Rename ReadCountModel.class to LikelihoodReadCountModel.class in Beast …

…#56
bioDS · Sep 12, 2024 · 7a0b39f · 7a0b39f
1 parent b93c323
commit 7a0b39f
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Showing 4 changed files with 17 additions and 17 deletions.
diff --git a/...lution/readcountmodel/ReadCountModel.java → ...dcountmodel/LikelihoodReadCountModel.java b/...lution/readcountmodel/ReadCountModel.java → ...dcountmodel/LikelihoodReadCountModel.java
@@ -14,7 +14,7 @@
 import java.util.Random;
 
 
-public class ReadCountModel extends Distribution {
+public class LikelihoodReadCountModel extends Distribution {
 
     public Input<Alignment> alignmentInput = new Input<>("alignment", "alignment");
     public Input<ReadCount> readCountInput = new Input<>("readCount", "nucleotide read counts");

diff --git a/...t/src/main/java/phylonco/beast/evolution/readcountmodel/TreeLikelihoodWithReadCounts.java b/...t/src/main/java/phylonco/beast/evolution/readcountmodel/TreeLikelihoodWithReadCounts.java
@@ -17,12 +17,12 @@ public class TreeLikelihoodWithReadCounts extends TreeLikelihood {
 //    public Input<RealParameter> epsilonInput = new Input<>("epsilon", "sequencing error");
 //    public Input<RealParameter> deltaInput = new Input<>("delta", "allelic dropout probability");
 
-    public Input<ReadCountModel> readCountModelInput = new Input<>("readCountModel", "read count model");
+    public Input<LikelihoodReadCountModel> readCountModelInput = new Input<>("readCountModel", "read count model");
 
     public Input<ReadCount> readCountdataInput = new Input<>("readcount", "read count data for the beast.tree", Input.Validate.REQUIRED);
 
 
-    private ReadCountModel readCountModel;
+    private LikelihoodReadCountModel likelihoodReadCountModel;
 
     @Override
     public void initAndValidate() {
@@ -135,7 +135,7 @@ protected int traverse(final Node node) {
                 int state = genotypeAlignment.getPattern(taxonIndex, patternIndex);
                 // update the leaf partials using read count model
                 int[] states = genotypeAlignment.getDataType().getStatesForCode(state);
-                readCountModel.calculateLogPLeaf(node, states);
+                likelihoodReadCountModel.calculateLogPLeaf(node, states);
             }
         }
         return update;

diff --git a/...on/readcountmodel/ReadCountModelTest.java → ...ntmodel/LikelihoodReadCountModelTest.java b/...on/readcountmodel/ReadCountModelTest.java → ...ntmodel/LikelihoodReadCountModelTest.java
@@ -21,7 +21,7 @@
 import static org.junit.Assert.assertEquals;
 
 
-public class ReadCountModelTest {
+public class LikelihoodReadCountModelTest {
 
     final double DELTA = 1e-10;
 
@@ -45,7 +45,7 @@ public void testAlignment() {
      */
     @Test
     public void testReadCountModel() throws IOException {
-        ReadCountModel readCountModel = new ReadCountModel();
+        LikelihoodReadCountModel likelihoodReadCountModel = new LikelihoodReadCountModel();
 
         // read from file
         Double epsilon = 0.06;
@@ -66,20 +66,20 @@ public void testReadCountModel() throws IOException {
         RealParameter sParam = new RealParameter(s);
 
         // init params
-        readCountModel.setInputValue("alignment", alignment);
-        readCountModel.setInputValue("readCount", readCounts);
-        readCountModel.setInputValue("epsilon", epsilon.toString());
-        readCountModel.setInputValue("delta", delta.toString());
-        readCountModel.setInputValue("t", t.toString());
-        readCountModel.setInputValue("v", v.toString());
-        readCountModel.setInputValue("s", sParam);
-        readCountModel.setInputValue("w", w.toString());
+        likelihoodReadCountModel.setInputValue("alignment", alignment);
+        likelihoodReadCountModel.setInputValue("readCount", readCounts);
+        likelihoodReadCountModel.setInputValue("epsilon", epsilon.toString());
+        likelihoodReadCountModel.setInputValue("delta", delta.toString());
+        likelihoodReadCountModel.setInputValue("t", t.toString());
+        likelihoodReadCountModel.setInputValue("v", v.toString());
+        likelihoodReadCountModel.setInputValue("s", sParam);
+        likelihoodReadCountModel.setInputValue("w", w.toString());
 
         // ...
 
-        readCountModel.initAndValidate();
+        likelihoodReadCountModel.initAndValidate();
 
-        double observedLogP = readCountModel.calculateLogP();
+        double observedLogP = likelihoodReadCountModel.calculateLogP();
         double expectedLogP = -35.6331962985386;
 
         assertEquals(expectedLogP, observedLogP, DELTA);

diff --git a/phylonco-beast/version.xml b/phylonco-beast/version.xml
@@ -35,7 +35,7 @@
         <provider classname="phylonco.beast.evolution.populationmodel.GompertzGrowth_t50"/>
         <provider classname="phylonco.beast.evolution.populationmodel.ConstantGrowth"/>
         <provider classname="phylonco.beast.evolution.populationmodel.StochasticVariableSelection"/>
-        <provider classname="phylonco.beast.evolution.readcountmodel.ReadCountModel"/>
+        <provider classname="phylonco.beast.evolution.readcountmodel.LikelihoodReadCountModel"/>
         <provider classname="phylonco.beast.evolution.datatype.ReadCount"/>
     </service>