List of usage examples for org.apache.commons.beanutils ConvertUtils convert
public static Object convert(String values[], Class clazz)
Convert an array of specified values to an array of objects of the specified class (if possible).
For more details see ConvertUtilsBean.
From source file:edu.scripps.fl.pubchem.app.RelatedCurveProcessor.java
public static void main(String[] args) throws Exception { CommandLineHandler clh = new CommandLineHandler(); args = clh.handle(args);/*from w w w . j a v a2s.c o m*/ Integer[] list = (Integer[]) ConvertUtils.convert(args, Integer[].class); Integer referenceAid = list[0]; Integer[] relatedAids = new Integer[list.length - 1]; System.arraycopy(list, 1, relatedAids, 0, list.length - 1); URL url = PipelineUtils.class.getClassLoader() .getResource("edu/scripps/fl/pubchem/RelatedCurvesPipeline.xml"); Pipeline pipeline = new PipelineUtils().createPipeline(url, Arrays.asList(relatedAids)); List<Stage> stages = pipeline.getStages(); BeanUtils.setProperty(stages.get(1), "referenceAID", referenceAid); pipeline.run(); new PipelineUtils().logErrors(pipeline); }
From source file:edu.scripps.fl.pubchem.app.AssayDownloader.java
public static void main(String[] args) throws Exception { CommandLineHandler clh = new CommandLineHandler() { public void configureOptions(Options options) { options.addOption(OptionBuilder.withLongOpt("data_url").withType("").withValueSeparator('=') .hasArg().create()); options.addOption(/*from ww w . j a v a 2 s .c o m*/ OptionBuilder.withLongOpt("days").withType(0).withValueSeparator('=').hasArg().create()); options.addOption(OptionBuilder.withLongOpt("mlpcn").withType(false).create()); options.addOption(OptionBuilder.withLongOpt("notInDb").withType(false).create()); } }; args = clh.handle(args); String data_url = clh.getCommandLine().getOptionValue("data_url"); if (null == data_url) data_url = "ftp://ftp.ncbi.nlm.nih.gov/pubchem/Bioassay/CSV/"; // data_url = "file:///C:/Home/temp/PubChemFTP/"; AssayDownloader main = new AssayDownloader(); main.dataUrl = new URL(data_url); if (clh.getCommandLine().hasOption("days")) main.days = Integer.parseInt(clh.getCommandLine().getOptionValue("days")); if (clh.getCommandLine().hasOption("mlpcn")) main.mlpcn = true; if (clh.getCommandLine().hasOption("notInDb")) main.notInDb = true; if (args.length == 0) main.process(); else { Long[] list = (Long[]) ConvertUtils.convert(args, Long[].class); List<Long> l = (List<Long>) Arrays.asList(list); log.info("AID to process: " + l); main.process(new HashSet<Long>(Arrays.asList(list))); } }
From source file:edu.scripps.fl.pubchem.app.ResultDownloader.java
public static void main(String[] args) throws Exception { CommandLineHandler clh = new CommandLineHandler() { public void configureOptions(Options options) { options.addOption(OptionBuilder.withLongOpt("data_url").withType("").withValueSeparator('=') .hasArg().create()); }//from w w w . jav a 2s .c o m }; args = clh.handle(args); String data_url = clh.getCommandLine().getOptionValue("data_url"); ResultDownloader rd = new ResultDownloader(); if (data_url != null) rd.setDataUrl(new URL(data_url)); else rd.setDataUrl(new URL("ftp://ftp.ncbi.nlm.nih.gov/pubchem/Bioassay/CSV/")); if (args.length == 0) rd.process(); else { Integer[] list = (Integer[]) ConvertUtils.convert(args, Integer[].class); rd.process(((List<Integer>) Arrays.asList(list)).iterator()); } }
From source file:net.eusashead.hateoas.header.impl.PropertyUtil.java
public static <V> V getValue(Object target, String name, Class<V> type) { return type.cast(ConvertUtils.convert(getValue(target, name), type)); }
From source file:com.github.dactiv.fear.commons.Casts.java
/** * value /*from w ww.jav a 2s . c o m*/ * * @param value * @param type class * * @param <T> * * @return ? */ public static <T> T cast(Object value, Class<T> type) { return (T) (value == null ? null : ConvertUtils.convert(value, type)); }
From source file:com.yahoo.elide.utils.coerce.CoerceUtil.java
/** * Convert value to target class./*from w w w .ja v a 2 s .c o m*/ * * @param value value to convert * @param cls class to convert to * @return coerced value */ public static Object coerce(Object value, Class<?> cls) { if (value == null || cls == null || cls.isAssignableFrom(value.getClass())) { return value; } try { return ConvertUtils.convert(value, cls); } catch (ConversionException | InvalidAttributeException | IllegalArgumentException e) { throw new InvalidValueException(value); } }
From source file:edu.scripps.fl.curves.CurveFit.java
public static void fit(Curve curve) { log.debug("Fitting Curve: " + curve); double y[] = (double[]) ConvertUtils.convert(curve.getResponses(), double[].class); double x[] = (double[]) ConvertUtils.convert(curve.getConcentrations(), double[].class); for (int ii = 0; ii < x.length; ii++) x[ii] = Math.log10(x[ii]); // max, min and range double minY = Double.MAX_VALUE; double maxY = -Double.MAX_VALUE; double maxResp = y[y.length - 1]; for (int i = 0; i < y.length; i++) { minY = Math.min(minY, y[i]); maxY = Math.max(maxY, y[i]); }//from ww w . j a v a 2s . co m curve.setResponseMin(minY); curve.setResponseMax(maxY); curve.setResponseRange(maxY - minY); curve.setMaxResponse(maxResp); // fit boolean flags[] = null; Map maps[] = null; double fitValues[] = null; Object fitResults[] = HillFit.doHill(x, y, null, HillConstants.FIT_ITER_NO, HillConstants.P4_FIT); if (fitResults != null) { flags = (boolean[]) fitResults[0]; fitValues = (double[]) fitResults[1]; maps = (Map[]) fitResults[2]; } if (fitValues != null) { curve.setYZero(fitValues[6]); curve.setLogEC50(fitValues[0]); curve.setYInflection(fitValues[1]); curve.setHillSlope(fitValues[2]); curve.setR2(fitValues[3]); double ec50 = 1000000D * Math.exp(Math.log(10D) * curve.getLogEC50()); double testEC50 = Math.pow(10, curve.getLogEC50()); Double ic50 = null; double logIC50 = BatchHill.iccalc(curve.getYZero(), curve.getYInflection(), curve.getLogEC50(), curve.getHillSlope(), 50D); if (logIC50 < 0.0D) ic50 = 1000000D * Math.exp(Math.log(10D) * logIC50); int dn = Math.max(1, x.length - 4); double df = dn; double p = HillStat.calcPValue(curve.getYZero(), curve.getYInflection(), curve.getLogEC50(), curve.getHillSlope(), x, y, flags); int mask = 0; for (int i = 0; i < x.length; i++) if (!flags[i]) mask++; double ss = HillStat.calcHillDeviation(curve.getLogEC50(), curve.getYZero(), curve.getYInflection(), curve.getHillSlope(), flags, null, x, y); curve.setEC50(ec50); curve.setIC50(ic50); curve.setPHill(p); curve.setSYX(ss / df); for (int ii = 0; ii < flags.length; ii++) { if (flags[ii] == true) { curve.setMasked(true); break; } } } else { curve.setLogEC50(null); curve.setHillSlope(null); curve.setR2(null); curve.setYInflection(null); curve.setYZero(null); curve.setEC50(null); curve.setIC50(null); curve.setPHill(null); curve.setSYX(null); curve.setMasked(false); flags = new boolean[x.length]; } // masks List<Boolean> masks = new ArrayList<Boolean>(flags.length); CollectionUtils.addAll(masks, (Boolean[]) ConvertUtils.convert(flags, Boolean[].class)); curve.setMask(masks); // classify curveClassification(curve, y, x, flags); // rank double rank = -BatchHill.calcRank(curve.getCurveClass(), curve.getMaxResponse(), curve.getResponseRange()); curve.setRank(rank); }
From source file:net.servicefixture.converter.CalendarConverter.java
public Object fromObject(Object source) { if (source == null) { return null; }//from w w w .j a v a 2 s .c o m if (source instanceof Calendar) { return source; } Date date = (Date) ConvertUtils.convert(source.toString(), Date.class); Calendar calendar = Calendar.getInstance(); calendar.setTimeInMillis(date.getTime()); return calendar; }
From source file:edu.scripps.fl.pubchem.app.util.ScrollableResultsIterator.java
public E next() { Object[] obj = results.get(); Object obj2 = ConvertUtils.convert(obj[0], clazz); return clazz.cast(obj2); }
From source file:edu.scripps.fl.pubchem.app.cids.FetchSDFStage.java
@Override public void process(Object obj) throws StageException { List<Number> ids = (List<Number>) obj; try {//from w ww . ja va 2 s . c o m int[] list = (int[]) ConvertUtils.convert(ids, int[].class); URL url = PUGSoapFactory.getInstance().getSDFilefromCIDs(list); System.out.println("SDF File URL: " + url); emit(url); } catch (Exception ex) { ex.printStackTrace(); throw new StageException(this, ex); } }