private int maxTagLength() {
int tl = 0;
for (String tag : gappedAlignments.keySet()) {
tl = Math.max(tl, tag.length());
}
return tl;
}
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;
}
private void mergeDiseaseFreeData(
Map<String, DiseaseFreeData> sourceMap, Map<String, DiseaseFreeData> destMap) {
for (String patientId : sourceMap.keySet()) {
DiseaseFreeData diseaseFreeData = sourceMap.get(patientId);
if (destMap.containsKey(patientId)) {
destMap.put(patientId, mergeDiseaseFreeData(destMap.get(patientId), diseaseFreeData));
} else {
destMap.put(patientId, diseaseFreeData);
}
}
}
private void mergeSurvivalData(
Map<String, SurvivalData> sourceMap, Map<String, SurvivalData> destMap) {
for (String patientId : sourceMap.keySet()) {
SurvivalData survivalData = sourceMap.get(patientId);
if (destMap.containsKey(patientId)) {
destMap.put(patientId, mergeSurvivalData(destMap.get(patientId), survivalData));
} else {
destMap.put(patientId, survivalData);
}
}
}
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;
}
/**
* 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();
}
/** 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);
}
}
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 List<String> computeOverallSurvivalMonths(Map<String, SurvivalData> survivalData) {
List<String> osStatusMonths = initializeList(canonicalPatientList.size());
for (String patientId : survivalData.keySet()) {
int osStatusMonthsIndex = canonicalPatientList.indexOf(patientId);
SurvivalData sd = survivalData.get(patientId);
if (VitalStatusAlive.has(sd.vitalStatus)) {
osStatusMonths.set(
osStatusMonthsIndex, convertDaysToMonths(sd.lastFollowUp, sd.lastKnownAlive));
} else if (VitalStatusDead.has(sd.vitalStatus)) {
osStatusMonths.set(osStatusMonthsIndex, convertDaysToMonths(sd.daysToDeath));
} else {
osStatusMonths.set(osStatusMonthsIndex, ClinicalAttribute.NA);
}
}
return osStatusMonths;
}
private List<String> computeDiseaseFreeStatus(Map<String, DiseaseFreeData> diseaseFreeData) {
List<String> dfStatus = initializeList(canonicalPatientList.size());
for (String patientId : diseaseFreeData.keySet()) {
int dfStatusIndex = canonicalPatientList.indexOf(patientId);
DiseaseFreeData df = diseaseFreeData.get(patientId);
if (patientIsDiseaseFree(df)) {
dfStatus.set(dfStatusIndex, DiseaseFreeStatus.DISEASE_FREE.toString());
} else {
try {
Integer.parseInt(df.daysToNewTumorEventAfterInitialTreatment);
dfStatus.set(dfStatusIndex, DiseaseFreeStatus.DISEASED.toString());
} catch (NumberFormatException e) {
dfStatus.set(dfStatusIndex, ClinicalAttribute.NA);
}
}
}
return dfStatus;
}
private List<String> computeDiseaseFreeMonths(Map<String, DiseaseFreeData> diseaseFreeData) {
List<String> dfStatusMonths = initializeList(canonicalPatientList.size());
for (String patientId : diseaseFreeData.keySet()) {
int dfStatusMonthsIndex = canonicalPatientList.indexOf(patientId);
DiseaseFreeData df = diseaseFreeData.get(patientId);
try {
if (patientIsDiseaseFree(df)) {
dfStatusMonths.set(
dfStatusMonthsIndex, convertDaysToMonths(df.lastFollowUp, df.lastKnownAlive));
} else {
int dfStatusDays = Integer.parseInt(df.daysToNewTumorEventAfterInitialTreatment);
dfStatusMonths.set(
dfStatusMonthsIndex, convertDaysToMonths(Integer.toString(dfStatusDays)));
}
} catch (NumberFormatException e) {
dfStatusMonths.set(dfStatusMonthsIndex, ClinicalAttribute.NA);
}
}
return dfStatusMonths;
}
private void discoverAndRunProcs(
Context context,
Set<TypeElement> annotationsPresent,
List<ClassSymbol> topLevelClasses,
List<PackageSymbol> packageInfoFiles) {
Map<String, TypeElement> unmatchedAnnotations =
new HashMap<String, TypeElement>(annotationsPresent.size());
for (TypeElement a : annotationsPresent) {
unmatchedAnnotations.put(a.getQualifiedName().toString(), a);
}
// Give "*" processors a chance to match
if (unmatchedAnnotations.size() == 0) unmatchedAnnotations.put("", null);
DiscoveredProcessors.ProcessorStateIterator psi = discoveredProcs.iterator();
// TODO: Create proper argument values; need past round
// information to fill in this constructor. Note that the 1
// st round of processing could be the last round if there
// were parse errors on the initial source files; however, we
// are not doing processing in that case.
Set<Element> rootElements = new LinkedHashSet<Element>();
rootElements.addAll(topLevelClasses);
rootElements.addAll(packageInfoFiles);
rootElements = Collections.unmodifiableSet(rootElements);
RoundEnvironment renv =
new JavacRoundEnvironment(false, false, rootElements, JavacProcessingEnvironment.this);
while (unmatchedAnnotations.size() > 0 && psi.hasNext()) {
ProcessorState ps = psi.next();
Set<String> matchedNames = new HashSet<String>();
Set<TypeElement> typeElements = new LinkedHashSet<TypeElement>();
for (Map.Entry<String, TypeElement> entry : unmatchedAnnotations.entrySet()) {
String unmatchedAnnotationName = entry.getKey();
if (ps.annotationSupported(unmatchedAnnotationName)) {
matchedNames.add(unmatchedAnnotationName);
TypeElement te = entry.getValue();
if (te != null) typeElements.add(te);
}
}
if (matchedNames.size() > 0 || ps.contributed) {
boolean processingResult = callProcessor(ps.processor, typeElements, renv);
ps.contributed = true;
ps.removeSupportedOptions(unmatchedProcessorOptions);
if (printProcessorInfo || verbose) {
log.printNoteLines(
"x.print.processor.info",
ps.processor.getClass().getName(),
matchedNames.toString(),
processingResult);
}
if (processingResult) {
unmatchedAnnotations.keySet().removeAll(matchedNames);
}
}
}
unmatchedAnnotations.remove("");
if (lint && unmatchedAnnotations.size() > 0) {
// Remove annotations processed by javac
unmatchedAnnotations.keySet().removeAll(platformAnnotations);
if (unmatchedAnnotations.size() > 0) {
log = Log.instance(context);
log.warning("proc.annotations.without.processors", unmatchedAnnotations.keySet());
}
}
// Run contributing processors that haven't run yet
psi.runContributingProcs(renv);
// Debugging
if (options.isSet("displayFilerState")) filer.displayState();
}
private Set<String> initUnmatchedProcessorOptions() {
Set<String> unmatchedProcessorOptions = new HashSet<String>();
unmatchedProcessorOptions.addAll(processorOptions.keySet());
return unmatchedProcessorOptions;
}
@SuppressWarnings("unchecked")
static Object bindInternal(
String name,
Class clazz,
Type type,
Annotation[] annotations,
Map<String, String[]> params,
String suffix,
String[] profiles) {
try {
Logger.trace("bindInternal: name [" + name + "] suffix [" + suffix + "]");
String[] value = params.get(name + suffix);
Logger.trace("bindInternal: value [" + value + "]");
Logger.trace("bindInternal: profile [" + Utils.join(profiles, ",") + "]");
// Let see if we have a BindAs annotation and a separator. If so, we need to split the values
// Look up for the BindAs annotation. Extract the profile if there is any.
// TODO: Move me somewhere else?
if (annotations != null) {
for (Annotation annotation : annotations) {
if ((clazz.isArray() || Collection.class.isAssignableFrom(clazz))
&& value != null
&& value.length > 0
&& annotation.annotationType().equals(As.class)) {
As as = ((As) annotation);
final String separator = as.value()[0];
value = value[0].split(separator);
}
if (annotation.annotationType().equals(NoBinding.class)) {
NoBinding bind = ((NoBinding) annotation);
String[] localUnbindProfiles = bind.value();
Logger.trace(
"bindInternal: localUnbindProfiles [" + Utils.join(localUnbindProfiles, ",") + "]");
if (localUnbindProfiles != null && contains(profiles, localUnbindProfiles)) {
return NO_BINDING;
}
}
}
}
// Arrays types
// The array condition is not so nice... We should find another way of doing this....
if (clazz.isArray()
&& (clazz != byte[].class
&& clazz != byte[][].class
&& clazz != File[].class
&& clazz != Upload[].class)) {
if (value == null) {
value = params.get(name + suffix + "[]");
}
if (value == null) {
return MISSING;
}
Object r = Array.newInstance(clazz.getComponentType(), value.length);
for (int i = 0; i <= value.length; i++) {
try {
Array.set(r, i, directBind(name, annotations, value[i], clazz.getComponentType()));
} catch (Exception e) {
// ?? One item was bad
}
}
return r;
}
// Enums
if (Enum.class.isAssignableFrom(clazz)) {
if (value == null || value.length == 0) {
return MISSING;
} else if (StringUtils.isEmpty(value[0])) {
return null;
}
return Enum.valueOf(clazz, value[0]);
}
// Map
if (Map.class.isAssignableFrom(clazz)) {
Class keyClass = String.class;
Class valueClass = String.class;
if (type instanceof ParameterizedType) {
keyClass = (Class) ((ParameterizedType) type).getActualTypeArguments()[0];
valueClass = (Class) ((ParameterizedType) type).getActualTypeArguments()[1];
}
// Special case Map<String, String>
// Multivalues composite params are binded to a Map<String, String>
// see http://play.lighthouseapp.com/projects/57987/tickets/443
if (keyClass == String.class && valueClass == String.class && isComposite(name, params)) {
Map<String, String> stringMap = Utils.filterParams(params, name);
if (stringMap.size() > 0) return stringMap;
}
// Search for all params
Map<Object, Object> r = new HashMap<Object, Object>();
for (String param : params.keySet()) {
Pattern p = Pattern.compile("^" + name + suffix + "\\[([^\\]]+)\\](.*)$");
Matcher m = p.matcher(param);
if (m.matches()) {
String key = m.group(1);
value = params.get(param);
Map<String, String[]> tP = new HashMap<String, String[]>();
tP.put("key", new String[] {key});
Object oKey = bindInternal("key", keyClass, keyClass, annotations, tP, "", value);
if (oKey != MISSING) {
if (isComposite(name + suffix + "[" + key + "]", params)) {
BeanWrapper beanWrapper = getBeanWrapper(valueClass);
Object oValue =
beanWrapper.bind(
"", type, params, name + suffix + "[" + key + "]", annotations);
r.put(oKey, oValue);
} else {
tP = new HashMap<String, String[]>();
tP.put("value", params.get(name + suffix + "[" + key + "]"));
Object oValue =
bindInternal("value", valueClass, valueClass, annotations, tP, "", value);
if (oValue != MISSING) {
r.put(oKey, oValue);
} else {
r.put(oKey, null);
}
}
}
}
}
return r;
}
// Collections types
if (Collection.class.isAssignableFrom(clazz)) {
if (clazz.isInterface()) {
if (clazz.equals(List.class)) {
clazz = ArrayList.class;
}
if (clazz.equals(Set.class)) {
clazz = HashSet.class;
}
if (clazz.equals(SortedSet.class)) {
clazz = TreeSet.class;
}
}
Collection r = (Collection) clazz.newInstance();
Class componentClass = String.class;
if (type instanceof ParameterizedType) {
componentClass = (Class) ((ParameterizedType) type).getActualTypeArguments()[0];
}
// Create a an array of the component class
if (value != null) {
Object customArray = Array.newInstance(componentClass, value.length);
// custom types
for (Class<?> c : supportedTypes.keySet()) {
if (c.isAssignableFrom(customArray.getClass())) {
Object[] ar =
(Object[])
supportedTypes
.get(c)
.bind("value", annotations, name, customArray.getClass(), null);
List l = Arrays.asList(ar);
if (clazz.equals(HashSet.class)) {
return new HashSet(l);
} else if (clazz.equals(TreeSet.class)) {
return new TreeSet(l);
}
return l;
}
}
}
if (value == null) {
value = params.get(name + suffix + "[]");
if (value == null && r instanceof List) {
for (String param : params.keySet()) {
Pattern p = Pattern.compile("^" + escape(name + suffix) + "\\[([0-9]+)\\](.*)$");
Matcher m = p.matcher(param);
if (m.matches()) {
int key = Integer.parseInt(m.group(1));
while (((List<?>) r).size() <= key) {
((List<?>) r).add(null);
}
if (isComposite(name + suffix + "[" + key + "]", params)) {
BeanWrapper beanWrapper = getBeanWrapper(componentClass);
Object oValue =
beanWrapper.bind(
"", type, params, name + suffix + "[" + key + "]", annotations);
((List) r).set(key, oValue);
} else {
Map<String, String[]> tP = new HashMap<String, String[]>();
tP.put("value", params.get(name + suffix + "[" + key + "]"));
Object oValue =
bindInternal(
"value", componentClass, componentClass, annotations, tP, "", value);
if (oValue != MISSING) {
((List) r).set(key, oValue);
}
}
}
}
return r.isEmpty() ? MISSING : r;
}
}
if (value == null) {
return MISSING;
}
for (String v : value) {
try {
r.add(directBind(name, annotations, v, componentClass));
} catch (Exception e) {
// ?? One item was bad
Logger.debug(e, "error:");
}
}
return r;
}
// Assume a Bean if isComposite
Logger.trace(
"bindInternal: class ["
+ clazz
+ "] name ["
+ name
+ "] annotation ["
+ Utils.join(annotations, " ")
+ "] isComposite ["
+ isComposite(name + suffix, params)
+ "]");
if (isComposite(name + suffix, params)) {
BeanWrapper beanWrapper = getBeanWrapper(clazz);
return beanWrapper.bind(name, type, params, suffix, annotations);
}
// Simple types
if (value == null || value.length == 0) {
return MISSING;
}
return directBind(name, annotations, value[0], clazz, type);
} catch (Exception e) {
Validation.addError(name + suffix, "validation.invalid");
return MISSING;
}
}