/**
* write log to screen
*
* @param writer XMLWriter
* @param branchRatesModelGenerator BranchRatesModelGenerator
*/
public void writeLogToScreen(
XMLWriter writer,
BranchRatesModelGenerator branchRatesModelGenerator,
SubstitutionModelGenerator substitutionModelGenerator) {
writer.writeComment("write log to screen");
writer.writeOpenTag(
LoggerParser.LOG,
new Attribute[] {
new Attribute.Default<String>(XMLParser.ID, "screenLog"),
new Attribute.Default<String>(LoggerParser.LOG_EVERY, options.echoEvery + "")
});
if (options.hasData()) {
writer.writeOpenTag(
ColumnsParser.COLUMN,
new Attribute[] {
new Attribute.Default<String>(ColumnsParser.LABEL, "Posterior"),
new Attribute.Default<String>(ColumnsParser.DECIMAL_PLACES, "4"),
new Attribute.Default<String>(ColumnsParser.WIDTH, "12")
});
writer.writeIDref(CompoundLikelihoodParser.POSTERIOR, "posterior");
writer.writeCloseTag(ColumnsParser.COLUMN);
}
writer.writeOpenTag(
ColumnsParser.COLUMN,
new Attribute[] {
new Attribute.Default<String>(ColumnsParser.LABEL, "Prior"),
new Attribute.Default<String>(ColumnsParser.DECIMAL_PLACES, "4"),
new Attribute.Default<String>(ColumnsParser.WIDTH, "12")
});
writer.writeIDref(CompoundLikelihoodParser.PRIOR, "prior");
writer.writeCloseTag(ColumnsParser.COLUMN);
if (options.hasData()) {
writer.writeOpenTag(
ColumnsParser.COLUMN,
new Attribute[] {
new Attribute.Default<String>(ColumnsParser.LABEL, "Likelihood"),
new Attribute.Default<String>(ColumnsParser.DECIMAL_PLACES, "4"),
new Attribute.Default<String>(ColumnsParser.WIDTH, "12")
});
writer.writeIDref(CompoundLikelihoodParser.LIKELIHOOD, "likelihood");
writer.writeCloseTag(ColumnsParser.COLUMN);
}
if (options.useStarBEAST) { // species
writer.writeOpenTag(
ColumnsParser.COLUMN,
new Attribute[] {
new Attribute.Default<String>(ColumnsParser.LABEL, "PopMean"),
new Attribute.Default<String>(ColumnsParser.DECIMAL_PLACES, "4"),
new Attribute.Default<String>(ColumnsParser.WIDTH, "12")
});
writer.writeIDref(
ParameterParser.PARAMETER,
TraitData.TRAIT_SPECIES + "." + options.starBEASTOptions.POP_MEAN);
writer.writeCloseTag(ColumnsParser.COLUMN);
}
for (PartitionTreeModel model : options.getPartitionTreeModels()) {
writer.writeOpenTag(
ColumnsParser.COLUMN,
new Attribute[] {
new Attribute.Default<String>(
ColumnsParser.LABEL, model.getPrefix() + TreeModelParser.ROOT_HEIGHT),
new Attribute.Default<String>(ColumnsParser.SIGNIFICANT_FIGURES, "6"),
new Attribute.Default<String>(ColumnsParser.WIDTH, "12")
});
writer.writeIDref(
ParameterParser.PARAMETER,
model.getPrefix() + TreeModel.TREE_MODEL + "." + TreeModelParser.ROOT_HEIGHT);
writer.writeCloseTag(ColumnsParser.COLUMN);
}
for (PartitionClockModel model : options.getPartitionClockModels()) {
writer.writeOpenTag(
ColumnsParser.COLUMN,
new Attribute[] {
new Attribute.Default<String>(
ColumnsParser.LABEL, branchRatesModelGenerator.getClockRateString(model)),
new Attribute.Default<String>(ColumnsParser.SIGNIFICANT_FIGURES, "6"),
new Attribute.Default<String>(ColumnsParser.WIDTH, "12")
});
branchRatesModelGenerator.writeAllClockRateRefs(model, writer);
// if (options.clockModelOptions.getRateOptionClockModel() == FixRateType.FIX_MEAN) {
// writer.writeIDref(ParameterParser.PARAMETER, "allClockRates");
// for (PartitionClockModel model : options.getPartitionClockModels()) {
// if (model.getClockType() == ClockType.UNCORRELATED_LOGNORMAL)
// writer.writeIDref(ParameterParser.PARAMETER, model.getPrefix() +
// ClockType.UCLD_STDEV);
// }
// } else {
// for (PartitionClockModel model : options.getPartitionClockModels()) {
// branchRatesModelGenerator.writeAllClockRateRefs(model, writer);
// }
// }
writer.writeCloseTag(ColumnsParser.COLUMN);
}
if (options.hasDiscreteIntegerTraitsExcludeSpecies()) {
for (PartitionSubstitutionModel model : options.getPartitionTraitsSubstitutionModels()) {
substitutionModelGenerator.writeStatisticLog(model, writer);
}
}
generateInsertionPoint(ComponentGenerator.InsertionPoint.IN_SCREEN_LOG, writer);
writer.writeCloseTag(LoggerParser.LOG);
generateInsertionPoint(ComponentGenerator.InsertionPoint.AFTER_SCREEN_LOG, writer);
}
