public static void verifyCommand(
String args[],
@SuppressWarnings("unused") String help,
Pattern[] patterns,
int low,
int high) {
String message = "";
if (args.length > high) {
message = "too many arguments";
} else if (args.length < low) {
message = "too few arguments";
} else {
for (int i = 0; patterns != null && i < patterns.length && i < args.length; i++) {
if (patterns[i] != null) {
Matcher m = patterns[i].matcher(args[i]);
if (!m.matches())
message +=
String.format(
"Argument %s (%s) does not match %s%n", i, args[i], patterns[i].pattern());
}
}
}
if (message.length() != 0) {
StringBuilder sb = new StringBuilder();
String del = "${";
for (String arg : args) {
sb.append(del);
sb.append(arg);
del = ";";
}
sb.append("}, is not understood. ");
sb.append(message);
throw new IllegalArgumentException(sb.toString());
}
}
private InstanceList readFile() throws IOException {
String NL = System.getProperty("line.separator");
Scanner scanner = new Scanner(new FileInputStream(fileName), encoding);
ArrayList<Pipe> pipeList = new ArrayList<Pipe>();
pipeList.add(new CharSequence2TokenSequence(Pattern.compile("\\p{L}\\p{L}+")));
pipeList.add(new TokenSequence2FeatureSequence());
InstanceList testing = new InstanceList(new SerialPipes(pipeList));
try {
while (scanner.hasNextLine()) {
String text = scanner.nextLine();
text = text.replaceAll("\\x0d", "");
Pattern patten = Pattern.compile("^(.*?),(.*?),(.*)$");
Matcher matcher = patten.matcher(text);
if (matcher.find()) {
docIds.add(matcher.group(1));
testing.addThruPipe(new Instance(matcher.group(3), null, "test instance", null));
}
}
} finally {
scanner.close();
}
return testing;
}
/**
* Get dependencies of a source file.
*
* @param path The canonical path of source file.
* @return Path of dependencies.
*/
private ArrayList<String> getDependencies(String path) {
if (!dependenceMap.containsKey(path)) {
ArrayList<String> dependencies = new ArrayList<String>();
Matcher m = PATTERN_REQUIRE.matcher(read(path, charset));
while (m.find()) {
// Decide which root path to use.
// Path wrapped in <> is related to root path.
// Path wrapped in "" is related to parent folder of the source file.
String root = null;
if (m.group(1).equals("<")) {
root = this.root;
} else {
root = new File(path).getParent();
}
// Get path of required file.
String required = m.group(2);
File f = new File(root, required);
if (f.exists()) {
dependencies.add(canonize(f));
} else {
App.exit("Cannot find required file " + required + " in " + path);
}
}
dependenceMap.put(path, dependencies);
}
return dependenceMap.get(path);
}
/**
* Import an XQuery library module from the given document. The namespace and preferred prefix of
* the module are extracted from the module itself. The MIME type of the document is set to
* "application/xquery" as a side-effect.
*
* @param module the non-XML document that holds the library module's source
* @return this service, to chain calls
* @throws DatabaseException if the module is an XML document, or the module declaration cannot be
* found at the top of the document
*/
public QueryService importModule(Document module) {
if (module instanceof XMLDocument)
throw new DatabaseException("module cannot be an XML document: " + module);
Matcher matcher = MODULE_DECLARATION_DQUOTE.matcher(module.contentsAsString());
if (!matcher.find()) {
matcher = MODULE_DECLARATION_SQUOTE.matcher(module.contentsAsString());
if (!matcher.find())
throw new DatabaseException("couldn't find a module declaration at the top of " + module);
}
module.metadata().setMimeType("application/xquery");
String moduleNamespace = matcher.group(1);
// TODO: should do URILiteral processing here to replace entity and character references and
// normalize
// whitespace, but since it seems that eXist doesn't do it either (bug?) there's no reason to
// rush.
Document prevModule = moduleMap.get(moduleNamespace);
if (prevModule != null && !prevModule.equals(module))
throw new DatabaseException(
"module "
+ moduleNamespace
+ " already bound to "
+ prevModule
+ ", can't rebind to "
+ module);
moduleMap.put(moduleNamespace, module);
return this;
}
public String parse(String format) {
StringBuffer buffer = new StringBuffer();
Matcher m = formatPattern.matcher(format);
while (m.find()) m.appendReplacement(buffer, getFormatSpecifierValue(m.group()));
m.appendTail(buffer);
return buffer.toString();
}
public static String getChrom(String chromName) {
Matcher m = chromPattern.matcher(chromName);
if (!m.matches()) {
return chromName;
}
return m.group(1);
}
public static String removePrimerLR(String pname) {
Matcher m = primerLRPattern.matcher(pname);
if (!m.matches()) {
throw new IllegalArgumentException(pname);
}
return m.group(1);
}
private static String expand(String str) {
if (str == null) {
return null;
}
StringBuilder result = new StringBuilder();
Pattern re = Pattern.compile("^(.*?)\\$\\{([^}]*)\\}(.*)");
while (true) {
Matcher matcher = re.matcher(str);
if (matcher.matches()) {
result.append(matcher.group(1));
String property = matcher.group(2);
if (property.equals("/")) {
property = "file.separator";
}
String value = System.getProperty(property);
if (value != null) {
result.append(value);
}
str = matcher.group(3);
} else {
result.append(str);
break;
}
}
return result.toString();
}
/**
* Takes a line and looks for an archive request tag. If one is found, the information from the
* tag is returned as an <CODE>ArchiveRequest</CODE>. If a tag is found, the data in the tag is
* stored in the <CODE>HashMap</CODE> provided.
*
* @param currentLine The line in which to look for the archive tag.
* @param group The <CODE>ArchiveGroup</CODE> to which to add the <CODE>ArchiveRequest</CODE>. Can
* be <CODE>null</CODE>.
* @param template The <CODE>Template</CODE> to which the <CODE>ArchiveRequest</CODE> belongs.
* @return The archive request tag data as an instance of <CODE>ArchiveRequest</CODE>, <CODE>null
* </CODE> if the line passed in does not contain an arFile tag.
*/
private ArchiveRequest parseArchiveRequestTag(
String currentLine, ArchiveGroup group, Template template) {
ArchiveRequest archiveTag;
Matcher currentMatcher = archiveRequestPattern.matcher(currentLine);
if (currentMatcher.find()) {
String fileName = currentMatcher.group(1);
archiveTag = template.getArchiveRequest(fileName);
if (archiveTag == null) {
archiveTag = new ArchiveRequest(fileName);
template.addArchiveRequest(archiveTag);
}
if (group != null) {
// Creating a new request object because the requests
// in the groups flagged as not in database will mean the
// group - request association is not in database. Requests
// in the archiveRequests map flagged as not in database
// means the request record is not there.
String requestFileName = archiveTag.getFileName();
String requestFileLocation = archiveTag.getFileLocation();
ArchiveRequest groupRequest = new ArchiveRequest(requestFileLocation, requestFileName);
group.addArchiveRequest(groupRequest);
}
} else archiveTag = null;
return archiveTag;
}
public void _sendString(String text) {
if (writeCommand == null) return;
/* intercept sessions -i and deliver it to a listener within armitage */
if (sessionListener != null) {
Matcher m = interact.matcher(text);
if (m.matches()) {
sessionListener.actionPerformed(new ActionEvent(this, 0, m.group(1)));
return;
}
}
Map read = null;
try {
synchronized (this) {
if (window != null && echo) {
window.append(window.getPromptText() + text);
}
}
if ("armitage.push".equals(writeCommand)) {
read = (Map) connection.execute(writeCommand, new Object[] {session, text});
} else {
connection.execute(writeCommand, new Object[] {session, text});
read = readResponse();
}
processRead(read);
fireSessionWroteEvent(text);
} catch (Exception ex) {
ex.printStackTrace();
}
}
public FileVisitResult preVisitDirectory(Path dir, BasicFileAttributes attrs)
throws IOException {
if (m != null) m.reset(root.relativize(dir).toString());
return m == null || m.matches() || m.hitEnd()
? FileVisitResult.CONTINUE
: FileVisitResult.SKIP_SUBTREE;
}
public String getArtifactIdFromCoord(String coord) {
Matcher m = COORD_P.matcher(coord);
if (m.matches()) {
return m.group(2);
} else {
return null;
}
}
public FileVisitResult visitFile(Path file, BasicFileAttributes attrs) throws IOException {
if (attrs.isRegularFile()) {
if (m != null) m.reset(root.relativize(file).toString());
if (m == null || m.matches())
futures.add(exec.submit(new FileLoader(root, file, blocSize)));
}
return FileVisitResult.CONTINUE;
}
public BasicSpellChecker(String file) throws IOException {
BufferedReader in = new BufferedReader(new FileReader(file));
Pattern p = Pattern.compile("\\w+");
for (String temp = ""; temp != null; temp = in.readLine()) {
Matcher m = p.matcher(temp.toLowerCase());
while (m.find())
nWords.put((temp = m.group()), nWords.containsKey(temp) ? nWords.get(temp) + 1 : 1);
}
in.close();
}
private List<String> convertFollowupPatientIds(List<String> patientIds) {
List<String> convertedPatientIds = new ArrayList<String>();
for (String patientId : patientIds) {
Matcher patientIdMatcher = FOLLOW_UP_PATIENT_ID_REGEX.matcher(patientId);
convertedPatientIds.add(patientIdMatcher.find() ? patientIdMatcher.group(1) : patientId);
}
return convertedPatientIds;
}
public URLFinder(String text) {
Matcher matcher = dfPattern.matcher(text);
urls = new ArrayList<String>();
locations = new ArrayList<Integer[]>();
while (matcher.find()) {
urls.add(matcher.group(1));
locations.add(new Integer[] {matcher.start(1), matcher.end(1)});
}
}
public static void main(String[] args) throws PatternSyntaxException {
Scanner in = new Scanner(System.in);
System.out.println("Enter pattern: ");
String patternString = in.nextLine();
Pattern pattern = Pattern.compile(patternString);
while (true) {
System.out.println("Enter string to match: ");
String input = in.nextLine();
if (input == null || input.equals("")) return;
Matcher matcher = pattern.matcher(input);
if (matcher.matches()) {
System.out.println("Match");
int g = matcher.groupCount();
if (g > 0) {
for (int i = 0; i < input.length(); i++) {
// Print any empty groups
for (int j = 1; j <= g; j++)
if (i == matcher.start(j) && i == matcher.end(j)) System.out.print("()");
// Print ( for non-empty groups starting here
for (int j = 1; j <= g; j++)
if (i == matcher.start(j) && i != matcher.end(j)) System.out.print('(');
System.out.print(input.charAt(i));
// Print ) for non-empty groups ending here
for (int j = 1; j <= g; j++)
if (i + 1 != matcher.start(j) && i + 1 == matcher.end(j)) System.out.print(')');
}
System.out.println();
}
} else System.out.println("No match");
}
}
// todo: give options for document splitting. A line or the whole file or
// sentence splitting as now
public Iterator<List<IN>> getIterator(Reader r) {
Tokenizer<IN> tokenizer = tokenizerFactory.getTokenizer(r);
// PTBTokenizer.newPTBTokenizer(r, false, true);
List<IN> words = new ArrayList<IN>();
IN previous = tokenFactory.makeToken();
StringBuilder prepend = new StringBuilder();
/*
* This changes SGML tags into whitespace -- it should maybe be moved
* elsewhere
*/
while (tokenizer.hasNext()) {
IN w = tokenizer.next();
String word = w.get(CoreAnnotations.TextAnnotation.class);
Matcher m = sgml.matcher(word);
if (m.matches()) {
String before = StringUtils.getNotNullString(w.get(CoreAnnotations.BeforeAnnotation.class));
String after = StringUtils.getNotNullString(w.get(CoreAnnotations.AfterAnnotation.class));
prepend.append(before).append(word);
String previousTokenAfter =
StringUtils.getNotNullString(previous.get(CoreAnnotations.AfterAnnotation.class));
previous.set(AfterAnnotation.class, previousTokenAfter + word + after);
// previous.appendAfter(w.word() + w.after());
} else {
String before = StringUtils.getNotNullString(w.get(CoreAnnotations.BeforeAnnotation.class));
if (prepend.length() > 0) {
w.set(BeforeAnnotation.class, prepend.toString() + before);
// w.prependBefore(prepend.toString());
prepend = new StringBuilder();
}
words.add(w);
previous = w;
}
}
List<List<IN>> sentences = wts.process(words);
String after = "";
IN last = null;
for (List<IN> sentence : sentences) {
int pos = 0;
for (IN w : sentence) {
w.set(PositionAnnotation.class, Integer.toString(pos));
after = StringUtils.getNotNullString(w.get(CoreAnnotations.AfterAnnotation.class));
w.remove(AfterAnnotation.class);
last = w;
}
}
if (last != null) {
last.set(AfterAnnotation.class, after);
}
return sentences.iterator();
}
protected RichText.Part text(PState s, String text, Map<? extends Attribute, ?> attrs)
throws IOException {
RichText.Part ret = null;
int p = 0;
while (true) {
Matcher m = urlpat.matcher(text);
if (!m.find(p)) break;
URL url;
try {
String su = text.substring(m.start(), m.end());
if (su.indexOf(':') < 0) su = "http://" + su;
url = new URL(su);
} catch (java.net.MalformedURLException e) {
p = m.end();
continue;
}
RichText.Part lead = new RichText.TextPart(text.substring(0, m.start()), attrs);
if (ret == null) ret = lead;
else ret.append(lead);
Map<Attribute, Object> na = new HashMap<Attribute, Object>(attrs);
na.putAll(urlstyle);
na.put(ChatAttribute.HYPERLINK, new FuckMeGentlyWithAChainsaw(url));
ret.append(new RichText.TextPart(text.substring(m.start(), m.end()), na));
p = m.end();
}
if (ret == null) ret = new RichText.TextPart(text, attrs);
else ret.append(new RichText.TextPart(text.substring(p), attrs));
return (ret);
}
// remove non-word characters and everything after ":::" from the
// program point name, leaving PackageName.ClassName.MethodName
private static String cleanup_pptname(String pptname) {
int index;
if ((index = pptname.indexOf("(")) > 0) {
pptname = pptname.substring(0, index);
}
if (pptname.endsWith(".")) pptname = pptname.substring(0, pptname.length() - 2);
Matcher m = non_word_pattern.matcher(pptname);
return m.replaceAll(".");
}
void search() {
int i=0;
Matcher matcher=new Matcher(a,b);
while (i<a.length-1) {
int j=i;
matcher.findBiggestMatchForFrom(i,j);
findbiggestmatchfrom(i,j,0);
}
}
public String getResult() {
if (result != null) {
return result;
}
matcher = RESULT_PATTERN.matcher(firstLine);
if (matcher.find()) {
result = matcher.group(1);
}
return result;
}
public int getStatus() {
if (status != null) {
return status;
}
matcher = STATUS_PATTERN.matcher(firstLine);
if (matcher.find()) {
status = Integer.parseInt(matcher.group(1));
}
return status;
}
public static int[] decodePrimerName(String pname) {
Matcher m = primerNamePattern.matcher(pname);
if (!m.matches()) {
throw new IllegalArgumentException(pname);
}
int[] a = new int[3];
a[0] = Integer.parseInt(m.group(1));
a[1] = Integer.parseInt(m.group(2));
a[2] = Integer.parseInt(m.group(3));
return a;
}
public ControllerRequest(Class<? extends Controller> controllerClass, Matcher matchedUrl) {
this.controllerClass = controllerClass;
if (matchedUrl.groupCount() > 0) {
List<String> argsList = new ArrayList<String>(matchedUrl.groupCount());
for (int i = 1; i <= matchedUrl.groupCount(); i++) {
argsList.add(matchedUrl.group(i));
}
this.args = argsList;
} else {
this.args = new ArrayList<String>(0);
}
}
void findRemoveDirectives(boolean clean) {
// if ( clean ) editor.startCompoundEdit();
Sketch sketch = editor.getSketch();
for (int i = 0; i < sketch.getCodeCount(); i++) {
SketchCode code = sketch.getCode(i);
String program = code.getProgram();
StringBuffer buffer = new StringBuffer();
Matcher m = pjsPattern.matcher(program);
while (m.find()) {
String mm = m.group();
// TODO this urgently needs tests ..
/* remove framing */
mm = mm.replaceAll("^\\/\\*\\s*@pjs", "").replaceAll("\\s*\\*\\/\\s*$", "");
/* fix multiline nice formatting */
mm = mm.replaceAll("[\\s]*([^;\\s\\n\\r]+)[\\s]*,[\\s]*[\\n\\r]+", "$1,");
/* fix multiline version without semicolons */
mm = mm.replaceAll("[\\s]*([^;\\s\\n\\r]+)[\\s]*[\\n\\r]+", "$1;");
mm = mm.replaceAll("\n", " ").replaceAll("\r", " ");
// System.out.println(mm);
if (clean) {
m.appendReplacement(buffer, "");
} else {
String[] directives = mm.split(";");
for (String d : directives) {
// System.out.println(d);
parseDirective(d);
}
}
}
if (clean) {
m.appendTail(buffer);
// TODO: not working!
code.setProgram(buffer.toString());
code.setModified(true);
}
}
if (clean) {
// editor.stopCompoundEdit();
editor.setText(sketch.getCurrentCode().getProgram());
sketch.setModified(false);
sketch.setModified(true);
}
}
/**
* Strips all non-article links from the given markup; anything like [[this]] is removed unless it
* goes to a wikipedia article, redirect, or disambiguation page.
*
* @param markup the text to be stripped
* @return the stripped text
*/
public static String stripIsolatedLinks(String markup) {
Vector<Integer> linkStack = new Vector<Integer>();
Pattern p = Pattern.compile("(\\[\\[|\\]\\])");
Matcher m = p.matcher(markup);
StringBuffer sb = new StringBuffer();
int lastIndex = 0;
while (m.find()) {
String tag = markup.substring(m.start(), m.end());
if (tag.equals("[[")) linkStack.add(m.start());
else {
if (!linkStack.isEmpty()) {
int linkStart = linkStack.lastElement();
linkStack.remove(linkStack.size() - 1);
if (linkStack.isEmpty()) {
sb.append(markup.substring(lastIndex, linkStart));
// we have the whole link, with other links nested inside if it's an image
String linkMarkup = markup.substring(linkStart + 2, m.start());
// System.out.println(" - " + linkStart + ", " + m.end() + ", " + markup.length()) ;
if (markup.substring(Math.max(0, linkStart - 10), linkStart).matches("(?s).*(\\W*)\n")
&& (m.end() >= markup.length() - 1
|| markup
.substring(m.end(), Math.min(markup.length() - 1, m.end() + 10))
.matches("(?s)(\\W*)(\n.*|$)"))) {
// discarding link
} else {
sb.append("[[");
sb.append(linkMarkup);
sb.append("]]");
}
lastIndex = m.end();
}
}
}
}
if (!linkStack.isEmpty())
System.err.println(
"MarkupStripper | Warning: links were not well formed, so we cannot guarantee that they were stripped out correctly. ");
sb.append(markup.substring(lastIndex));
return sb.toString();
}
/**
* Initializes the date format.
*
* @param d input
* @param e example format
* @param ii input info
* @throws QueryException query exception
*/
final void date(final byte[] d, final String e, final InputInfo ii) throws QueryException {
final Matcher mt = DATE.matcher(Token.string(d).trim());
if (!mt.matches()) throw dateError(d, e, ii);
yea = toLong(mt.group(1), false, ii);
// +1 is added to BC values to simplify computations
if (yea < 0) yea++;
mon = (byte) (Strings.toInt(mt.group(3)) - 1);
day = (byte) (Strings.toInt(mt.group(4)) - 1);
if (mon < 0 || mon >= 12 || day < 0 || day >= dpm(yea, mon)) throw dateError(d, e, ii);
if (yea <= MIN_YEAR || yea > MAX_YEAR) throw DATERANGE_X_X.get(ii, type, chop(d, ii));
zone(mt, 5, d, ii);
}
/**
* Returns an integer corresponding to the given experiment name. If the argument matches an
* experiment name exactly, then that index is returned. Otherwise, the argument is treated as a
* regexp, and the index of some experiment that matches it is returned.
*
* @param key The name, or regexp for the name, of the experiment to find.
* @return The array index of the experiment, or -1 if not found.
*/
public int findExperiment(String key) {
if (exptIndices.containsKey(key)) {
return exptIndices.get(key);
}
Pattern p = Pattern.compile(key);
for (String k : exptIndices.keySet()) {
Matcher m = p.matcher(k);
if (m.matches()) {
return exptIndices.get(k);
}
}
return -1;
}
@Override
public StorageResults fetch(Expression userQuery) {
Expression expression = userQuery.normalize();
Matcher matcher = expression.accept(new MatcherCreator());
List<DataRecord> matchRecords = new LinkedList<DataRecord>();
for (DataRecord dataRecord : storage) {
if (matcher.match(dataRecord)) {
matchRecords.add(dataRecord);
}
}
List<DataRecord> filteredRecords = expression.accept(new Filter(matchRecords));
return new InMemoryStorageResults(filteredRecords);
}
