/**
* If the outbound level is BINARY, convert the string field to binary, then pad to the left with
* the appropriate number of zero bits to reach a number of bits specified by the bitLength
* attribute of the TDT definition file.
*/
private void binaryPadding(Map<String, String> extraparams, Field tdtfield) {
String fieldname = tdtfield.getName();
int reqbitlength = tdtfield.getBitLength();
String value;
String binaryValue = fieldToBinary(tdtfield, extraparams);
if (binaryValue.length() < reqbitlength) {
int extraBitLength = reqbitlength - binaryValue.length();
StringBuilder zeroPaddedBinaryValue = new StringBuilder("");
for (int i = 0; i < extraBitLength; i++) {
zeroPaddedBinaryValue.append("0");
}
zeroPaddedBinaryValue.append(binaryValue);
value = zeroPaddedBinaryValue.toString();
} else {
if (binaryValue.length() > reqbitlength)
throw new TDTException(
"Binary value ["
+ binaryValue
+ "] for field "
+ fieldname
+ " exceeds maximum allowed "
+ reqbitlength
+ " bits. Decimal value was "
+ extraparams.get(fieldname));
value = binaryValue;
}
extraparams.put(fieldname, value);
}
/** {@inheritDoc} */
protected void getNewMonitors(Map<String, Monitor> map) throws MonitorException {
assert Thread.holdsLock(this);
int used = prologue.getUsed();
long modificationTime = prologue.getModificationTimeStamp();
if ((used > lastUsed) || (lastModificationTime > modificationTime)) {
lastUsed = used;
lastModificationTime = modificationTime;
Monitor monitor = getNextMonitorEntry();
while (monitor != null) {
String name = monitor.getName();
// guard against duplicate entries
if (!map.containsKey(name)) {
map.put(name, monitor);
/*
* insertedMonitors is null when called from pollFor()
* via buildMonitorMap(). Since we update insertedMonitors
* at the end of buildMonitorMap(), it's ok to skip the
* add here.
*/
if (insertedMonitors != null) {
insertedMonitors.add(monitor);
}
}
monitor = getNextMonitorEntry();
}
}
}
/**
* 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;
}
PCNode insertFullName(String full_name, boolean cl, boolean weavable) {
int dotpos = full_name.indexOf('.');
String head;
String rest;
if (dotpos == -1) {
head = full_name;
rest = null;
} else {
head = full_name.substring(0, dotpos);
rest = full_name.substring(dotpos + 1);
}
PCNode child;
if (!inners.containsKey(head)) {
child = new PCNode(head, this, root);
inners.put(head, child);
} else {
child = (PCNode) inners.get(head);
}
if (rest != null) {
return child.insertFullName(rest, cl, weavable);
} else {
child.is_class |= cl;
child.is_weavable |= weavable;
return child;
}
}
/** @return matching bloc B bloc -> A bloc */
public static Map<Integer, Integer> diff(FileDesc a, FileDesc b) {
Map<Integer, List<IndexedHash>> blocA = new HashMap<Integer, List<IndexedHash>>();
int i = 0;
for (Bloc bloc : a.blocs) {
List<IndexedHash> l = blocA.get(bloc.roll);
if (l == null) {
l = new ArrayList<IndexedHash>();
blocA.put(bloc.roll, l);
}
l.add(new IndexedHash(i++, bloc.hash));
}
Map<Integer, Integer> map = new HashMap<Integer, Integer>();
loop:
for (i = 0; i < b.blocs.length; i++) {
Bloc blocB = b.blocs[i];
List<IndexedHash> list = blocA.get(blocB.roll);
if (list != null) {
for (IndexedHash bloc : list) {
if (blocB.hash.equals(bloc.h)) {
map.put(i, bloc.i);
continue loop;
}
}
}
}
return map;
}
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);
}
/** Parse the given string, return resulting data if appropriate. */
ParseResult internalParse(
String s, Map<String, Integer> targetUnionDecisions, boolean mustConsumeStr) {
//
// If there's no target decision, then go ahead and try all branches.
//
if (targetUnionDecisions == null || targetUnionDecisions.get(name) == null) {
for (InferredType subelt : unionTypes) {
ParseResult pr = subelt.internalParse(s, targetUnionDecisions, false);
if (pr != null
&& (!mustConsumeStr
|| (mustConsumeStr && pr.getRemainingString().trim().length() == 0))) {
return new ParseResult(pr.getData(), pr.hasData(), pr.getRemainingString());
}
}
return null;
}
//
// If there is a target decision, then carry it out.
//
InferredType subelt = unionTypes.get(targetUnionDecisions.get(name));
ParseResult pr = subelt.internalParse(s, targetUnionDecisions, false);
if (pr != null
&& (!mustConsumeStr || (mustConsumeStr && pr.getRemainingString().trim().length() == 0))) {
return new ParseResult(pr.getData(), pr.hasData(), pr.getRemainingString());
}
return null;
}
public List getUserListAT() {
List<Map> list = new ArrayList<Map>();
String[][] data = {
{"3537255778", "Alex Chen"},
{"2110989338", "Brian Wang"},
{"3537640807", "David Hsieh"},
{"5764816553", "James Yu"},
{"3756404948", "K.C."},
{"2110994764", "Neil Weinstock"},
{"6797798390", "Owen Chen"},
{"3831206627", "Randy Chen"},
{"6312460903", "Tony Shen"},
{"2110993498", "Yee Liaw"}
};
for (int i = 0; i < data.length; i++) {
Map map = new HashMap();
String userRef = data[i][0];
String userName = data[i][1];
map.put("userObjectId", userRef);
map.put("userName", userName);
list.add(map);
}
return list;
}
public void processMethodMapping(
String className,
int firstLineNumber,
int lastLineNumber,
String methodReturnType,
String methodName,
String methodArguments,
String newMethodName) {
// Original class name -> obfuscated method names.
Map methodMap = (Map) classMethodMap.get(className);
if (methodMap == null) {
methodMap = new HashMap();
classMethodMap.put(className, methodMap);
}
// Obfuscated method name -> methods.
Set methodSet = (Set) methodMap.get(newMethodName);
if (methodSet == null) {
methodSet = new LinkedHashSet();
methodMap.put(newMethodName, methodSet);
}
// Add the method information.
methodSet.add(
new MethodInfo(
firstLineNumber, lastLineNumber, methodReturnType, methodArguments, methodName));
}
/**
* Reads the file that specifies method calls that should be replaced by other method calls. The
* file is of the form:
*
* <p>[regex] [orig-method-def] [new-method-name]
*
* <p>where the orig_method-def is of the form:
*
* <p>fully-qualified-method-name (args)
*
* <p>Blank lines and // comments are ignored. The orig-method-def is replaced by a call to
* new-method-name with the same arguments in any classfile that matches the regular expressions.
* All method names and argument types should be fully qualified.
*/
public void read_map_file(File map_file) throws IOException {
LineNumberReader lr = new LineNumberReader(new FileReader(map_file));
MapFileError mfe = new MapFileError(lr, map_file);
Pattern current_regex = null;
Map<MethodDef, MethodInfo> map = new LinkedHashMap<MethodDef, MethodInfo>();
for (String line = lr.readLine(); line != null; line = lr.readLine()) {
line = line.replaceFirst("//.*$", "");
if (line.trim().length() == 0) continue;
if (line.startsWith(" ")) {
if (current_regex == null)
throw new IOException("No current class regex on line " + lr.getLineNumber());
StrTok st = new StrTok(line, mfe);
st.stok.wordChars('.', '.');
MethodDef md = parse_method(st);
String new_method = st.need_word();
map.put(md, new MethodInfo(new_method));
} else {
if (current_regex != null) {
MethodMapInfo mmi = new MethodMapInfo(current_regex, map);
map_list.add(mmi);
map = new LinkedHashMap<MethodDef, MethodInfo>();
}
current_regex = Pattern.compile(line);
}
}
if (current_regex != null) {
MethodMapInfo mmi = new MethodMapInfo(current_regex, map);
map_list.add(mmi);
}
dump_map_list();
}
/**
* method to make adjustments for known counter problems. This method depends on the availability
* of certain counters, which is generally guaranteed by the synchWithTarget() method.
*/
protected void kludge(Map<String, Monitor> map) {
if (Boolean.getBoolean("sun.jvmstat.perfdata.disableKludge")) {
// bypass all kludges
return;
}
String name = "java.vm.version";
StringMonitor jvm_version = (StringMonitor) map.get(name);
if (jvm_version == null) {
jvm_version = (StringMonitor) findByAlias(name);
}
name = "java.vm.name";
StringMonitor jvm_name = (StringMonitor) map.get(name);
if (jvm_name == null) {
jvm_name = (StringMonitor) findByAlias(name);
}
name = "hotspot.vm.args";
StringMonitor args = (StringMonitor) map.get(name);
if (args == null) {
args = (StringMonitor) findByAlias(name);
}
assert ((jvm_name != null) && (jvm_version != null) && (args != null));
if (jvm_name.stringValue().indexOf("HotSpot") >= 0) {
if (jvm_version.stringValue().startsWith("1.4.2")) {
kludgeMantis(map, args);
}
}
}
/**
* This is called when JPM runs in the background to start jobs
*
* @throws Exception
*/
public void daemon() throws Exception {
Runtime.getRuntime()
.addShutdownHook(
new Thread("Daemon shutdown") {
public void run() {
for (Service service : startedByDaemon) {
try {
reporter.error("Stopping " + service);
service.stop();
reporter.error("Stopped " + service);
} catch (Exception e) {
// Ignore
}
}
}
});
List<ServiceData> services = getServices();
Map<String, ServiceData> map = new HashMap<String, ServiceData>();
for (ServiceData d : services) {
map.put(d.name, d);
}
List<ServiceData> start = new ArrayList<ServiceData>();
Set<ServiceData> set = new HashSet<ServiceData>();
for (ServiceData sd : services) {
checkStartup(map, start, sd, set);
}
if (start.isEmpty()) reporter.warning("No services to start");
for (ServiceData sd : start) {
try {
Service service = getService(sd.name);
reporter.trace("Starting " + service);
String result = service.start();
if (result != null) reporter.error("Started error " + result);
else startedByDaemon.add(service);
reporter.trace("Started " + service);
} catch (Exception e) {
reporter.error("Cannot start daemon %s, due to %s", sd.name, e);
}
}
while (true) {
for (Service sd : startedByDaemon) {
try {
if (!sd.isRunning()) {
reporter.error("Starting due to failure " + sd);
String result = sd.start();
if (result != null) reporter.error("Started error " + result);
}
} catch (Exception e) {
reporter.error("Cannot start daemon %s, due to %s", sd, e);
}
}
Thread.sleep(10000);
}
}
public static void testConfigurableForNonPrimitives() {
Map<String, String> p = new HashMap<String, String>();
C config = Configurable.createConfigurable(C.class, p);
assertNull(config.port());
p.put("port", "10");
config = Configurable.createConfigurable(C.class, p);
assertEquals(Integer.valueOf(10), config.port()); // property port is
// not set
}
public Map<String, String> getFormatSpecifierDescriptions() {
Map<String, String> m = new LinkedHashMap<String, String>();
Iterator<String> keys = scoreBoardValues.keySet().iterator();
while (keys.hasNext()) {
String k = keys.next();
m.put(k, scoreBoardValues.get(k).getDescription());
}
return m;
}
/**
* Finds the original field name(s), appending the first one to the out line, and any additional
* alternatives to the extra lines.
*/
private void originalFieldName(
String className,
String obfuscatedFieldName,
String type,
StringBuffer outLine,
List extraOutLines) {
int extraIndent = -1;
// Class name -> obfuscated field names.
Map fieldMap = (Map) classFieldMap.get(className);
if (fieldMap != null) {
// Obfuscated field names -> fields.
Set fieldSet = (Set) fieldMap.get(obfuscatedFieldName);
if (fieldSet != null) {
// Find all matching fields.
Iterator fieldInfoIterator = fieldSet.iterator();
while (fieldInfoIterator.hasNext()) {
FieldInfo fieldInfo = (FieldInfo) fieldInfoIterator.next();
if (fieldInfo.matches(type)) {
// Is this the first matching field?
if (extraIndent < 0) {
extraIndent = outLine.length();
// Append the first original name.
if (verbose) {
outLine.append(fieldInfo.type).append(' ');
}
outLine.append(fieldInfo.originalName);
} else {
// Create an additional line with the proper
// indentation.
StringBuffer extraBuffer = new StringBuffer();
for (int counter = 0; counter < extraIndent; counter++) {
extraBuffer.append(' ');
}
// Append the alternative name.
if (verbose) {
extraBuffer.append(fieldInfo.type).append(' ');
}
extraBuffer.append(fieldInfo.originalName);
// Store the additional line.
extraOutLines.add(extraBuffer);
}
}
}
}
}
// Just append the obfuscated name if we haven't found any matching
// fields.
if (extraIndent < 0) {
outLine.append(obfuscatedFieldName);
}
}
private void putMap(String name, Map m) {
_put(OBJECT, name);
final int sizePos = _buf.position();
_buf.putInt(0);
for (Object key : m.keySet()) _putObjectField(key.toString(), m.get(key));
_buf.put(EOO);
_buf.putInt(sizePos, _buf.position() - sizePos);
}
static boolean isComposite(String name, Map<String, String[]> params) {
for (String pName : params.keySet()) {
if (pName.startsWith(name + ".")
&& params.get(pName) != null
&& params.get(pName).length > 0) {
return true;
}
}
return false;
}
@Override
public Node execute(ExecutionContext ec, Template tmpl) throws IOException { // {{{
Map<String, StartNamedBlock> blocks = tmpl.getBlocks();
Node n = blocks.get(this.blockName);
if (blocks.containsKey(this.blockName)) {
return blocks.get(this.blockName).getExecuteNode();
} else {
return this.executeNode;
}
// return this.getNextNode();
} // }}}
public List getUserList() {
List<Map> list = new ArrayList<Map>();
try {
/*
String apiUrl=rallyApiHost+"/user?query="+
"((TeamMemberships%20%3D%20https%3A%2F%2Frally1.rallydev.com%2Fslm%2Fwebservice%2F1.34%2Fproject%2F6169133135)%20or%20"+
"(TeamMemberships%20%3D%20https%3A%2F%2Frally1.rallydev.com%2Fslm%2Fwebservice%2F1.34%2Fproject%2F6083311244))"+
"&fetch=true&order=Name&start=1&pagesize=100";
*/
String apiUrl =
rallyApiHost
+ "/user?query=(Disabled%20=%20false)"
+ "&fetch=true&order=Name&start=1&pagesize=100";
log.info("apiUrl=" + apiUrl);
String responseXML = getRallyXML(apiUrl);
org.jdom.input.SAXBuilder bSAX = new org.jdom.input.SAXBuilder();
org.jdom.Document doc = bSAX.build(new StringReader(responseXML));
Element root = doc.getRootElement();
XPath xpath = XPath.newInstance("//Object");
List xlist = xpath.selectNodes(root);
Iterator iter = xlist.iterator();
while (iter.hasNext()) {
Map map = new HashMap();
Element item = (Element) iter.next();
String userRef = item.getAttribute("ref").getValue();
String userName = item.getAttribute("refObjectName").getValue();
String userObjectId = item.getChildText("ObjectID");
map.put("userRef", userRef);
map.put("userObjectId", userObjectId);
map.put("userName", userName);
list.add(map);
}
} catch (Exception ex) {
log.error("", ex);
}
return list;
}
public static void main(String[] args) {
long start = System.currentTimeMillis();
Scanner input = new Scanner(System.in);
int numberOfTestCases = input.nextInt();
ArrayList<Integer> order = new ArrayList<Integer>(numberOfTestCases);
int previousKey = -1;
int previousValue = 0;
int cycleNumber = 0;
Map<Integer, Integer> testCases = new TreeMap<Integer, Integer>();
for (int i = 0; i < numberOfTestCases; i++) {
int numberOfCycles = input.nextInt();
testCases.put(numberOfCycles, 1);
order.add(numberOfCycles);
}
for (Map.Entry<Integer, Integer> entry : testCases.entrySet()) {
int numberOfCycles;
int initialHeight;
if (previousKey == -1) {
numberOfCycles = entry.getKey();
initialHeight = entry.getValue();
} else {
numberOfCycles = entry.getKey() - previousKey;
initialHeight = previousValue;
}
for (int i = 0; i < numberOfCycles; i++) {
if (cycleNumber % 2 == 0) {
initialHeight *= 2;
} else {
initialHeight += 1;
}
cycleNumber++;
}
entry.setValue(initialHeight);
previousKey = entry.getKey();
previousValue = initialHeight;
}
for (Integer element : order) {
System.out.println(testCases.get(element));
}
long elapsed = System.currentTimeMillis() - start;
System.out.println("time: " + elapsed);
}
public void run() {
Map read;
boolean shouldRead = go_read;
String command = null;
long last = 0;
try {
/* swallow the banner if requested to do so */
if (swallow) {
readResponse();
}
while (shouldRead) {
synchronized (listeners) {
if (commands.size() > 0) {
command = (String) commands.removeFirst();
}
}
if (command != null) {
_sendString(command);
command = null;
lastRead = System.currentTimeMillis();
}
long now = System.currentTimeMillis();
if (this.window != null && !this.window.isShowing() && (now - last) < 1500) {
/* check if our window is not showing... if not, then we're going to switch to a very reduced
read schedule. */
} else {
read = readResponse();
if (read == null || "failure".equals(read.get("result") + "")) {
break;
}
processRead(read);
last = System.currentTimeMillis();
}
Thread.sleep(100);
synchronized (listeners) {
shouldRead = go_read;
}
}
} catch (Exception javaSucksBecauseItMakesMeCatchEverythingFuckingThing) {
javaSucksBecauseItMakesMeCatchEverythingFuckingThing.printStackTrace();
}
}
public Set /*<PCNode>*/ matchSpecific(Pattern simple_name_pattern) {
Set matches = new HashSet();
Iterator ii = inners.keySet().iterator();
while (ii.hasNext()) {
String inner = (String) ii.next();
// System.out.print("Matching "+inner+" against "+simple_name_pattern.pattern()+": ");
if (simple_name_pattern.matcher(inner).matches()) {
// System.out.println("true");
matches.add(inners.get(inner));
} else {
// System.out.println("false");
}
}
return matches;
}
private List<String> computeOverallSurvivalStatus(Map<String, SurvivalData> survivalData) {
List<String> osStatus = initializeList(canonicalPatientList.size());
for (String patientId : survivalData.keySet()) {
int osStatusIndex = canonicalPatientList.indexOf(patientId);
SurvivalData sd = survivalData.get(patientId);
if (VitalStatusAlive.has(sd.vitalStatus)) {
osStatus.set(osStatusIndex, VitalStatusAlive.LIVING.toString());
} else if (VitalStatusDead.has(sd.vitalStatus)) {
osStatus.set(osStatusIndex, VitalStatusDead.DECEASED.toString());
} else {
osStatus.set(osStatusIndex, ClinicalAttribute.NA);
}
}
return osStatus;
}
private Map<String, DiseaseFreeData> getDiseaseFreeDataForMatrix(DataMatrix dataMatrix) {
Map<String, DiseaseFreeData> diseaseFreeDataMap = new HashMap<String, DiseaseFreeData>();
List<String> patientIds = getPatientIds(dataMatrix);
for (int lc = 0; lc < patientIds.size(); lc++) {
String patientId = patientIds.get(lc);
DiseaseFreeData df = getDiseaseFreeDataForPatient(lc, dataMatrix);
if (diseaseFreeDataMap.containsKey(patientId)) {
df = mergeDiseaseFreeData(diseaseFreeDataMap.get(patientId), df);
}
diseaseFreeDataMap.put(patientId, df);
}
return diseaseFreeDataMap;
}
/**
* The convert method translates a String input to a specified outbound level of the same coding
* scheme. For example, the input string value may be a tag-encoding URI and the outbound level
* specified by string outboundlevel may be BINARY, in which case the return value is a binary
* representation expressed as a string.
*
* @param input the identifier to be converted.
* @param inputParameters additional parameters which need to be provided because they cannot
* always be determined from the input value alone. Examples include the taglength,
* companyprefixlength and filter values.
* @param outputLevel the outbound level required for the ouput. Permitted values include BINARY,
* TAG_ENCODING, PURE_IDENTITY, LEGACY and ONS_HOSTNAME.
* @return the identifier converted to the output level.
*/
public String convert(
String input, Map<String, String> inputParameters, LevelTypeList outputLevel) {
TagLengthList tagLength = null;
if (inputParameters.containsKey("taglength")) {
// in principle, the user should provide a
// TagLengthList object in the parameter list.
String s = inputParameters.get("taglength");
tagLength = TagLengthList.valueOf(s);
}
PrefixMatch match = findPrefixMatch(input, tagLength);
return convertLevel(match.getScheme(), match.getLevel(), input, inputParameters, outputLevel);
}
private Map<String, SurvivalData> getSurvivalDataForMatrix(DataMatrix dataMatrix) {
Map<String, SurvivalData> survivalDataMap = new HashMap<String, SurvivalData>();
List<String> patientIds = getPatientIds(dataMatrix);
for (int lc = 0; lc < patientIds.size(); lc++) {
String patientId = patientIds.get(lc);
SurvivalData sd = getSurvivalDataForPatient(lc, dataMatrix);
if (survivalDataMap.containsKey(patientId)) {
sd = mergeSurvivalData(survivalDataMap.get(patientId), sd);
}
survivalDataMap.put(patientId, sd);
}
return survivalDataMap;
}
/** Method to dump debugging information */
private void dumpAll(Map map, int lvmid) {
if (DEBUG) {
Set keys = map.keySet();
System.err.println("Dump for " + lvmid);
int j = 0;
for (Iterator i = keys.iterator(); i.hasNext(); j++) {
Monitor monitor = (Monitor) map.get(i.next());
System.err.println(j + "\t" + monitor.getName() + "=" + monitor.getValue());
}
System.err.println("nextEntry = " + nextEntry + " pollForEntry = " + pollForEntry);
System.err.println("Buffer info:");
System.err.println("buffer = " + buffer);
}
}
/**
* returns the multiple alignment as a string in a fashion identical to that in a file of
* ALN/CLUSTALW format (except from the fact that info about residues' match is missing. Aka, the
* 3rd line of a file of ALN/CLUSTALW ('*', '.', ':' chars) is missing).
*
* <p>(Note: CLUSTALW doesn't necessarily have the match characters... -Tim)
*/
public String toString() {
StringBuilder sb = new StringBuilder();
int tl = maxTagLength();
int i = 0, last = gappedAlignments.keySet().size() - 1;
for (String tag : gappedAlignments.keySet()) {
sb.append(StringUtils.padString(tag, tl));
sb.append(" ");
sb.append(gappedAlignments.get(tag).gappedString());
if (i < last) {
sb.append("\n");
}
i += 1;
}
return sb.toString();
}
private int parse() throws IOException {
String line;
BufferedReader reader = new BufferedReader(new FileReader(inputFile));
int count = 0;
line = reader.readLine(); // Quality Scores;
String[] array = line.split("\t");
qualityScores = new Integer[array.length - offset];
for (int i = offset; i < array.length; i++) {
qualityScores[i - offset] = Integer.parseInt(array[i]);
}
line = reader.readLine(); // Experiment Names
array = line.split("\t");
experiments = new String[array.length - offset];
for (int i = offset; i < array.length; i++) {
experiments[i - offset] = array[i];
exptIndices.put(array[i], i - offset);
}
// Reads the rest of the table.
while ((line = reader.readLine()) != null) {
array = line.split("\t");
String id = array[0]; // first column is the ID
if (array.length != experiments.length + offset) {
System.err.println(
String.format(
"Line %s has length %d != %d", id, array.length, experiments.length + offset));
} else {
// we're going to skip the second column (an index value), and
// put the rest of the values in the array. Any parsing exceptions
// indicate missing (NULL) values.
Float[] values = new Float[experiments.length];
for (int i = 0; i < experiments.length; i++) {
try {
values[i] = Float.parseFloat(array[i + offset]);
count += 1;
} catch (NumberFormatException nfe) {
values[i] = null;
}
}
table.put(id, values);
}
}
reader.close();
return count;
}
protected Map<String, String> getAttributes() {
if (attributes != null) {
return attributes;
}
attributes = new HashMap<String, String>();
matcher = ADDITIONAL_ATTRIBUTES_PATTERN.matcher(firstLine);
if (matcher.find()) {
String s;
Matcher attributeMatcher;
s = matcher.group(2);
attributeMatcher = ADDITIONAL_ATTRIBUTE_PATTERN.matcher(s);
while (attributeMatcher.find()) {
String key;
String value;
key = attributeMatcher.group(1);
value = attributeMatcher.group(2);
attributes.put(key.toLowerCase(Locale.ENGLISH), value);
}
}
return attributes;
}