private boolean matches(
BEASTInterface plugin2, String sConditionalAttribute, String sConditionalValue) {
if (sConditionalAttribute.equals("id") && plugin2.getID().equals(sConditionalValue))
return true;
if (sConditionalAttribute.equals("type")
&& plugin2.getClass().getName().equals(sConditionalValue)) return true;
if (sConditionalAttribute.equals("type!")
&& !plugin2.getClass().getName().equals(sConditionalValue)) return true;
return false;
}
private void findPriorityBeastObjects(
BEASTInterface beastObject, List<BEASTInterface> priorityBeastObjects)
throws IllegalArgumentException, IllegalAccessException {
if (beastObject.getClass().equals(Alignment.class)) {
priorityBeastObjects.add(beastObject);
}
if (beastObject instanceof TraitSet) {
priorityBeastObjects.add(beastObject);
}
for (BEASTInterface beastObject2 : beastObject.listActiveBEASTObjects()) {
findPriorityBeastObjects(beastObject2, priorityBeastObjects);
}
}
@SuppressWarnings("unchecked")
public void sync(int iPartition) {
if (parentInputs.size() > 0 && _input.get() != null) {
Input<?> input = parentInputs.get(iPartition);
if (bIsList) {
List<Object> list = (List<Object>) _input.get();
List<Object> targetList = ((List<Object>) input.get());
// targetList.clear();
// only clear former members
for (BEASTInterface plugin : startInputs) {
targetList.remove(plugin);
}
targetList.addAll(list);
// sync outputs of items in list
for (Object o : list) {
if (o instanceof BEASTInterface) {
((BEASTInterface) o).getOutputs().add(parentPlugins.get(iPartition));
}
}
} else {
try {
// System.err.println("sync " + parentPlugins.get(iPartition) + "[" + input.getName() + "]
// = " + _input.get());
input.setValue(_input.get(), parentPlugins.get(iPartition));
} catch (Exception e) {
e.printStackTrace();
}
}
}
}
/**
* create new instance of src object, connecting all inputs from src object Note if input is a
* SubstModel, it is duplicated as well.
*
* @param src object to be copied
* @param i index used to extend ID with.
* @return copy of src object
*/
private Object duplicate(BEASTInterface src, int i) {
if (src == null) {
return null;
}
BEASTInterface copy;
try {
copy = src.getClass().newInstance();
copy.setID(src.getID() + "_" + i);
} catch (InstantiationException | IllegalAccessException e) {
e.printStackTrace();
throw new RuntimeException(
"Programmer error: every object in the model should have a default constructor that is publicly accessible: "
+ src.getClass().getName());
}
for (Input<?> input : src.listInputs()) {
if (input.get() != null) {
if (input.get() instanceof List) {
// handle lists
// ((List)copy.getInput(input.getName())).clear();
for (Object o : (List<?>) input.get()) {
if (o instanceof BEASTInterface) {
// make sure it is not already in the list
copy.setInputValue(input.getName(), o);
}
}
} else if (input.get() instanceof SubstitutionModel) {
// duplicate subst models
BEASTInterface substModel = (BEASTInterface) duplicate((BEASTInterface) input.get(), i);
copy.setInputValue(input.getName(), substModel);
} else {
// it is some other value
copy.setInputValue(input.getName(), input.get());
}
}
}
copy.initAndValidate();
return copy;
}
/** Find the input associated with this panel based on the path Input. */
@SuppressWarnings("unchecked")
public Input<?> resolveInput(BeautiDoc doc, int iPartition) {
try {
// if (parentPlugins != null && parentPlugins.size() > 0 && _input != null)
// System.err.println("sync " + parentPlugins.get(iPartition) + "[?] = " +
// _input.get());
List<BEASTInterface> plugins;
if (bHasPartitionsInput.get() == Partition.none) {
plugins = new ArrayList<BEASTInterface>();
plugins.add(doc.mcmc.get());
} else {
plugins = doc.getPartitions(bHasPartitionsInput.get().toString());
}
parentPlugins = new ArrayList<BEASTInterface>();
parentInputs = new ArrayList<Input<?>>();
parentPlugins.add(doc);
parentInputs.add(doc.mcmc);
type = doc.mcmc.getType();
bIsList = false;
for (int i = 0; i < sPathComponents.length; i++) {
List<BEASTInterface> oldPlugins = plugins;
plugins = new ArrayList<BEASTInterface>();
parentPlugins = new ArrayList<BEASTInterface>();
parentInputs = new ArrayList<Input<?>>();
for (BEASTInterface plugin : oldPlugins) {
Input<?> namedInput = plugin.getInput(sPathComponents[i]);
type = namedInput.getType();
if (namedInput.get() instanceof List<?>) {
bIsList = true;
List<?> list = (List<?>) namedInput.get();
if (sConditionalAttribute[i] == null) {
for (Object o : list) {
BEASTInterface plugin2 = (BEASTInterface) o;
plugins.add(plugin2);
parentPlugins.add(plugin);
parentInputs.add(namedInput);
}
// throw new Exception ("Don't know which element to pick from the list. List
// component should come with a condition. " + m_sPathComponents[i]);
} else {
int nMatches = 0;
for (int j = 0; j < list.size(); j++) {
BEASTInterface plugin2 = (BEASTInterface) list.get(j);
if (matches(plugin2, sConditionalAttribute[i], sConditionalValue[i])) {
plugins.add(plugin2);
parentPlugins.add(plugin);
parentInputs.add(namedInput);
nMatches++;
break;
}
}
if (nMatches == 0) {
parentInputs.add(namedInput);
parentPlugins.add(plugin);
}
}
} else if (namedInput.get() instanceof BEASTInterface) {
bIsList = false;
if (sConditionalAttribute[i] == null) {
plugins.add((BEASTInterface) namedInput.get());
parentPlugins.add(plugin);
parentInputs.add(namedInput);
} else {
if (matches(plugin, sConditionalAttribute[i], sConditionalValue[i])) {
// if ((m_sConditionalAttribute[i].equals("id") &&
// plugin.getID().equals(m_sConditionalValue[i])) ||
// (m_sConditionalAttribute[i].equals("type") &&
// plugin.getClass().getName().equals(m_sConditionalValue[i]))) {
plugins.add(plugin);
parentPlugins.add(plugin);
parentInputs.add(namedInput);
}
}
} else {
throw new Exception("input " + sPathComponents[i] + " is not a plugin or list");
}
}
}
if (sTypeInput.get() != null) {
type = Class.forName(sTypeInput.get());
}
// sanity check
if (!bIsList && (bHasPartitionsInput.get() == Partition.none) && plugins.size() > 1) {
System.err.println("WARNING: multiple plugins match, but hasPartitions=none");
// this makes sure that all mathing plugins are available in one go
bIsList = true;
// this suppresses syncing
parentInputs.clear();
}
inputs.clear();
startInputs.clear();
for (BEASTInterface plugin : plugins) {
inputs.add(plugin);
startInputs.add(plugin);
}
if (!bIsList) {
_input = new FlexibleInput<BEASTInterface>();
} else {
_input = new FlexibleInput<ArrayList<BEASTInterface>>(new ArrayList<BEASTInterface>());
}
_input.setRule(Validate.REQUIRED);
syncTo(iPartition);
// if (parentPlugins != null && parentPlugins.size() > 0)
// System.err.println("sync " + parentPlugins.get(iPartition) + "[?] = " +
// _input.get());
if (bIsList) {
checkForDups((List<Object>) _input.get());
}
return _input;
} catch (Exception e) {
System.err.println(
"Warning: could not find objects in path " + Arrays.toString(sPathComponents));
}
return null;
} // resolveInputs
public String toXML(BEASTInterface beastObject, Collection<BEASTInterface> others) {
try {
StringBuffer buf = new StringBuffer();
buf.append(
"<"
+ XMLParser.BEAST_ELEMENT
+ " version='2.0' 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 =
xml.substring(0, endIndex) // + "\n\n<!-- " + DO_NOT_EDIT_WARNING + " \n\n" +
// extras + "\n\n-->\n\n"
+ endBeastString;
xml = xml.replaceAll("xmlns=\"http://www.w3.org/TR/xhtml1/strict\"", "");
xml = dedupName(xml);
xml = sortTags(xml);
// insert newlines in alignments
int k = xml.indexOf("<data ");
StringBuffer buf2 = new StringBuffer(xml);
while (k > 0) {
while (xml.charAt(k) != '>') {
if (xml.charAt(k) == ' ' && !xml.startsWith("idref", k + 1)) {
buf2.setCharAt(k, '\n');
}
k++;
}
k = xml.indexOf("<data ", k + 1);
}
return buf2.toString();
} catch (Exception e) {
e.printStackTrace();
return null;
}
} // toXML
/**
* produce elements for a beast object with name name, putting results in buf. It tries to create
* XML conforming to the XML transformation rules (see XMLParser) that is moderately readable.
*/
@SuppressWarnings("rawtypes")
void beastObjectToXML(
BEASTInterface beastObject, StringBuffer buf, String name, boolean isTopLevel)
throws Exception {
// determine element name, default is input, otherswise find one of the defaults
String elementName = "input";
for (String key : element2ClassMap.keySet()) {
String className = element2ClassMap.get(key);
Class _class = Class.forName(className);
if (_class.equals(beastObject.getClass())) {
elementName = key;
}
}
// if (beastObject instanceof Alignment) {
// elementName = XMLParser.DATA_ELEMENT;
// }
// if (beastObject instanceof Sequence) {
// elementName = XMLParser.SEQUENCE_ELEMENT;
// }
// if (beastObject instanceof State) {
// elementName = XMLParser.STATE_ELEMENT;
// }
// if (beastObject instanceof Distribution) {
// elementName = XMLParser.DISTRIBUTION_ELEMENT;
// }
// if (beastObject instanceof Logger) {
// elementName = XMLParser.LOG_ELEMENT;
// }
// if (beastObject instanceof Operator) {
// elementName = XMLParser.OPERATOR_ELEMENT;
// }
// if (beastObject instanceof RealParameter) {
// elementName = XMLParser.REAL_PARAMETER_ELEMENT;
// }
// if (beastObject instanceof Tree) {
// elementName = XMLParser.TREE_ELEMENT;
// }
if (isTopLevel) {
elementName = XMLParser.RUN_ELEMENT;
}
for (int i = 0; i < indent; i++) {
buf.append(" ");
}
indent++;
// open element
buf.append("<").append(elementName);
boolean skipInputs = false;
if (isDone.stream().anyMatch(x -> x == beastObject)) {
// XML is already produced, we can idref it
buf.append(" idref='" + normalise(beastObject.getID()) + "'");
skipInputs = true;
} else {
// see whether a reasonable id can be generated
if (beastObject.getID() != null && !beastObject.getID().equals("")) {
String id = beastObject.getID();
// ensure ID is unique
if (IDs.contains(id)) {
int k = 1;
while (IDs.contains(id + k)) {
k++;
}
id = id + k;
}
buf.append(" id='" + normalise(id) + "'");
IDs.add(id);
}
isDone.add(beastObject);
}
String className = beastObject.getClass().getName();
if (skipInputs == false
&& (!element2ClassMap.containsKey(elementName)
|| !element2ClassMap.get(elementName).equals(className))) {
// only add spec element if it cannot be deduced otherwise (i.e., by idref or default mapping
buf.append(" spec='" + className + "'");
}
if (name != null && !name.equals(elementName)) {
// only add name element if it differs from element = default name
buf.append(" name='" + name + "'");
}
if (!skipInputs) {
// process inputs of this beast object
// first, collect values as attributes
List<Input<?>> inputs = beastObject.listInputs();
for (Input<?> input : inputs) {
Object value = input.get();
inputToXML(input, value, beastObject, buf, true);
}
// next, collect values as input elements
StringBuffer buf2 = new StringBuffer();
for (Input input : inputs) {
Object value = input.get();
inputToXML(input, value, beastObject, buf2, false);
}
if (buf2.length() == 0) {
// if nothing was added by the inputs, close element
indent--;
buf.append("/>\n");
} else {
// add contribution of inputs
if (buf2.indexOf("<") >= 0) {
buf.append(">\n");
buf.append(buf2);
indent--;
for (int i = 0; i < indent; i++) {
buf.append(" ");
}
} else {
buf.append(">");
buf.append(buf2.toString().trim());
indent--;
}
// add closing element
buf.append("</" + elementName + ">\n");
}
} else {
// close element
indent--;
buf.append("/>\n");
}
if (indent < 2) {
buf.append("\n");
}
} // pluginToXML
/**
* Produce JSON fragment for a beast object with given name, putting results in buf. It tries to
* create JSON conforming to the JSON transformation rules (see JSONParser) that is moderately
* readable.
*/
void beastObjectToJSON(
BEASTInterface beastObject,
Class<?> defaultType,
StringBuffer buf,
String name,
boolean isTopLevel)
throws Exception {
// determine element name, default is input, otherwise find one of the defaults
String indent = "";
for (int i = 0; i < indentCount; i++) {
indent += "\t";
// buf.append(" ");
}
indentCount++;
// open element
boolean needsComma = false;
if (name != null) {
// buf.append((indentCount == 1 ? "" : indent.substring(1)) + " \"" + name + "\": {");
buf.append((indentCount == 1 ? "" : indent.substring(1)) + " " + name + ": {");
} else {
buf.append(indent + "{");
}
boolean skipInputs = false;
if (isDone.contains(beastObject)) {
// JSON is already produced, we can idref it
buf.append((needsComma == true) ? ",\n" + indent + " " : "");
buf.append("idref: \"" + beastObject.getID() + "\" ");
needsComma = true;
skipInputs = true;
} else {
// see whether a reasonable id can be generated
if (beastObject.getID() != null && !beastObject.getID().equals("")) {
String id = beastObject.getID();
// ensure ID is unique
if (IDs.contains(id)) {
int k = 1;
while (IDs.contains(id + k)) {
k++;
}
id = id + k;
}
buf.append((needsComma == true) ? ",\n" + indent + " " : "");
buf.append("id: \"" + normalise(null, id) + "\"");
needsComma = true;
IDs.add(id);
}
isDone.add(beastObject);
}
String className = beastObject.getClass().getName();
if (skipInputs == false) {
// only add spec element if it cannot be deduced otherwise (i.e., by idref)
if (defaultType != null && !defaultType.getName().equals(className)) {
buf.append((needsComma == true) ? ",\n" + indent + " " : "");
// buf.append("\"spec\": \"" + className + "\"");
buf.append("spec: \"" + className + "\"");
needsComma = true;
}
}
if (!skipInputs) {
// process inputs of this beastObject
// first, collect values as attributes
List<Input<?>> inputs = beastObject.listInputs();
// List<InputType> inputs = XMLParserUtils.listInputs(beastObject.getClass(), beastObject);
for (Input<?> input : inputs) {
StringBuffer buf2 = new StringBuffer();
Object value = input.get();
inputToJSON(input, value, beastObject, buf2, true, indent);
if (buf2.length() > 0) {
buf.append((needsComma == true) ? "," : "");
buf.append(buf2);
needsComma = true;
}
}
// next, collect values as input elements
StringBuffer buf2 = new StringBuffer();
for (Input<?> input : inputs) {
StringBuffer buf3 = new StringBuffer();
Object value = input.get();
inputToJSON(input, value, beastObject, buf3, false, indent);
if (buf3.length() > 0) {
buf2.append((needsComma == true) ? ",\n" : "\n");
buf2.append(buf3);
needsComma = true;
}
}
if (buf2.length() != 0) {
buf.append(buf2);
}
indentCount--;
if (needsComma) {
buf.append("\n" + indent);
}
needsComma = true;
} else {
// close element
indentCount--;
buf.append("");
needsComma = true;
}
// if (m_nIndent < 2) {
// collapse newlines if there are no sub-objects
String str = buf.toString();
if (str.indexOf('}') < 0 && str.length() < 1024) {
str = str.replaceAll("\\s+", " ");
buf.delete(0, buf.length());
buf.append(indent);
buf.append(str);
}
buf.append("}");
// }
} // beastObjectToJSON