protected final void printCallInfo(
final VariantContext vc,
final double[] log10AlleleFrequencyPriors,
final long runtimeNano,
final AFCalcResult result) {
printCallElement(vc, "type", "ignore", vc.getType());
int allelei = 0;
for (final Allele a : vc.getAlleles())
printCallElement(vc, "allele", allelei++, a.getDisplayString());
for (final Genotype g : vc.getGenotypes())
printCallElement(vc, "PL", g.getSampleName(), g.getLikelihoodsString());
for (int priorI = 0; priorI < log10AlleleFrequencyPriors.length; priorI++)
printCallElement(vc, "priorI", priorI, log10AlleleFrequencyPriors[priorI]);
printCallElement(vc, "runtime.nano", "ignore", runtimeNano);
printCallElement(vc, "log10PosteriorOfAFEq0", "ignore", result.getLog10PosteriorOfAFEq0());
printCallElement(vc, "log10PosteriorOfAFGt0", "ignore", result.getLog10PosteriorOfAFGT0());
for (final Allele allele : result.getAllelesUsedInGenotyping()) {
if (allele.isNonReference()) {
printCallElement(vc, "MLE", allele, result.getAlleleCountAtMLE(allele));
printCallElement(
vc, "pNonRefByAllele", allele, result.getLog10PosteriorOfAFGt0ForAllele(allele));
}
}
callReport.flush();
}
/**
* automatically generate non-existing help html files for existing commands in the CommandLoader
*
* @param cl the CommandLoader where you look for the existing commands
*/
public void createHelpText(CommandLoader cl) {
File dir = new File((getClass().getResource("..").getPath()));
dir = new File(dir, language);
if (!dir.exists() && !dir.mkdirs()) {
System.out.println("Failed to create " + dir.getAbsolutePath());
return;
}
for (String mnemo : cl.getMnemoList()) {
if (!exists(mnemo)) {
File file = new File(dir, mnemo + ".htm");
try {
file.createNewFile();
BufferedOutputStream os = new BufferedOutputStream(new FileOutputStream(file));
PrintStream ps = new PrintStream(os);
ps.println("<html>\n<head>\n<title>" + mnemo + "\n</title>\n</head>\n<body>");
ps.println("Command: " + mnemo.toUpperCase() + "<br>");
ps.println("arguments: <br>");
ps.println("effects: <br>");
ps.println("flags to be set: <br>");
ps.println("approx. clockcycles: <br>");
ps.println("misc: <br>");
ps.println("</body>\n</html>");
ps.flush();
ps.close();
} catch (IOException e) {
System.out.println("failed to create " + file.getAbsolutePath());
}
}
}
}
static void processFile(String fname, PrintStream out) throws IOException {
System.err.println("Processing: " + fname);
FileInputStream fio = new FileInputStream(new File(fname));
InputStreamReader fread = new InputStreamReader(fio, JetTest.encoding);
BufferedReader fp = new BufferedReader(fread);
StringBuffer buf = new StringBuffer();
int docno = 0, allsents = 0, processedsents = 0;
while (true) {
String line = fp.readLine();
// EOF or an empty line: the end of a Document.
if (line == null || line.equals("")) {
if (0 < buf.length()) {
SGMLProcessor.allTags = true;
Document doc = SGMLProcessor.sgmlToDoc(buf.toString(), (String[]) null);
doc.setSGMLwrapMargin(0);
System.err.println(
"Doc-" + docno + ": sents=" + allsents + ", processed=" + processedsents);
processDoc1(doc, docno);
writeDoc1(doc, out);
out.flush();
buf = new StringBuffer();
docno++;
allsents = 0;
processedsents = 0;
}
if (line == null) {
break;
} else {
continue;
}
}
if (line.startsWith("#")) {
// "#" indicates a comment line.
buf.append(line + "\n");
} else {
allsents++;
if (processedsents < MaxProcessSentences) {
buf.append("<sentence>");
String[] words = line.split(" ");
for (int i = 0; i < words.length; i++) {
if (0 != words[i].length()) {
buf.append("<token>" + words[i] + " </token>");
}
}
buf.append("</sentence>\n");
processedsents++;
}
}
}
fp.close();
fread.close();
fio.close();
return;
}
/**
* Closes down connections to the underlying process. This method will be used only if the
* supporting Java Native Interface library could be loaded.
*/
private synchronized void native_close(PrintStream out) {
try {
in.close();
out.flush();
out.close();
} catch (IOException ioe) {
}
}
/**
* Logs the event message to the output stream.
*
* @param out Stream to which the message is logged.
* @param event Message to be logged.
*/
private void log(PrintStream out, String event) {
if (null == log) {
out.println(event);
out.flush();
} else {
log.log(event);
}
}
public static void main(String args[]) throws Exception {
int testCases = Integer.parseInt(in.readLine());
for (int i = 0; i < testCases; i++) {
char[] path = in.readLine().toCharArray();
output(path);
out.println();
}
out.flush();
}
protected static void writeReferencePositions(String filePath, ArrayList<Position> positions)
throws FileNotFoundException {
PrintStream os = new PrintStream(new File(filePath));
for (Position pos : positions) {
os.format(
"%.5f %.5f %.4f\n",
pos.getLatitude().degrees, pos.getLongitude().degrees, pos.getElevation());
}
os.flush();
}
/**
* Render status using a given printer.
*
* @param status the IRunStatus to render to String
* @param printer the IRunStatusPrinter to use (defaults to AJC_PRINTER if null)
* @return the String rendering of the status, or "((IRunStatus) null)" if null
*/
public static String render(IRunStatus status, IRunStatusPrinter printer) {
if (null == status) {
return "((IRunStatus) null)";
}
if (null == printer) {
printer = RunUtils.AJC_PRINTER;
}
ByteArrayOutputStream outStream = new ByteArrayOutputStream();
PrintStream out = new PrintStream(outStream);
printer.printRunStatus(out, status);
out.flush();
return outStream.toString();
}
public static void main(String args[]) throws Exception {
StringTokenizer tokenizer = new StringTokenizer(in.readLine());
int n = Integer.parseInt(tokenizer.nextToken()), m = Integer.parseInt(tokenizer.nextToken());
Graph graph = new Graph(n, m);
for (long i = 0; i < m; i++) {
tokenizer = new StringTokenizer(in.readLine());
int from = Integer.parseInt(tokenizer.nextToken()),
to = Integer.parseInt(tokenizer.nextToken());
graph.connect(from, to);
}
output(graph, n);
out.println();
out.flush();
}
// made synchronized for 0087
// attempted to remove synchronized for 0136 to fix bug #775 (no luck tho)
// http://dev.processing.org/bugs/show_bug.cgi?id=775
public synchronized void message(String s) {
// System.out.println("M" + s.length() + ":" + s.trim()); // + "MMM" + s.length());
// this eats the CRLFs on the lines.. oops.. do it later
// if (s.trim().length() == 0) return;
// this is PApplet sending a message (via System.out.println)
// that signals that the applet has been quit.
if (s.indexOf(PApplet.EXTERNAL_STOP) == 0) {
// System.out.println("external: quit");
if (editor != null) {
// editor.internalCloseRunner(); // [091124]
// editor.handleStop(); // prior to 0192
editor.internalCloseRunner(); // 0192
}
return;
}
// this is the PApplet sending us a message that the applet
// is being moved to a new window location
if (s.indexOf(PApplet.EXTERNAL_MOVE) == 0) {
String nums = s.substring(s.indexOf(' ') + 1).trim();
int space = nums.indexOf(' ');
int left = Integer.parseInt(nums.substring(0, space));
int top = Integer.parseInt(nums.substring(space + 1));
// this is only fired when connected to an editor
editor.setSketchLocation(new Point(left, top));
// System.out.println("external: move to " + left + " " + top);
return;
}
// these are used for debugging, in case there are concerns
// that some errors aren't coming through properly
// if (s.length() > 2) {
// System.err.println(newMessage);
// System.err.println("message " + s.length() + ":" + s);
// }
// always shove out the message, since it might not fall under
// the same setup as we're expecting
sketchErr.print(s);
// System.err.println("[" + s.length() + "] " + s);
sketchErr.flush();
}
public static void main(String args[]) throws Exception {
int testCases = Integer.parseInt(in.readLine());
for (int i = 0; i < testCases; i++) {
StringTokenizer tokenizer = new StringTokenizer(in.readLine());
int n = Integer.parseInt(tokenizer.nextToken());
Party party = new Party();
for (int j = 0; j < n; j++) {
Person person = new Person(j);
tokenizer = new StringTokenizer(in.readLine());
while (tokenizer.hasMoreTokens()) person.add(Integer.parseInt(tokenizer.nextToken()));
party.invite(person);
}
output(party);
out.println();
}
out.flush();
}
/**
* Closes down connections to the underlying process. This method will be used only if the
* supporting Java Native Interface library could not be loaded.
*/
private synchronized void pure_close(PrintStream out) {
/*
* Try to close this process for at least 30 seconds.
*/
for (int i = 0; i < 30; i++) {
try {
in.close();
err.close();
out.flush();
out.close();
} catch (IOException ioe) {
}
try {
exit_code = p.waitFor();
p.destroy();
break;
} catch (InterruptedException ie) {
}
try {
Thread.sleep(1000);
} catch (InterruptedException ie) {
}
}
}
public HTTPResponse post(String host, int port, boolean isKeepAlive) {
HTTPResponse httpRes = new HTTPResponse();
setConnection((isKeepAlive == true) ? HTTP.KEEP_ALIVE : HTTP.CLOSE);
boolean isHeaderRequest = isHeadRequest();
OutputStream out = null;
InputStream in = null;
try {
if (postSocket == null) postSocket = new Socket(host, port);
out = postSocket.getOutputStream();
PrintStream pout = new PrintStream(out);
pout.print(getHeader());
pout.print(HTTP.CRLF);
boolean isChunkedRequest = isChunked();
String content = getContentString();
int contentLength = 0;
if (content != null) contentLength = content.length();
if (0 < contentLength) {
if (isChunkedRequest == true) {
String chunSizeBuf = Long.toString(contentLength);
pout.print(chunSizeBuf);
pout.print(HTTP.CRLF);
}
pout.print(content);
if (isChunkedRequest == true) pout.print(HTTP.CRLF);
}
if (isChunkedRequest == true) {
pout.print("0");
pout.print(HTTP.CRLF);
}
pout.flush();
in = postSocket.getInputStream();
httpRes.set(in, isHeaderRequest);
} catch (Exception e) {
httpRes.setStatusCode(HTTPStatus.INTERNAL_SERVER_ERROR);
} finally {
if (isKeepAlive == false) {
try {
in.close();
} catch (Exception e) {
}
;
if (in != null)
try {
out.close();
} catch (Exception e) {
}
;
if (out != null)
try {
postSocket.close();
} catch (Exception e) {
}
;
postSocket = null;
}
}
return httpRes;
}
/**
* ** Encodes the specified DBRecordKyes into XML and writes it to ** a specified PrintStream
* ** @param out The PrintStream ** @param dbrk The list of DBRecordKeys
*/
public static void printXML(PrintStream out, DBRecordKey... dbrk) {
if (out != null) {
DBRecordKey.printXML(new PrintWriter(out), dbrk);
out.flush();
}
}
/** Finalizes output file. */
public void finished() {
m_printstream.flush();
}
/** Starts main program with the specified arguments. */
public synchronized boolean run(String args[]) {
ok = true;
if (!parseArgs(args)) {
return false;
}
try {
if (cflag || uflag) {
if (fname != null) {
// The name of the zip file as it would appear as its own
// zip file entry. We use this to make sure that we don't
// add the zip file to itself.
zname = fname.replace(File.separatorChar, '/');
if (zname.startsWith("./")) {
zname = zname.substring(2);
}
}
}
if (cflag) {
Manifest manifest = null;
InputStream in = null;
if (!Mflag) {
if (mname != null) {
in = new FileInputStream(mname);
manifest = new Manifest(new BufferedInputStream(in));
} else {
manifest = new Manifest();
}
addVersion(manifest);
addCreatedBy(manifest);
if (isAmbiguousMainClass(manifest)) {
if (in != null) {
in.close();
}
return false;
}
if (ename != null) {
addMainClass(manifest, ename);
}
if (pname != null) {
if (!addProfileName(manifest, pname)) {
if (in != null) {
in.close();
}
return false;
}
}
}
OutputStream out;
if (fname != null) {
out = new FileOutputStream(fname);
} else {
out = new FileOutputStream(FileDescriptor.out);
if (vflag) {
// Disable verbose output so that it does not appear
// on stdout along with file data
// error("Warning: -v option ignored");
vflag = false;
}
}
expand(null, files, false);
create(new BufferedOutputStream(out, 4096), manifest);
if (in != null) {
in.close();
}
out.close();
} else if (uflag) {
File inputFile = null, tmpFile = null;
FileInputStream in;
FileOutputStream out;
if (fname != null) {
inputFile = new File(fname);
tmpFile = createTempFileInSameDirectoryAs(inputFile);
in = new FileInputStream(inputFile);
out = new FileOutputStream(tmpFile);
} else {
in = new FileInputStream(FileDescriptor.in);
out = new FileOutputStream(FileDescriptor.out);
vflag = false;
}
InputStream manifest = (!Mflag && (mname != null)) ? (new FileInputStream(mname)) : null;
expand(null, files, true);
boolean updateOk = update(in, new BufferedOutputStream(out), manifest, null);
if (ok) {
ok = updateOk;
}
in.close();
out.close();
if (manifest != null) {
manifest.close();
}
if (ok && fname != null) {
// on Win32, we need this delete
inputFile.delete();
if (!tmpFile.renameTo(inputFile)) {
tmpFile.delete();
throw new IOException(getMsg("error.write.file"));
}
tmpFile.delete();
}
} else if (tflag) {
replaceFSC(files);
if (fname != null) {
list(fname, files);
} else {
InputStream in = new FileInputStream(FileDescriptor.in);
try {
list(new BufferedInputStream(in), files);
} finally {
in.close();
}
}
} else if (xflag) {
replaceFSC(files);
if (fname != null && files != null) {
extract(fname, files);
} else {
InputStream in =
(fname == null) ? new FileInputStream(FileDescriptor.in) : new FileInputStream(fname);
try {
extract(new BufferedInputStream(in), files);
} finally {
in.close();
}
}
} else if (iflag) {
genIndex(rootjar, files);
}
} catch (IOException e) {
fatalError(e);
ok = false;
} catch (Error ee) {
ee.printStackTrace();
ok = false;
} catch (Throwable t) {
t.printStackTrace();
ok = false;
}
out.flush();
err.flush();
return ok;
}
static void writeDocRaw(Document doc, PrintStream out) throws IOException {
out.println(doc.writeSGML(null).toString());
out.flush();
return;
}
public static final void print(Object msg) {
out.print(msg);
out.flush();
}
public static void main(String argv[]) {
try {
BufferedReader buf1 = new BufferedReader(new FileReader("./index/pIndex"));
FileOutputStream out = new FileOutputStream("finalindex");
PrintStream p = new PrintStream(out);
String nline1, nline2, term1, term2, term3, term, t1, t2;
StringBuffer sbuff = new StringBuffer();
StringBuffer sbuff1;
long df, postings = 0, line = 0;
String[] id;
int flag = 0;
while (true) {
nline1 = buf1.readLine();
// System.out.println(nline1);
if (nline1 == null) break;
line++;
String[] words = nline1.split(" ");
String search_word = words[0];
char ch = search_word.charAt(0);
// System.out.println("c"+ch);
id = words[1].split(",");
df = id.length;
flag = 0;
sbuff1 = new StringBuffer(); // System.out.println(df);
if (df > 30000 && ((ch == 't') || ch == 'o' || ch == 'c')) {
int count = 0;
postings = 0;
System.out.println("before df" + df + ";line" + line); // System.out.println("here\n");
while (count < df) {
String temp1 = id[count];
String temp[] = temp1.split(":");
int t = Integer.parseInt(temp[1]);
// System.out.println("t:"+t);
if (t != 1) {
if (flag == 0) {
// System.out.println("here\n");
sbuff1.append(search_word);
sbuff1.append(" ");
sbuff1.append(temp1);
flag = 1;
} else {
sbuff1.append(",");
sbuff1.append(temp1);
postings++;
}
}
count++;
}
// System.out.println(sbuff1);
System.out.println("postings size after:" + postings + ";line" + line);
p.println(sbuff1.toString());
p.flush();
} else {
p.println(nline1);
p.flush();
}
}
} catch (IOException E) {
}
}
public String sendKommando(String kommando) throws IOException {
System.out.println("send: " + kommando);
ud.println(kommando);
ud.flush(); // sørg for at data sendes til værten før vi læser svar
return læsSvar();
}
