Switch AscertainedForParsimonyUninformativeFilteredAlignment to spec FilteredAlignment#19
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Switch AscertainedForParsimonyUninformativeFilteredAlignment to spec FilteredAlignment#19
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…FilteredAlignment 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.
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Summary
beast.base.evolution.alignment.FilteredAlignmentis@Deprecatedin beast3 with a Javadoc pointer tobeast.base.spec.evolution.alignment.FilteredAlignment. This was the only remaining Java migration item formorph-models— surfaced by the beast3-migration analyzer.The spec
FilteredAlignmentstill extends the (non-deprecated)Alignment, so all the inherited fields the existing override relies on —isAscertainedInput,excludefromInput,excludetoInput,setupAscertainment()— remain available unchanged. Only the import andextendsclause needed updating; one line of real change.Test plan
mvn test— 8/8 pass (LewisMKTest)mvn -q -DskipTests compileandtest-compile— cleanFilteredAlignmentpreserves)