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Better/new user messages when using sampled ancestor trees #100

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Lars-B wants to merge 4 commits into from
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Better/new user messages when using sampled ancestor trees #100

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e137382
Gracefully exit when sampled ancestors are present and CA heights are…
Lars-B May 26, 2025
120e606
warning about using CCDs with SA trees, not directly supported but wi…
Lars-B May 26, 2025
240e781
commenting never used bits of code
Lars-B May 26, 2025
61ac206
adding option to set seed for alignment generation
Lars-B Jul 28, 2025
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29 changes: 25 additions & 4 deletions src/beastfx/app/seqgen/SimulatedAlignment.java
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Original file line number Diff line number Diff line change
Expand Up @@ -6,6 +6,7 @@
import beast.base.core.Description;
import beast.base.core.Input;
import beast.base.core.Input.Validate;
import beast.base.core.Log;
import beast.base.evolution.alignment.Alignment;
import beast.base.evolution.alignment.Sequence;
import beast.base.evolution.branchratemodel.BranchRateModel;
Expand All @@ -32,7 +33,12 @@ public class SimulatedAlignment extends Alignment {
final public Input<Integer> m_sequenceLengthInput = new Input<>("sequencelength", "nr of samples to generate (default 1000).", 1000);
final public Input<String> m_outputFileNameInput = new Input<>(
"outputFileName",
"If provided, simulated alignment is additionally written to this file.");
"If provided, simulated alignment is additionally written to this file.");
final public Input<Long> localSeedInput = new Input<>(
"seed",
"Optional local random seed for simulating this alignment. If not set, global seed is used.",
Input.Validate.OPTIONAL
);

/**
* nr of samples to generate *
Expand Down Expand Up @@ -87,9 +93,24 @@ public void initAndValidate() {
m_outputFileName = m_outputFileNameInput.get();

sequenceInput.get().clear();

simulate();


Long customSeed = localSeedInput.get();
long originalSeed = Randomizer.getSeed();
long seedToUse = customSeed != null ? customSeed : originalSeed;

if (customSeed != null) {
Log.info.println();
Log.info.println("Random number seed for alignment simulation: " + customSeed);
Log.info.println();
}

try {
Randomizer.setSeed(seedToUse);
simulate();
} finally {
Randomizer.setSeed(originalSeed);
}

// Write simulated alignment to disk if requested:
if (m_outputFileName != null) {
PrintStream pstream;
Expand Down
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