removeTaxa function #412

examples/coalescent/jcCoalescent.lphy

@@ -6,4 +6,5 @@ model {
   Θ ~ LogNormal(meanlog=3.0, sdlog=1.0);
   ψ ~ Coalescent(theta=Θ, taxa=taxa);
   D ~ PhyloCTMC(tree=ψ, L=L, Q=jukesCantor());
+  E = rmTaxa(names=1:3, alignment=D);
 }

lphy-base/src/main/java/lphy/base/function/alignment/RemoveTaxa.java

@@ -0,0 +1,73 @@
+package lphy.base.function.alignment;
+
+import jebl.evolution.sequences.SequenceType;
+import lphy.base.evolution.Taxa;
+import lphy.base.evolution.Taxon;
+import lphy.base.evolution.alignment.Alignment;
+import lphy.base.evolution.alignment.AlignmentUtils;
+import lphy.base.evolution.alignment.SimpleAlignment;
+import lphy.core.model.DeterministicFunction;
+import lphy.core.model.Value;
+import lphy.core.model.annotation.GeneratorCategory;
+import lphy.core.model.annotation.GeneratorInfo;
+import lphy.core.model.annotation.ParameterInfo;
+
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+
+import static lphy.base.evolution.alignment.AlignmentUtils.ALIGNMENT_PARAM_NAME;
+
+public class RemoveTaxa extends DeterministicFunction<Alignment> {
+
+    public static final String taxaParamName = "names";
+
+    public RemoveTaxa(@ParameterInfo(name = taxaParamName,
+            description = "an array of objects representing taxa names") Value<Object[]> taxaNames,
+                      @ParameterInfo(name = AlignmentUtils.ALIGNMENT_PARAM_NAME,
+                              description = "the original alignment.") Value<Alignment> originalAlignment) {
+        setParam(taxaParamName, taxaNames);
+        setParam(ALIGNMENT_PARAM_NAME, originalAlignment);
+    }
+
+    @GeneratorInfo(name="rmTaxa", category = GeneratorCategory.TAXA_ALIGNMENT,
+            examples = {"jcCoalescent.lphy"}, description = "Remove a set of taxa from the given alignment.")
+    public Value<Alignment> apply() {
+        Value<Object[]> namesVal = getParams().get(taxaParamName);
+        Value<Alignment> alignmentVal = getParams().get(ALIGNMENT_PARAM_NAME);
+
+        List<String> unwantedNameList = Arrays.stream(namesVal.value())
+                .map(Object::toString).toList();
+
+        final Alignment original = alignmentVal.value();
+        List<Taxon> newTaxonList = new ArrayList<>();
+        for (Taxon t : original.getTaxonArray()) {
+            // rm all taxon if it is in
+            if (!unwantedNameList.contains(t.getName()))
+                newTaxonList.add(t);
+        }
+        Taxa newTaxa = Taxa.createTaxa(newTaxonList.toArray(Taxon[]::new));
+        int nchar = original.nchar();
+        SequenceType sequenceType = original.getSequenceType();
+        Alignment newAlignment = new SimpleAlignment(newTaxa, nchar, sequenceType);
+
+        int tmpS;
+        // set states
+        for (int i = 0; i < newAlignment.ntaxa(); i++) {
+            String name = newAlignment.getTaxonName(i);
+            int originalIdx = original.indexOfTaxon(name);
+            if (originalIdx < 0)
+                throw new IllegalArgumentException("Cannot find the taxon " + name + " in the given alignment : " +
+                        Arrays.toString(original.getTaxaNames()));
+
+            for (int j = 0; j < original.nchar(); j++) {
+                // original taxon index
+                tmpS = original.getState(originalIdx, j);
+                // new taxon index
+                newAlignment.setState(i, j, tmpS);
+            }
+        }
+
+        return new Value<>(null, newAlignment, this);
+    }
+}

lphy-base/src/main/java/lphy/base/spi/LPhyBaseImpl.java

@@ -89,7 +89,7 @@ public class LPhyBaseImpl implements LPhyExtension {
             // Taxa
             CreateTaxa.class, ExtantTaxa.class, NCharFunction.class, NTaxaFunction.class, TaxaFunction.class,
             // Alignment
-            SelectSitesByMissingFraction.class,
+            SelectSitesByMissingFraction.class, RemoveTaxa.class,
             VariableSites.class, InvariableSites.class, CopySites.class,
             // Tree
             LocalBranchRates.class, ExtantTree.class, PruneTree.class, //NodeCount.class, TreeLength.class,