Examples with SimpleAlignment dr.evolution.alignment.SimpleAlignment used on opensource projects

Example 6 with SimpleAlignment

use of dr.evolution.alignment.SimpleAlignment in project beast-mcmc by beast-dev.

the class AlignmentParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    final SimpleAlignment alignment = new SimpleAlignment();
    final DataType dataType = DataTypeUtils.getDataType(xo);
    if (dataType == null) {
        throw new XMLParseException("dataType attribute expected for alignment element");
    }
    alignment.setDataType(dataType);
    for (int i = 0; i < xo.getChildCount(); i++) {
        final Object child = xo.getChild(i);
        if (child instanceof Sequence) {
            alignment.addSequence((Sequence) child);
        } else if (child instanceof DataType) {
        // already dealt with
        } else {
            throw new XMLParseException("Unknown child element found in alignment");
        }
    }
    final Logger logger = Logger.getLogger("dr.evoxml");
    logger.info("\nRead alignment" + (xo.hasAttribute(XMLParser.ID) ? ": " + xo.getId() : "") + "\n  Sequences = " + alignment.getSequenceCount() + "\n      Sites = " + alignment.getSiteCount() + "\n   Datatype = " + alignment.getDataType().getDescription());
    return alignment;
}

Example 7 with SimpleAlignment

use of dr.evolution.alignment.SimpleAlignment in project beast-mcmc by beast-dev.

the class MainFrame method generateNumberOfSimulations.

// END: doExport
// threading, UI, exceptions handling
private void generateNumberOfSimulations(final File outFile) {
    setBusy();
    SwingWorker<Void, Void> worker = new SwingWorker<Void, Void>() {

        ArrayList<TreeModel> simulatedTreeModelList = new ArrayList<TreeModel>();

        // Executed in background thread
        public Void doInBackground() {
            try {
                if (BeagleSequenceSimulatorApp.VERBOSE) {
                    Utils.printPartitionDataList(dataList);
                    System.out.println();
                }
                long startingSeed = dataList.startingSeed;
                for (int i = 0; i < dataList.simulationsCount; i++) {
                    String fullPath = Utils.getMultipleWritePath(outFile, dataList.outputFormat.toString().toLowerCase(), i);
                    PrintWriter writer = new PrintWriter(new FileWriter(fullPath));
                    ArrayList<Partition> partitionsList = new ArrayList<Partition>();
                    for (PartitionData data : dataList) {
                        if (data.record == null) {
                            writer.close();
                            throw new RuntimeException("Set data in Partitions tab for " + (partitionsList.size() + 1) + " partition.");
                        } else {
                            TreeModel treeModel = data.createTreeModel();
                            simulatedTreeModelList.add(treeModel);
                            // create partition
                            Partition partition = new Partition(//
                            treeModel, //
                            data.createBranchModel(), //
                            data.createSiteRateModel(), //
                            data.createClockRateModel(), //
                            data.createFrequencyModel(), // from
                            data.from - 1, // to
                            data.to - 1, // every
                            data.every);
                            if (data.ancestralSequenceString != null) {
                                partition.setRootSequence(data.createAncestralSequence());
                            }
                            partitionsList.add(partition);
                        }
                    }
                    if (dataList.setSeed) {
                        MathUtils.setSeed(startingSeed);
                        startingSeed += 1;
                    }
                    beagleSequenceSimulator = new BeagleSequenceSimulator(partitionsList);
                    SimpleAlignment alignment = beagleSequenceSimulator.simulate(dataList.useParallel, dataList.outputAncestralSequences);
                    alignment.setOutputType(dataList.outputFormat);
                    //                        if (dataList.outputFormat == SimpleAlignment.OutputType.NEXUS) {
                    //                            alignment.setOutputType(dataList.outputFormat);
                    //                        } else if(dataList.outputFormat == SimpleAlignment.OutputType.XML) {
                    //                        	alignment.setOutputType(dataList.outputFormat);
                    //                        }else {
                    //                        	//
                    //                        }
                    writer.println(alignment.toString());
                    writer.close();
                }
            // END: simulationsCount loop
            } catch (Exception e) {
                Utils.handleException(e);
                setStatus("Exception occured.");
                setIdle();
            }
            return null;
        }

        // END: doInBackground
        // Executed in event dispatch thread
        public void done() {
            //            	LinkedHashMap<Integer, LinkedHashMap<NodeRef, int[]>> partitionSequencesMap = beagleSequenceSimulator.getPartitionSequencesMap();
            terminalPanel.setText(Utils.partitionDataListToString(dataList, simulatedTreeModelList));
            setStatus("Generated " + Utils.getSiteCount(dataList) + " sites.");
            setIdle();
        }
    };
    worker.execute();
}

Example 8 with SimpleAlignment

use of dr.evolution.alignment.SimpleAlignment in project beast-mcmc by beast-dev.

the class BeastImporter method readAlignment.

private Alignment readAlignment(Element e, TaxonList taxa) throws Importer.ImportException {
    SimpleAlignment alignment = new SimpleAlignment();
    List children = e.getChildren();
    for (Object aChildren : children) {
        Element child = (Element) aChildren;
        if (child.getName().equalsIgnoreCase(SequenceParser.SEQUENCE)) {
            alignment.addSequence(readSequence(child, taxa));
        }
    }
    return alignment;
}

Example 9 with SimpleAlignment

use of dr.evolution.alignment.SimpleAlignment in project beast-mcmc by beast-dev.

the class FastaImporter method importAlignment.

/**
     * importAlignment.
     */
public Alignment importAlignment() throws IOException, ImportException {
    SimpleAlignment alignment = null;
    try {
        // find fasta line start
        while (read() != FASTA_FIRST_CHAR) {
        }
        do {
            final String name = readLine().trim();
            StringBuffer seq = new StringBuffer();
            readSequence(seq, dataType, "" + FASTA_FIRST_CHAR, Integer.MAX_VALUE, "-", "?", "", "");
            if (alignment == null) {
                alignment = new SimpleAlignment();
            }
            alignment.addSequence(new Sequence(new Taxon(name.toString()), seq.toString()));
        } while (getLastDelimiter() == FASTA_FIRST_CHAR);
    } catch (EOFException e) {
    // catch end of file the ugly way.
    }
    return alignment;
}

Example 10 with SimpleAlignment

use of dr.evolution.alignment.SimpleAlignment in project beast-mcmc by beast-dev.

the class NexusImporter method readDataBlock.

/**
     * Reads a 'DATA' block.
     */
private Alignment readDataBlock() throws /*TaxonList taxonList*/
ImportException, IOException {
    taxonCount = 0;
    siteCount = 0;
    dataType = null;
    readDataBlockHeader("MATRIX", DATA_BLOCK);
    SimpleAlignment alignment = new SimpleAlignment();
    readSequenceData(alignment, null);
    alignment.updateSiteCount();
    findEndBlock();
    return alignment;
}