List of usage examples for org.apache.commons.configuration2.builder BasicConfigurationBuilder getConfiguration
@Override public T getConfiguration() throws ConfigurationException
From source file:Executable.Output.java
/** * Write the control file (for the final imputation step) * @param config The configuration to write * @throws OutputException If there is an IO problem *//* w ww . j a va 2s.com*/ public void writeControl(List<ImmutableNode> config) throws OutputException { BasicConfigurationBuilder<ExtendedXMLConfiguration> builder = new BasicConfigurationBuilder<>( ExtendedXMLConfiguration.class).configure(new Parameters().xml()); ExtendedXMLConfiguration c; try { c = builder.getConfiguration(); } catch (ConfigurationException ex) { throw new ProgrammerException(ex); } c.setRootElementName("linkimputepro"); c.addNodes(null, config); FileHandler handler = new FileHandler(c); try { handler.save(control); } catch (ConfigurationException ex) { if (ex.getCause() instanceof IOException) { IOException tex = (IOException) ex.getCause(); throw new OutputException("Problem writing imputation control file", tex); } throw new ProgrammerException(ex); } }
From source file:Executable.LinkImputeR.java
private static XMLConfiguration convert(File ini) throws INIException, VCFInputException { FileBasedConfigurationBuilder<INIConfiguration> inibuilder = new FileBasedConfigurationBuilder<>( INIConfiguration.class).configure(new Parameters().fileBased().setFile(ini)); INIConfiguration config;// www . j a v a 2 s . c o m try { config = inibuilder.getConfiguration(); } catch (ConfigurationException ex) { throw new INIException( "There's a problem reading the ini file. " + "Does it exist? Is it formatted correctly?", ex); } List<ImmutableNode> xml = new ArrayList<>(); xml.add(new ImmutableNode.Builder().name("mode").value("accuracy").create()); String[] sdepths = config.getString("Global.depth").split(","); int[] depths = new int[sdepths.length]; for (int i = 0; i < sdepths.length; i++) { try { depths[i] = Integer.parseInt(sdepths[i]); } catch (NumberFormatException ex) { throw new INIException("Values for the depth option must be integers"); } if (depths[i] <= 0) { throw new INIException("Values for the depth option must be positive"); } } int maxDepth = NumberUtils.max(depths); int minDepth = NumberUtils.min(depths); double error; try { error = config.getDouble("Global.error", 0.01); } catch (ConversionException ex) { throw new INIException("Values for the error option must be a number"); } if ((error <= 0.0) || (error > 1.0)) { throw new INIException("Values for error must be between 0 and 1"); } File input = new File(config.getString("Input.filename")); List<PositionFilter> inputfilters = new ArrayList<>(); int numSnps = VCF.numberPositionsFromFile(input); for (HierarchicalConfiguration<ImmutableNode> i : config.childConfigurationsAt("InputFilters")) { switch (i.getRootElementName()) { //ADD FILTERS case "maf": double maf; try { maf = i.getDouble(null); } catch (ConversionException ex) { throw new INIException("Parameter for the MAF Filter must be a number"); } if ((maf <= 0) | (maf >= 0.5)) { throw new INIException("Parameter for the MAF filter must be between 0 and 0.5"); } inputfilters.add(new MAFFilter(maf, 8, 100, error)); break; case "hw": double sig; try { sig = i.getDouble(null); } catch (ConversionException ex) { throw new INIException("Parameter for the HW Filter must be a number"); } if ((sig <= 0) | (sig >= 1.0)) { throw new INIException("Parameter for the HWS filter must be between 0 and 1"); } inputfilters.add(new ParalogHWFilter(sig / numSnps, error)); break; case "positionmissing": double missing; try { missing = i.getDouble(null); } catch (ConversionException ex) { throw new INIException("Parameter for the Position Missing filter must be a number"); } if ((missing <= 0) | (missing >= 1.0)) { throw new INIException("Parameter for the Position Missing filter must be between 0 and 1"); } inputfilters.add(new PositionMissing(i.getDouble(null), minDepth)); break; } } String saveString = config.getString("Input.save", null); File save = (saveString == null) ? null : new File(saveString); String readsformat = config.getString("Input.readsformat", null); if ((readsformat != null) && (readsformat.split(",").length > 2)) { throw new INIException("readsformat must be either a single format or two" + "formats comma separated (LinkImputeR currently only works on" + "biallelic SNPs)"); } int maxInDepth; try { maxInDepth = config.getInt("Input.maxdepth", 100); } catch (ConversionException ex) { throw new INIException("Parameter values for the maxdepth option must be an integer."); } Input o = new Input(input, inputfilters, save, maxInDepth, readsformat); xml.add(o.getConfig()); String sampleMethod = config.getString("Accuracy.maskmethod", "all"); Method sm; switch (sampleMethod) { case "bysnp": sm = Method.BYSNP; break; case "bysample": sm = Method.BYSAMPLE; break; case "all": sm = Method.ALL; break; default: throw new INIException("maskmethod must be either \"bysnp\", \"bysample\" or \"all\"."); } int numberMasked; try { numberMasked = config.getInt("Accuracy.numbermasked", 10000); } catch (ConversionException ex) { throw new INIException("Parameter values for the numbermasked option must be an integer."); } int minMaskDepth; try { minMaskDepth = config.getInt("Accuracy.mindepth", 30); } catch (ConversionException ex) { throw new INIException("Parameter values for the maxdepth option must be an integer"); } DepthMaskFactory dmf = new DepthMaskFactory(numberMasked, minMaskDepth, maxDepth, sm); xml.add(dmf.getConfig()); String accuracyMethod = config.getString("Accuracy.accuracymethod", "correct"); AccuracyMethod am; switch (accuracyMethod) { case "correlation": am = AccuracyMethod.CORRELATION; break; case "correct": am = AccuracyMethod.CORRECT; break; default: throw new INIException("accuractymethod must be either \"correlation\" or \"correct\"."); } Caller caller = new BinomialCaller(error); String statsRoot = config.getString("Stats.root"); boolean partial; try { partial = config.getBoolean("Stats.partial", false); } catch (ConversionException ex) { throw new INIException("Stats partial must be convertible to a boolean. Try \"yes\" or \"no\"."); } boolean eachMasked; try { eachMasked = config.getBoolean("Stats.eachmasked", false); } catch (ConversionException ex) { throw new INIException("Stats eachmasked must be convertible to a boolean. Try \"yes\" or \"no\"."); } int casenum = 1; for (int depth : depths) { List<List<VCFFilter>> cases = new ArrayList<>(); cases.add(new ArrayList<>()); for (HierarchicalConfiguration<ImmutableNode> i : config.childConfigurationsAt("CaseFilters")) { List<List<VCFFilter>> newcases = new ArrayList<>(); String[] options = i.getString(null).split(","); for (String opt : options) { VCFFilter f; switch (i.getRootElementName()) { case "maf": double maf; try { maf = Double.parseDouble(opt); } catch (NumberFormatException ex) { throw new INIException("Parameter for the MAF Filter must be a number"); } if ((maf <= 0) | (maf >= 0.5)) { throw new INIException("Parameter for the MAF filter must be between 0 and 0.5"); } f = new MAFFilter(maf, 8, 100, error); for (List<VCFFilter> c : cases) { List<VCFFilter> nc = new ArrayList<>(c); nc.add(f); newcases.add(nc); } break; case "missing": double missing; try { missing = Double.parseDouble(opt); } catch (NumberFormatException ex) { throw new INIException("Parameter for the Missing filter must be a number"); } if ((missing <= 0) | (missing >= 1.0)) { throw new INIException("Parameter for the Missing filter must be between 0 and 1"); } VCFFilter fp = new PositionMissing(missing, depth); VCFFilter fs = new SampleMissing(missing, depth); for (List<VCFFilter> c : cases) { List<VCFFilter> nc = new ArrayList<>(c); nc.add(fp); nc.add(fs); newcases.add(nc); } break; case "samplemissing": double smissing; try { smissing = Double.parseDouble(opt); } catch (NumberFormatException ex) { throw new INIException("Parameter for the Missing filter must be a number"); } if ((smissing <= 0) | (smissing >= 1.0)) { throw new INIException("Parameter for the Missing filter must be between 0 and 1"); } f = new SampleMissing(smissing, depth); for (List<VCFFilter> c : cases) { List<VCFFilter> nc = new ArrayList<>(c); nc.add(f); newcases.add(nc); } break; case "positionmissing": double pmissing; try { pmissing = Double.parseDouble(opt); } catch (NumberFormatException ex) { throw new INIException("Parameter for the Missing filter must be a number"); } if ((pmissing <= 0) | (pmissing >= 1.0)) { throw new INIException("Parameter for the Missing filter must be between 0 and 1"); } f = new PositionMissing(pmissing, depth); for (List<VCFFilter> c : cases) { List<VCFFilter> nc = new ArrayList<>(c); nc.add(f); newcases.add(nc); } break; //NEED TO THINK ABOUT WHAT TO DO WITH SIGNIFICANCE! //POSSIBLY CHANGES IN CASE???? /*case "hw": f = new ParalogHWFilter(Double.parseDouble(opt),error); for (List<VCFFilter> c: cases) { List<VCFFilter> nc = new ArrayList<>(c); nc.add(f); newcases.add(nc); } break; */ } } cases = newcases; } ImputationOption imputer = new ImputationOption(new KnniLDProbOptimizedCalls(depth, am)); CombinerOption combiner = new CombinerOption(new MaxDepthCombinerOptimizedCalls(depth, am)); for (List<VCFFilter> filters : cases) { String name = "Case " + casenum; File prettyStats = null; File genoStats = null; File depthStats = null; File dgStats = null; File eachMaskedFile = null; switch (config.getString("Stats.level", "sum")) { case "sum": break; case "pretty": prettyStats = new File(statsRoot + "pretty_" + casenum + ".dat"); break; case "table": prettyStats = new File(statsRoot + "pretty_" + casenum + ".dat"); genoStats = new File(statsRoot + "geno_" + casenum + ".dat"); depthStats = new File(statsRoot + "depth_" + casenum + ".dat"); dgStats = new File(statsRoot + "dg_" + casenum + ".dat"); break; default: throw new INIException("Stats level must be either \"sum\", \"pretty\" or \"table\"."); } if (eachMasked) { eachMaskedFile = new File(statsRoot + "each_" + casenum + ".dat"); } PrintStats print = new PrintStats(prettyStats, genoStats, depthStats, dgStats, eachMaskedFile, partial); Case cas = new Case(name, filters, caller, imputer, combiner, print, "Depth(" + depth + ")"); xml.add(cas.getConfig()); casenum++; } } File sum = new File(statsRoot + "sum.dat"); File control = new File(config.getString("Output.control")); File table; if (config.getString("Stats.level").equals("table")) { table = new File(statsRoot + "table.dat"); } else { table = null; } Output out = new Output(sum, table, control, partial); xml.add(out.getConfig()); File log; String ls = config.getString("Log.file", null); if (ls != null) { log = new File(ls); } else { log = null; } Level level; switch (config.getString("Log.level", "critical").toLowerCase()) { case "brief": level = Log.Level.BRIEF; break; case "detail": level = Log.Level.DETAIL; break; case "debug": level = Log.Level.DEBUG; break; case "critical": level = Log.Level.CRITICAL; break; default: throw new INIException("log level must be either \"critical\", \"brief\", \"details\" or \"debug\"."); } xml.add(Log.getConfig(level, log)); BasicConfigurationBuilder<ExtendedXMLConfiguration> xmlbuilder = new BasicConfigurationBuilder<>( ExtendedXMLConfiguration.class).configure(new Parameters().xml()); ExtendedXMLConfiguration c; try { c = xmlbuilder.getConfiguration(); } catch (ConfigurationException ex) { throw new ProgrammerException(ex); } c.setRootElementName("linkimputer"); c.addNodes(null, xml); return c; }
From source file:org.demoiselle.internal.implementation.ConfigurationLoader.java
private void loadConfiguration() { Configuration config;//from w w w.j ava 2s . c o m BasicConfigurationBuilder<? extends Configuration> builder = createConfiguration(); if (builder instanceof FileBasedConfigurationBuilder) { Parameters params = new Parameters(); ((FileBasedConfigurationBuilder) builder) .configure(params.fileBased().setURL(Reflections.getResourceAsURL(this.resource))); } try { config = builder.getConfiguration(); } catch (org.apache.commons.configuration2.ex.ConfigurationException e) { getLogger().warning(getBundle().getString("file-not-found", this.resource)); config = null; } this.configuration = config; }