Examples with ImportException dr.evolution.io.Importer.ImportException used on opensource projects

Example 11 with ImportException

use of dr.evolution.io.Importer.ImportException in project beast-mcmc by beast-dev.

the class BEAUTiImporter method importBEASTFile.

// xml
private void importBEASTFile(File file) throws IOException, ImportException, JDOMException {
    try {
        FileReader reader = new FileReader(file);
        BeastImporter importer = new BeastImporter(reader);
        List<TaxonList> taxonLists = new ArrayList<TaxonList>();
        List<Alignment> alignments = new ArrayList<Alignment>();
        importer.importBEAST(taxonLists, alignments);
        TaxonList taxa = taxonLists.get(0);
        int count = 1;
        for (Alignment alignment : alignments) {
            String name = file.getName();
            if (alignment.getId() != null && alignment.getId().length() > 0) {
                name = alignment.getId();
            } else {
                if (alignments.size() > 1) {
                    name += count;
                }
            }
            setData(name, taxa, alignment, null, null, null, null);
            count++;
        }
        // assume that any additional taxon lists are taxon sets...
        for (int i = 1; i < taxonLists.size(); i++) {
            Taxa taxonSet = (Taxa) taxonLists.get(i);
            options.taxonSets.add(taxonSet);
            options.taxonSetsMono.put(taxonSet, false);
            options.taxonSetsIncludeStem.put(taxonSet, false);
            options.taxonSetsTreeModel.put(taxonSet, options.getPartitionTreeModels().get(0));
        }
        reader.close();
    } catch (JDOMException e) {
        throw new JDOMException(e.getMessage());
    } catch (ImportException e) {
        throw new ImportException(e.getMessage());
    } catch (IOException e) {
        throw new IOException(e.getMessage());
    }
}

Example 12 with ImportException

use of dr.evolution.io.Importer.ImportException in project beast-mcmc by beast-dev.

the class BeagleSeqSimTest method ancestralSequenceTree.

//END: simulateRandomBranchAssignment
static void ancestralSequenceTree() {
    try {
        LinkedHashMap<NodeRef, int[]> sequenceMap = new LinkedHashMap<NodeRef, int[]>();
        DataType dataType = Nucleotides.INSTANCE;
        // create tree
        NewickImporter importer = new NewickImporter("(SimSeq1:73.7468,(SimSeq2:25.256989999999995,SimSeq3:45.256989999999995):18.48981);");
        Tree tree = importer.importTree(null);
        TreeModel treeModel = new TreeModel(tree);
        for (NodeRef node : treeModel.getNodes()) {
            if (treeModel.isExternal(node)) {
                int[] seq = new int[] { 1, 1, 1 };
                sequenceMap.put(node, seq);
            } else {
                int[] seq = new int[] { 2, 2, 2 };
                sequenceMap.put(node, seq);
            }
        }
        // END: nodes loop
        AncestralSequenceTrait ancestralSequence = new AncestralSequenceTrait(sequenceMap, dataType);
        TreeTraitProvider[] treeTraitProviders = new TreeTraitProvider[] { ancestralSequence };
        StringBuffer buffer = new StringBuffer();
        NumberFormat format = NumberFormat.getNumberInstance(Locale.ENGLISH);
        boolean useTipLabels = true;
        //
        TreeUtils.newick(//
        treeModel, //
        treeModel.getRoot(), //
        useTipLabels, //
        TreeUtils.BranchLengthType.LENGTHS_AS_TIME, //
        format, //
        null, //
        treeTraitProviders, null, buffer);
        System.out.println(buffer);
    } catch (IOException e) {
        e.printStackTrace();
    } catch (ImportException e) {
        e.printStackTrace();
    }
// END: try-catch
}

Example 13 with ImportException

use of dr.evolution.io.Importer.ImportException in project beast-mcmc by beast-dev.

the class DataModelImporter method importBEASTFile.

// xml
private void importBEASTFile(File file, DateGuesser guesser, Map dataModel) throws IOException, ImportException {
    try {
        FileReader reader = new FileReader(file);
        BeastImporter importer = new BeastImporter(reader);
        List<TaxonList> taxonLists = new ArrayList<TaxonList>();
        List<Alignment> alignments = new ArrayList<Alignment>();
        importer.importBEAST(taxonLists, alignments);
        TaxonList taxa = taxonLists.get(0);
        int count = 1;
        for (Alignment alignment : alignments) {
            String name = file.getName();
            if (alignment.getId() != null && alignment.getId().length() > 0) {
                name = alignment.getId();
            } else {
                if (alignments.size() > 1) {
                    name += count;
                }
            }
            setData(dataModel, guesser, name, taxa, taxonLists, alignment, null, null, null);
            count++;
        }
        reader.close();
    } catch (JDOMException e) {
        throw new ImportException(e.getMessage());
    } catch (ImportException e) {
        throw new ImportException(e.getMessage());
    } catch (IOException e) {
        throw new IOException(e.getMessage());
    }
}

Example 14 with ImportException

use of dr.evolution.io.Importer.ImportException in project beast-mcmc by beast-dev.

the class BeagleSequenceSimulatorConsoleApp method simulate.

// END: constructor
public void simulate(String[] args) {
    try {
        // /////////////////////////////////
        // ---SPLIT PARTITION ARGUMENTS---//
        // /////////////////////////////////
        int from = 0;
        int to = 0;
        ArrayList<String[]> argsList = new ArrayList<String[]>();
        for (String arg : args) {
            if (arg.equalsIgnoreCase(SPLIT_PARTITION)) {
                argsList.add(Arrays.copyOfRange(args, from, to));
                from = to + 1;
            }
            // END: split check
            to++;
        }
        if (args[0].contains(HELP)) {
            gracefullyExit(null);
        } else if (argsList.size() == 0) {
            gracefullyExit("Empty or incorrect arguments list.");
        }
        // END: failed split check
        String[] leftoverArguments = Arrays.copyOfRange(args, from, args.length);
        if (leftoverArguments.length > 2) {
            gracefullyExit("Unrecognized option " + leftoverArguments[2]);
        }
        ArrayList<Partition> partitionsList = new ArrayList<Partition>();
        for (String[] partitionArgs : argsList) {
            // /////////////
            // ---PARSE---//
            // /////////////
            arguments.parseArguments(partitionArgs);
            // ///////////////////
            // ---INTERROGATE---//
            // ///////////////////
            PartitionData data = new PartitionData();
            String option = null;
            double[] values = null;
            if (partitionArgs.length == 0 || arguments.hasOption(HELP)) {
                gracefullyExit(null);
            }
            // Tree / Taxa
            if (arguments.hasOption(TREE_FILE)) {
                File treeFile = new File(arguments.getStringOption(TREE_FILE));
                Tree tree = Utils.importTreeFromFile(treeFile);
                data.record = new TreesTableRecord(treeFile.getName(), tree);
            } else if (arguments.hasOption(TAXA_SET)) {
                File taxaFile = new File(arguments.getStringOption(TAXA_SET));
                Taxa taxa = Utils.importTaxaFromFile(taxaFile);
                data.record = new TreesTableRecord(taxaFile.getName(), taxa);
            } else {
                throw new RuntimeException("Tree file / Taxa set not specified.");
            }
            // Demographic Model
            if (arguments.hasOption(DEMOGRAPHIC_MODEL)) {
                option = arguments.getStringOption(DEMOGRAPHIC_MODEL);
                if (option.equalsIgnoreCase(NO_DEMOGRAPHIC_MODEL)) {
                    int index = 0;
                    data.demographicModelIndex = index;
                } else if (option.equalsIgnoreCase(CONSTANT_POPULATION)) {
                    int index = 1;
                    data.demographicModelIndex = index;
                    if (arguments.hasOption(CONSTANT_POPULATION_PARAMETER_VALUES)) {
                        values = arguments.getRealArrayOption(CONSTANT_POPULATION_PARAMETER_VALUES);
                        parseDemographicValues(index, values, data);
                    }
                } else if (option.equalsIgnoreCase(EXPONENTIAL_GROWTH_RATE)) {
                    int index = 2;
                    data.demographicModelIndex = index;
                    if (arguments.hasOption(EXPONENTIAL_GROWTH_RATE_PARAMETER_VALUES)) {
                        values = arguments.getRealArrayOption(EXPONENTIAL_GROWTH_RATE_PARAMETER_VALUES);
                        parseDemographicValues(index, values, data);
                    }
                } else if (option.equalsIgnoreCase(EXPONENTIAL_DOUBLING_TIME)) {
                    int index = 3;
                    data.demographicModelIndex = index;
                    if (arguments.hasOption(EXPONENTIAL_GROWTH_DOUBLING_TIME_PARAMETER_VALUES)) {
                        values = arguments.getRealArrayOption(EXPONENTIAL_GROWTH_DOUBLING_TIME_PARAMETER_VALUES);
                        parseDemographicValues(index, values, data);
                    }
                } else {
                    gracefullyExit("Unrecognized option.");
                }
            }
            // Branch Substitution Model
            if (arguments.hasOption(BRANCH_SUBSTITUTION_MODEL)) {
                option = arguments.getStringOption(BRANCH_SUBSTITUTION_MODEL);
                if (option.equalsIgnoreCase(HKY)) {
                    int index = 0;
                    data.substitutionModelIndex = index;
                    if (arguments.hasOption(HKY_SUBSTITUTION_PARAMETER_VALUES)) {
                        values = arguments.getRealArrayOption(HKY_SUBSTITUTION_PARAMETER_VALUES);
                        parseSubstitutionValues(index, values, data);
                    }
                } else if (option.equalsIgnoreCase(GTR)) {
                    int index = 1;
                    data.substitutionModelIndex = index;
                    if (arguments.hasOption(GTR_SUBSTITUTION_PARAMETER_VALUES)) {
                        values = arguments.getRealArrayOption(GTR_SUBSTITUTION_PARAMETER_VALUES);
                        parseSubstitutionValues(index, values, data);
                    }
                } else if (option.equalsIgnoreCase(TN93)) {
                    int index = 2;
                    data.substitutionModelIndex = index;
                    if (arguments.hasOption(TN93_SUBSTITUTION_PARAMETER_VALUES)) {
                        values = arguments.getRealArrayOption(TN93_SUBSTITUTION_PARAMETER_VALUES);
                        parseSubstitutionValues(index, values, data);
                    }
                } else if (option.equalsIgnoreCase(GY94_CODON_MODEL)) {
                    int index = 3;
                    data.substitutionModelIndex = index;
                    if (arguments.hasOption(GY94_SUBSTITUTION_PARAMETER_VALUES)) {
                        values = arguments.getRealArrayOption(GY94_SUBSTITUTION_PARAMETER_VALUES);
                        parseSubstitutionValues(index, values, data);
                    }
                } else {
                    gracefullyExit("Unrecognized option.");
                }
            }
            // Site Rate Model
            if (arguments.hasOption(SITE_RATE_MODEL)) {
                option = arguments.getStringOption(SITE_RATE_MODEL);
                if (option.equalsIgnoreCase(NO_SITE_RATE_MODEL)) {
                    int index = 0;
                    data.siteRateModelIndex = index;
                } else if (option.equalsIgnoreCase(GAMMA_SITE_RATE_MODEL)) {
                    int index = 1;
                    data.siteRateModelIndex = index;
                    if (arguments.hasOption(GAMMA_SITE_RATE_MODEL_PARAMETER_VALUES)) {
                        values = arguments.getRealArrayOption(GAMMA_SITE_RATE_MODEL_PARAMETER_VALUES);
                        parseSiteRateValues(index, values, data);
                    }
                } else {
                    gracefullyExit("Unrecognized option.");
                }
            }
            // Clock Rate Model
            if (arguments.hasOption(CLOCK_RATE_MODEL)) {
                option = arguments.getStringOption(CLOCK_RATE_MODEL);
                if (option.equalsIgnoreCase(STRICT_CLOCK)) {
                    int index = 0;
                    data.clockModelIndex = index;
                    if (arguments.hasOption(STRICT_CLOCK_PARAMETER_VALUES)) {
                        values = arguments.getRealArrayOption(STRICT_CLOCK_PARAMETER_VALUES);
                        parseClockValues(index, values, data);
                    }
                } else if (option.equalsIgnoreCase(LOGNORMAL_RELAXED_CLOCK)) {
                    int index = 1;
                    data.clockModelIndex = index;
                    if (arguments.hasOption(LOGNORMAL_RELAXED_CLOCK_PARAMETER_VALUES)) {
                        values = arguments.getRealArrayOption(LOGNORMAL_RELAXED_CLOCK_PARAMETER_VALUES);
                        parseClockValues(index, values, data);
                    }
                    // set to true/false
                    if (arguments.hasOption(LRC_PARAMETERS_IN_REAL_SPACE)) {
                        boolean lrcParametersInRealSpace = (arguments.getStringOption(LRC_PARAMETERS_IN_REAL_SPACE).equalsIgnoreCase(TRUE) ? true : false);
                        data.lrcParametersInRealSpace = lrcParametersInRealSpace;
                    }
                } else if (option.equalsIgnoreCase(EXPONENTIAL_RELAXED_CLOCK)) {
                    int index = 2;
                    data.clockModelIndex = index;
                    if (arguments.hasOption(EXPONENTIAL_RELAXED_CLOCK_PARAMETER_VALUES)) {
                        values = arguments.getRealArrayOption(EXPONENTIAL_RELAXED_CLOCK_PARAMETER_VALUES);
                        parseClockValues(index, values, data);
                    }
                } else if (option.equalsIgnoreCase(INVERSE_GAUSSIAN_RELAXED_CLOCK)) {
                    int index = 3;
                    data.clockModelIndex = index;
                    if (arguments.hasOption(INVERSE_GAUSSIAN_RELAXED_CLOCK_PARAMETER_VALUES)) {
                        values = arguments.getRealArrayOption(INVERSE_GAUSSIAN_RELAXED_CLOCK_PARAMETER_VALUES);
                        parseClockValues(index, values, data);
                    }
                } else {
                    gracefullyExit("Unrecognized option.");
                }
            }
            // Frequency Model
            if (arguments.hasOption(BASE_FREQUENCIES)) {
                option = arguments.getStringOption(BASE_FREQUENCIES);
                if (option.equalsIgnoreCase(NUCLEOTIDE_FREQUENCIES)) {
                    int index = 0;
                    data.frequencyModelIndex = index;
                    if (arguments.hasOption(NUCLEOTIDE_FREQUENCY_PARAMETER_VALUES)) {
                        values = arguments.getRealArrayOption(NUCLEOTIDE_FREQUENCY_PARAMETER_VALUES);
                        parseFrequencyValues(index, values, data);
                    }
                } else if (option.equalsIgnoreCase(CODON_FREQUENCIES)) {
                    int index = 1;
                    data.frequencyModelIndex = index;
                    if (arguments.hasOption(CODON_FREQUENCY_PARAMETER_VALUES)) {
                        values = arguments.getRealArrayOption(CODON_FREQUENCY_PARAMETER_VALUES);
                        parseFrequencyValues(index, values, data);
                    }
                } else {
                    gracefullyExit("Unrecognized option.");
                }
            }
            if (arguments.hasOption(FROM)) {
                data.from = arguments.getIntegerOption(FROM);
            }
            if (arguments.hasOption(TO)) {
                data.to = arguments.getIntegerOption(TO);
            }
            if (arguments.hasOption(EVERY)) {
                data.every = arguments.getIntegerOption(EVERY);
            }
            // END: EVERY option check
            // create partition
            Partition partition = new Partition(//
            data.createTreeModel(), //
            data.createBranchModel(), //
            data.createSiteRateModel(), //
            data.createClockRateModel(), //
            data.createFrequencyModel(), // from
            data.from - 1, // to
            data.to - 1, // every
            data.every);
            if (arguments.hasOption(ROOT_SEQUENCE)) {
                data.ancestralSequenceString = arguments.getStringOption(ROOT_SEQUENCE);
                partition.setRootSequence(data.createAncestralSequence());
            }
            // END: ANCESTRAL_SEQUENCE option check
            partitionsList.add(partition);
            //                System.err.println(data.from);
            dataList.add(data);
        }
        if (this.VERBOSE) {
            //        		System.out.println(dataList.get(0).from + " " + dataList.get(1).from);
            Utils.printPartitionDataList(dataList);
            System.out.println();
        }
        SimpleAlignment alignment = new SimpleAlignment();
        String outputFile = null;
        if (leftoverArguments.length > 0) {
            outputFile = leftoverArguments[0];
            String[] file = outputFile.split("\\.", 2);
            if (file.length > 1) {
                String extension = outputFile.split("\\.", 2)[1];
                // TODO Delegate here to enum-class; switches are not generic
                if (extension.equalsIgnoreCase(SimpleAlignment.OutputType.FASTA.getText()) || extension.equalsIgnoreCase("fst")) {
                    dataList.outputFormat = SimpleAlignment.OutputType.FASTA;
                } else if (extension.equalsIgnoreCase(SimpleAlignment.OutputType.NEXUS.getText()) || extension.equalsIgnoreCase("nxs")) {
                    dataList.outputFormat = SimpleAlignment.OutputType.NEXUS;
                } else if (extension.equalsIgnoreCase(SimpleAlignment.OutputType.XML.getText())) {
                    dataList.outputFormat = SimpleAlignment.OutputType.XML;
                } else {
                    dataList.outputFormat = SimpleAlignment.OutputType.FASTA;
                }
            //END: extension check
            } else {
                outputFile = file[0] + "." + SimpleAlignment.OutputType.FASTA.toString().toLowerCase();
                dataList.outputFormat = SimpleAlignment.OutputType.FASTA;
            }
        //END: 
        }
        if (leftoverArguments.length > 1) {
            dataList.startingSeed = Long.parseLong(leftoverArguments[1]);
            dataList.setSeed = true;
        }
        if (dataList.setSeed) {
            MathUtils.setSeed(dataList.startingSeed);
        }
        if (leftoverArguments.length > 2) {
            dataList.outputAncestralSequences = Boolean.parseBoolean(leftoverArguments[2]);
        }
        if (leftoverArguments.length > 3) {
            dataList.useParallel = Boolean.parseBoolean(leftoverArguments[3]);
        }
        BeagleSequenceSimulator beagleSequenceSimulator = new BeagleSequenceSimulator(partitionsList);
        alignment = beagleSequenceSimulator.simulate(dataList.useParallel, dataList.outputAncestralSequences);
        alignment.setOutputType(dataList.outputFormat);
        PrintWriter writer = new PrintWriter(new FileWriter(outputFile));
        writer.println(alignment.toString());
        writer.close();
    } catch (ArgumentException e) {
        System.out.println();
        printUsage(arguments);
        System.out.println();
        System.out.println(e.getMessage());
        e.printStackTrace();
        System.exit(1);
    } catch (IOException e) {
        System.out.println();
        printUsage(arguments);
        System.out.println();
        System.out.println(e.getMessage());
        e.printStackTrace();
        System.exit(1);
    } catch (ImportException e) {
        System.out.println();
        printUsage(arguments);
        System.out.println();
        System.out.println(e.getMessage());
        e.printStackTrace();
        System.exit(1);
    }
// END: try-catch block
}