List of usage examples for java.lang ClassCastException getMessage
public String getMessage()
From source file:tuit.java
@SuppressWarnings("ConstantConditions") public static void main(String[] args) { System.out.println(licence);//from w w w . j a v a2 s. com //Declare variables File inputFile; File outputFile; File tmpDir; File blastnExecutable; File properties; File blastOutputFile = null; // TUITPropertiesLoader tuitPropertiesLoader; TUITProperties tuitProperties; // String[] parameters = null; // Connection connection = null; MySQL_Connector mySQL_connector; // Map<Ranks, TUITCutoffSet> cutoffMap; // BLASTIdentifier blastIdentifier = null; // RamDb ramDb = null; CommandLineParser parser = new GnuParser(); Options options = new Options(); options.addOption(tuit.IN, "input<file>", true, "Input file (currently fasta-formatted only)"); options.addOption(tuit.OUT, "output<file>", true, "Output file (in " + tuit.TUIT_EXT + " format)"); options.addOption(tuit.P, "prop<file>", true, "Properties file (XML formatted)"); options.addOption(tuit.V, "verbose", false, "Enable verbose output"); options.addOption(tuit.B, "blast_output<file>", true, "Perform on a pre-BLASTed output"); options.addOption(tuit.DEPLOY, "deploy", false, "Deploy the taxonomic databases"); options.addOption(tuit.UPDATE, "update", false, "Update the taxonomic databases"); options.addOption(tuit.USE_DB, "usedb", false, "Use RDBMS instead of RAM-based taxonomy"); Option option = new Option(tuit.REDUCE, "reduce", true, "Pack identical (100% similar sequences) records in the given sample file"); option.setArgs(Option.UNLIMITED_VALUES); options.addOption(option); option = new Option(tuit.COMBINE, "combine", true, "Combine a set of given reduction files into an HMP Tree-compatible taxonomy"); option.setArgs(Option.UNLIMITED_VALUES); options.addOption(option); options.addOption(tuit.NORMALIZE, "normalize", false, "If used in combination with -combine ensures that the values are normalized by the root value"); HelpFormatter formatter = new HelpFormatter(); try { //Get TUIT directory final File tuitDir = new File( new File(tuit.class.getProtectionDomain().getCodeSource().getLocation().toURI().getPath()) .getParent()); final File ramDbFile = new File(tuitDir, tuit.RAM_DB); //Setup logger Log.getInstance().setLogName("tuit.log"); //Read command line final CommandLine commandLine = parser.parse(options, args, true); //Check if the REDUCE option is on if (commandLine.hasOption(tuit.REDUCE)) { final String[] fileList = commandLine.getOptionValues(tuit.REDUCE); for (String s : fileList) { final Path path = Paths.get(s); Log.getInstance().log(Level.INFO, "Processing " + path.toString() + "..."); final NucleotideFastaSequenceReductor nucleotideFastaSequenceReductor = NucleotideFastaSequenceReductor .fromPath(path); ReductorFileOperator.save(nucleotideFastaSequenceReductor, path.resolveSibling(path.getFileName().toString() + ".rdc")); } Log.getInstance().log(Level.FINE, "Task done, exiting..."); return; } //Check if COMBINE is on if (commandLine.hasOption(tuit.COMBINE)) { final boolean normalize = commandLine.hasOption(tuit.NORMALIZE); final String[] fileList = commandLine.getOptionValues(tuit.COMBINE); //TODO: implement a test for format here final List<TreeFormatter.TreeFormatterFormat.HMPTreesOutput> hmpTreesOutputs = new ArrayList<>(); final TreeFormatter treeFormatter = TreeFormatter .newInstance(new TreeFormatter.TuitLineTreeFormatterFormat()); for (String s : fileList) { final Path path = Paths.get(s); Log.getInstance().log(Level.INFO, "Merging " + path.toString() + "..."); treeFormatter.loadFromPath(path); final TreeFormatter.TreeFormatterFormat.HMPTreesOutput output = TreeFormatter.TreeFormatterFormat.HMPTreesOutput .newInstance(treeFormatter.toHMPTree(normalize), s.substring(0, s.indexOf("."))); hmpTreesOutputs.add(output); treeFormatter.erase(); } final Path destination; if (commandLine.hasOption(OUT)) { destination = Paths.get(commandLine.getOptionValue(tuit.OUT)); } else { destination = Paths.get("merge.tcf"); } CombinatorFileOperator.save(hmpTreesOutputs, treeFormatter, destination); Log.getInstance().log(Level.FINE, "Task done, exiting..."); return; } if (!commandLine.hasOption(tuit.P)) { throw new ParseException("No properties file option found, exiting."); } else { properties = new File(commandLine.getOptionValue(tuit.P)); } //Load properties tuitPropertiesLoader = TUITPropertiesLoader.newInstanceFromFile(properties); tuitProperties = tuitPropertiesLoader.getTuitProperties(); //Create tmp directory and blastn executable tmpDir = new File(tuitProperties.getTMPDir().getPath()); blastnExecutable = new File(tuitProperties.getBLASTNPath().getPath()); //Check for deploy if (commandLine.hasOption(tuit.DEPLOY)) { if (commandLine.hasOption(tuit.USE_DB)) { NCBITablesDeployer.fastDeployNCBIDatabasesFromNCBI(connection, tmpDir); } else { NCBITablesDeployer.fastDeployNCBIRamDatabaseFromNCBI(tmpDir, ramDbFile); } Log.getInstance().log(Level.FINE, "Task done, exiting..."); return; } //Check for update if (commandLine.hasOption(tuit.UPDATE)) { if (commandLine.hasOption(tuit.USE_DB)) { NCBITablesDeployer.updateDatabasesFromNCBI(connection, tmpDir); } else { //No need to specify a different way to update the database other than just deploy in case of the RAM database NCBITablesDeployer.fastDeployNCBIRamDatabaseFromNCBI(tmpDir, ramDbFile); } Log.getInstance().log(Level.FINE, "Task done, exiting..."); return; } //Connect to the database if (commandLine.hasOption(tuit.USE_DB)) { mySQL_connector = MySQL_Connector.newDefaultInstance( "jdbc:mysql://" + tuitProperties.getDBConnection().getUrl().trim() + "/", tuitProperties.getDBConnection().getLogin().trim(), tuitProperties.getDBConnection().getPassword().trim()); mySQL_connector.connectToDatabase(); connection = mySQL_connector.getConnection(); } else { //Probe for ram database if (ramDbFile.exists() && ramDbFile.canRead()) { Log.getInstance().log(Level.INFO, "Loading RAM taxonomic map..."); try { ramDb = RamDb.loadSelfFromFile(ramDbFile); } catch (IOException ie) { if (ie instanceof java.io.InvalidClassException) throw new IOException("The RAM-based taxonomic database needs to be updated."); } } else { Log.getInstance().log(Level.SEVERE, "The RAM database either has not been deployed, or is not accessible." + "Please use the --deploy option and check permissions on the TUIT directory. " + "If you were looking to use the RDBMS as a taxonomic reference, plese use the -usedb option."); return; } } if (commandLine.hasOption(tuit.B)) { blastOutputFile = new File(commandLine.getOptionValue(tuit.B)); if (!blastOutputFile.exists() || !blastOutputFile.canRead()) { throw new Exception("BLAST output file either does not exist, or is not readable."); } else if (blastOutputFile.isDirectory()) { throw new Exception("BLAST output file points to a directory."); } } //Check vital parameters if (!commandLine.hasOption(tuit.IN)) { throw new ParseException("No input file option found, exiting."); } else { inputFile = new File(commandLine.getOptionValue(tuit.IN)); Log.getInstance().setLogName(inputFile.getName().split("\\.")[0] + ".tuit.log"); } //Correct the output file option if needed if (!commandLine.hasOption(tuit.OUT)) { outputFile = new File((inputFile.getPath()).split("\\.")[0] + tuit.TUIT_EXT); } else { outputFile = new File(commandLine.getOptionValue(tuit.OUT)); } //Adjust the output level if (commandLine.hasOption(tuit.V)) { Log.getInstance().setLevel(Level.FINE); Log.getInstance().log(Level.INFO, "Using verbose output for the log"); } else { Log.getInstance().setLevel(Level.INFO); } //Try all files if (inputFile != null) { if (!inputFile.exists() || !inputFile.canRead()) { throw new Exception("Input file either does not exist, or is not readable."); } else if (inputFile.isDirectory()) { throw new Exception("Input file points to a directory."); } } if (!properties.exists() || !properties.canRead()) { throw new Exception("Properties file either does not exist, or is not readable."); } else if (properties.isDirectory()) { throw new Exception("Properties file points to a directory."); } //Create blast parameters final StringBuilder stringBuilder = new StringBuilder(); for (Database database : tuitProperties.getBLASTNParameters().getDatabase()) { stringBuilder.append(database.getUse()); stringBuilder.append(" ");//Gonna insert an extra space for the last database } String remote; String entrez_query; if (tuitProperties.getBLASTNParameters().getRemote().getDelegate().equals("yes")) { remote = "-remote"; entrez_query = "-entrez_query"; parameters = new String[] { "-db", stringBuilder.toString(), remote, entrez_query, tuitProperties.getBLASTNParameters().getEntrezQuery().getValue(), "-evalue", tuitProperties.getBLASTNParameters().getExpect().getValue() }; } else { if (!commandLine.hasOption(tuit.B)) { if (tuitProperties.getBLASTNParameters().getEntrezQuery().getValue().toUpperCase() .startsWith("NOT") || tuitProperties.getBLASTNParameters().getEntrezQuery().getValue().toUpperCase() .startsWith("ALL")) { parameters = new String[] { "-db", stringBuilder.toString(), "-evalue", tuitProperties.getBLASTNParameters().getExpect().getValue(), "-negative_gilist", TUITFileOperatorHelper.restrictToEntrez(tmpDir, tuitProperties.getBLASTNParameters().getEntrezQuery().getValue() .toUpperCase().replace("NOT", "OR")) .getAbsolutePath(), "-num_threads", tuitProperties.getBLASTNParameters().getNumThreads().getValue() }; } else if (tuitProperties.getBLASTNParameters().getEntrezQuery().getValue().toUpperCase() .equals("")) { parameters = new String[] { "-db", stringBuilder.toString(), "-evalue", tuitProperties.getBLASTNParameters().getExpect().getValue(), "-num_threads", tuitProperties.getBLASTNParameters().getNumThreads().getValue() }; } else { parameters = new String[] { "-db", stringBuilder.toString(), "-evalue", tuitProperties.getBLASTNParameters().getExpect().getValue(), /*"-gilist", TUITFileOperatorHelper.restrictToEntrez( tmpDir, tuitProperties.getBLASTNParameters().getEntrezQuery().getValue()).getAbsolutePath(),*/ //TODO remove comment!!!!! "-num_threads", tuitProperties.getBLASTNParameters().getNumThreads().getValue() }; } } } //Prepare a cutoff Map if (tuitProperties.getSpecificationParameters() != null && tuitProperties.getSpecificationParameters().size() > 0) { cutoffMap = new HashMap<Ranks, TUITCutoffSet>(tuitProperties.getSpecificationParameters().size()); for (SpecificationParameters specificationParameters : tuitProperties .getSpecificationParameters()) { cutoffMap.put(Ranks.valueOf(specificationParameters.getCutoffSet().getRank()), TUITCutoffSet.newDefaultInstance( Double.parseDouble( specificationParameters.getCutoffSet().getPIdentCutoff().getValue()), Double.parseDouble(specificationParameters.getCutoffSet() .getQueryCoverageCutoff().getValue()), Double.parseDouble( specificationParameters.getCutoffSet().getAlpha().getValue()))); } } else { cutoffMap = new HashMap<Ranks, TUITCutoffSet>(); } final TUITFileOperatorHelper.OutputFormat format; if (tuitProperties.getBLASTNParameters().getOutputFormat().getFormat().equals("rdp")) { format = TUITFileOperatorHelper.OutputFormat.RDP_FIXRANK; } else { format = TUITFileOperatorHelper.OutputFormat.TUIT; } try (TUITFileOperator<NucleotideFasta> nucleotideFastaTUITFileOperator = NucleotideFastaTUITFileOperator .newInstance(format, cutoffMap);) { nucleotideFastaTUITFileOperator.setInputFile(inputFile); nucleotideFastaTUITFileOperator.setOutputFile(outputFile); final String cleanupString = tuitProperties.getBLASTNParameters().getKeepBLASTOuts().getKeep(); final boolean cleanup; if (cleanupString.equals("no")) { Log.getInstance().log(Level.INFO, "Temporary BLAST files will be deleted."); cleanup = true; } else { Log.getInstance().log(Level.INFO, "Temporary BLAST files will be kept."); cleanup = false; } //Create blast identifier ExecutorService executorService = Executors.newSingleThreadExecutor(); if (commandLine.hasOption(tuit.USE_DB)) { if (blastOutputFile == null) { blastIdentifier = TUITBLASTIdentifierDB.newInstanceFromFileOperator(tmpDir, blastnExecutable, parameters, nucleotideFastaTUITFileOperator, connection, cutoffMap, Integer.parseInt( tuitProperties.getBLASTNParameters().getMaxFilesInBatch().getValue()), cleanup); } else { try { blastIdentifier = TUITBLASTIdentifierDB.newInstanceFromBLASTOutput( nucleotideFastaTUITFileOperator, connection, cutoffMap, blastOutputFile, Integer.parseInt( tuitProperties.getBLASTNParameters().getMaxFilesInBatch().getValue()), cleanup); } catch (JAXBException e) { Log.getInstance().log(Level.SEVERE, "Error reading " + blastOutputFile.getName() + ", please check input. The file must be XML formatted."); } catch (Exception e) { e.printStackTrace(); } } } else { if (blastOutputFile == null) { blastIdentifier = TUITBLASTIdentifierRAM.newInstanceFromFileOperator(tmpDir, blastnExecutable, parameters, nucleotideFastaTUITFileOperator, cutoffMap, Integer.parseInt( tuitProperties.getBLASTNParameters().getMaxFilesInBatch().getValue()), cleanup, ramDb); } else { try { blastIdentifier = TUITBLASTIdentifierRAM.newInstanceFromBLASTOutput( nucleotideFastaTUITFileOperator, cutoffMap, blastOutputFile, Integer.parseInt( tuitProperties.getBLASTNParameters().getMaxFilesInBatch().getValue()), cleanup, ramDb); } catch (JAXBException e) { Log.getInstance().log(Level.SEVERE, "Error reading " + blastOutputFile.getName() + ", please check input. The file must be XML formatted."); } catch (Exception e) { e.printStackTrace(); } } } Future<?> runnableFuture = executorService.submit(blastIdentifier); runnableFuture.get(); executorService.shutdown(); } } catch (ParseException pe) { Log.getInstance().log(Level.SEVERE, (pe.getMessage())); formatter.printHelp("tuit", options); } catch (SAXException saxe) { Log.getInstance().log(Level.SEVERE, saxe.getMessage()); } catch (FileNotFoundException fnfe) { Log.getInstance().log(Level.SEVERE, fnfe.getMessage()); } catch (TUITPropertyBadFormatException tpbfe) { Log.getInstance().log(Level.SEVERE, tpbfe.getMessage()); } catch (ClassCastException cce) { Log.getInstance().log(Level.SEVERE, cce.getMessage()); } catch (JAXBException jaxbee) { Log.getInstance().log(Level.SEVERE, "The properties file is not well formatted. Please ensure that the XML is consistent with the io.properties.dtd schema."); } catch (ClassNotFoundException cnfe) { //Probably won't happen unless the library deleted from the .jar Log.getInstance().log(Level.SEVERE, cnfe.getMessage()); //cnfe.printStackTrace(); } catch (SQLException sqle) { Log.getInstance().log(Level.SEVERE, "A database communication error occurred with the following message:\n" + sqle.getMessage()); //sqle.printStackTrace(); if (sqle.getMessage().contains("Access denied for user")) { Log.getInstance().log(Level.SEVERE, "Please use standard database login: " + NCBITablesDeployer.login + " and password: " + NCBITablesDeployer.password); } } catch (Exception e) { Log.getInstance().log(Level.SEVERE, e.getMessage()); e.printStackTrace(); } finally { if (connection != null) { try { connection.close(); } catch (SQLException sqle) { Log.getInstance().log(Level.SEVERE, "Problem closing the database connection: " + sqle); } } Log.getInstance().log(Level.FINE, "Task done, exiting..."); } }
From source file:Main.java
@SuppressWarnings("unchecked") public static final <E extends View> E getView(View parent, int id) { try {/*from w w w.ja va 2 s . co m*/ return (E) parent.findViewById(id); } catch (ClassCastException ex) { Log.e("ImagPageUtil", "Could not cast View to concrete class \n" + ex.getMessage()); throw ex; } }
From source file:com.comcast.cats.service.util.YAMLUtils.java
@SuppressWarnings("unchecked") public static synchronized <T> T loadFromYAML(String filePath, T resultObject, Constructor constructor) throws IllegalClassException, IOException { Yaml yaml;//from www. j a v a 2 s .c o m FileInputStream fileIS = null; if (constructor != null) { yaml = new Yaml(constructor); } else { yaml = new Yaml(); } try { fileIS = new FileInputStream(filePath); resultObject = (T) yaml.load(fileIS); } catch (FileNotFoundException exception) { File file = new File(filePath); file.createNewFile(); // create file if one does not exist. fileIS = new FileInputStream(filePath); resultObject = (T) yaml.load(fileIS); } catch (ClassCastException e) { logger.warn( "YAML content found at " + filePath + " does not conform to passed object " + e.getMessage()); throw new IllegalClassException( "YAML content found at " + filePath + " does not conform to passed object " + e.getMessage()); } finally { if (fileIS != null) { fileIS.close(); } } return resultObject; }
From source file:com.feilong.core.lang.ObjectUtilTemp.java
/** * ?? {@link java.util.Iterator}.//from ww w . ja va2s. com * <p> * ??,,???with no copying<br> * ?, ClassCastException ,Rats -- ,arrayList ?arrayList.iterator() * </p> * <p> * <b>:</b>{@link Arrays#asList(Object...)} list {@link Array} ArrayList, * {@link java.util.AbstractList#add(int, Object)} ,<br> * listadd?, {@link java.lang.UnsupportedOperationException} * </p> * * @param <T> * the generic type * @param arrays * ,? , * @return (null == arrays) null;<br> * ?arrays?Object[], {@link Arrays#asList(Object...)}?list,? {@link List#iterator() * t}<br> * ,? Object[],?, {@link Array#getLength(Object)}?, {@link Array#get(Object, int)} list * @see Arrays#asList(Object...) * @see Array#getLength(Object) * @see Array#get(Object, int) * @see List#iterator() * @deprecated */ @Deprecated @SuppressWarnings({ "unchecked" }) public static <T> Iterator<T> toIterator(Object arrays) { if (null == arrays) { return null; } List<T> list = null; try { // ??,,???with no copying Object[] objArrays = (Object[]) arrays; list = (List<T>) toList(objArrays); } catch (ClassCastException e) { LOGGER.debug("arrays can not cast to Object[],maybe primitive type,values is:{},{}", arrays, e.getMessage()); // Rats -- int length = Array.getLength(arrays); list = new ArrayList<T>(length); for (int i = 0; i < length; ++i) { Object object = Array.get(arrays, i); list.add((T) object); } } return list.iterator(); }
From source file:org.apache.synapse.util.PayloadHelper.java
public static DataHandler getBinaryPayload(SOAPEnvelope envelope) { OMElement el = getXMLPayload(envelope); if (el == null) return null; if (!el.getQName().equals(BINARYELT)) { log.error("Wrong QName" + el.getQName()); return null; }// w w w .j av a 2 s.c o m OMNode textNode = el.getFirstOMChild(); if (textNode.getType() != OMNode.TEXT_NODE) { log.error("Text Node not found"); return null; } OMText text = (OMText) textNode; try { return (DataHandler) text.getDataHandler(); } catch (ClassCastException ce) { log.error("cannot get DataHandler" + ce.getMessage()); return null; } }
From source file:com.netflix.astyanax.thrift.ThriftUtils.java
@SuppressWarnings({ "rawtypes", "unchecked" })
private static Object populateObject(Object obj, Map<String, Object> map) throws Exception {
org.apache.thrift.TBase entity = (org.apache.thrift.TBase) obj;
Field field = entity.getClass().getDeclaredField("metaDataMap");
Map<org.apache.thrift.TFieldIdEnum, org.apache.thrift.meta_data.FieldMetaData> fields = (Map<org.apache.thrift.TFieldIdEnum, FieldMetaData>) field
.get(entity);//from w w w .j av a 2s . c om
for (Entry<TFieldIdEnum, FieldMetaData> f : fields.entrySet()) {
Object value = map.get(f.getKey().getFieldName());
if (value != null) {
ThriftTypes type = ThriftTypes.values()[f.getValue().valueMetaData.type];
switch (type) {
case VOID:
break;
case BYTE:
case BOOL:
case DOUBLE:
case I16:
case I32:
case I64:
case STRING:
try {
entity.setFieldValue(f.getKey(), valueForBasicType(value, f.getValue().valueMetaData.type));
} catch (ClassCastException e) {
if (e.getMessage().contains(ByteBuffer.class.getCanonicalName())) {
entity.setFieldValue(f.getKey(), ByteBuffer.wrap(Base64.decodeBase64((String) value)));
} else {
throw e;
}
}
break;
case ENUM: {
org.apache.thrift.meta_data.EnumMetaData meta = (org.apache.thrift.meta_data.EnumMetaData) f
.getValue().valueMetaData;
Object e = meta.enumClass;
entity.setFieldValue(f.getKey(), Enum.valueOf((Class<Enum>) e, (String) value));
break;
}
case MAP: {
org.apache.thrift.meta_data.MapMetaData meta = (org.apache.thrift.meta_data.MapMetaData) f
.getValue().valueMetaData;
if (!meta.keyMetaData.isStruct() && !meta.keyMetaData.isContainer()) {
Map<Object, Object> childMap = (Map<Object, Object>) value;
Map<Object, Object> childEntityMap = Maps.newHashMap();
entity.setFieldValue(f.getKey(), childEntityMap);
if (!meta.keyMetaData.isStruct() && !meta.keyMetaData.isContainer()) {
for (Entry<Object, Object> entry : childMap.entrySet()) {
Object childKey = valueForBasicType(entry.getKey(), meta.keyMetaData.type);
Object childValue = valueForBasicType(entry.getValue(), meta.valueMetaData.type);
childEntityMap.put(childKey, childValue);
}
}
} else {
LOG.error(String.format("Unable to serializer field '%s' key type '%s' not supported",
f.getKey().getFieldName(), meta.keyMetaData.getTypedefName()));
}
break;
}
case LIST: {
Map<String, Object> childMap = (Map<String, Object>) value;
org.apache.thrift.meta_data.ListMetaData listMeta = (org.apache.thrift.meta_data.ListMetaData) f
.getValue().valueMetaData;
// Create an empty list and attach to the parent entity
List<Object> childList = Lists.newArrayList();
entity.setFieldValue(f.getKey(), childList);
if (listMeta.elemMetaData instanceof org.apache.thrift.meta_data.StructMetaData) {
org.apache.thrift.meta_data.StructMetaData structMeta = (org.apache.thrift.meta_data.StructMetaData) listMeta.elemMetaData;
for (Entry<String, Object> childElement : childMap.entrySet()) {
org.apache.thrift.TBase childEntity = structMeta.structClass.newInstance();
populateObject(childEntity, (Map<String, Object>) childElement.getValue());
childList.add(childEntity);
}
}
break;
}
case STRUCT: {
break;
}
case SET:
default:
LOG.error("Unhandled value : " + f.getKey().getFieldName() + " " + type);
break;
}
}
}
return entity;
}
From source file:com.cinchapi.concourse.lang.Parser.java
/** * Go through a list of symbols and group the expressions together in a * {@link Expression} object./*from www . j av a 2 s .c o m*/ * * @param symbols * @return the expression */ protected static List<Symbol> groupExpressions(List<Symbol> symbols) { // visible // for // testing try { List<Symbol> grouped = Lists.newArrayList(); ListIterator<Symbol> it = symbols.listIterator(); while (it.hasNext()) { Symbol symbol = it.next(); if (symbol instanceof KeySymbol) { // NOTE: We are assuming that the list of symbols is well // formed, and, as such, the next elements will be an // operator and one or more symbols. If this is not the // case, this method will throw a ClassCastException OperatorSymbol operator = (OperatorSymbol) it.next(); ValueSymbol value = (ValueSymbol) it.next(); Expression expression; if (operator.getOperator() == Operator.BETWEEN) { ValueSymbol value2 = (ValueSymbol) it.next(); expression = Expression.create((KeySymbol) symbol, operator, value, value2); } else { expression = Expression.create((KeySymbol) symbol, operator, value); } grouped.add(expression); } else if (symbol instanceof TimestampSymbol) { // Add the // timestamp to the // previously // generated // Expression ((Expression) Iterables.getLast(grouped)).setTimestamp((TimestampSymbol) symbol); } else { grouped.add(symbol); } } return grouped; } catch (ClassCastException e) { throw new SyntaxException(e.getMessage()); } }
From source file:org.filteredpush.qc.sciname.services.GBIFService.java
public static NameUsage parseNameUsageFromJSON(String targetName, String json) { JSONParser parser = new JSONParser(); try {// w w w . j a v a 2 s . co m JSONArray array = new JSONArray(); try { JSONObject o = (JSONObject) parser.parse(json); if (o.get("results") != null) { array = (JSONArray) o.get("results"); } else { // array = (JSONArray)parser.parse(json); } } catch (ClassCastException e) { logger.debug(e.getMessage(), e); array = (JSONArray) parser.parse(json); } Iterator<JSONObject> i = array.iterator(); while (i.hasNext()) { JSONObject obj = i.next(); // System.out.println(obj.toJSONString()); NameUsage name = new NameUsage(obj); if (name.getCanonicalName().equals(targetName)) { return name; } } } catch (ParseException e) { logger.debug(e.getMessage(), e); } return null; }
From source file:org.exoplatform.commons.notification.template.TemplateUtils.java
/** * Generate the Groovy Template//from www . j a va 2 s . c o m * @param context The template context * @param element The GroovyElemt * @param out The Writer to writer template * @return */ public static void loadGroovy(TemplateContext context, Element element, Writer out) { try { String groovyTemplate = element.getTemplate(); if (groovyTemplate == null) { groovyTemplate = loadGroovyTemplate(element.getTemplateConfig().getTemplatePath()); element.template(groovyTemplate); } if (groovyTemplate != null && groovyTemplate.length() > 0) { GroovyTemplate gTemplate = new GroovyTemplate(groovyTemplate); gTemplate.render(out, context); } } catch (ClassCastException e) { throw new IllegalArgumentException("The function only load groovy with GroovyElement type."); } catch (Exception e) { LOG.warn("Failed to load groovy template of plugin " + context.getPluginId() + "\n" + e.getMessage()); } }
From source file:com.discovery.darchrow.lang.ArrayUtil.java
/** * ?? {@link java.util.Iterator}.//w w w. j a v a2 s.com * <p> * ??,???with no copying<br> * ?, ClassCastException ,Rats -- ,arrayList ?arrayList.iterator() * </p> * <p> * <b>:</b>{@link Arrays#asList(Object...)} list {@link Array} ArrayList, * {@link java.util.AbstractList#add(int, Object)} ,<br> * listadd?, {@link java.lang.UnsupportedOperationException} * </p> * * @param <T> * the generic type * @param arrays * ,? , * @return if (null == arrays) return null;<br> * ?arrays?Object[], {@link Arrays#asList(Object...)}?list,? {@link List#iterator() * t}<br> * ,? Object[],?, {@link Array#getLength(Object)}?, {@link Array#get(Object, int)} list * @see Arrays#asList(Object...) * @see Array#getLength(Object) * @see Array#get(Object, int) * @see List#iterator() */ @SuppressWarnings({ "unchecked" }) public static <T> Iterator<T> toIterator(Object arrays) { if (null == arrays) { return null; } List<T> list = null; try { // ??,???with no copying Object[] objArrays = (Object[]) arrays; list = (List<T>) toList(objArrays); } catch (ClassCastException e) { if (LOGGER.isDebugEnabled()) { LOGGER.debug("arrays can not cast to Object[],maybe primitive type,values is:{},{}", arrays, e.getMessage()); } // Rats -- int length = Array.getLength(arrays); list = new ArrayList<T>(length); for (int i = 0; i < length; ++i) { Object object = Array.get(arrays, i); list.add((T) object); } } return list.iterator(); }