Examples with BEASTInterface beast.core.BEASTInterface used on opensource projects

Example 26 with BEASTInterface

use of beast.core.BEASTInterface in project beast2 by CompEvol.

the class JSONParser method processInput.

// setInputs
private void processInput(String name, JSONObject node, List<NameValuePair> map, List<InputType> inputs) throws JSONParserException, JSONException {
    if (node.has(name)) {
        if (!(name.equals("id") || name.equals("idref") || name.equals("spec") || name.equals("name"))) {
            Object o = node.get(name);
            if (o instanceof String) {
                String value = (String) o;
                if (value.startsWith("@")) {
                    String IDRef = value.substring(1);
                    JSONObject element = new JSONObject();
                    element.put("idref", IDRef);
                    BEASTInterface beastObject = createObject(element, BEAST_OBJECT_CLASS);
                    map.add(new NameValuePair(name, beastObject));
                // setInput(node, parent, name, beastObject);
                } else {
                    map.add(new NameValuePair(name, value));
                // setInput(node, parent, name, value);
                }
            } else if (o instanceof Number) {
                map.add(new NameValuePair(name, o));
            // parent.setInputValue(name, o);
            } else if (o instanceof Boolean) {
                map.add(new NameValuePair(name, o));
            // parent.setInputValue(name, o);
            } else if (o instanceof JSONObject) {
                JSONObject child = (JSONObject) o;
                String className = getClassName(child, name, inputs);
                BEASTInterface childItem = createObject(child, className);
                if (childItem != null) {
                    map.add(new NameValuePair(name, childItem));
                // setInput(node, parent, name, childItem);
                }
            // childElements++;
            } else if (o instanceof JSONArray) {
                JSONArray list = (JSONArray) o;
                for (int i = 0; i < list.length(); i++) {
                    Object o2 = list.get(i);
                    if (o2 instanceof JSONObject) {
                        JSONObject child = (JSONObject) o2;
                        String className = getClassName(child, name, inputs);
                        BEASTInterface childItem = createObject(child, className);
                        if (childItem != null) {
                            map.add(new NameValuePair(name, childItem));
                        // setInput(node, parent, name, childItem);
                        }
                    } else {
                        map.add(new NameValuePair(name, o2));
                    // parent.setInputValue(name, o2);
                    }
                }
            } else {
                throw new RuntimeException("Developer error: Don't know how to handle this JSON construction");
            }
        }
    }
}

Example 27 with BEASTInterface

use of beast.core.BEASTInterface in project beast2 by CompEvol.

the class JSONProducer method main.

public static void main(String[] args) throws SAXException, IOException, ParserConfigurationException, XMLParserException {
    // convert BEAST 2 XML to BEAST JSON file
    XMLParser parser = new XMLParser();
    BEASTInterface beastObject = parser.parseFile(new File(args[0]));
    String JSONFile = args[0].replace(".xml", ".json");
    PrintStream out;
    if (JSONFile.endsWith(".json")) {
        out = new PrintStream(new File(JSONFile));
    } else {
        out = System.out;
    }
    JSONProducer writer = new JSONProducer();
    String JSON = writer.toJSON(beastObject);
    out.println(JSON);
    out.close();
}

Example 28 with BEASTInterface

use of beast.core.BEASTInterface in project beast2 by CompEvol.

the class JSONProducer method toJSON.

public String toJSON(BEASTInterface beastObject, Collection<BEASTInterface> others) {
    try {
        StringBuffer buf = new StringBuffer();
        // buf.append("{\"version\": \"2.0\",\n\"namespace\": \"" + DEFAULT_NAMESPACE + "\",\n\n" +
        // "\"" + JSONParser.ANALYSIS_ELEMENT + "\": [\n");
        buf.append("{version: \"" + (new BEASTVersion2()).getMajorVersion() + "\",\nnamespace: \"" + DEFAULT_NAMESPACE + "\",\n\n" + XMLParser.BEAST_ELEMENT + ": [\n");
        // buf.append("\n\n");
        isDone = new HashSet<>();
        isInputsDone = new HashMap<>();
        IDs = new HashSet<>();
        indentCount = 1;
        List<BEASTInterface> priorityBeastObjects = new ArrayList<>();
        findPriorityBeastObjects(beastObject, priorityBeastObjects);
        for (BEASTInterface beastObject2 : priorityBeastObjects) {
            if (!isDone.contains(beastObject2)) {
                // name = name.substring(name.lastIndexOf('.') + 1).toLowerCase();
                beastObjectToJSON(beastObject2, BEASTInterface.class, buf, null, true);
                buf.append(",");
            }
        }
        buf.append("\n\n");
        beastObjectToJSON(beastObject, BEASTInterface.class, buf, null, true);
        String end = "\n]\n}";
        buf.append(end);
        String JSON = buf.toString();
        String[] nameSpaces = DEFAULT_NAMESPACE.split(":");
        for (String nameSpace : nameSpaces) {
            // JSON = JSON.replaceAll("\"spec\": \"" + nameSpace + ".", "\"spec\": \"");
            JSON = JSON.replaceAll("spec: \"" + nameSpace + ".", "spec: \"");
        }
        return JSON;
    } catch (Exception e) {
        e.printStackTrace();
        return null;
    }
}

Example 29 with BEASTInterface

use of beast.core.BEASTInterface in project beast2 by CompEvol.

the class NexusParser method processSets.

protected void processSets() {
    // does not already have a calibration associated with it
    for (TaxonSet taxonset : taxonsets) {
        boolean found = false;
        for (BEASTInterface o : taxonset.getOutputs()) {
            if (o instanceof MRCAPrior) {
                found = true;
                break;
            }
        }
        if (!found) {
            MRCAPrior prior = new MRCAPrior();
            prior.isMonophyleticInput.setValue(true, prior);
            prior.taxonsetInput.setValue(taxonset, prior);
            prior.setID(taxonset.getID() + ".prior");
            // should set Tree before initialising, but we do not know the tree yet...
            if (calibrations == null) {
                calibrations = new ArrayList<>();
            }
            calibrations.add(prior);
        }
    }
}

Example 30 with BEASTInterface

use of beast.core.BEASTInterface in project beast2 by CompEvol.

the class XMLProducer method toXML.

public String toXML(BEASTInterface beastObject, Collection<BEASTInterface> others) {
    try {
        StringBuffer buf = new StringBuffer();
        Set<String> requiredPacakges = getPackagesAndVersions(beastObject);
        String required = requiredPacakges.toString();
        required = required.substring(1, required.length() - 1);
        required = required.replaceAll(", ", ":");
        buf.append("<" + XMLParser.BEAST_ELEMENT + " version='" + new BEASTVersion2().getMajorVersion() + "'" + " required='" + required + "'" + " namespace='" + DEFAULT_NAMESPACE + "'>\n");
        for (String element : element2ClassMap.keySet()) {
            if (!reservedElements.contains(element)) {
                buf.append("<map name='" + element + "'>" + element2ClassMap.get(element) + "</map>\n");
            }
        }
        buf.append("\n\n");
        isDone = new HashSet<>();
        isInputsDone = new HashMap<>();
        IDs = new HashSet<>();
        indent = 0;
        beastObjectToXML(beastObject, buf, null, true);
        String endBeastString = "</" + XMLParser.BEAST_ELEMENT + ">";
        buf.append(endBeastString);
        // return buf.toString();
        // beautify XML hierarchy
        String xml = cleanUpXML(buf.toString(), m_sXMLBeuatifyXSL);
        // TODO: fix m_sIDRefReplacementXSL script to deal with nested taxon sets
        // String xml2 = cleanUpXML(xml, m_sIDRefReplacementXSL);
        String xml2 = xml;
        xml = findPlates(xml2);
        // beatify by applying name spaces to spec attributes
        String[] nameSpaces = DEFAULT_NAMESPACE.split(":");
        for (String nameSpace : nameSpaces) {
            xml = xml.replaceAll("spec=\"" + nameSpace + ".", "spec=\"");
        }
        buf = new StringBuffer();
        if (others.size() > 0) {
            for (BEASTInterface beastObject2 : others) {
                if (!IDs.contains(beastObject2.getID())) {
                    beastObjectToXML(beastObject2, buf, null, false);
                }
            }
        }
        int endIndex = xml.indexOf(endBeastString);
        String extras = buf.toString();
        // prevent double -- inside XML comment, this can happen in sequences
        extras = extras.replaceAll("--", "- - ");
        xml = // + "\n\n<!-- " + DO_NOT_EDIT_WARNING + " \n\n" +
        xml.substring(0, endIndex) + // extras +  "\n\n-->\n\n"
        endBeastString;
        xml = xml.replaceAll("xmlns=\"http://www.w3.org/TR/xhtml1/strict\"", "");
        xml = dedupName(xml);
        xml = sortTags(xml);
        // return buf2.toString();
        return xml;
    } catch (Exception e) {
        e.printStackTrace();
        return null;
    }
}