Pierre Gruet pushed to branch upstream at Debian Med / jebl2
Commits:
664633f1 by Pierre Gruet at 2026-05-29T12:18:35+02:00
New upstream version 0.1+git20231105.51da3b1
- - - - -
1 changed file:
- src/jebl/evolution/io/NewickImporter.java
Changes:
=====================================
src/jebl/evolution/io/NewickImporter.java
=====================================
@@ -23,6 +23,8 @@ public class NewickImporter implements TreeImporter {
private final ImportHelper helper;
private boolean unquotedLabels;
+ private String lastLabel = null;
+
/**
* Constructor
* @param reader tree text
@@ -154,7 +156,7 @@ public class NewickImporter implements TreeImporter {
*/
private Node readInternalNode(SimpleRootedTree tree) throws IOException,
ImportException
{
- List<Node> children = new ArrayList<Node>();
+ List<Node> children = new ArrayList<>();
// read the opening '('
helper.readCharacter();
@@ -175,7 +177,7 @@ public class NewickImporter implements TreeImporter {
// should have had a closing ')'
if (helper.getLastDelimiter() != ')') {
- throw new ImportException.BadFormatException("Missing closing ')'
in tree");
+ throw new ImportException.BadFormatException("Missing closing ')'
in tree" + (lastLabel != null ? " - after tip " + lastLabel : ""));
}
final Node node = tree.createInternalNode(children);
@@ -212,6 +214,7 @@ public class NewickImporter implements TreeImporter {
if ("".equals(label)) {
throw new ImportException.UnknownTaxonException("Emtpy node names
are not allowed.");
}
+ lastLabel = label;
try {
return tree.createExternalNode(Taxon.getTaxon(label));
} catch (IllegalArgumentException e) {
View it on GitLab:
https://salsa.debian.org/med-team/jebl2/-/commit/664633f19a51c262c70ea0666b45d7f2050b6df1
--
View it on GitLab:
https://salsa.debian.org/med-team/jebl2/-/commit/664633f19a51c262c70ea0666b45d7f2050b6df1
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