/**
* 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;
}
/**
* produce XML for an input of a beast object, both as attribute/value pairs for primitive inputs
* (if isShort=true) and as individual elements (if isShort=false)
*
* @param input: name of the input
* @param beastObject: beast object to produce this input XML for
* @param buf: gets XML results are appended
* @param isShort: flag to indicate attribute/value format (true) or element format (false)
* @throws Exception
*/
void inputToXML(
Input<?> input, Object value, BEASTInterface beastObject, StringBuffer buf, boolean isShort)
throws Exception {
// if (input.getName().equals("*")) {
// this can happen with beast.core.parameter.Map
// and * is not a valid XML attribute name
// return;
// }
if (value != null) {
if (value instanceof Map) {
// distinguish between List, Map, BEASTInterface and primitive input types
if (isShort) {
@SuppressWarnings("unchecked")
Map<String, ?> map = (Map<String, ?>) value;
// determine label width
int whiteSpaceWidth = 0;
List<String> keys = new ArrayList<>();
keys.addAll(map.keySet());
Collections.sort(keys);
for (String key : keys) {
whiteSpaceWidth = Math.max(whiteSpaceWidth, key.length());
}
for (String key : map.keySet()) {
// buf.append(" <input name='" + key + "'>");
buf.append("\n " + key);
for (int k = key.length(); k < whiteSpaceWidth; k++) {
buf.append(' ');
}
buf.append("=\"" + normalise(map.get(key).toString()) + "\"");
}
}
return;
} else if (value instanceof List) {
if (!isShort) {
int k = 0;
List<?> list = (List<?>) value;
for (Object o2 : list) {
if (o2 instanceof BEASTInterface) {
beastObjectToXML((BEASTInterface) o2, buf, input.getName(), false);
} else {
k++;
buf.append(o2.toString());
if (k < list.size()) {
buf.append(' ');
}
}
}
}
return;
} else if (value instanceof BEASTInterface) {
if (!value.equals(input.defaultValue)) {
if (isShort && isDone.contains(value)) {
buf.append(
" " + input.getName() + "='@" + normalise(((BEASTInterface) value).getID()) + "'");
if (!isInputsDone.containsKey(beastObject)) {
isInputsDone.put(beastObject, new HashSet<>());
}
isInputsDone.get(beastObject).add(input.getName());
}
if (!isShort
&& (!isInputsDone.containsKey(beastObject)
|| !isInputsDone.get(beastObject).contains(input.getName()))) {
beastObjectToXML((BEASTInterface) value, buf, input.getName(), false);
}
}
return;
} else {
if (!value.equals(input.defaultValue)) {
// primitive type
String valueString = value.toString();
if (isShort) {
if (valueString.indexOf('\n') < 0) {
buf.append(" " + input.getName() + "='" + normalise(value.toString()) + "'");
}
} else {
if (valueString.indexOf('\n') >= 0) {
for (int j = 0; j < indent; j++) {
buf.append(" ");
}
if (input.getName().equals("value")) {
buf.append(normalise(value.toString()));
} else {
buf.append(
"<input name='"
+ input.getName()
+ "'>"
+ normalise(value.toString())
+ "</input>\n");
}
}
}
}
return;
}
} else {
// value=null, no XML to produce
return;
}
} // inputToXML
/** Ensure the class behaves properly, even when inputs are not specified. */
@Override
public void initAndValidate() throws Exception {
boolean sortNodesAlphabetically = false;
if (dataInput.get() != null) {
labels = dataInput.get().getTaxaNames();
} else if (m_taxonset.get() != null) {
if (labels == null) {
labels = m_taxonset.get().asStringList();
} else { // else labels were set by TreeParser c'tor
sortNodesAlphabetically = true;
}
} else {
if (isLabelledNewickInput.get()) {
if (m_initial.get() != null) {
labels = m_initial.get().getTaxonset().asStringList();
} else {
labels = new ArrayList<>();
createUnrecognizedTaxa = true;
sortNodesAlphabetically = true;
}
} else {
if (m_initial.get() != null) {
// try to pick up taxa from initial tree
final Tree tree = m_initial.get();
if (tree.m_taxonset.get() != null) {
labels = tree.m_taxonset.get().asStringList();
} else {
// m_sLabels = null;
}
} else {
// m_sLabels = null;
}
}
// m_bIsLabelledNewick = false;
}
final String newick = newickInput.get();
if (newick == null || newick.equals("")) {
// can happen while initalising Beauti
final Node dummy = new Node();
setRoot(dummy);
} else {
try {
setRoot(parseNewick(newickInput.get()));
} catch (ParseCancellationException e) {
throw new RuntimeException(
"TreeParser cannot make sense of the Newick string "
+ "provided. It gives the following clue:\n"
+ e.getMessage());
}
}
super.initAndValidate();
if (sortNodesAlphabetically) {
// correct for node ordering: ensure order is alphabetical
for (int i = 0; i < getNodeCount() && i < labels.size(); i++) {
m_nodes[i].setID(labels.get(i));
}
Node[] nodes = new Node[labels.size()];
System.arraycopy(m_nodes, 0, nodes, 0, labels.size());
Arrays.sort(nodes, (o1, o2) -> o1.getID().compareTo(o2.getID()));
for (int i = 0; i < labels.size(); i++) {
m_nodes[i] = nodes[i];
nodes[i].setNr(i);
}
}
if (m_initial.get() != null) processTraits(m_initial.get().m_traitList.get());
else processTraits(m_traitList.get());
if (timeTraitSet != null) {
adjustTreeNodeHeights(root);
} else if (adjustTipHeightsInput.get()) {
double treeLength = TreeUtils.getTreeLength(this, getRoot());
double extraTreeLength = 0.0;
double maxTipHeight = 0.0;
// all nodes should be at zero height if no date-trait is available
for (int i = 0; i < getLeafNodeCount(); i++) {
double height = getNode(i).getHeight();
if (maxTipHeight < height) {
maxTipHeight = height;
}
extraTreeLength += height;
getNode(i).setHeight(0);
}
double scaleFactor = (treeLength + extraTreeLength) / treeLength;
final double SCALE_FACTOR_THRESHOLD = 0.001;
// if the change in total tree length is more than 0.1% then give the user a warning!
if (scaleFactor > 1.0 + SCALE_FACTOR_THRESHOLD) {
DecimalFormat format = new DecimalFormat("#.##");
Log.info.println(
"WARNING: Adjust tip heights attribute set to 'true' in " + getClass().getSimpleName());
Log.info.println(
" has resulted in significant (>"
+ format.format(SCALE_FACTOR_THRESHOLD * 100.0)
+ "%) change in tree length.");
Log.info.println(
" Use "
+ adjustTipHeightsInput.getName()
+ "='false' to override this default.");
Log.info.printf(" original max tip age = %8.3f\n", maxTipHeight);
Log.info.printf(" new max tip age = %8.3f\n", 0.0);
Log.info.printf(" original tree length = %8.3f\n", treeLength);
Log.info.printf(" new tree length = %8.3f\n", treeLength + extraTreeLength);
Log.info.printf(" TL scale factor = %8.3f\n", scaleFactor);
}
}
if (m_taxonset.get() == null && labels != null && isLabelledNewickInput.get()) {
m_taxonset.setValue(new TaxonSet(Taxon.createTaxonList(labels)), this);
}
initStateNodes();
} // init
/**
* produce JSON for an input of a beastObject, both as attribute/value pairs for primitive inputs
* (if isShort=true) and as individual elements (if isShort=false)
*
* @param input0: name of the input
* @param beastObject: beastObject to produce this input JSON for
* @param buf: gets JSON results are appended
* @param isShort: flag to indicate attribute/value format (true) or element format (false)
* @throws Exception
*/
@SuppressWarnings({"rawtypes", "unchecked"})
private void inputToJSON(
Input input,
Object value,
BEASTInterface beastObject,
StringBuffer buf,
boolean isShort,
String indent)
throws Exception {
if (value != null) {
// distinguish between Map, List, BEASTObject and primitive input types
if (value instanceof Map) {
if (!isShort) {
Map<String, ?> map = (Map<String, ?>) value;
StringBuffer buf2 = new StringBuffer();
// determine label width
int whiteSpaceWidth = 0;
for (String key : map.keySet()) {
whiteSpaceWidth = Math.max(whiteSpaceWidth, key.length());
}
boolean needsComma = false;
List<String> keys = new ArrayList<>();
keys.addAll(map.keySet());
Collections.sort(keys);
for (String key : keys) {
if (needsComma) {
buf2.append(",\n");
}
buf2.append(indent + " " + key);
for (int k = key.length(); k < whiteSpaceWidth; k++) {
buf2.append(' ');
}
buf2.append(" :\"" + map.get(key) + "\"");
needsComma = true;
}
buf.append(buf2);
}
return;
} else if (value instanceof List) {
if (!isShort) {
StringBuffer buf2 = new StringBuffer();
// buf2.append(indent + " \"" + input0 + "\": [\n");
buf2.append(indent + " " + input.getName() + ": [\n");
boolean needsComma = false;
int oldLen = buf2.length();
for (Object o2 : (List) value) {
if (needsComma) {
buf2.append(",\n");
}
StringBuffer buf3 = new StringBuffer();
if (o2 instanceof BEASTInterface) {
beastObjectToJSON((BEASTInterface) o2, input.getType(), buf3, null, false);
} else {
buf2.append(o2.toString());
}
buf2.append(buf3);
needsComma = oldLen < buf2.length();
}
if (buf2.length() != oldLen) {
buf.append(buf2);
buf.append("\n" + indent + " ]");
}
}
return;
} else if (value instanceof BEASTInterface) {
if (!value.equals(input.defaultValue)) {
// Parameters can use short hand notation if they are not in the state
// Note this means lower and upper bounds are lost -- no problem for BEAST, but maybe for
// BEAUti
if (value instanceof Parameter.Base) {
Parameter.Base parameter = (Parameter.Base) value;
boolean isInState = false;
for (Object o : parameter.getOutputs()) {
if (o instanceof State) {
isInState = true;
break;
}
}
if (!isInState) {
if (isShort) {
buf.append(" " + input.getName() + ": \"" + parameter.getValue() + "\"");
} else {
return;
}
}
}
if (isShort && isDone.contains(value)) {
buf.append(" " + input.getName() + ": \"@" + ((BEASTInterface) value).getID() + "\"");
if (!isInputsDone.containsKey(beastObject)) {
isInputsDone.put(beastObject, new HashSet<>());
}
isInputsDone.get(beastObject).add(input.getName());
}
if (!isShort
&& (!isInputsDone.containsKey(beastObject)
|| !isInputsDone.get(beastObject).contains(input.getName()))) {
beastObjectToJSON((BEASTInterface) value, input.getType(), buf, input.getName(), false);
}
}
return;
} else {
// primitive type
if (!value.equals(input.defaultValue)) {
String valueString = value.toString();
if (isShort) {
if (valueString.indexOf('\n') < 0) {
buf.append(" " + input.getName() + ": " + normalise(input, value.toString()) + "");
}
} else {
if (valueString.indexOf('\n') >= 0) {
buf.append(
indent + "" + input.getName() + ": " + normalise(input, value.toString()) + "");
}
}
}
return;
}
} else {
// value=null, no JSON to produce
return;
}
} // inputToJSON