/** convert plain text string to JSON string, replacing some entities * */
private String normalise(Input<?> input, String str) {
str = str.replaceAll("\\\\", "\\\\\\\\");
str = str.replaceAll("/", "\\\\/");
str = str.replaceAll("\b", "\\\\b");
str = str.replaceAll("\f", "\\\\f");
str = str.replaceAll("\t", "\\\\t");
str = str.replaceAll("\\r", "\\\\r");
str = str.replaceAll("\"", "\\\\\"");
str = str.replaceAll("\n", "\\\\n");
if (input != null
&& !input.getType().equals(Double.class)
&& !input.getType().equals(Integer.class)
&& !input.getType().equals(Boolean.class)) {
str = "\"" + str + "\"";
}
return str;
}
/** 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
/**
* 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