--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/scripts/annotator.bf	Tue Apr 20 10:29:30 2021 +0000
@@ -0,0 +1,102 @@
+LoadFunctionLibrary ("libv3/tasks/trees.bf");
+LoadFunctionLibrary ("libv3/tasks/alignments.bf");
+LoadFunctionLibrary ("libv3/convenience/regexp.bf");
+LoadFunctionLibrary ("libv3/IOFunctions.bf");
+
+tags = {
+    "^Node" : "Internal"
+};
+
+
+
+
+tree = trees.LoadAnnotatedTopology (TRUE);
+ts = tree[^"terms.trees.newick_with_lengths"];
+root_node = io.PromptUserForString ("Root on this node");
+
+
+
+Topology T = ts;
+ts = RerootTree (T, root_node);
+ACCEPT_ROOTED_TREES = FALSE;
+Topology T = ts;
+ACCEPT_ROOTED_TREES = TRUE;
+Topology TR = ts;
+
+
+NORMALIZE_SEQUENCE_NAMES = FALSE;
+SetDialogPrompt ("File with the sequences to label as the in-clade");
+DataSet query = ReadDataFile (PROMPT_FOR_FILE);
+GetString (seqNames,query,-1);
+
+label = io.PromptUserForString ("Use this label");
+
+
+for (s;in;seqNames) {
+    tags [s && 6] = label;
+}
+
+reg_exp = Rows (tags);
+
+
+node_labels = {};
+for (_regexp_, _leaves_; in; regexp.PartitionByRegularExpressions (BranchName (T,-1), reg_exp)) {
+    tag = tags[_regexp_];
+    
+    if (tag != "Internal") {    
+    
+        if (Abs (tag) == 0) {
+            tag = "Reference";
+        }
+    
+        for (l; in; _leaves_) {
+            node_labels[l] = tag;
+        }
+    }
+}
+
+node_labelsR = {};
+for (_regexp_, _leaves_; in; regexp.PartitionByRegularExpressions (BranchName (TR,-1), reg_exp)) {
+    tag = tags[_regexp_];
+    
+    if (tag != "Internal") {    
+    
+        if (Abs (tag) == 0) {
+            tag = "Reference";
+        }
+    
+        for (l; in; _leaves_) {
+            node_labelsR[l] = tag;
+        }
+    }
+}
+
+
+leaf_labels = node_labels;
+node_labelsF = node_labels;
+node_labels * ((trees.ParsimonyLabel ("T", node_labels))["labels"]);
+node_labelsR * ((trees.ParsimonyLabel ("T", node_labelsR))["labels"]);
+node_labelsF * ((trees.ParsimonyLabel ("T", node_labelsF))["labels"]);
+
+output_to = io.PromptUserForString ("Write output to this prefix");
+
+fprintf (output_to + "labels.json", CLEAR_FILE, leaf_labels);
+fprintf (output_to + "int.nwk", CLEAR_FILE, tree.Annotate ("T", "relabel_and_annotate", "{}", FALSE));
+fprintf (output_to + "clade.nwk", CLEAR_FILE, tree.Annotate ("TR", "relabel_and_annotate_full", "{}", FALSE));
+fprintf (output_to + "full.nwk", CLEAR_FILE, tree.Annotate ("T", "relabel_and_annotate_full", "{}", FALSE));
+
+function relabel_and_annotate (node_name) {
+    _label = "";
+    if (node_labels / node_name && leaf_labels / node_name == FALSE) {
+        _label = "{" + node_labels[node_name] + "}";
+    }
+    return node_name + _label;
+}
+
+function relabel_and_annotate_full (node_name) {
+    _label = "";
+    if (node_labelsR / node_name) {
+        _label = "{" + node_labelsR[node_name] + "}";
+    }
+    return node_name + _label;
+}