/**
* To reduce the search space we will only consider routes that start and end at one city
* (whichever is first in the collection). All other possible routes are equivalent to one of
* these routes since start city is irrelevant in determining the shortest cycle.
*
* @param cities The list of destinations, each of which must be visited once.
* @param progressListener Call-back for receiving the status of the algorithm as it progresses.
* May be null.
* @return The shortest route that visits each of the specified cities once.
*/
public List<String> calculateShortestRoute(
Collection<String> cities, ProgressListener progressListener) {
Iterator<String> iterator = cities.iterator();
String startCity = iterator.next();
Collection<String> destinations = new ArrayList<String>(cities.size() - 1);
while (iterator.hasNext()) {
destinations.add(iterator.next());
}
FitnessEvaluator<List<String>> evaluator = new RouteEvaluator(distances);
PermutationGenerator<String> generator = new PermutationGenerator<String>(destinations);
long totalPermutations = generator.getTotalPermutations();
long count = 0;
List<String> shortestRoute = null;
double shortestDistance = Double.POSITIVE_INFINITY;
List<String> currentRoute = new ArrayList<String>(cities.size());
while (generator.hasMore()) {
List<String> route = generator.nextPermutationAsList(currentRoute);
route.add(0, startCity);
double distance = evaluator.getFitness(route, null);
if (distance < shortestDistance) {
shortestDistance = distance;
shortestRoute = new ArrayList<String>(route);
}
++count;
if (count % 1000 == 0 && progressListener != null) {
progressListener.updateProgress(((double) count) / totalPermutations * 100);
}
}
if (progressListener != null) {
progressListener.updateProgress(100); // Finished.
}
return shortestRoute;
}
public void analyzeInnerClasses(ProgressListener pl, double done, double scale) {
double subScale = scale / innerComplexity;
// If output should be immediate, we delay analyzation to output.
// Note that this may break anonymous classes, but the user
// has been warned.
if ((Options.options & Options.OPTION_IMMEDIATE) != 0) return;
// Now analyze the inner classes.
for (int j = 0; j < inners.length; j++) {
if (pl != null) {
double innerCompl = inners[j].getComplexity() * subScale;
if (innerCompl > STEP_COMPLEXITY) {
double innerscale = subScale * inners[j].methodComplexity;
inners[j].analyze(pl, done, innerscale);
inners[j].analyzeInnerClasses(null, done + innerscale, innerCompl - innerscale);
} else {
pl.updateProgress(done, inners[j].name);
inners[j].analyze(null, 0.0, 0.0);
inners[j].analyzeInnerClasses(null, 0.0, 0.0);
}
done += innerCompl;
} else {
inners[j].analyze(null, 0.0, 0.0);
inners[j].analyzeInnerClasses(null, 0.0, 0.0);
}
}
// Now analyze the method scoped classes.
for (int j = 0; j < methods.length; j++) methods[j].analyzeInnerClasses();
}
public void dumpJavaFile(TabbedPrintWriter writer, ProgressListener pl) throws IOException {
imports.init(clazz.getName());
LocalInfo.init();
initialize();
double done = 0.05;
double scale = (0.75) * methodComplexity / (methodComplexity + innerComplexity);
analyze(pl, INITIALIZE_COMPLEXITY, scale);
done += scale;
analyzeInnerClasses(pl, done, 0.8 - done);
makeDeclaration(new SimpleSet());
imports.dumpHeader(writer);
dumpSource(writer, pl, 0.8, 0.2);
if (pl != null) pl.updateProgress(1.0, name);
}
public void dumpBlock(TabbedPrintWriter writer, ProgressListener pl, double done, double scale)
throws IOException {
double subScale = scale / getComplexity();
writer.pushScope(this);
boolean needFieldNewLine = false;
boolean needNewLine = false;
Set declared = null;
if ((Options.options & Options.OPTION_IMMEDIATE) != 0) declared = new SimpleSet();
for (int i = 0; i < fields.length; i++) {
if (blockInitializers[i] != null) {
if (needNewLine) writer.println();
writer.openBrace();
writer.tab();
blockInitializers[i].dumpSource(writer);
writer.untab();
writer.closeBrace();
needFieldNewLine = needNewLine = true;
}
if ((Options.options & Options.OPTION_IMMEDIATE) != 0) {
// We now do the analyzation we skipped before.
fields[i].analyze();
fields[i].makeDeclaration(declared);
}
if (fields[i].skipWriting()) continue;
if (needFieldNewLine) writer.println();
fields[i].dumpSource(writer);
needNewLine = true;
}
if (blockInitializers[fields.length] != null) {
if (needNewLine) writer.println();
writer.openBrace();
writer.tab();
blockInitializers[fields.length].dumpSource(writer);
writer.untab();
writer.closeBrace();
needNewLine = true;
}
for (int i = 0; i < inners.length; i++) {
if (needNewLine) writer.println();
if ((Options.options & Options.OPTION_IMMEDIATE) != 0) {
// We now do the analyzation we skipped before.
inners[i].analyze(null, 0.0, 0.0);
inners[i].analyzeInnerClasses(null, 0.0, 0.0);
inners[i].makeDeclaration(declared);
}
if (pl != null) {
double innerCompl = inners[i].getComplexity() * subScale;
if (innerCompl > STEP_COMPLEXITY) inners[i].dumpSource(writer, pl, done, innerCompl);
else {
pl.updateProgress(done, name);
inners[i].dumpSource(writer);
}
done += innerCompl;
} else inners[i].dumpSource(writer);
needNewLine = true;
}
for (int i = 0; i < methods.length; i++) {
if ((Options.options & Options.OPTION_IMMEDIATE) != 0) {
// We now do the analyzation we skipped before.
if (!methods[i].isConstructor()) methods[i].analyze(null, 0.0, 0.0);
methods[i].analyzeInnerClasses();
methods[i].makeDeclaration(declared);
}
if (methods[i].skipWriting()) continue;
if (needNewLine) writer.println();
if (pl != null) {
double methodCompl = methods[i].getComplexity() * subScale;
pl.updateProgress(done, methods[i].getName());
methods[i].dumpSource(writer);
done += methodCompl;
} else methods[i].dumpSource(writer);
needNewLine = true;
}
writer.popScope();
clazz.dropInfo(clazz.KNOWNATTRIBS | clazz.UNKNOWNATTRIBS);
}
public void analyze(ProgressListener pl, double done, double scale) {
if (GlobalOptions.verboseLevel > 0) GlobalOptions.err.println("Class " + name);
double subScale = scale / methodComplexity;
if (pl != null) pl.updateProgress(done, name);
imports.useClass(clazz);
if (clazz.getSuperclass() != null) imports.useClass(clazz.getSuperclass());
ClassInfo[] interfaces = clazz.getInterfaces();
for (int j = 0; j < interfaces.length; j++) imports.useClass(interfaces[j]);
if (fields == null) {
/* This means that the class could not be loaded.
* give up.
*/
return;
}
// First analyze constructors and synthetic fields:
constrAna = null;
if (constructors.length > 0) {
for (int j = 0; j < constructors.length; j++) {
if (pl != null) {
double constrCompl = constructors[j].getComplexity() * subScale;
if (constrCompl > STEP_COMPLEXITY) constructors[j].analyze(pl, done, constrCompl);
else {
pl.updateProgress(done, name);
constructors[j].analyze(null, 0.0, 0.0);
}
done += constrCompl;
} else constructors[j].analyze(null, 0.0, 0.0);
}
constrAna = new TransformConstructors(this, false, constructors);
constrAna.removeSynthInitializers();
}
if (staticConstructor != null) {
if (pl != null) {
double constrCompl = staticConstructor.getComplexity() * subScale;
if (constrCompl > STEP_COMPLEXITY) staticConstructor.analyze(pl, done, constrCompl);
else {
pl.updateProgress(done, name);
staticConstructor.analyze(null, 0.0, 0.0);
}
done += constrCompl;
} else staticConstructor.analyze(null, 0.0, 0.0);
}
// If output should be immediate, we delay analyzation to output.
// Note that this may break anonymous classes, but the user
// has been warned.
if ((Options.options & Options.OPTION_IMMEDIATE) != 0) return;
// Analyze fields
for (int j = 0; j < fields.length; j++) fields[j].analyze();
// Now analyze remaining methods.
for (int j = 0; j < methods.length; j++) {
if (!methods[j].isConstructor())
if (pl != null) {
double methodCompl = methods[j].getComplexity() * subScale;
if (methodCompl > STEP_COMPLEXITY) methods[j].analyze(pl, done, methodCompl);
else {
pl.updateProgress(done, methods[j].getName());
methods[j].analyze(null, 0.0, 0.0);
}
done += methodCompl;
} else methods[j].analyze(null, 0.0, 0.0);
}
}
/**
* Construct the singular value decomposition
*
* @param Arg Rectangular matrix
* @return Structure to access U, S and V.
*/
public SingularValueDecomposition(
double[][] A, ProgressListener progressListener, ThreadMaster threadMaster) {
// Derived from LINPACK code.
// Initialize.
m = A.length;
n = A[0].length;
int nu = Math.min(m, n);
s = new double[Math.min(m + 1, n)];
U = new double[m][nu];
V = new double[n][n];
double[] e = new double[n];
double[] work = new double[m];
boolean wantu = true;
boolean wantv = true;
// Reduce A to bidiagonal form, storing the diagonal elements
// in s and the super-diagonal elements in e.
int nct = Math.min(m - 1, n);
int nrt = Math.max(0, Math.min(n - 2, m));
if (progressListener != null)
progressListener.startProgress("Initializing SVD...", 0, Math.max(nct, nrt));
for (int k = 0; k < Math.max(nct, nrt); k++) {
if (progressListener != null) progressListener.updateProgress(k);
if (threadMaster != null && threadMaster.threadMustDie()) return;
if (k < nct) {
// Compute the transformation for the k-th column and
// place the k-th diagonal in s[k].
// Compute 2-norm of k-th column without under/overflow.
s[k] = 0;
for (int i = k; i < m; i++) {
s[k] = hypot(s[k], A[i][k]);
}
if (s[k] != 0.0) {
if (A[k][k] < 0.0) {
s[k] = -s[k];
}
for (int i = k; i < m; i++) {
A[i][k] /= s[k];
}
A[k][k] += 1.0;
}
s[k] = -s[k];
}
for (int j = k + 1; j < n; j++) {
if ((k < nct) & (s[k] != 0.0)) {
// Apply the transformation.
double t = 0;
for (int i = k; i < m; i++) {
t += A[i][k] * A[i][j];
}
t = -t / A[k][k];
for (int i = k; i < m; i++) {
A[i][j] += t * A[i][k];
}
}
// Place the k-th row of A into e for the
// subsequent calculation of the row transformation.
e[j] = A[k][j];
}
if (wantu & (k < nct)) {
// Place the transformation in U for subsequent back
// multiplication.
for (int i = k; i < m; i++) {
U[i][k] = A[i][k];
}
}
if (k < nrt) {
// Compute the k-th row transformation and place the
// k-th super-diagonal in e[k].
// Compute 2-norm without under/overflow.
e[k] = 0;
for (int i = k + 1; i < n; i++) {
e[k] = hypot(e[k], e[i]);
}
if (e[k] != 0.0) {
if (e[k + 1] < 0.0) {
e[k] = -e[k];
}
for (int i = k + 1; i < n; i++) {
e[i] /= e[k];
}
e[k + 1] += 1.0;
}
e[k] = -e[k];
if ((k + 1 < m) & (e[k] != 0.0)) {
// Apply the transformation.
for (int i = k + 1; i < m; i++) {
work[i] = 0.0;
}
for (int j = k + 1; j < n; j++) {
for (int i = k + 1; i < m; i++) {
work[i] += e[j] * A[i][j];
}
}
for (int j = k + 1; j < n; j++) {
double t = -e[j] / e[k + 1];
for (int i = k + 1; i < m; i++) {
A[i][j] += t * work[i];
}
}
}
if (wantv) {
// Place the transformation in V for subsequent
// back multiplication.
for (int i = k + 1; i < n; i++) {
V[i][k] = e[i];
}
}
}
}
// Set up the final bidiagonal matrix or order p.
int p = Math.min(n, m + 1);
if (nct < n) {
s[nct] = A[nct][nct];
}
if (m < p) {
s[p - 1] = 0.0;
}
if (nrt + 1 < p) {
e[nrt] = A[nrt][p - 1];
}
e[p - 1] = 0.0;
// If required, generate U.
if (wantu) {
if (progressListener != null)
progressListener.startProgress("generating eigenvalues...", 0, nct);
for (int j = nct; j < nu; j++) {
for (int i = 0; i < m; i++) {
U[i][j] = 0.0;
}
U[j][j] = 1.0;
}
for (int k = nct - 1; k >= 0; k--) {
if (progressListener != null) progressListener.updateProgress(nct - k);
if (threadMaster != null && threadMaster.threadMustDie()) return;
if (s[k] != 0.0) {
for (int j = k + 1; j < nu; j++) {
double t = 0;
for (int i = k; i < m; i++) {
t += U[i][k] * U[i][j];
}
t = -t / U[k][k];
for (int i = k; i < m; i++) {
U[i][j] += t * U[i][k];
}
}
for (int i = k; i < m; i++) {
U[i][k] = -U[i][k];
}
U[k][k] = 1.0 + U[k][k];
for (int i = 0; i < k - 1; i++) {
U[i][k] = 0.0;
}
} else {
for (int i = 0; i < m; i++) {
U[i][k] = 0.0;
}
U[k][k] = 1.0;
}
}
}
// If required, generate V.
if (wantv) {
if (progressListener != null)
progressListener.startProgress("generating eigenvectors...", 0, n);
for (int k = n - 1; k >= 0; k--) {
if (progressListener != null) progressListener.updateProgress(n - k);
if (threadMaster != null && threadMaster.threadMustDie()) return;
if ((k < nrt) & (e[k] != 0.0)) {
for (int j = k + 1; j < nu; j++) {
double t = 0;
for (int i = k + 1; i < n; i++) {
t += V[i][k] * V[i][j];
}
t = -t / V[k + 1][k];
for (int i = k + 1; i < n; i++) {
V[i][j] += t * V[i][k];
}
}
}
for (int i = 0; i < n; i++) {
V[i][k] = 0.0;
}
V[k][k] = 1.0;
}
}
// Main iteration loop for the singular values.
int pp = p - 1;
int iter = 0;
double eps = Math.pow(2.0, -52.0);
if (progressListener != null)
progressListener.startProgress("locating negligible elements...", 0, pp + 1);
while (p > 0) {
if (progressListener != null) progressListener.updateProgress(pp - p);
if (threadMaster != null && threadMaster.threadMustDie()) return;
int k, kase;
// Here is where a test for too many iterations would go.
// This section of the program inspects for
// negligible elements in the s and e arrays. On
// completion the variables kase and k are set as follows.
// kase = 1 if s(p) and e[k-1] are negligible and k<p
// kase = 2 if s(k) is negligible and k<p
// kase = 3 if e[k-1] is negligible, k<p, and
// s(k), ..., s(p) are not negligible (qr step).
// kase = 4 if e(p-1) is negligible (convergence).
for (k = p - 2; k >= -1; k--) {
if (k == -1) {
break;
}
if (Math.abs(e[k]) <= eps * (Math.abs(s[k]) + Math.abs(s[k + 1]))) {
e[k] = 0.0;
break;
}
}
if (k == p - 2) {
kase = 4;
} else {
int ks;
for (ks = p - 1; ks >= k; ks--) {
if (ks == k) {
break;
}
double t = (ks != p ? Math.abs(e[ks]) : 0.) + (ks != k + 1 ? Math.abs(e[ks - 1]) : 0.);
if (Math.abs(s[ks]) <= eps * t) {
s[ks] = 0.0;
break;
}
}
if (ks == k) {
kase = 3;
} else if (ks == p - 1) {
kase = 1;
} else {
kase = 2;
k = ks;
}
}
k++;
// Perform the task indicated by kase.
switch (kase) {
// Deflate negligible s(p).
case 1:
{
double f = e[p - 2];
e[p - 2] = 0.0;
for (int j = p - 2; j >= k; j--) {
double t = hypot(s[j], f);
double cs = s[j] / t;
double sn = f / t;
s[j] = t;
if (j != k) {
f = -sn * e[j - 1];
e[j - 1] = cs * e[j - 1];
}
if (wantv) {
for (int i = 0; i < n; i++) {
t = cs * V[i][j] + sn * V[i][p - 1];
V[i][p - 1] = -sn * V[i][j] + cs * V[i][p - 1];
V[i][j] = t;
}
}
}
}
break;
// Split at negligible s(k).
case 2:
{
double f = e[k - 1];
e[k - 1] = 0.0;
for (int j = k; j < p; j++) {
double t = hypot(s[j], f);
double cs = s[j] / t;
double sn = f / t;
s[j] = t;
f = -sn * e[j];
e[j] = cs * e[j];
if (wantu) {
for (int i = 0; i < m; i++) {
t = cs * U[i][j] + sn * U[i][k - 1];
U[i][k - 1] = -sn * U[i][j] + cs * U[i][k - 1];
U[i][j] = t;
}
}
}
}
break;
// Perform one qr step.
case 3:
{
// Calculate the shift.
double scale =
Math.max(
Math.max(
Math.max(
Math.max(Math.abs(s[p - 1]), Math.abs(s[p - 2])), Math.abs(e[p - 2])),
Math.abs(s[k])),
Math.abs(e[k]));
double sp = s[p - 1] / scale;
double spm1 = s[p - 2] / scale;
double epm1 = e[p - 2] / scale;
double sk = s[k] / scale;
double ek = e[k] / scale;
double b = ((spm1 + sp) * (spm1 - sp) + epm1 * epm1) / 2.0;
double c = (sp * epm1) * (sp * epm1);
double shift = 0.0;
if ((b != 0.0) | (c != 0.0)) {
shift = Math.sqrt(b * b + c);
if (b < 0.0) {
shift = -shift;
}
shift = c / (b + shift);
}
double f = (sk + sp) * (sk - sp) + shift;
double g = sk * ek;
// Chase zeros.
for (int j = k; j < p - 1; j++) {
double t = hypot(f, g);
double cs = f / t;
double sn = g / t;
if (j != k) {
e[j - 1] = t;
}
f = cs * s[j] + sn * e[j];
e[j] = cs * e[j] - sn * s[j];
g = sn * s[j + 1];
s[j + 1] = cs * s[j + 1];
if (wantv) {
for (int i = 0; i < n; i++) {
t = cs * V[i][j] + sn * V[i][j + 1];
V[i][j + 1] = -sn * V[i][j] + cs * V[i][j + 1];
V[i][j] = t;
}
}
t = hypot(f, g);
cs = f / t;
sn = g / t;
s[j] = t;
f = cs * e[j] + sn * s[j + 1];
s[j + 1] = -sn * e[j] + cs * s[j + 1];
g = sn * e[j + 1];
e[j + 1] = cs * e[j + 1];
if (wantu && (j < m - 1)) {
for (int i = 0; i < m; i++) {
t = cs * U[i][j] + sn * U[i][j + 1];
U[i][j + 1] = -sn * U[i][j] + cs * U[i][j + 1];
U[i][j] = t;
}
}
}
e[p - 2] = f;
iter = iter + 1;
}
break;
// Convergence.
case 4:
{
// Make the singular values positive.
if (s[k] <= 0.0) {
s[k] = (s[k] < 0.0 ? -s[k] : 0.0);
if (wantv) {
for (int i = 0; i <= pp; i++) {
V[i][k] = -V[i][k];
}
}
}
// Order the singular values.
while (k < pp) {
if (s[k] >= s[k + 1]) {
break;
}
double t = s[k];
s[k] = s[k + 1];
s[k + 1] = t;
if (wantv && (k < n - 1)) {
for (int i = 0; i < n; i++) {
t = V[i][k + 1];
V[i][k + 1] = V[i][k];
V[i][k] = t;
}
}
if (wantu && (k < m - 1)) {
for (int i = 0; i < m; i++) {
t = U[i][k + 1];
U[i][k + 1] = U[i][k];
U[i][k] = t;
}
}
k++;
}
iter = 0;
p--;
}
break;
}
}
}
/**
* Downloads to a directory represented by a {@link File} object, determining the file name from
* the Content-Disposition header.
*
* @param url URL of file
* @param base base directory in which the download is saved
* @return the absolute file path of the downloaded file, or an empty string if the file could not
* be downloaded
*/
public String download(String url, File base) {
if (mHTTPClient == null) {
mHTTPClient = createHTTPClient(mPrivateKey, mCertificate, mValidateCertificate);
if (mHTTPClient == null) return "";
}
LOGGER.info("downloading file from URL=" + url + "...");
mCurrentRequest = new HttpGet(url);
// execute request
CloseableHttpResponse response;
try {
response = mHTTPClient.execute(mCurrentRequest);
} catch (IOException ex) {
LOGGER.log(Level.WARNING, "can't execute request", ex);
return "";
}
try {
int code = response.getStatusLine().getStatusCode();
// HTTP/1.1 200 OK -- other codes should throw Exceptions
if (code != 200) {
LOGGER.warning("invalid response code: " + code);
return "";
}
// get filename
Header dispHeader = response.getFirstHeader("Content-Disposition");
if (dispHeader == null) {
LOGGER.warning("no content header");
return "";
}
String filename = parseContentDisposition(dispHeader.getValue());
// never trust incoming data
filename = filename != null ? new File(filename).getName() : "";
if (filename.isEmpty()) {
LOGGER.warning("no filename in content: " + dispHeader.getValue());
return "";
}
// get file size
long s = -1;
Header lengthHeader = response.getFirstHeader("Content-Length");
if (lengthHeader == null) {
LOGGER.warning("no length header");
} else {
try {
s = Long.parseLong(lengthHeader.getValue());
} catch (NumberFormatException ex) {
LOGGER.log(Level.WARNING, "can' parse file size", ex);
}
}
final long fileSize = s;
mListener.updateProgress(s < 0 ? -2 : 0);
// TODO should check for content-disposition parsing here
// and choose another filename if necessary
HttpEntity entity = response.getEntity();
if (entity == null) {
LOGGER.warning("no entity in response");
return "";
}
File destination = new File(base, filename);
if (destination.exists()) {
LOGGER.warning("file already exists: " + destination.getAbsolutePath());
return "";
}
try (FileOutputStream out = new FileOutputStream(destination)) {
CountingOutputStream cOut =
new CountingOutputStream(out) {
@Override
protected synchronized void afterWrite(int n) {
if (fileSize <= 0) return;
// inform listener
mListener.updateProgress((int) (this.getByteCount() / (fileSize * 1.0) * 100));
}
};
entity.writeTo(cOut);
} catch (IOException ex) {
LOGGER.log(Level.WARNING, "can't download file", ex);
return "";
}
LOGGER.info("... download successful!");
return destination.getAbsolutePath();
} finally {
try {
response.close();
} catch (IOException ex) {
LOGGER.log(Level.WARNING, "can't close response", ex);
}
}
}
// TODO unused
public void abort() {
if (mCurrentRequest != null) mCurrentRequest.abort();
mListener.updateProgress(-3);
}
