[beast-mcmc] r4811 committed - More fixes

[beast...@googlecode.com]

Revision: 4811
Author: rambaut
Date: Fri Mar 9 07:49:10 2012
Log: More fixes
http://code.google.com/p/beast-mcmc/source/detail?r=4811

Modified:
/trunk/src/dr/evomodel/antigenic/AntigenicLikelihood.java

=======================================
--- /trunk/src/dr/evomodel/antigenic/AntigenicLikelihood.java Fri Mar 9
07:44:23 2012
+++ /trunk/src/dr/evomodel/antigenic/AntigenicLikelihood.java Fri Mar 9
07:49:10 2012
@@ -205,7 +205,7 @@
columnLabels.toArray(labelArray);

((Parameter.Abstract)this.columnEffectsParameter).setDimensionNames(labelArray);
for (int i = 0; i < maxColumnTitre.length; i++) {
- this.columnEffectsParameter.setParameterValue(i,
maxColumnTitre[i]);
+ this.columnEffectsParameter.setParameterValueQuietly(i,
maxColumnTitre[i]);
}

if (rowParameter == null) {
@@ -220,7 +220,7 @@
rowLabels.toArray(labelArray);

((Parameter.Abstract)this.rowEffectsParameter).setDimensionNames(labelArray);
for (int i = 0; i < maxRowTitre.length; i++) {
- this.rowEffectsParameter.setParameterValue(i, maxRowTitre[i]);
+ this.rowEffectsParameter.setParameterValueQuietly(i,
maxRowTitre[i]);
}

StringBuilder sb = new StringBuilder();
@@ -249,7 +249,8 @@
locationChanged = new
boolean[this.locationsParameter.getRowDimension()];
logLikelihoods = new double[measurements.size()];
storedLogLikelihoods = new double[measurements.size()];
- likelihoodKnown = false;
+
+ makeDirty();
}

protected void setupLocationsParameter(MatrixParameter
locationsParameter, List<String> strains) {
@@ -270,8 +271,11 @@
if (variable == locationsParameter) {
locationChanged[index / mdsDimension] = true;
} else if (variable == mdsPrecisionParameter) {
+ setLocationChangedFlags(true);
} else if (variable == columnEffectsParameter) {
+ setLocationChangedFlags(true);
} else if (variable == rowEffectsParameter) {
+ setLocationChangedFlags(true);
} else {
// could be a derived class's parameter
// throw new IllegalArgumentException("Unknown parameter");
@@ -354,14 +358,14 @@

likelihoodKnown = true;

- clearLocationChangedFlags();
+ setLocationChangedFlags(false);

return logLikelihood;
}

- private void clearLocationChangedFlags() {
+ private void setLocationChangedFlags(boolean flag) {
for (int i = 0; i < locationChanged.length; i++) {
- locationChanged[i] = false;
+ locationChanged[i] = flag;
}
}

@@ -448,7 +452,8 @@
@Override
public void makeDirty() {
likelihoodKnown = false;
- }
+ setLocationChangedFlags(true);
+ }

private class Measurement {
private Measurement(final int column, final int columnStrain,
final int row, final int rowStrain, final MeasurementType type, final
double minTitre, final double maxTitre) {