set ids of trees parsed from NEXUS file. fixes CompEvol/BeastFX#87

CompEvol · Sep 16, 2024 · c520aaf · c520aaf
1 parent fe85402
commit c520aaf
Showing 1 changed file with 13 additions and 0 deletions.
diff --git a/src/beast/base/parser/NexusParser.java b/src/beast/base/parser/NexusParser.java
@@ -522,10 +522,20 @@ protected void parseTreesBlock(final BufferedReader fin) throws IOException {
  }
 
  // read trees
+ int current = 0;
  while (nextCommand != null && !nextCommand.isEndOfBlock()) {
  if (nextCommand.isCommand("tree")) {
  String treeString = nextCommand.arguments;
  final int i = treeString.indexOf('(');
+
+
+ String id = "" + current;
+ try {
+ id = treeString.substring(5, i).split("=")[0].trim();
+ } catch (Exception e) {
+ // ignore
+ }
+
  if (i > 0) {
  treeString = treeString.substring(i);
  }
@@ -546,8 +556,11 @@ protected void parseTreesBlock(final BufferedReader fin) throws IOException {
  listener.treeParsed(trees.size(), treeParser);
  }
 
+ treeParser.setID(id);
+
  // this must come after listener or trees.size() gives the wrong index to treeParsed
  trees.add(treeParser);
+ current++;
 
  }
  nextCommand = readNextCommand(fin);