[beast-mcmc] r6737 committed - maybe Compund model is enough

[beast...@googlecode.com]

Revision: 6737
Author: fbielejec
Date: Wed Apr 15 14:12:08 2015 UTC
Log: maybe Compund model is enough
https://code.google.com/p/beast-mcmc/source/detail?r=6737

Modified:

/trunk/src/dr/app/beagle/evomodel/branchmodel/lineagespecific/BeagleBranchLikelihood.java

/trunk/src/dr/app/beagle/evomodel/branchmodel/lineagespecific/DirichletProcessOperator.java

=======================================
---
/trunk/src/dr/app/beagle/evomodel/branchmodel/lineagespecific/BeagleBranchLikelihood.java
Tue Apr 14 13:25:00 2015 UTC
+++
/trunk/src/dr/app/beagle/evomodel/branchmodel/lineagespecific/BeagleBranchLikelihood.java
Wed Apr 15 14:12:08 2015 UTC
@@ -8,9 +8,11 @@
import dr.evomodel.tree.TreeModel;
import dr.inference.loggers.LogColumn;
import dr.inference.loggers.NumberColumn;
+import dr.inference.model.CompoundModel;
import dr.inference.model.Likelihood;
import dr.inference.model.Model;
import dr.inference.model.Parameter;
+import dr.inference.model.Likelihood.Abstract;

@SuppressWarnings("serial")
public class BeagleBranchLikelihood implements Likelihood {
@@ -18,15 +20,19 @@
private TreeModel treeModel;
private List<Likelihood> uniqueLikelihoods;

- // size of z:
private List<Likelihood> branchLikelihoods;
private Parameter categoriesParameter;

private String id = null;
-
+ private boolean used = false;
+
// for discrete categories
private CountableBranchCategoryProvider categoriesProvider;

+ //TODO
+ private final CompoundModel compoundModel = new
CompoundModel("compoundModel");
+
+
public BeagleBranchLikelihood(TreeModel treeModel,
List<Likelihood> likelihoods,
Parameter categoriesParameter) {
@@ -50,7 +56,7 @@

public List<Likelihood> getBranchLikelihoods() {

- // TODO: if no tree then read them in supplied order
+ // linked list preserves order
List<Likelihood> loglikes = new LinkedList<Likelihood>();

if (treeModel != null) {
@@ -61,26 +67,30 @@

int branchCategory = categoriesProvider.getBranchCategory(
treeModel, branch);
- int zIndex = (int) categoriesParameter
+ int index = (int) categoriesParameter
.getParameterValue(branchCategory);

- Likelihood branchLikelihood = uniqueLikelihoods.get(zIndex);
+// System.out.println("branchCategory: " + branchCategory);
+// System.out.println("index: " + index);
+
+ Likelihood branchLikelihood = uniqueLikelihoods.get(index);

// branchLikelihoods.add(new
// Holder(branchLikelihood).value);
loglikes.add(branchLikelihood);
-
+ //TODO
+ compoundModel.addModel(branchLikelihood.getModel());
+
}
}// END: branch loop

- } else {
+ } else {// if no tree then read them in supplied order

int dim = categoriesParameter.getDimension();
if (dim != uniqueLikelihoods.size()) {
throw new RuntimeException("Dimensionality mismatch!");
- }
+ }// END: size of categoriesParameter check

- // TODO: does this preserve order? check!
loglikes.addAll(uniqueLikelihoods);

}// END: tree check
@@ -102,11 +112,16 @@
public double getLogLikelihood() {

double loglike = 0;
- for(Likelihood like : getBranchLikelihoods()) {
-
+// for(Likelihood like : getBranchLikelihoods()) {
+//
+// loglike += like.getLogLikelihood();
+//
+// }//END: loglikes loop
+
+ for(Likelihood like : branchLikelihoods) {
loglike += like.getLogLikelihood();
-
- }//END: loglikes loop
+ }
+

return loglike;
}//END: getLogLikelihood
@@ -127,52 +142,56 @@
public LogColumn[] getColumns() {
return new dr.inference.loggers.LogColumn[] { new LikelihoodColumn(
getId() == null ? "likelihood" : getId()) };
- }
+ }//END: getColumns

@Override
public String getId() {
return this.id;
- }
+ }//END: getId

@Override
public void setId(String id) {
this.id = id;
- }
+ }//END: setId

@Override
public Model getModel() {
- // TODO Auto-generated method stub
- return null;
+ // TODO
+//return null;
+ return compoundModel;
}


@Override
public void makeDirty() {
- // TODO Auto-generated method stub
+
+ for( Likelihood likelihood : uniqueLikelihoods ) {
+ likelihood.makeDirty();
+ }

- }
+ }//END: makeDirty

@Override
public String prettyName() {
- // TODO Auto-generated method stub
- return null;
- }
+ return Abstract.getPrettyName(this);
+ }//END: prettyName

@Override
public boolean isUsed() {
- // TODO Auto-generated method stub
- return false;
- }
+ return used;
+ }//END: isUsed

@Override
public void setUsed() {
- // TODO Auto-generated method stub
+ used = true;
+ for (Likelihood like : branchLikelihoods) {
+ like.setUsed();
+ }

- }
+ }//END: setUsed

@Override
public boolean evaluateEarly() {
- // TODO Auto-generated method stub
return false;
}

=======================================
---
/trunk/src/dr/app/beagle/evomodel/branchmodel/lineagespecific/DirichletProcessOperator.java
Tue Apr 14 13:25:00 2015 UTC
+++
/trunk/src/dr/app/beagle/evomodel/branchmodel/lineagespecific/DirichletProcessOperator.java
Wed Apr 15 14:12:08 2015 UTC
@@ -10,6 +10,10 @@
import dr.inference.operators.SimpleMCMCOperator;
import dr.math.MathUtils;

+
+/**
+ * @author Filip Bielejec
+ */
@SuppressWarnings("serial")
public class DirichletProcessOperator extends SimpleMCMCOperator implements
GibbsOperator {