/src/main/java/com/yahoo/labs/samoa/moa/core/Statistics.java +++ /dev/null @@ -1,1107 +0,0 @@ -package com.yahoo.labs.samoa.moa.core; - -/* - * #%L - * SAMOA - * %% - * Copyright (C) 2014 - 2015 Apache Software Foundation - * %% - * Licensed under the Apache License, Version 2.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.apache.org/licenses/LICENSE-2.0 - * - * Unless required by applicable law or agreed to in writing, software - * distributed under the License is distributed on an "AS IS" BASIS, - * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - * See the License for the specific language governing permissions and - * limitations under the License. - * #L% - */ - -public class Statistics { - - /** Some constants */ - protected static final double MACHEP = 1.11022302462515654042E-16; - protected static final double MAXLOG = 7.09782712893383996732E2; - protected static final double MINLOG = -7.451332191019412076235E2; - protected static final double MAXGAM = 171.624376956302725; - protected static final double SQTPI = 2.50662827463100050242E0; - protected static final double SQRTH = 7.07106781186547524401E-1; - protected static final double LOGPI = 1.14472988584940017414; - - protected static final double big = 4.503599627370496e15; - protected static final double biginv = 2.22044604925031308085e-16; - - /************************************************* - * COEFFICIENTS FOR METHOD normalInverse() * - *************************************************/ - /* approximation for 0 <= |y - 0.5| <= 3/8 */ - protected static final double P0[] = { - -5.99633501014107895267E1, - 9.80010754185999661536E1, - -5.66762857469070293439E1, - 1.39312609387279679503E1, - -1.23916583867381258016E0, - }; - protected static final double Q0[] = { - /* 1.00000000000000000000E0, */ - 1.95448858338141759834E0, - 4.67627912898881538453E0, - 8.63602421390890590575E1, - -2.25462687854119370527E2, - 2.00260212380060660359E2, - -8.20372256168333339912E1, - 1.59056225126211695515E1, - -1.18331621121330003142E0, - }; - - /* - * Approximation for interval z = sqrt(-2 log y ) between 2 and 8 i.e., y - * between exp(-2) = .135 and exp(-32) = 1.27e-14. - */ - protected static final double P1[] = { - 4.05544892305962419923E0, - 3.15251094599893866154E1, - 5.71628192246421288162E1, - 4.40805073893200834700E1, - 1.46849561928858024014E1, - 2.18663306850790267539E0, - -1.40256079171354495875E-1, - -3.50424626827848203418E-2, - -8.57456785154685413611E-4, - }; - protected static final double Q1[] = { - /* 1.00000000000000000000E0, */ - 1.57799883256466749731E1, - 4.53907635128879210584E1, - 4.13172038254672030440E1, - 1.50425385692907503408E1, - 2.50464946208309415979E0, - -1.42182922854787788574E-1, - -3.80806407691578277194E-2, - -9.33259480895457427372E-4, - }; - - /* - * Approximation for interval z = sqrt(-2 log y ) between 8 and 64 i.e., y - * between exp(-32) = 1.27e-14 and exp(-2048) = 3.67e-890. - */ - protected static final double P2[] = { - 3.23774891776946035970E0, - 6.91522889068984211695E0, - 3.93881025292474443415E0, - 1.33303460815807542389E0, - 2.01485389549179081538E-1, - 1.23716634817820021358E-2, - 3.01581553508235416007E-4, - 2.65806974686737550832E-6, - 6.23974539184983293730E-9, - }; - protected static final double Q2[] = { - /* 1.00000000000000000000E0, */ - 6.02427039364742014255E0, - 3.67983563856160859403E0, - 1.37702099489081330271E0, - 2.16236993594496635890E-1, - 1.34204006088543189037E-2, - 3.28014464682127739104E-4, - 2.89247864745380683936E-6, - 6.79019408009981274425E-9, - }; - - /** - * Computes standard error for observed values of a binomial random variable. - * - * @param p - * the probability of success - * @param n - * the size of the sample - * @return the standard error - */ - public static double binomialStandardError(double p, int n) { - - if (n == 0) { - return 0; - } - return Math.sqrt((p * (1 - p)) / (double) n); - } - - /** - * Returns chi-squared probability for given value and degrees of freedom. (The probability that the chi-squared - * variate will be greater than x for the given degrees of freedom.) - * - * @param x - * the value - * @param v - * the number of degrees of freedom - * @return the chi-squared probability - */ - public static double chiSquaredProbability(double x, double v) { - - if (x < 0.0 || v < 1.0) - return 0.0; - return incompleteGammaComplement(v / 2.0, x / 2.0); - } - - /** - * Computes probability of F-ratio. - * - * @param F - * the F-ratio - * @param df1 - * the first number of degrees of freedom - * @param df2 - * the second number of degrees of freedom - * @return the probability of the F-ratio. - */ - public static double FProbability(double F, int df1, int df2) { - - return incompleteBeta(df2 / 2.0, df1 / 2.0, df2 / (df2 + df1 * F)); - } - - /** - * Returns the area under the Normal (Gaussian) probability density function, integrated from minus infinity to - * <tt>x</tt> (assumes mean is zero, variance is one). - * - * <pre> - * x - * - - * 1 | | 2 - * normal(x) = --------- | exp( - t /2 ) dt - * sqrt(2pi) | | - * - - * -inf. - * - * = ( 1 + erf(z) ) / 2 - * = erfc(z) / 2 - * </pre> - * - * where <tt>z = x/sqrt(2)</tt>. Computation is via the functions <tt>errorFunction</tt> and - * <tt>errorFunctionComplement</tt>. - * - * @param a - * the z-value - * @return the probability of the z value according to the normal pdf - */ - public static double normalProbability(double a) { - - double x, y, z; - - x = a * SQRTH; - z = Math.abs(x); - - if (z < SQRTH) - y = 0.5 + 0.5 * errorFunction(x); - else { - y = 0.5 * errorFunctionComplemented(z); - if (x > 0) - y = 1.0 - y; - } - return y; - } - - /** - * Returns the value, <tt>x</tt>, for which the area under the Normal (Gaussian) probability density function - * (integrated from minus infinity to <tt>x</tt>) is equal to the argument <tt>y</tt> (assumes mean is zero, variance - * is one). - * <p> - * For small arguments <tt>0 < y < exp(-2)</tt>, the program computes <tt>z = sqrt( -2.0 * log(y) )</tt>; then the - * approximation is <tt>x = z - log(z)/z - (1/z) P(1/z) / Q(1/z)</tt>. There are two rational functions P/Q, one for - * <tt>0 < y < exp(-32)</tt> and the other for <tt>y</tt> up to <tt>exp(-2)</tt>. For larger arguments, - * <tt>w = y - 0.5</tt>, and <tt>x/sqrt(2pi) = w + w**3 R(w**2)/S(w**2))</tt>. - * - * @param y0 - * the area under the normal pdf - * @return the z-value - */ - public static double normalInverse(double y0) { - - double x, y, z, y2, x0, x1; - int code; - - final double s2pi = Math.sqrt(2.0 * Math.PI); - - if (y0 <= 0.0) - throw new IllegalArgumentException(); - if (y0 >= 1.0) - throw new IllegalArgumentException(); - code = 1; - y = y0; - if (y > (1.0 - 0.13533528323661269189)) { /* 0.135... = exp(-2) */ - y = 1.0 - y; - code = 0; - } - - if (y > 0.13533528323661269189) { - y = y - 0.5; - y2 = y * y; - x = y + y * (y2 * polevl(y2, P0, 4) / p1evl(y2, Q0, 8)); - x = x * s2pi; - return (x); - } - - x = Math.sqrt(-2.0 * Math.log(y)); - x0 = x - Math.log(x) / x; - - z = 1.0 / x; - if (x < 8.0) /* y > exp(-32) = 1.2664165549e-14 */ - x1 = z * polevl(z, P1, 8) / p1evl(z, Q1, 8); - else - x1 = z * polevl(z, P2, 8) / p1evl(z, Q2, 8); - x = x0 - x1; - if (code != 0) - x = -x; - return (x); - } - - /** - * Returns natural logarithm of gamma function. - * - * @param x - * the value - * @return natural logarithm of gamma function - */ - public static double lnGamma(double x) { - - double p, q, w, z; - - double A[] = { - 8.11614167470508450300E-4, - -5.95061904284301438324E-4, - 7.93650340457716943945E-4, - -2.77777777730099687205E-3, - 8.33333333333331927722E-2 - }; - double B[] = { - -1.37825152569120859100E3, - -3.88016315134637840924E4, - -3.31612992738871184744E5, - -1.16237097492762307383E6, - -1.72173700820839662146E6, - -8.53555664245765465627E5 - }; - double C[] = { - /* 1.00000000000000000000E0, */ - -3.51815701436523470549E2, - -1.70642106651881159223E4, - -2.20528590553854454839E5, - -1.13933444367982507207E6, - -2.53252307177582951285E6, - -2.01889141433532773231E6 - }; - - if (x < -34.0) { - q = -x; - w = lnGamma(q); - p = Math.floor(q); - if (p == q) - throw new ArithmeticException("lnGamma: Overflow"); - z = q - p; - if (z > 0.5) { - p += 1.0; - z = p - q; - } - z = q * Math.sin(Math.PI * z); - if (z == 0.0) - throw new ArithmeticException("lnGamma: Overflow"); - z = LOGPI - Math.log(z) - w; - return z; - } - - if (x < 13.0) { - z = 1.0; - while (x >= 3.0) { - x -= 1.0; - z *= x; - } - while (x < 2.0) { - if (x == 0.0) - throw new ArithmeticException("lnGamma: Overflow"); - z /= x; - x += 1.0; - } - if (z < 0.0) - z = -z; - if (x == 2.0) - return Math.log(z); - x -= 2.0; - p = x * polevl(x, B, 5) / p1evl(x, C, 6); - return (Math.log(z) + p); - } - - if (x > 2.556348e305) - throw new ArithmeticException("lnGamma: Overflow"); - - q = (x - 0.5) * Math.log(x) - x + 0.91893853320467274178; - - if (x > 1.0e8) - return (q); - - p = 1.0 / (x * x); - if (x >= 1000.0) - q += ((7.9365079365079365079365e-4 * p - - 2.7777777777777777777778e-3) * p - + 0.0833333333333333333333) / x; - else - q += polevl(p, A, 4) / x; - return q; - } - - /** - * Returns the error function of the normal distribution. The integral is - * - * <pre> - * x - * - - * 2 | | 2 - * erf(x) = -------- | exp( - t ) dt. - * sqrt(pi) | | - * - - * 0 - * </pre> - * - * <b>Implementation:</b> For <tt>0 <= |x| < 1, erf(x) = x * P4(x**2)/Q5(x**2)</tt>; otherwise - * <tt>erf(x) = 1 - erfc(x)</tt>. - * <p> - * Code adapted from the <A HREF="http://www.sci.usq.edu.au/staff/leighb/graph/Top.html";> Java 2D Graph Package - * 2.4</A>, which in turn is a port from the <A HREF="http://people.ne.mediaone.net/moshier/index.html#Cephes";>Cephes - * 2.2</A> Math Library (C). - * - * @param a - * the argument to the function. - */ - public static double errorFunction(double x) { - double y, z; - final double T[] = { - 9.60497373987051638749E0, - 9.00260197203842689217E1, - 2.23200534594684319226E3, - 7.00332514112805075473E3, - 5.55923013010394962768E4 - }; - final double U[] = { - // 1.00000000000000000000E0, - 3.35617141647503099647E1, - 5.21357949780152679795E2, - 4.59432382970980127987E3, - 2.26290000613890934246E4, - 4.92673942608635921086E4 - }; - - if (Math.abs(x) > 1.0) - return (1.0 - errorFunctionComplemented(x)); - z = x * x; - y = x * polevl(z, T, 4) / p1evl(z, U, 5); - return y; - } - - /** - * Returns the complementary Error function of the normal distribution. - * - * <pre> - * 1 - erf(x) = - * - * inf. - * - - * 2 | | 2 - * erfc(x) = -------- | exp( - t ) dt - * sqrt(pi) | | - * - - * x - * </pre> - * - * <b>Implementation:</b> For small x, <tt>erfc(x) = 1 - erf(x)</tt>; otherwise rational approximations are computed. - * <p> - * Code adapted from the <A HREF="http://www.sci.usq.edu.au/staff/leighb/graph/Top.html";> Java 2D Graph Package - * 2.4</A>, which in turn is a port from the <A HREF="http://people.ne.mediaone.net/moshier/index.html#Cephes";>Cephes - * 2.2</A> Math Library (C). - * - * @param a - * the argument to the function. - */ - public static double errorFunctionComplemented(double a) { - double x, y, z, p, q; - - double P[] = { - 2.46196981473530512524E-10, - 5.64189564831068821977E-1, - 7.46321056442269912687E0, - 4.86371970985681366614E1, - 1.96520832956077098242E2, - 5.26445194995477358631E2, - 9.34528527171957607540E2, - 1.02755188689515710272E3, - 5.57535335369399327526E2 - }; - double Q[] = { - // 1.0 - 1.32281951154744992508E1, - 8.67072140885989742329E1, - 3.54937778887819891062E2, - 9.75708501743205489753E2, - 1.82390916687909736289E3, - 2.24633760818710981792E3, - 1.65666309194161350182E3, - 5.57535340817727675546E2 - }; - - double R[] = { - 5.64189583547755073984E-1, - 1.27536670759978104416E0, - 5.01905042251180477414E0, - 6.16021097993053585195E0, - 7.40974269950448939160E0, - 2.97886665372100240670E0 - }; - double S[] = { - // 1.00000000000000000000E0, - 2.26052863220117276590E0, - 9.39603524938001434673E0, - 1.20489539808096656605E1, - 1.70814450747565897222E1, - 9.60896809063285878198E0, - 3.36907645100081516050E0 - }; - - if (a < 0.0) - x = -a; - else - x = a; - - if (x < 1.0) - return 1.0 - errorFunction(a); - - z = -a * a; - - if (z < -MAXLOG) { - if (a < 0) - return (2.0); - else - return (0.0); - } - - z = Math.exp(z); - - if (x < 8.0) { - p = polevl(x, P, 8); - q = p1evl(x, Q, 8); - } else { - p = polevl(x, R, 5); - q = p1evl(x, S, 6); - } - - y = (z * p) / q; - - if (a < 0) - y = 2.0 - y; - - if (y == 0.0) { - if (a < 0) - return 2.0; - else - return (0.0); - } - return y; - } - - /** - * Evaluates the given polynomial of degree <tt>N</tt> at <tt>x</tt>. Evaluates polynomial when coefficient of N is - * 1.0. Otherwise same as <tt>polevl()</tt>. - * - * <pre> - * 2 N - * y = C + C x + C x +...+ C x - * 0 1 2 N - * - * Coefficients are stored in reverse order: - * - * coef[0] = C , ..., coef[N] = C . - * N 0 - * </pre> - * - * The function <tt>p1evl()</tt> assumes that <tt>coef[N] = 1.0</tt> and is omitted from the array. Its calling - * arguments are otherwise the same as <tt>polevl()</tt>. - * <p> - * In the interest of speed, there are no checks for out of bounds arithmetic. - * - * @param x - * argument to the polynomial. - * @param coef - * the coefficients of the polynomial. - * @param N - * the degree of the polynomial. - */ - public static double p1evl(double x, double coef[], int N) { - - double ans; - ans = x + coef[0]; - - for (int i = 1; i < N; i++) - ans = ans * x + coef[i]; - - return ans; - } - - /** - * Evaluates the given polynomial of degree <tt>N</tt> at <tt>x</tt>. - * - * <pre> - * 2 N - * y = C + C x + C x +...+ C x - * 0 1 2 N - * - * Coefficients are stored in reverse order: - * - * coef[0] = C , ..., coef[N] = C . - * N 0 - * </pre> - * - * In the interest of speed, there are no checks for out of bounds arithmetic. - * - * @param x - * argument to the polynomial. - * @param coef - * the coefficients of the polynomial. - * @param N - * the degree of the polynomial. - */ - public static double polevl(double x, double coef[], int N) { - - double ans; - ans = coef[0]; - - for (int i = 1; i <= N; i++) - ans = ans * x + coef[i]; - - return ans; - } - - /** - * Returns the Incomplete Gamma function. - * - * @param a - * the parameter of the gamma distribution. - * @param x - * the integration end point. - */ - public static double incompleteGamma(double a, double x) - { - - double ans, ax, c, r; - - if (x <= 0 || a <= 0) - return 0.0; - - if (x > 1.0 && x > a) - return 1.0 - incompleteGammaComplement(a, x); - - /* Compute x**a * exp(-x) / gamma(a) */ - ax = a * Math.log(x) - x - lnGamma(a); - if (ax < -MAXLOG) - return (0.0); - - ax = Math.exp(ax); - - /* power series */ - r = a; - c = 1.0; - ans = 1.0; - - do { - r += 1.0; - c *= x / r; - ans += c; - } while (c / ans > MACHEP); - - return (ans * ax / a); - } - - /** - * Returns the Complemented Incomplete Gamma function. - * - * @param a - * the parameter of the gamma distribution. - * @param x - * the integration start point. - */ - public static double incompleteGammaComplement(double a, double x) { - - double ans, ax, c, yc, r, t, y, z; - double pk, pkm1, pkm2, qk, qkm1, qkm2; - - if (x <= 0 || a <= 0) - return 1.0; - - if (x < 1.0 || x < a) - return 1.0 - incompleteGamma(a, x); - - ax = a * Math.log(x) - x - lnGamma(a); - if (ax < -MAXLOG) - return 0.0; - - ax = Math.exp(ax); - - /* continued fraction */ - y = 1.0 - a; - z = x + y + 1.0; - c = 0.0; - pkm2 = 1.0; - qkm2 = x; - pkm1 = x + 1.0; - qkm1 = z * x; - ans = pkm1 / qkm1; - - do { - c += 1.0; - y += 1.0; - z += 2.0; - yc = y * c; - pk = pkm1 * z - pkm2 * yc; - qk = qkm1 * z - qkm2 * yc; - if (qk != 0) { - r = pk / qk; - t = Math.abs((ans - r) / r); - ans = r; - } else - t = 1.0; - - pkm2 = pkm1; - pkm1 = pk; - qkm2 = qkm1; - qkm1 = qk; - if (Math.abs(pk) > big) { - pkm2 *= biginv; - pkm1 *= biginv; - qkm2 *= biginv; - qkm1 *= biginv; - } - } while (t > MACHEP); - - return ans * ax; - } - - /** - * Returns the Gamma function of the argument. - */ - public static double gamma(double x) { - - double P[] = { - 1.60119522476751861407E-4, - 1.19135147006586384913E-3, - 1.04213797561761569935E-2, - 4.76367800457137231464E-2, - 2.07448227648435975150E-1, - 4.94214826801497100753E-1, - 9.99999999999999996796E-1 - }; - double Q[] = { - -2.31581873324120129819E-5, - 5.39605580493303397842E-4, - -4.45641913851797240494E-3, - 1.18139785222060435552E-2, - 3.58236398605498653373E-2, - -2.34591795718243348568E-1, - 7.14304917030273074085E-2, - 1.00000000000000000320E0 - }; - - double p, z; - int i; - - double q = Math.abs(x); - - if (q > 33.0) { - if (x < 0.0) { - p = Math.floor(q); - if (p == q) - throw new ArithmeticException("gamma: overflow"); - i = (int) p; - z = q - p; - if (z > 0.5) { - p += 1.0; - z = q - p; - } - z = q * Math.sin(Math.PI * z); - if (z == 0.0) - throw new ArithmeticException("gamma: overflow"); - z = Math.abs(z); - z = Math.PI / (z * stirlingFormula(q)); - - return -z; - } else { - return stirlingFormula(x); - } - } - - z = 1.0; - while (x >= 3.0) { - x -= 1.0; - z *= x; - } - - while (x < 0.0) { - if (x == 0.0) { - throw new ArithmeticException("gamma: singular"); - } else if (x > -1.E-9) { - return (z / ((1.0 + 0.5772156649015329 * x) * x)); - } - z /= x; - x += 1.0; - } - - while (x < 2.0) { - if (x == 0.0) { - throw new ArithmeticException("gamma: singular"); - } else if (x < 1.e-9) { - return (z / ((1.0 + 0.5772156649015329 * x) * x)); - } - z /= x; - x += 1.0; - } - - if ((x == 2.0) || (x == 3.0)) - return z; - - x -= 2.0; - p = polevl(x, P, 6); - q = polevl(x, Q, 7); - return z * p / q; - } - - /** - * Returns the Gamma function computed by Stirling's formula. The polynomial STIR is valid for 33 <= x <= 172. - */ - public static double stirlingFormula(double x) { - - double STIR[] = { - 7.87311395793093628397E-4, - -2.29549961613378126380E-4, - -2.68132617805781232825E-3, - 3.47222221605458667310E-3, - 8.33333333333482257126E-2, - }; - double MAXSTIR = 143.01608; - - double w = 1.0 / x; - double y = Math.exp(x); - - w = 1.0 + w * polevl(w, STIR, 4); - - if (x > MAXSTIR) { - /* Avoid overflow in Math.pow() */ - double v = Math.pow(x, 0.5 * x - 0.25); - y = v * (v / y); - } else { - y = Math.pow(x, x - 0.5) / y; - } - y = SQTPI * y * w; - return y; - } - - /** - * Returns the Incomplete Beta Function evaluated from zero to <tt>xx</tt>. - * - * @param aa - * the alpha parameter of the beta distribution. - * @param bb - * the beta parameter of the beta distribution. - * @param xx - * the integration end point. - */ - public static double incompleteBeta(double aa, double bb, double xx) { - - double a, b, t, x, xc, w, y; - boolean flag; - - if (aa <= 0.0 || bb <= 0.0) - throw new ArithmeticException("ibeta: Domain error!"); - - if ((xx <= 0.0) || (xx >= 1.0)) { - if (xx == 0.0) - return 0.0; - if (xx == 1.0) - return 1.0; - throw new ArithmeticException("ibeta: Domain error!"); - } - - flag = false; - if ((bb * xx) <= 1.0 && xx <= 0.95) { - t = powerSeries(aa, bb, xx); - return t; - } - - w = 1.0 - xx; - - /* Reverse a and b if x is greater than the mean. */ - if (xx > (aa / (aa + bb))) { - flag = true; - a = bb; - b = aa; - xc = xx; - x = w; - } else { - a = aa; - b = bb; - xc = w; - x = xx; - } - - if (flag && (b * x) <= 1.0 && x <= 0.95) { - t = powerSeries(a, b, x); - if (t <= MACHEP) - t = 1.0 - MACHEP; - else - t = 1.0 - t; - return t; - } - - /* Choose expansion for better convergence. */ - y = x * (a + b - 2.0) - (a - 1.0); - if (y < 0.0) - w = incompleteBetaFraction1(a, b, x); - else - w = incompleteBetaFraction2(a, b, x) / xc; - - /* - * Multiply w by the factor a b _ _ _ x (1-x) | (a+b) / ( a | (a) | (b) ) . - */ - - y = a * Math.log(x); - t = b * Math.log(xc); - if ((a + b) < MAXGAM && Math.abs(y) < MAXLOG && Math.abs(t) < MAXLOG) { - t = Math.pow(xc, b); - t *= Math.pow(x, a); - t /= a; - t *= w; - t *= gamma(a + b) / (gamma(a) * gamma(b)); - if (flag) { - if (t <= MACHEP) - t = 1.0 - MACHEP; - else - t = 1.0 - t; - } - return t; - } - /* Resort to logarithms. */ - y += t + lnGamma(a + b) - lnGamma(a) - lnGamma(b); - y += Math.log(w / a); - if (y < MINLOG) - t = 0.0; - else - t = Math.exp(y); - - if (flag) { - if (t <= MACHEP) - t = 1.0 - MACHEP; - else - t = 1.0 - t; - } - return t; - } - - /** - * Continued fraction expansion #1 for incomplete beta integral. - */ - public static double incompleteBetaFraction1(double a, double b, double x) { - - double xk, pk, pkm1, pkm2, qk, qkm1, qkm2; - double k1, k2, k3, k4, k5, k6, k7, k8; - double r, t, ans, thresh; - int n; - - k1 = a; - k2 = a + b; - k3 = a; - k4 = a + 1.0; - k5 = 1.0; - k6 = b - 1.0; - k7 = k4; - k8 = a + 2.0; - - pkm2 = 0.0; - qkm2 = 1.0; - pkm1 = 1.0; - qkm1 = 1.0; - ans = 1.0; - r = 1.0; - n = 0; - thresh = 3.0 * MACHEP; - do { - xk = -(x * k1 * k2) / (k3 * k4); - pk = pkm1 + pkm2 * xk; - qk = qkm1 + qkm2 * xk; - pkm2 = pkm1; - pkm1 = pk; - qkm2 = qkm1; - qkm1 = qk; - - xk = (x * k5 * k6) / (k7 * k8); - pk = pkm1 + pkm2 * xk; - qk = qkm1 + qkm2 * xk; - pkm2 = pkm1; - pkm1 = pk; - qkm2 = qkm1; - qkm1 = qk; - - if (qk != 0) - r = pk / qk; - if (r != 0) { - t = Math.abs((ans - r) / r); - ans = r; - } else - t = 1.0; - - if (t < thresh) - return ans; - - k1 += 1.0; - k2 += 1.0; - k3 += 2.0; - k4 += 2.0; - k5 += 1.0; - k6 -= 1.0; - k7 += 2.0; - k8 += 2.0; - - if ((Math.abs(qk) + Math.abs(pk)) > big) { - pkm2 *= biginv; - pkm1 *= biginv; - qkm2 *= biginv; - qkm1 *= biginv; - } - if ((Math.abs(qk) < biginv) || (Math.abs(pk) < biginv)) { - pkm2 *= big; - pkm1 *= big; - qkm2 *= big; - qkm1 *= big; - } - } while (++n < 300); - - return ans; - } - - /** - * Continued fraction expansion #2 for incomplete beta integral. - */ - public static double incompleteBetaFraction2(double a, double b, double x) { - - double xk, pk, pkm1, pkm2, qk, qkm1, qkm2; - double k1, k2, k3, k4, k5, k6, k7, k8; - double r, t, ans, z, thresh; - int n; - - k1 = a; - k2 = b - 1.0; - k3 = a; - k4 = a + 1.0; - k5 = 1.0; - k6 = a + b; - k7 = a + 1.0; - ; - k8 = a + 2.0; - - pkm2 = 0.0; - qkm2 = 1.0; - pkm1 = 1.0; - qkm1 = 1.0; - z = x / (1.0 - x); - ans = 1.0; - r = 1.0; - n = 0; - thresh = 3.0 * MACHEP; - do { - xk = -(z * k1 * k2) / (k3 * k4); - pk = pkm1 + pkm2 * xk; - qk = qkm1 + qkm2 * xk; - pkm2 = pkm1; - pkm1 = pk; - qkm2 = qkm1; - qkm1 = qk; - - xk = (z * k5 * k6) / (k7 * k8); - pk = pkm1 + pkm2 * xk; - qk = qkm1 + qkm2 * xk; - pkm2 = pkm1; - pkm1 = pk; - qkm2 = qkm1; - qkm1 = qk; - - if (qk != 0) - r = pk / qk; - if (r != 0) { - t = Math.abs((ans - r) / r); - ans = r; - } else - t = 1.0; - - if (t < thresh) - return ans; - - k1 += 1.0; - k2 -= 1.0; - k3 += 2.0; - k4 += 2.0; - k5 += 1.0; - k6 += 1.0; - k7 += 2.0; - k8 += 2.0; - - if ((Math.abs(qk) + Math.abs(pk)) > big) { - pkm2 *= biginv; - pkm1 *= biginv; - qkm2 *= biginv; - qkm1 *= biginv; - } - if ((Math.abs(qk) < biginv) || (Math.abs(pk) < biginv)) { - pkm2 *= big; - pkm1 *= big; - qkm2 *= big; - qkm1 *= big; - } - } while (++n < 300); - - return ans; - } - - /** - * Power series for incomplete beta integral. Use when b*x is small and x not too close to 1. - */ - public static double powerSeries(double a, double b, double x) { - - double s, t, u, v, n, t1, z, ai; - - ai = 1.0 / a; - u = (1.0 - b) * x; - v = u / (a + 1.0); - t1 = v; - t = u; - n = 2.0; - s = 0.0; - z = MACHEP * ai; - while (Math.abs(v) > z) { - u = (n - b) * x / n; - t *= u; - v = t / (a + n); - s += v; - n += 1.0; - } - s += t1; - s += ai; - - u = a * Math.log(x); - if ((a + b) < MAXGAM && Math.abs(u) < MAXLOG) { - t = gamma(a + b) / (gamma(a) * gamma(b)); - s = s * t * Math.pow(x, a); - } else { - t = lnGamma(a + b) - lnGamma(a) - lnGamma(b) + u + Math.log(s); - if (t < MINLOG) - s = 0.0; - else - s = Math.exp(t); - } - return s; - } - -} http://git-wip-us.apache.org/repos/asf/incubator-samoa/blob/9b178f63/samoa-api/src/main/java/com/yahoo/labs/samoa/moa/core/StringUtils.java ---------------------------------------------------------------------- diff --git a/samoa-api/src/main/java/com/yahoo/labs/samoa/moa/core/StringUtils.java b/samoa-api/src/main/java/com/yahoo/labs/samoa/moa/core/StringUtils.java deleted file mode 100644 index b143ba3..0000000 --- a/samoa-api/src/main/java/com/yahoo/labs/samoa/moa/core/StringUtils.java +++ /dev/null @@ -1,96 +0,0 @@ -package com.yahoo.labs.samoa.moa.core; - -/* - * #%L - * SAMOA - * %% - * Copyright (C) 2014 - 2015 Apache Software Foundation - * %% - * Licensed under the Apache License, Version 2.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.apache.org/licenses/LICENSE-2.0 - * - * Unless required by applicable law or agreed to in writing, software - * distributed under the License is distributed on an "AS IS" BASIS, - * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - * See the License for the specific language governing permissions and - * limitations under the License. - * #L% - */ - -import java.text.DecimalFormat; - -/** - * Class implementing some string utility methods. - * - * @author Richard Kirkby ([email protected]) - * @version $Revision: 7 $ - */ -public class StringUtils { - - public static final String newline = System.getProperty("line.separator"); - - public static String doubleToString(double value, int fractionDigits) { - return doubleToString(value, 0, fractionDigits); - } - - public static String doubleToString(double value, int minFractionDigits, - int maxFractionDigits) { - DecimalFormat numberFormat = new DecimalFormat(); - numberFormat.setMinimumFractionDigits(minFractionDigits); - numberFormat.setMaximumFractionDigits(maxFractionDigits); - return numberFormat.format(value); - } - - public static void appendNewline(StringBuilder out) { - out.append(newline); - } - - public static void appendIndent(StringBuilder out, int indent) { - for (int i = 0; i < indent; i++) { - out.append(' '); - } - } - - public static void appendIndented(StringBuilder out, int indent, String s) { - appendIndent(out, indent); - out.append(s); - } - - public static void appendNewlineIndented(StringBuilder out, int indent, - String s) { - appendNewline(out); - appendIndented(out, indent, s); - } - - public static String secondsToDHMSString(double seconds) { - if (seconds < 60) { - return doubleToString(seconds, 2, 2) + 's'; - } - long secs = (int) (seconds); - long mins = secs / 60; - long hours = mins / 60; - long days = hours / 24; - secs %= 60; - mins %= 60; - hours %= 24; - StringBuilder result = new StringBuilder(); - if (days > 0) { - result.append(days); - result.append('d'); - } - if ((hours > 0) || (days > 0)) { - result.append(hours); - result.append('h'); - } - if ((hours > 0) || (days > 0) || (mins > 0)) { - result.append(mins); - result.append('m'); - } - result.append(secs); - result.append('s'); - return result.toString(); - } -}
