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Closes CompEvol/BeastFX#105 #106

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Merged
merged 3 commits into from
Nov 20, 2025
Merged

Closes CompEvol/BeastFX#105 #106

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c0002bb
Target tree option now does what it should, CompEvol/BeastFX#105
Lars-B Nov 19, 2025
776f609
Cleaner fix: no need to pass target twice
Lars-B Nov 19, 2025
45e5f00
clean up, removing the targetTreeFileName parameter
Lars-B Nov 19, 2025
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54 changes: 22 additions & 32 deletions src/beastfx/app/treeannotator/TreeAnnotator.java
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Original file line number Diff line number Diff line change
Expand Up @@ -36,7 +36,6 @@
import beast.base.core.Description;
import beast.base.core.Input;
import beast.base.core.Log;
import beast.base.evolution.alignment.TaxonSet;
import beast.base.evolution.tree.Node;
import beast.base.evolution.tree.Tree;
import beast.base.evolution.tree.TreeParser;
Expand All @@ -61,7 +60,7 @@ public class TreeAnnotator extends beast.base.inference.Runnable {
final public Input<Integer> burnInPercentageInput = new Input<>("burnin", "percentage of trees to used as burn-in (and will be ignored)", 10);
final public Input<Double> limitInput = new Input<>("limit", "the minimum posterior probability for a node to be annotated", 0.0);
final public Input<String> topologyInput = new Input<> ("topology", "name of the method for determining topology", "MCC");
final public Input<String> targetInput = new Input<> ("target", "target_file_name, specifies a user target tree to be annotated");
final public Input<String> targetInput = new Input<> ("target", "target_file_name, specifies a user target tree to be annotated", "");
final public Input<Boolean> forceDiscreteInput = new Input<> ("forceDiscrete", "forces integer traits to be treated as discrete traits.");
final public Input<Boolean> lowMemInput = new Input<> ("lowMem", "use less memory, which is a bit slower.");
final public Input<Double> hpd2DInput = new Input<> ("hpd2D", "the HPD interval to be used for the bivariate traits");
Expand Down Expand Up @@ -544,21 +543,15 @@ public void run(final int burninPercentage,
// HeightsSummary heightsOption,
double posteriorLimit,
double hpd2D,
// Target targetOption,
String targetTreeFileName,
String inputFileName,
String outputFileName
) throws IOException {

topologySettingService = getTopologySettingService();
nodeHeightSettingService = getNodeHeightSettingService();

// Get citations, only print if eihter of them is not empty.


// Get citations, only print if either of them is not empty.
String nodeCitation = nodeHeightSettingService.getCitations();


String topoCitation = topologySettingService.getCitations();

if (!nodeCitation.isBlank() || !topoCitation.isBlank()) {
Expand Down Expand Up @@ -619,11 +612,19 @@ public void run(final int burninPercentage,
}
}

Tree targetTree = topologySettingService.setTopology(treeSet, progressStream, this);
if (targetInput.get() != null && !targetInput.get().isEmpty()) {
String current = topologySettingService.getServiceName();
String required = UserTargetTreeTopologyService.SERVICE_NAME;
if (!required.equals(current)) {
Log.info("Setting topology to be the target tree...");
topologyInput.setValue("target", this);
topologySettingService = getTopologySettingService();
}
}


Tree targetTree = topologySettingService.setTopology(treeSet, progressStream, this);
cladeSystem = getCladeSystem(targetTree);

// progressStream.println("Collecting node information...");
// progressStream.println("0 25 50 75 100");
// progressStream.println("|--------------|--------------|--------------|--------------|");
Expand Down Expand Up @@ -684,18 +685,18 @@ public void run(final int burninPercentage,

progressStream.println("Writing annotated tree....");


processMetaData(targetTree.getRoot());
try {
final PrintStream stream = outputFileName != null ?
new PrintStream(new FileOutputStream(outputFileName)) :
System.out;
targetTree.init(stream);
stream.println();
stream.print("tree TREE_" +
topologySettingService.getServiceName() + "_" +
nodeHeightSettingService.getServiceName() + " = ");

stream.print("tree TREE_" +
topologySettingService.getServiceName() + "_" +
nodeHeightSettingService.getServiceName() + " = ");
int[] dummy = new int[1];
String newick = targetTree.getRoot().toSortedNewick(dummy, true);
stream.print(newick);
Expand Down Expand Up @@ -1175,7 +1176,7 @@ private void annotate2DHPDAttribute(Node node, String preLabel, String postLabel
private final List<TreeAnnotationPlugin> beastObjects = new ArrayList<>();

Set<String> attributeNames = new HashSet<>();
TaxonSet taxa = null;
// TaxonSet taxa = null;

static boolean processBivariateAttributes = true;

Expand Down Expand Up @@ -1387,8 +1388,7 @@ public void run() throws Exception {
for (String versionFile : versionFileInput.get()) {
BEASTClassLoader.addServices(versionFile);
}

String targetTreeFileName = null;

String inputFileName = null;
String outputFileName = null;

Expand Down Expand Up @@ -1453,20 +1453,12 @@ public void run() throws Exception {
hpd2D = hpd2DInput.get();
if (hpd2D <= 0 || hpd2D >=1) {
Log.err.println("hpd2D is a fraction and should be in between 0.0 and 1.0.");
System.exit(1);
System.exit(1);
}
processBivariateAttributes = true;
}


// Target target = Target.MAX_CLADE_CREDIBILITY;
// if (targetInput.get() != null) {
// target = Target.USER_TARGET_TREE;
// targetTreeFileName = arguments.getStringOption("target");
// }

final List<File> args2 = filesInput.get();


switch (args2.size()) {
case 2:
Expand All @@ -1484,9 +1476,7 @@ public void run() throws Exception {
}

try {
run(burninPercentage, lowMem, posteriorLimit, hpd2D, targetTreeFileName, inputFileName, outputFileName);
//} catch (IOException e) {
// throw e;
run(burninPercentage, lowMem, posteriorLimit, hpd2D, inputFileName, outputFileName);
} catch (Exception e) {
e.printStackTrace();
}
Expand Down
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