From 6aee70263b5913573186954842df29d2010b51fd Mon Sep 17 00:00:00 2001 From: Alexei Drummond Date: Thu, 7 May 2026 21:57:06 +1200 Subject: [PATCH] Switch AscertainedForParsimonyUninformativeFilteredAlignment to spec FilteredAlignment MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit beast.base.evolution.alignment.FilteredAlignment is @Deprecated in beast3 and replaced by beast.base.spec.evolution.alignment.FilteredAlignment. The spec class still extends Alignment (the legacy StateNode, not itself deprecated), so all the inherited fields the override relies on — isAscertainedInput, excludefromInput, excludetoInput, setupAscertainment() — remain available unchanged. Only the import and extends clause needed updating. mvn test: 8/8 pass. Found via the beast3-migration analyzer: the only remaining Java migration item for morph-models. --- .../AscertainedForParsimonyUninformativeFilteredAlignment.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/main/java/morphmodels/evolution/alignment/AscertainedForParsimonyUninformativeFilteredAlignment.java b/src/main/java/morphmodels/evolution/alignment/AscertainedForParsimonyUninformativeFilteredAlignment.java index c343ff4..f8b7a3c 100644 --- a/src/main/java/morphmodels/evolution/alignment/AscertainedForParsimonyUninformativeFilteredAlignment.java +++ b/src/main/java/morphmodels/evolution/alignment/AscertainedForParsimonyUninformativeFilteredAlignment.java @@ -1,7 +1,7 @@ package morphmodels.evolution.alignment; import beast.base.core.Input; -import beast.base.evolution.alignment.FilteredAlignment; +import beast.base.spec.evolution.alignment.FilteredAlignment; import java.util.HashSet; import java.util.Set;