List of usage examples for org.apache.commons.configuration CompositeConfiguration getString
public String getString(String key, String defaultValue)
From source file:ffx.xray.parsers.MTZFilter.java
/** * {@inheritDoc}/*from w ww .j a v a 2 s . com*/ */ @Override public ReflectionList getReflectionList(File mtzFile, CompositeConfiguration properties) { ByteOrder byteOrder = ByteOrder.nativeOrder(); FileInputStream fileInputStream; DataInputStream dataInputStream; try { fileInputStream = new FileInputStream(mtzFile); dataInputStream = new DataInputStream(fileInputStream); byte headerOffset[] = new byte[4]; byte bytes[] = new byte[80]; int offset = 0; // Eat "MTZ" title. dataInputStream.read(bytes, offset, 4); String mtzstr = new String(bytes); // Header offset. dataInputStream.read(headerOffset, offset, 4); // Machine stamp. dataInputStream.read(bytes, offset, 4); ByteBuffer byteBuffer = ByteBuffer.wrap(bytes); int stamp = byteBuffer.order(ByteOrder.BIG_ENDIAN).getInt(); String stampstr = Integer.toHexString(stamp); switch (stampstr.charAt(0)) { case '1': case '3': if (byteOrder.equals(ByteOrder.LITTLE_ENDIAN)) { byteOrder = ByteOrder.BIG_ENDIAN; } break; case '4': if (byteOrder.equals(ByteOrder.BIG_ENDIAN)) { byteOrder = ByteOrder.LITTLE_ENDIAN; } break; } byteBuffer = ByteBuffer.wrap(headerOffset); int headerOffsetI = byteBuffer.order(byteOrder).getInt(); // skip to header and parse dataInputStream.skipBytes((headerOffsetI - 4) * 4); for (Boolean parsing = true; parsing; dataInputStream.read(bytes, offset, 80)) { mtzstr = new String(bytes); parsing = parseHeader(mtzstr); } } catch (EOFException e) { String message = " MTZ end of file reached."; logger.log(Level.WARNING, message, e); return null; } catch (IOException e) { String message = " MTZ IO exception."; logger.log(Level.WARNING, message, e); return null; } // column identifiers foString = sigFoString = rFreeString = null; if (properties != null) { foString = properties.getString("fostring", null); sigFoString = properties.getString("sigfostring", null); rFreeString = properties.getString("rfreestring", null); } h = k = l = fo = sigFo = rFree = -1; fPlus = sigFPlus = fMinus = sigFMinus = rFreePlus = rFreeMinus = -1; fc = phiC = -1; boolean print = false; parseColumns(print); parseFcColumns(print); if (fo < 0 && fPlus < 0 && sigFo < 0 && sigFPlus < 0 && fc < 0 && phiC < 0) { logger.info(" The MTZ header contains insufficient information to generate the reflection list."); logger.info(" For non-default column labels set fostring/sigfostring in the properties file."); return null; } Column column; if (fo > 0) { column = (Column) columns.get(fo); } else if (fPlus > 0) { column = (Column) columns.get(fPlus); } else { column = (Column) columns.get(fc); } Dataset dataSet = (Dataset) dataSets.get(column.id - dsetOffset); if (logger.isLoggable(Level.INFO)) { StringBuilder sb = new StringBuilder(); sb.append(format("\n Reading %s\n\n", mtzFile.getName())); sb.append(format(" Setting up reflection list based on MTZ file.\n")); sb.append(format(" Space group number: %d (name: %s)\n", spaceGroupNum, SpaceGroup.spaceGroupNames[spaceGroupNum - 1])); sb.append(format(" Resolution: %8.3f\n", 0.999999 * resHigh)); sb.append(format(" Cell: %8.3f %8.3f %8.3f %8.3f %8.3f %8.3f\n", dataSet.cell[0], dataSet.cell[1], dataSet.cell[2], dataSet.cell[3], dataSet.cell[4], dataSet.cell[5])); logger.info(sb.toString()); } Crystal crystal = new Crystal(dataSet.cell[0], dataSet.cell[1], dataSet.cell[2], dataSet.cell[3], dataSet.cell[4], dataSet.cell[5], SpaceGroup.spaceGroupNames[spaceGroupNum - 1]); double sampling = 0.6; if (properties != null) { sampling = properties.getDouble("sampling", 0.6); } Resolution resolution = new Resolution(0.999999 * resHigh, sampling); return new ReflectionList(crystal, resolution, properties); }
From source file:ro.nextreports.server.web.ApplicationLoaderListener.java
private void config() { LOG.info("NextReports Server " + ReleaseInfo.getVersion() + " starting ... "); CompositeConfiguration config = new CompositeConfiguration(); config.addConfiguration(new SystemConfiguration()); try {/*from w w w .jav a 2 s . c om*/ config.addConfiguration(new PropertiesConfiguration(getClass().getResource("/nextserver.properties"))); } catch (ConfigurationException e) { // TODO e.printStackTrace(); } File defaultNextServerHomeFolder = new File(System.getProperty("user.home"), ".nextserver"); String defaultNextServerHome = defaultNextServerHomeFolder.getPath(); String nextServerHome = config.getString("nextserver.home", defaultNextServerHome); LOG.info("nextserver.home = " + nextServerHome); String demo = System.getProperty("DEMO"); LOG.info("DEMO=" + demo); boolean installWithDemo = Boolean.valueOf(demo); File nextServerHomeFolder = new File(nextServerHome); if (!nextServerHomeFolder.exists()) { try { if (installWithDemo) { deployDemoData(nextServerHome); } else { if (LOG.isDebugEnabled()) { LOG.debug("Create nextserver home folder: '" + nextServerHomeFolder + "'"); } FileUtils.forceMkdir(nextServerHomeFolder); } } catch (IOException e) { // TODO e.printStackTrace(); } } System.setProperty("nextserver.home", nextServerHome); // File defaultJaspersHomeFolder = new File(nextServerHome, "jaspers"); // String defaultJaspersHome = defaultJaspersHomeFolder.getPath(); // String jaspersHome = config.getString("jaspers.home", defaultJaspersHome); // System.setProperty("jaspers.home", jaspersHome); // if (LOG.isDebugEnabled()) { // LOG.debug("jaspers.home = " + jaspersHome); // } // indexing.file ClassPathResource classPathResource = new ClassPathResource("indexing.xml"); String indexingFile = null; try { indexingFile = classPathResource.getFile().getAbsolutePath(); } catch (IOException e) { // TODO e.printStackTrace(); } System.setProperty("indexing.file", indexingFile); if (LOG.isDebugEnabled()) { LOG.debug("indexing.file = " + indexingFile); } // String baseUrl = config.getString("nextserver.baseUrl"); // String reportsUrl = config.getString("reports.url"); // if (LOG.isDebugEnabled()) { // LOG.debug("nextserver.baseUrl = " + baseUrl); // LOG.debug("reports.url = " + reportsUrl); // } }
From source file:umich.ms.batmass.gui.viewers.map2d.components.Map2DZoomLevel.java
private RangeNormalizer createNormalizer(double minNonZero, double max) { double curRange = max - minNonZero; CompositeConfiguration config = Map2DOptions.getInstance().getConfig(); // TODO: the default value is set here, in case the user config is messed up String normalizerName = config.getString("intensityNormalizer", "LOG"); RangeNormalizers norm = RangeNormalizers.valueOf(normalizerName); RangeNormalizer rangeNormalizer = norm.getRangeNormalizer(); rangeNormalizer.configure(max, minNonZero, targetRange); return rangeNormalizer; // return new RangeNormalizerImplDoNothing(); // TODO: replaced this version, which was not doing any normalization in the intensity // range was smaller than the defined threshold, with the above two lines (i.e. the // normalization is always executed) // It worked better this way for metabolomics Agilent data, where we had signals // of very small and very large intensity. Don't know why, though... // if (curRange <= targetRange) { // // TODO: exp int this case // // if the range is smaller than target, then find exp base // return new RangeNormalizerImplDoNothing(); // } else { // // if the range is larger than target, then find log base // double base = FastMath.exp((FastMath.log(max) - FastMath.log(minNonZero)) / targetRange); // return new RangeNormalizerImplLog(base); // }//from w ww .j a v a 2s . c om }