if there is a special Tree Logger, then do not log this tree using no…

…rmal Tree Logger #161 LinguaPhylo/linguaPhylo#488

lphybeast/src/main/java/lphybeast/BEASTContext.java

@@ -1126,6 +1126,10 @@ public List<Loggable> getExtraLoggables() {
         return extraLoggables;
     }
 
+    public List<Loggable> getSkipLoggables() {
+        return skipLoggables;
+    }
+
     public List<LoggerHelper> getExtraLoggers() {
         return extraLoggers;
     }
@@ -1139,6 +1143,10 @@ public void addExtraLoggable(Loggable loggable) {
         extraLoggables.add(loggable);
     }
 
+    public void addSkipLoggable(Loggable loggable) {
+        skipLoggables.add(loggable);
+    }
+
     /**
      * {@link LoggerHelper} creates BEAST2 {@link Logger}.
      */

lphybeast/src/main/java/lphybeast/tobeast/generators/UCLNRelaxedClockToBEAST.java

@@ -49,24 +49,26 @@ public UCRelaxedClockModel generatorToBEAST(UCLNMean1 ucln, BEASTInterface value
             }
         }
 
+        GraphicalModelNode branchRates = context.getGraphicalModelNode(value);
         if (value instanceof RealParameter rates) {
             ucRelaxedClockModel.setInputValue("rates", rates);
 
             // branch rates LogNormal prior, which is same LogNormal as UCLN
             Prior ratesPrior = BEASTContext.createPrior(logNormDist, rates);
             context.addBEASTObject(ratesPrior, ucln);
 
+            // rm rates from log
+            context.addSkipLoggable(rates);
+            // replaced by <log id="" ... branchratemodel="@" tree="@"/>
+            RateStatistic rateStatistic = LoggerUtils.createRateStatistic("RatesStat." + branchRates.getUniqueId(), ucRelaxedClockModel, beastTree);
+            context.addExtraLoggable(rateStatistic);
+
         } else throw new IllegalArgumentException("Value sampled from LPhy UCLN should be mapped to RealParameter ! " + value);
 
         ucRelaxedClockModel.initAndValidate();
-        GraphicalModelNode branchRates = context.getGraphicalModelNode(value);
         // in case to duplicate with RandomValue id also called "branchRates"
         ucRelaxedClockModel.setID(branchRates.getUniqueId() + ".model");
 
-        //TODO rm rates from log, replaced by <log id="" ... branchratemodel="@" tree="@"/>
-        RateStatistic rateStatistic = LoggerUtils.createRateStatistic("RatesStat." + branchRates.getUniqueId(), ucRelaxedClockModel, beastTree);
-        context.addExtraLoggable(rateStatistic);
-
         // Extra Logger <log ... branchratemodel="@..." tree="@..."/>
         MetaDataTreeLogger metaDataTreeLogger = new MetaDataTreeLogger(ucRelaxedClockModel, beastTree, context);
         context.addExtraLogger(metaDataTreeLogger);

lphybeast/src/main/java/lphybeast/tobeast/loggers/LoggerFactory.java

@@ -60,10 +60,23 @@ public List<Logger> createLoggers(long logEvery, String logFileStem) {
         List<TreeInterface> trees = getTrees();
         boolean multipleTrees = trees.size() > 1;
         for (TreeInterface tree : trees) {
-            TreeLoggerHelper treeLogger = new TreeLoggerCreator(tree);
-            treeLogger.setFileName(logFileStem, multipleTrees);
+            boolean create = true;
+            // if there is already a special Tree Logger, e.g. TreeWithMetaDataLogger, for this tree,
+            // then do not log it using normal Tree Logger
+            for (LoggerHelper loggerHelper : context.getExtraLoggers()) {
+                if (loggerHelper instanceof TreeLoggerHelper treeLoggerHelper) {
+                    TreeInterface extraTree = treeLoggerHelper.getTree();
+                    if (extraTree.equals(tree))
+                        create = false;
+                }
+            }
+
+            if (create) {
+                TreeLoggerHelper treeLogger = new TreeLoggerCreator(tree);
+                treeLogger.setFileName(logFileStem, multipleTrees);
 
-            loggers.add(treeLogger.createLogger(logEvery, elements));
+                loggers.add(treeLogger.createLogger(logEvery, elements));
+            }
         }
 
         // extraLoggers, create a seperated logger each time
@@ -117,6 +130,11 @@ public List<Loggable> getLoggables() {
             nonTrees.addAll(context.getExtraLoggables());
         }
 
+        // rm loggable if it is in skipLoggables
+        for (Loggable loggable : context.getSkipLoggables()) {
+            nonTrees.remove(loggable);
+        }
+
 //        for (Loggable loggable : extraLoggables) {
 //            // fix StructuredCoalescent log
 //            if (loggable instanceof Constant) {
@@ -168,13 +186,14 @@ public TreeLoggerCreator(TreeInterface tree) {
             this.tree = tree;
         }
 
+        @Deprecated
         private boolean logMetaData() {
             TreeInterface tree = getTree();
             Map<BEASTInterface, GraphicalModelNode<?>> BEASTToLPHYMap = context.getBEASTToLPHYMap();
             GraphicalModelNode graphicalModelNode = BEASTToLPHYMap.get(tree);
             Generator generator = ((RandomVariable) graphicalModelNode).getGenerator();
 
-            // TODO more general?
+            //TODO it'd better to use MetaDataTreeLogger
             return generator instanceof SkylineCoalescent ||
                     generator instanceof StructuredCoalescent;
         }

lphybeast/src/main/java/lphybeast/tobeast/loggers/MetaDataTreeLogger.java

@@ -15,6 +15,8 @@
 
 /**
  * Log branch rates with tree.
+ * This is for the scenario that cannot use {@link LoggerFactory.TreeLoggerCreator},
+ * which relies on the generator of lphy's tree.
  * @see TreeWithMetaDataLogger
  * @author Walter Xie
  */
@@ -25,8 +27,14 @@ public class MetaDataTreeLogger implements TreeLoggerHelper {
     final TreeInterface tree;
     String fileName;
 
+    /**
+     * create Tree Logger, using TreeWithMetaDataLogger
+     * @param branchRateModel   can be null, if so, no branchratemodel=""
+     * @param tree              cannot be null
+     * @param context           central config
+     */
     public MetaDataTreeLogger(BranchRateModel branchRateModel, TreeInterface tree, BEASTContext context) {
-        this.branchRateModel = Objects.requireNonNull(branchRateModel);
+        this.branchRateModel = branchRateModel;
         this.tree = Objects.requireNonNull(tree);
         this.context = context;
     }
@@ -41,7 +49,8 @@ public Logger createLogger(long logEvery, Multimap<BEASTInterface, GraphicalMode
 
         TreeWithMetaDataLogger treeWithMetaDataLogger = new TreeWithMetaDataLogger();
         treeWithMetaDataLogger.setInputValue("tree", tree);
-        treeWithMetaDataLogger.setInputValue("branchratemodel", branchRateModel);
+        if (branchRateModel != null)
+            treeWithMetaDataLogger.setInputValue("branchratemodel", branchRateModel);
 
         logger.setInputValue("log", treeWithMetaDataLogger);
         logger.initAndValidate();