static void initWords(int size, Object[] key, Object[] abs) {
String fileName = "testwords.txt";
int ki = 0;
int ai = 0;
try {
FileInputStream fr = new FileInputStream(fileName);
BufferedInputStream in = new BufferedInputStream(fr);
while (ki < size || ai < size) {
StringBuffer sb = new StringBuffer();
for (; ; ) {
int c = in.read();
if (c < 0) {
if (ki < size) randomWords(key, ki, size);
if (ai < size) randomWords(abs, ai, size);
in.close();
return;
}
if (c == '\n') {
String s = sb.toString();
if (ki < size) key[ki++] = s;
else abs[ai++] = s;
break;
}
sb.append((char) c);
}
}
in.close();
} catch (IOException ex) {
System.out.println("Can't read words file:" + ex);
throw new Error(ex);
}
}
protected String getDropSQL(DatabaseObjectType type, String name) {
SQLObject foundDropQuery = null;
String sqlStatement = "DROP " + type.toString() + " " + name;
for (SQLObject dropQuery : catalogStore.getDropStatements()) {
if (type == dropQuery.getType()) {
foundDropQuery = dropQuery;
break;
}
}
if (foundDropQuery != null
&& foundDropQuery.getSql() != null
&& !foundDropQuery.getSql().isEmpty()) {
String dropStatement = foundDropQuery.getSql();
StringBuffer sqlBuffer = new StringBuffer(dropStatement.length() + name.length());
int identifier = dropStatement.indexOf('?');
sqlBuffer
.append(dropStatement.substring(0, identifier))
.append(name)
.append(dropStatement.substring(identifier + 1));
sqlStatement = sqlBuffer.toString();
}
return sqlStatement;
}
private Set<String> getListenerClassNames(final String xml, final String path)
throws IOException, SAXException {
final Digester digester = getDigester();
digester.addObjectCreate(XmlConfiguration.listeners, ArrayList.class);
digester.addObjectCreate(path, StringBuffer.class); // TODO rather than StringBuffer can
digester.addCallMethod(path, "append", 0); // TODO this be a String?
digester.addSetRoot(path, "add");
final Set<String> classNames = new HashSet<String>();
final StringReader includeReader = new StringReader(xml);
Object o = digester.parse(includeReader);
if (o == null) {
// return empty Set
return classNames;
}
Collection<StringBuffer> classNamesAsStringBuffers = (Collection<StringBuffer>) o;
/** When the configuration contains no listener settings, return the empty Set */
if (classNamesAsStringBuffers == null) {
return classNames;
}
for (StringBuffer classNamesAsStringBuffer : classNamesAsStringBuffers) {
classNames.add(classNamesAsStringBuffer.toString());
}
return classNames;
}
/**
* ** Reads a line from the specified socket's input stream ** @param socket The socket to read a
* line from ** @param maxLen The maximum length of of the line to read ** @param sb The string
* buffer to use ** @throws IOException if an error occurs or the server has stopped
*/
protected static String socketReadLine(Socket socket, int maxLen, StringBuffer sb)
throws IOException {
if (socket != null) {
int dataLen = 0;
StringBuffer data = (sb != null) ? sb : new StringBuffer();
InputStream input = socket.getInputStream();
while ((maxLen < 0) || (maxLen > dataLen)) {
int ch = input.read();
// Print.logInfo("ReadLine char: " + ch);
if (ch < 0) {
// this means that the server has stopped
throw new IOException("End of input");
} else if (ch == LineTerminatorChar) {
// include line terminator in String
data.append((char) ch);
dataLen++;
break;
} else {
// append character
data.append((char) ch);
dataLen++;
}
}
return data.toString();
} else {
return null;
}
}
/**
* Returns a String representation of the <code><saml:Attribute></code> element.
*
* @param includeNS Determines whether or not the namespace qualifier is prepended to the Element
* when converted
* @param declareNS Determines whether or not the namespace is declared within the Element.
* @return A string containing the valid XML for this element
*/
public String toString(boolean includeNS, boolean declareNS) {
StringBuffer result = new StringBuffer(1000);
String prefix = "";
String uri = "";
if (includeNS) {
prefix = SAMLConstants.ASSERTION_PREFIX;
}
if (declareNS) {
uri = SAMLConstants.assertionDeclareStr;
}
result
.append("<")
.append(prefix)
.append("Attribute")
.append(uri)
.append(" AttributeName=\"")
.append(_attributeName)
.append("\" AttributeNamespace=\"")
.append(_attributeNameSpace)
.append("\">\n");
Iterator iter = _attributeValue.iterator();
while (iter.hasNext()) {
result.append(XMLUtils.printAttributeValue((Element) iter.next(), prefix)).append("\n");
}
result.append("</").append(prefix).append("Attribute>\n");
return result.toString();
}
public boolean shutdown(int port, boolean ssl) {
try {
String protocol = "http" + (ssl ? "s" : "");
URL url = new URL(protocol, "127.0.0.1", port, "shutdown");
HttpURLConnection conn = (HttpURLConnection) url.openConnection();
conn.setRequestMethod("GET");
conn.setRequestProperty("servicemanager", "shutdown");
conn.connect();
StringBuffer sb = new StringBuffer();
BufferedReader br = new BufferedReader(new InputStreamReader(conn.getInputStream(), "UTF-8"));
int n;
char[] cbuf = new char[1024];
while ((n = br.read(cbuf, 0, cbuf.length)) != -1) sb.append(cbuf, 0, n);
br.close();
String message = sb.toString().replace("<br>", "\n");
if (message.contains("Goodbye")) {
cp.appendln("Shutting down the server:");
String[] lines = message.split("\n");
for (String line : lines) {
cp.append("...");
cp.appendln(line);
}
return true;
}
} catch (Exception ex) {
}
cp.appendln("Unable to shutdown CTP");
return false;
}
private void parse(String filename) throws Exception {
BufferedReader br = new BufferedReader(new InputStreamReader(new FileInputStream(filename)));
StringBuffer sb = new StringBuffer();
int j;
while ((j = br.read()) != -1) {
char next = (char) j;
if (next >= 'A' && next <= 'z') {
sb.append(next);
}
if (sb.length() == 4) {
String qGram = sb.toString().toUpperCase();
sb = new StringBuffer();
int frequency = 0;
if (map.containsKey(qGram)) {
frequency = map.get(qGram);
}
frequency++;
map.put(qGram, frequency);
}
}
br.close();
}
public String toString() {
StringBuffer buf = new StringBuffer();
for (int i = 0; i < m_Size; i++) {
buf.append(getBit(i) ? '1' : '0');
}
return buf.toString();
}
/** Converts a normal string to a html conform string */
public static String conv2Html(String st) {
StringBuffer buf = new StringBuffer();
for (int i = 0; i < st.length(); i++) {
buf.append(conv2Html(st.charAt(i)));
}
return buf.toString();
}
public static String text(NodeList nodeList) {
StringBuffer sb = new StringBuffer();
for (int i = 0; i < nodeList.getLength(); i++) {
sb.append(text(nodeList.item(i)));
}
return sb.toString();
}
public static void LCS(String str, String str2) {
int len = str.length();
int len2 = str2.length();
int[][] storage = new int[len + 1][len2 + 1];
for (int i = 0; i <= len; i++) {
for (int j = 0; j <= len2; j++) {
if (i == 0 || j == 0) {
storage[i][j] = 0;
} else if (str.charAt(i - 1) == str2.charAt(j - 1)) {
storage[i][j] = 1 + storage[i - 1][j - 1];
} else {
storage[i][j] = Math.max(storage[i - 1][j], storage[i][j - 1]);
}
}
}
int i = len;
int j = len2;
StringBuffer sb = new StringBuffer();
while (storage[i][j] > 0) {
if (str.charAt(i - 1) == str2.charAt(j - 1)) {
sb.insert(0, str.charAt(i - 1));
i--;
j--;
} else if (storage[i - 1][j] > storage[i][j - 1]) {
i--;
} else {
j--;
}
}
System.out.println(sb.toString());
}
private ClassLoaderStrategy getClassLoaderStrategy(String fullyQualifiedClassName)
throws Exception {
try {
// Get just the package name
StringBuffer sb = new StringBuffer(fullyQualifiedClassName);
sb.delete(sb.lastIndexOf("."), sb.length());
currentPackage = sb.toString();
// Retrieve the Java classpath from the system properties
String cp = System.getProperty("java.class.path");
String sepChar = System.getProperty("path.separator");
String[] paths = StringUtils.pieceList(cp, sepChar.charAt(0));
ClassLoaderStrategy cl =
ClassLoaderUtil.getClassLoader(ClassLoaderUtil.FILE_SYSTEM_CLASS_LOADER, new String[] {});
// Iterate through paths until class with the specified name is found
String classpath = StringUtils.replaceChar(currentPackage, '.', File.separatorChar);
for (int i = 0; i < paths.length; i++) {
Class[] classes = cl.getClasses(paths[i] + File.separatorChar + classpath, currentPackage);
for (int j = 0; j < classes.length; j++) {
if (classes[j].getName().equals(fullyQualifiedClassName)) {
return ClassLoaderUtil.getClassLoader(
ClassLoaderUtil.FILE_SYSTEM_CLASS_LOADER, new String[] {paths[i]});
}
}
}
throw new Exception("Class could not be found.");
} catch (Exception e) {
System.err.println("Exception creating class loader strategy.");
System.err.println(e.getMessage());
throw e;
}
}
/**
* Return the number of characters that will be printed when the specified character is echoed to
* the screen. Adapted from cat by Torbjorn Granlund, as repeated in stty by David MacKenzie.
*/
StringBuffer getPrintableCharacters(char ch) {
StringBuffer sbuff = new StringBuffer();
if (ch >= 32) {
if (ch < 127) {
sbuff.append(ch);
} else if (ch == 127) {
sbuff.append('^');
sbuff.append('?');
} else {
sbuff.append('M');
sbuff.append('-');
if (ch >= (128 + 32)) {
if (ch < (128 + 127)) {
sbuff.append((char) (ch - 128));
} else {
sbuff.append('^');
sbuff.append('?');
}
} else {
sbuff.append('^');
sbuff.append((char) (ch - 128 + 64));
}
}
} else {
sbuff.append('^');
sbuff.append((char) (ch + 64));
}
return sbuff;
}
/**
* Starts a new column, possibly closing the current column if needed
*
* @param ret the output buffer to put LaTeX into
* @param p the properties from the <code><td></code> tag
*/
public void startCol(StringBuffer ret, Properties p) {
endCol(ret);
int span = hasNumProp("colspan", p);
if (colcnt > 0) {
ret.append(" & ");
}
String align = hasProp("align", p);
if (align != null && span < 0) span = 1;
if (span > 0) {
ret.append("\\multicolumn{" + span + "}{");
if (border && colcnt == 0) ret.append("|");
String cc =
""
+ (char) ('a' + (colcnt / (26 * 26)))
+ (char) ((colcnt / 26) + 'a')
+ (char) ((colcnt % 26) + 'a');
if (align != null) {
String h = align.substring(0, 1);
if ("rR".indexOf(h) >= 0) ret.append("r");
else if ("lL".indexOf(h) >= 0) ret.append("p{\\tbl" + tc + "c" + cc + "w}");
else if ("cC".indexOf(h) >= 0) ret.append("p{\\tbl" + tc + "c" + cc + "w}");
} else ret.append("p{\\tbl" + tc + "c" + cc + "w}");
if (border) ret.append("|");
ret.append("}");
}
String wid = p.getProperty("texwidth");
ret.append("{");
if (wid != null) {
ret.append("\\parbox{" + wid + "}{\\vskip 1ex ");
parboxed = true;
}
colcnt++;
colopen = true;
}
private String mkStr(char kar, int num) {
StringBuffer sb = new StringBuffer(num);
for (int ix = 0; ix < num; ix++) {
sb.append(kar);
}
return sb.toString();
}
public String toString() {
StringBuffer buffer = new StringBuffer("Queue:\n"); // $NON-NLS-1$
for (int i = this.start; i <= this.end; i++) {
buffer.append(this.names[i]).append('\n');
}
return buffer.toString();
}
// ----------------------------------------------------------------------
// for "SrvTypeRqst"
// get the list of service types for specified scope & naming authority
// ----------------------------------------------------------------------
public synchronized String getServiceTypeList(String na, String scope) {
Vector typelist = new Vector(5);
Iterator values = table.values().iterator();
while (values.hasNext()) {
Entry e = (Entry) values.next();
if (!e.getDeleted()
&& // nor deleted
scope.equalsIgnoreCase(e.getScope())
&& // match scope
(na.equals("*")
|| // NA wildcard
na.equalsIgnoreCase(e.getNA()))
&& // match NA
!typelist.contains(e.getType())) {
typelist.addElement(e.getType());
}
}
StringBuffer tl = new StringBuffer();
for (int i = 0; i < typelist.size(); i++) {
String s = (String) typelist.elementAt(i);
if (tl.length() > 0) tl.append(",");
tl.append(s);
}
return tl.toString();
}
/** ** Reads/returns the specified CompileTime template file */
private static String readTemplate(File tf, String pkgName) {
/* read template data */
byte templData[] = FileTools.readFile(tf);
if (templData == null) {
Print.errPrintln("\nUnable to read Input/Template file: " + tf);
return null;
} else if (templData.length == 0) {
Print.errPrintln("\nInput/Template file is empty: " + tf);
return null;
}
/* return template String */
String templateText = StringTools.toStringValue(templData);
if (!StringTools.isBlank(pkgName) && !StringTools.isBlank(templateText)) {
String lines[] = StringTools.split(templateText, '\n', false);
for (int i = 0; i < lines.length; i++) {
if (lines[i].trim().startsWith(JAVA_PACKAGE_)) {
lines[i] = CompiletimeVars.packageLine(pkgName);
return StringTools.join(lines, '\n') + "\n";
}
}
StringBuffer sb = new StringBuffer();
sb.append(CompiletimeVars.packageLine(pkgName)).append("\n");
sb.append(templateText);
return sb.toString();
} else {
return templateText;
}
}
private String addNewInteraction(String fingerprint, BiologicalInteraction interaction)
throws SQLException {
String sql =
String.format(
"INSERT IGNORE INTO interaction (fingerprint) VALUES (%s)",
SqlUtil.toSqlVarchar(fingerprint));
if (1 != DBUtil.update(sql)) {
System.out.println("SQL update failed? " + sql);
}
String interaction_id = DBUtil.querySingle("SELECT LAST_INSERT_ID()");
Iterator<BiologicalEntity> iter = interaction.getEntityIterator();
StringBuffer sb =
new StringBuffer(
"INSERT IGNORE INTO interaction_pool (interaction_id, gene_id, entity_src_table, role) VALUES ");
while (iter.hasNext()) {
BiologicalEntity entity = iter.next();
sb.append("(")
.append(interaction_id)
.append(", ")
.append(SqlUtil.toSqlVarchar(entity.getId()))
.append(", '")
.append(srcTableLookup.get(entity.getId_src()))
.append("', '")
.append(entity.getRole())
.append("')");
if (iter.hasNext()) sb.append(", ");
}
if (DBUtil.update(sb.toString()) != interaction.getEnvolvedEntityCount()) {
System.out.println("SQL update failed? " + sb);
}
return interaction_id;
}
/**
* Returns the full URL of the request including the query string.
*
* <p>Used as a convenience method for logging purposes.
*
* @param request the request object.
* @return the full URL of the request including the query string.
*/
protected String getRequestURL(HttpServletRequest request) {
StringBuffer sb = request.getRequestURL();
if (request.getQueryString() != null) {
sb.append("?").append(request.getQueryString());
}
return sb.toString();
}
/**
* convert email address mapping<br>
* <code>user-</code> will be replace by the email address of the user as stored in the user
* repository <code>group-</code> will
*/
public String convertEmailList(String mailTo) {
StringBuffer ret = new StringBuffer();
String[] list = mailTo.split(";");
if (list == null) {
return "";
}
for (int i = 0; i < list.length; i++) { // for each item
String userName = list[i];
if (i != 0) {
ret.append("\n");
}
if (userName.startsWith(MailConstants.PREFIX_USER)) {
userName = StringUtils.removeStart(userName, MailConstants.PREFIX_USER);
if (log.isDebugEnabled()) {
log.debug("username =" + userName);
}
ret.append(getUserMail(userName));
} else if (userName.startsWith(MailConstants.PREFIX_GROUP)) {
} else if (userName.startsWith(MailConstants.PREFIX_ROLE)) {
} else {
// none of the above, just add the mail to the list
ret.append(userName);
}
}
return ret.toString();
}
public void addDataSet(Color color, String legend, Data data[]) throws Exception {
/* init */
this._initChart();
/* dataset color/legend/markers */
String hexColor = ColorTools.toHexString(color, false);
this.addDatasetColor(hexColor);
this.addDatasetLegend(legend);
this.addShapeMarker("d," + hexColor + "," + this.dataSetCount + ",-1,7,1");
/* data */
StringBuffer xv = new StringBuffer();
StringBuffer yv = new StringBuffer();
for (int i = 0; i < data.length; i++) {
GetScaledExtendedEncodedValue(yv, data[i].getTempC(), this.minTempC, this.maxTempC);
GetScaledExtendedEncodedValue(xv, data[i].getTimestamp(), this.minDateTS, this.maxDateTS);
}
if (StringTools.isBlank(this.chd)) {
this.chd = "e:";
} else {
this.chd += ",";
}
this.chd += xv.toString() + "," + yv.toString();
/* count data set */
this.dataSetCount++;
}
/**
* Adds <code>AttributeValue</code> to the Attribute.
*
* @param value A String representing <code>AttributeValue</code>.
* @exception SAMLException
*/
public void addAttributeValue(String value) throws SAMLException {
if (value == null || value.length() == 0) {
if (SAMLUtilsCommon.debug.messageEnabled()) {
SAMLUtilsCommon.debug.message("addAttributeValue: Input is null");
}
throw new SAMLRequesterException(SAMLUtilsCommon.bundle.getString("nullInput"));
}
StringBuffer sb = new StringBuffer(300);
sb.append("<")
.append(SAMLConstants.ASSERTION_PREFIX)
.append("AttributeValue")
.append(SAMLConstants.assertionDeclareStr)
.append(">")
.append(value)
.append("</")
.append(SAMLConstants.ASSERTION_PREFIX)
.append("AttributeValue>");
try {
Element ele =
XMLUtils.toDOMDocument(sb.toString().trim(), SAMLUtilsCommon.debug).getDocumentElement();
if (_attributeValue == null) {
_attributeValue = new ArrayList();
}
if (!(_attributeValue.add(ele))) {
if (SAMLUtilsCommon.debug.messageEnabled()) {
SAMLUtilsCommon.debug.message(
"Attribute: failed to " + "add to the attribute value list.");
}
throw new SAMLRequesterException(SAMLUtilsCommon.bundle.getString("addListError"));
}
} catch (Exception e) {
SAMLUtilsCommon.debug.error("addAttributeValue error", e);
throw new SAMLRequesterException("Exception in addAttributeValue" + e.getMessage());
}
}
public static String randomHash(int length) {
StringBuffer buffer = new StringBuffer();
for (int i = 0; i < length; i++) {
buffer.append(DIC[(int) (System.nanoTime() % 32)]);
}
return buffer.toString();
}
/**
* @description: Decodes the supplied lzw encoded string
* @method decode
* @param {string} s
* @param {function} callback
*/
public static String decode(List<Integer> encoded) {
// Build the dictionary.
int dictSize = 256;
Map<Integer, String> dictionary = new HashMap<Integer, String>();
for (int i = 0; i < 256; i++) {
dictionary.put(i, "" + (char) i);
}
String w = "" + (char) (int) encoded.remove(0);
StringBuffer result = new StringBuffer(w);
for (int k : encoded) {
String entry;
if (dictionary.containsKey(k)) {
entry = dictionary.get(k);
} else if (k == dictSize) {
entry = w + w.charAt(0);
} else {
throw new IllegalArgumentException("Bad compressed k: " + k);
}
result.append(entry);
// Add w+entry[0] to the dictionary.
dictionary.put(dictSize++, w + entry.charAt(0));
w = entry;
}
return result.toString();
}
/**
* ************************************************************************ Lineas de Remesa
*
* @param whereClause where clause or null (starting with AND)
* @return lines
*/
public MRemesaLine[] getLines(String whereClause, String orderClause) {
ArrayList list = new ArrayList();
StringBuffer sql = new StringBuffer("SELECT * FROM C_RemesaLine WHERE C_Remesa_ID=? ");
if (whereClause != null) sql.append(whereClause);
if (orderClause != null) sql.append(" ").append(orderClause);
PreparedStatement pstmt = null;
try {
pstmt = DB.prepareStatement(sql.toString(), get_TrxName());
pstmt.setInt(1, getC_Remesa_ID());
ResultSet rs = pstmt.executeQuery();
while (rs.next()) list.add(new MRemesaLine(getCtx(), rs));
rs.close();
pstmt.close();
pstmt = null;
} catch (Exception e) {
log.saveError("getLines - " + sql, e);
} finally {
try {
if (pstmt != null) pstmt.close();
} catch (Exception e) {
}
pstmt = null;
}
//
MRemesaLine[] lines = new MRemesaLine[list.size()];
list.toArray(lines);
return lines;
} // getLines
public void run() {
StringBuffer data = new StringBuffer();
Print.logDebug("Client:InputThread started");
while (true) {
data.setLength(0);
boolean timeout = false;
try {
if (this.readTimeout > 0L) {
this.socket.setSoTimeout((int) this.readTimeout);
}
ClientSocketThread.socketReadLine(this.socket, -1, data);
} catch (InterruptedIOException ee) { // SocketTimeoutException ee) {
// error("Read interrupted (timeout) ...");
if (getRunStatus() != THREAD_RUNNING) {
break;
}
timeout = true;
// continue;
} catch (Throwable t) {
Print.logError("Client:InputThread - " + t);
t.printStackTrace();
break;
}
if (!timeout || (data.length() > 0)) {
ClientSocketThread.this.handleMessage(data.toString());
}
}
synchronized (this.threadLock) {
this.isRunning = false;
Print.logDebug("Client:InputThread stopped");
this.threadLock.notify();
}
}
public void cutPlaylist() throws Exception {
if (logger.isDebugEnabled()) logger.debug("Cut Playlist.");
String st;
PrintWriter pw =
new PrintWriter(new BufferedWriter(new FileWriter(new File(this.NAME + ".dec"))));
BufferedReader br = new BufferedReader(new FileReader(new File(this.NAME)));
if ((st = br.readLine()) != null) {
String st2[];
st = new File(st).toURL().toString();
st2 = st.split("/");
StringBuffer stb = new StringBuffer(st2[st2.length - 1]);
StringBuffer stb2 = stb.reverse();
String st3 = new String(stb2);
int i = 0;
while (st3.charAt(i) != '.') i++;
String a = st3.substring(i + 1, st3.length());
pw.print(new StringBuffer(a).reverse());
}
while ((st = br.readLine()) != null) {
pw.println();
String st2[];
st = new File(st).toURL().toString();
st2 = st.split("/");
StringBuffer stb = new StringBuffer(st2[st2.length - 1]);
StringBuffer stb2 = stb.reverse();
String st3 = new String(stb2);
int i = 0;
while (st3.charAt(i) != '.') i++;
String a = st3.substring(i + 1, st3.length());
pw.print(new StringBuffer(a).reverse());
}
pw.close();
br.close();
}
/**
* @param section
* @param index
* @return
* @throws IOException
*/
final String getStringFromSection(final Section section, final int index) throws IOException {
if (index > section.getSize()) {
return "";
}
final StringBuffer str = new StringBuffer();
// Most string symbols will be less than 50 bytes in size
final byte[] tmp = new byte[50];
this.efile.seek(section.getFileOffset() + index);
while (true) {
int len = this.efile.read(tmp);
for (int i = 0; i < len; i++) {
if (tmp[i] == 0) {
len = 0;
break;
}
str.append((char) tmp[i]);
}
if (len <= 0) {
break;
}
}
return str.toString();
}
/** @return nick(id) */
public String getNickAndId() {
StringBuffer sb = new StringBuffer(getNick());
sb.append('(');
sb.append(Long.toString(getId()));
sb.append(')');
return sb.toString();
}
