Example 1 with XMLWriter
use of dr.app.beauti.util.XMLWriter in project beast-mcmc by beast-dev.
the class GetDateFromTree method outputBDSSXML.
private static void outputBDSSXML(String curD, int index, double[][] tips, double[] origin, Tree[] trees) throws IOException {
XMLWriter w = writeHeadAndTaxa(curD, index, tips);
w.flush();
w.writeText("\t<!-- Stadler et al (2011) : Estimating the basic reproductive number from viral sequence data, Submitted.-->\n" + // logTransformed=\"true\">\n" +
"\t<birthDeathSerialSampling id=\"bdss\" units=\"substitutions\" hasFinalSample=\"false\">\n" + "\t\t<birthRate>\n" + "\t\t\t<parameter id=\"bdss.birthRate\" value=\"8.23E-4\" lower=\"0.0\" upper=\"1000.0\"/>\n" + "\t\t</birthRate>\n");
if (isRelativeDeath) {
w.writeText("\t\t<relativeDeathRate>\n" + "\t\t\t<parameter id=\"bdss.relativeDeathRate\" value=\"0.107\" lower=\"0.0\" upper=\"100.0\"/>\n" + "\t\t</relativeDeathRate>\n");
} else {
w.writeText("\t\t<deathRate>\n" + "\t\t\t<parameter id=\"bdss.deathRate\" value=\"9.46e-5\" lower=\"0.0\" upper=\"1000.0\"/>\n" + "\t\t</deathRate>\n");
}
w.writeText("\t\t<sampleProbability>\n" + "\t\t\t<parameter id=\"bdss.sampleProbability\" value=\"0.01\" lower=\"0.0\" upper=\"1.0\"/>\n" + "\t\t</sampleProbability>\n" + "\t\t<psi>\n" + "\t\t\t<parameter id=\"bdss.psi\" value=\"2.78E-4\" lower=\"0.0\" upper=\"100.0\"/>\n" + "\t\t</psi>\n" + "\t\t<origin>\n" + "\t\t\t<parameter id=\"bdss.origin\" value=\"" + origin[0] + "\" lower=\"0.0\" upper=\"14000.0\"/>\n" + "\t\t</origin>\n" + "\t\t<sampleBecomesNonInfectiousProb>\n" + "\t\t\t<parameter id=\"bdss.r\" value=\"1.0\"/>\n" + "\t\t</sampleBecomesNonInfectiousProb>\n" + "\t</birthDeathSerialSampling>\n");
for (int tree = 2; tree <= combiTrees; tree++) {
w.writeText("\t<!-- Stadler et al (2011) : Estimating the basic reproductive number from viral sequence data, Submitted.-->\n" + "\t<birthDeathSerialSampling id=\"bdss" + tree + // logTransformed=\"true\">\n" +
"\" units=\"substitutions\" hasFinalSample=\"false\">\n" + "\t\t<birthRate>\n" + "\t\t\t<parameter idref=\"bdss.birthRate\"/>\n" + "\t\t</birthRate>\n");
if (isRelativeDeath) {
w.writeText("\t\t<relativeDeathRate>\n" + "\t\t\t<parameter idref=\"bdss.relativeDeathRate\"/>\n" + "\t\t</relativeDeathRate>\n");
} else {
w.writeText("\t\t<deathRate>\n" + "\t\t\t<parameter idref=\"bdss.deathRate\"/>\n" + "\t\t</deathRate>\n");
}
w.writeText("\t\t<sampleProbability>\n" + "\t\t\t<parameter idref=\"bdss.sampleProbability\"/>\n" + "\t\t</sampleProbability>\n" + "\t\t<psi>\n" + "\t\t\t<parameter idref=\"bdss.psi\"/>\n" + "\t\t</psi>\n" + "\t\t<origin>\n" + "\t\t\t<parameter id=\"bdss" + tree + ".origin\" value=\"" + origin[tree - 1] + "\" lower=\"0.0\" upper=\"14000.0\"/>\n" + "\t\t</origin>\n" + "\t\t<sampleBecomesNonInfectiousProb>\n" + "\t\t\t<parameter idref=\"bdss.r\"/>\n" + "\t\t</sampleBecomesNonInfectiousProb>\n" + "\t</birthDeathSerialSampling>\n");
}
w.flush();
// w.writeText("\t<RPNcalculator id=\"mur\">\n" +
// "\t\t<variable name=\"b\">\n" +
// "\t\t\t<parameter idref=\"bdss.birthRate\"/>\n" +
// "\t\t</variable>\n" +
// "\t\t<variable name=\"d\">\n" +
// "\t\t\t<parameter idref=\"bdss.deathRate\"/>\n" +
// "\t\t</variable>\n" +
// "\t\t<expression name=\"mur\">d b /</expression> <!-- d/b -->\n" +
// "\t</RPNcalculator>\n" +
// "\t<RPNcalculator id=\"R0\">\n" +
// "\t\t<variable name=\"b\">\n" +
// "\t\t\t<parameter idref=\"bdss.birthRate\"/>\n" +
// "\t\t</variable>\n" +
// "\t\t<variable name=\"d\">\n" +
// "\t\t\t<parameter idref=\"bdss.deathRate\"/>\n" +
// "\t\t</variable>\n" +
// "\t\t<variable name=\"s\">\n" +
// "\t\t\t<parameter idref=\"bdss.psi\"/>\n" +
// "\t\t</variable>\n" +
// "\t\t<variable name=\"r\">\n" +
// "\t\t\t<parameter idref=\"bdss.r\"/>\n" +
// "\t\t</variable>\n" +
// "\t\t<expression name=\"R0\">b d s r * + /</expression> <!-- b/(d+s*r) -->\n" +
// "\t</RPNcalculator>\n");
// w.writeText("\t<RPNcalculator id=\"td\">\n" +
// "\t\t<variable name=\"d\">\n" +
// "\t\t\t<parameter idref=\"bdss.deathRate\"/>\n" +
// "\t\t</variable>\n" +
// "\t\t<variable name=\"s\">\n" +
// "\t\t\t<parameter idref=\"bdss.psi\"/>\n" +
// "\t\t</variable>\n" +
// "\t\t<expression name=\"td\">d s + </expression> <!-- d + s -->\n" +
// "\t</RPNcalculator>\n");
// w.writeText("\t<RPNcalculator id=\"expp\">\n" +
// "\t\t<variable name=\"p\">\n" +
// "\t\t\t<parameter idref=\"bdss.psi\"/>\n" +
// "\t\t</variable>\n" +
// "\t\t<expression name=\"expp\">\n" +
// "\t\t\tp exp\n" +
// "\t\t</expression>\n" +
// "\t</RPNcalculator>\n");
// for (int tree = 2; tree <= combiTrees; tree++) {
// w.writeText("\t<RPNcalculator id=\"R0" + tree + "\">\n" +
// "\t\t<variable name=\"b\">\n" +
// "\t\t\t<parameter idref=\"bdss" + tree + ".birthRate\"/>\n" +
// "\t\t</variable>\n" +
// "\t\t<variable name=\"d\">\n" +
// "\t\t\t<parameter idref=\"bdss" + tree + ".deathRate\"/>\n" +
// "\t\t</variable>\n" +
// "\t\t<variable name=\"s\">\n" +
// "\t\t\t<parameter idref=\"bdss" + tree + ".psi\"/>\n" +
// "\t\t</variable>\n" +
// "\t\t<variable name=\"r\">\n" +
// "\t\t\t<parameter idref=\"bdss.r\"/>\n" +
// "\t\t</variable>\n" +
// "\t\t<expression name=\"R0" + tree + "\">\n" +
// "\t\t\tb b d * s r * + /\n" +
// "\t\t</expression>\n" +
// "\t</RPNcalculator>\n");
// }
w.flush();
w.writeText("\n" + "\t<!-- Generate a random starting tree under the coalescent process -->\n" + "\t<newick id=\"startingTree\">\n");
w.write(trees[0].toString());
w.writeText("\n" + "\t</newick>\n");
w.flush();
for (int tree = 2; tree <= combiTrees; tree++) {
w.writeText("\n" + "\t<!-- Generate a random starting tree under the coalescent process -->\n" + "\t<newick id=\"startingTree" + tree + "\">\n");
w.write(insetTreeIndex(tree, trees[tree - 1].toString()));
w.writeText("\n" + "\t</newick>\n");
w.flush();
}
w.writeText("\n" + "\t<!-- Generate a tree model -->\n" + "\t<treeModel id=\"treeModel\">\n" + "\t\t<coalescentTree idref=\"startingTree\"/>\n" + "\t\t<rootHeight>\n" + "\t\t\t<parameter id=\"treeModel.rootHeight\"/>\n" + "\t\t</rootHeight>\n" + "\t\t<nodeHeights internalNodes=\"true\">\n" + "\t\t\t<parameter id=\"treeModel.internalNodeHeights\"/>\n" + "\t\t</nodeHeights>\n" + "\t\t<nodeHeights internalNodes=\"true\" rootNode=\"true\">\n" + "\t\t\t<parameter id=\"treeModel.allInternalNodeHeights\"/>\n" + "\t\t</nodeHeights>\n" + "\n" + "\t\t<!-- END Tip date sampling -->\n" + "\t</treeModel>\n");
for (int tree = 2; tree <= combiTrees; tree++) {
w.writeText("\n" + "\t<!-- Generate a tree model -->\n" + "\t<treeModel id=\"treeModel" + tree + "\">\n" + "\t\t<coalescentTree idref=\"startingTree" + tree + "\"/>\n" + "\t\t<rootHeight>\n" + "\t\t\t<parameter id=\"treeModel" + tree + ".rootHeight\"/>\n" + "\t\t</rootHeight>\n" + "\t\t<nodeHeights internalNodes=\"true\">\n" + "\t\t\t<parameter id=\"treeModel" + tree + ".internalNodeHeights\"/>\n" + "\t\t</nodeHeights>\n" + "\t\t<nodeHeights internalNodes=\"true\" rootNode=\"true\">\n" + "\t\t\t<parameter id=\"treeModel" + tree + ".allInternalNodeHeights\"/>\n" + "\t\t</nodeHeights>\n" + "\n" + "\t\t<!-- END Tip date sampling -->\n" + "\t</treeModel>\n");
}
w.flush();
w.writeText("\n" + "\t<!-- Generate a speciation likelihood for Yule or Birth Death -->\n" + "\t<speciationLikelihood id=\"speciation\">\n" + "\t\t<model>\n" + "\t\t\t<birthDeathSerialSampling idref=\"bdss\"/>\n" + "\t\t</model>\n" + "\t\t<speciesTree>\n" + "\t\t\t<treeModel idref=\"treeModel\"/>\n" + "\t\t</speciesTree>\n" + "\t</speciationLikelihood>\n");
for (int tree = 2; tree <= combiTrees; tree++) {
w.writeText("\n" + "\t<!-- Generate a speciation likelihood for Yule or Birth Death -->\n" + "\t<speciationLikelihood id=\"speciation" + tree + "\">\n" + "\t\t<model>\n" + "\t\t\t<birthDeathSerialSampling idref=\"bdss" + tree + "\"/>\n" + "\t\t</model>\n" + "\t\t<speciesTree>\n" + "\t\t\t<treeModel idref=\"treeModel" + tree + "\"/>\n" + "\t\t</speciesTree>\n" + "\t</speciationLikelihood>\n");
}
w.writeText("\n" + "\t<!-- Define operators -->\n" + "\t<operators id=\"operators\">\n" + // "\t\t</randomWalkOperator>\n" +
"\t\t<scaleOperator scaleFactor=\"0.75\" weight=\"10\">\n" + "\t\t\t<parameter idref=\"bdss.birthRate\"/>\n" + "\t\t</scaleOperator>\n" + "\t\t<scaleOperator scaleFactor=\"0.75\" weight=\"10\">\n");
if (isRelativeDeath) {
w.writeText("\t\t\t<parameter idref=\"bdss.relativeDeathRate\"/>\n");
} else {
w.writeText("\t\t\t<parameter idref=\"bdss.deathRate\"/>\n");
}
w.writeText("\t\t</scaleOperator>\n");
if (!isRelativeDeath) {
w.writeText("\t\t<upDownOperator scaleFactor=\"0.75\" weight=\"10\">\n" + "\t\t\t<up>\n" + "\t\t\t\t<parameter idref=\"bdss.birthRate\"/>\n" + "\t\t\t\t<parameter idref=\"bdss.deathRate\"/>\n" + "\t\t\t</up>\n" + "\t\t\t<down/>\n" + "\t\t</upDownOperator>\n");
}
// "\t\t<randomWalkOperator windowSize=\"1.0\" weight=\"10\">\n" +
// "\t\t\t<parameter idref=\"bdss.psi\"/>\n" +
// "\t\t</randomWalkOperator>\n" +
// "\t\t<scaleOperator scaleFactor=\"0.75\" weight=\"10\">\n" +
// "\t\t\t<parameter idref=\"bdss.psi\"/>\n" +
// "\t\t</scaleOperator>\n"+
w.writeText("\t\t<scaleOperator scaleFactor=\"0.75\" weight=\"10\">\n" + "\t\t\t<parameter idref=\"bdss.origin\"/>\n" + "\t\t</scaleOperator>\n");
for (int tree = 2; tree <= combiTrees; tree++) {
w.writeText("\n" + // "\t\t</scaleOperator>\n" +
"\t\t<scaleOperator scaleFactor=\"0.75\" weight=\"10\">\n" + "\t\t\t<parameter idref=\"bdss" + tree + ".origin\"/>\n" + "\t\t</scaleOperator>\n");
}
w.writeText("\n" + "\t</operators>");
w.flush();
w.writeText("\n" + "\t<!-- Define MCMC -->\n" + "\t<mcmc id=\"mcmc\" chainLength=\"10000000\" autoOptimize=\"true\">\n" + "\t\t<posterior id=\"posterior\">\n" + "\t\t\t<prior id=\"prior\">\n" + "\t\t\t\t<uniformPrior lower=\"0.0\" upper=\"1000.0\">\n" + "\t\t\t\t\t<parameter idref=\"bdss.birthRate\"/>\n" + "\t\t\t\t</uniformPrior>\n");
// "\t\t\t\t</oneOnXPrior>\n" +
if (isRelativeDeath) {
w.writeText("\t\t\t\t<uniformPrior lower=\"0.0\" upper=\"100.0\">\n" + "\t\t\t<parameter idref=\"bdss.relativeDeathRate\"/>\n");
} else {
w.writeText("\t\t\t\t<uniformPrior lower=\"0.0\" upper=\"1000.0\">\n" + "\t\t\t<parameter idref=\"bdss.deathRate\"/>\n");
}
w.writeText("\t\t\t\t</uniformPrior>\n");
// "\t\t\t\t<oneOnXPrior>\n" +
// "\t\t\t\t\t<parameter idref=\"bdss.psi\"/>\n" +
// "\t\t\t\t</oneOnXPrior>\n" +
// for (int tree = 2; tree <= combiTrees; tree++) {
// w.writeText("\t\t\t\t<uniformPrior lower=\"0.0\" upper=\"100000.0\">\n" +
// "\t\t\t\t\t<parameter idref=\"bdss" + tree + ".birthRate\"/>\n" +
// "\t\t\t\t</uniformPrior>\n" +
// "\t\t\t\t<uniformPrior lower=\"0.0\" upper=\"1000.0\">\n" +
// "\t\t\t\t\t<parameter idref=\"bdss" + tree + ".deathRate\"/>\n" +
// "\t\t\t\t</uniformPrior>\n" +
// "\t\t\t\t<uniformPrior lower=\"0.0\" upper=\"100.0\">\n" +
// "\t\t\t\t\t<parameter idref=\"bdss" + tree + ".psi\"/>\n" +
// "\t\t\t\t</uniformPrior>\n");
// }
w.writeText("\n" + "\t\t\t\t<uniformPrior lower=\"0.0\" upper=\"1.7976931348623157E308\">\n" + "\t\t\t\t\t<parameter idref=\"bdss.origin\"/>\n" + "\t\t\t\t</uniformPrior>\n");
for (int tree = 2; tree <= combiTrees; tree++) {
w.writeText("\n" + "\t\t\t\t<uniformPrior lower=\"0.0\" upper=\"1.7976931348623157E308\">\n" + "\t\t\t\t\t<parameter idref=\"bdss" + tree + ".origin\"/>\n" + "\t\t\t\t</uniformPrior>\n");
}
w.writeText("\n" + "\t\t\t</prior>\n" + "\t\t\t<likelihood id=\"likelihood\">\n" + "\t\t\t\t<speciationLikelihood idref=\"speciation\"/>\n");
for (int tree = 2; tree <= combiTrees; tree++) {
w.writeText("\t\t\t\t<speciationLikelihood idref=\"speciation" + tree + "\"/>\n");
}
w.writeText("\t\t\t</likelihood>\n" + "\t\t</posterior>\n" + "\t\t<operators idref=\"operators\"/>\n");
w.flush();
w.writeText("\n" + "\t\t<!-- write log to screen -->\n" + "\t\t<log id=\"screenLog\" logEvery=\"100000\">\n" + "\t\t\t<column label=\"Posterior\" dp=\"4\" width=\"12\">\n" + "\t\t\t\t<posterior idref=\"posterior\"/>\n" + "\t\t\t</column>\n" + "\t\t\t<column label=\"Prior\" dp=\"4\" width=\"12\">\n" + "\t\t\t\t<prior idref=\"prior\"/>\n" + "\t\t\t</column>\n" + "\t\t\t<column label=\"speciation\" dp=\"4\" width=\"12\">\n" + "\t\t\t\t<likelihood idref=\"speciation\"/>\n" + "\t\t\t</column>\n" + "\t\t\t<column label=\"rootHeight\" sf=\"6\" width=\"12\">\n" + "\t\t\t\t<parameter idref=\"treeModel.rootHeight\"/>\n" + "\t\t\t</column>\n" + "\t\t\t<parameter idref=\"bdss.birthRate\"/>\n");
if (isRelativeDeath) {
w.writeText("\t\t\t<parameter idref=\"bdss.relativeDeathRate\"/>\n");
} else {
w.writeText("\t\t\t<parameter idref=\"bdss.deathRate\"/>\n");
}
w.writeText("\t\t\t<parameter idref=\"bdss.psi\"/>\n" + "\t\t\t<parameter idref=\"bdss.r\"/>\n");
for (int tree = 2; tree <= combiTrees; tree++) {
w.writeText("\t\t\t<parameter idref=\"treeModel" + tree + ".rootHeight\"/>\n" + // "\t\t\t<RPNcalculator idref=\"R0" + tree + "\"/>\n" +
"\t\t\t<parameter idref=\"bdss" + tree + ".origin\"/>\n");
}
w.writeText("\t\t</log>\n" + "\n" + "\t\t<!-- write log to file -->\n" + "\t\t<log id=\"fileLog\" logEvery=\"1000\" fileName=\"T" + curD + "_" + Integer.toString(index) + ".log\" overwrite=\"false\">\n" + "\t\t\t<posterior idref=\"posterior\"/>\n" + "\t\t\t<prior idref=\"prior\"/>\n" + "\t\t\t<parameter idref=\"treeModel.rootHeight\"/>\n" + "\t\t\t<parameter idref=\"bdss.birthRate\"/>\n");
if (isRelativeDeath) {
w.writeText("\t\t\t<parameter idref=\"bdss.relativeDeathRate\"/>\n");
} else {
w.writeText("\t\t\t<parameter idref=\"bdss.deathRate\"/>\n");
}
w.writeText("\t\t\t<parameter idref=\"bdss.sampleProbability\"/>\n" + "\t\t\t<parameter idref=\"bdss.psi\"/>\n" + "\t\t\t<parameter idref=\"bdss.origin\"/>\n" + "\t\t\t<parameter idref=\"bdss.r\"/>\n");
for (int tree = 2; tree <= combiTrees; tree++) {
w.writeText("\t\t\t<parameter idref=\"treeModel" + tree + ".rootHeight\"/>\n" + // "\t\t\t<RPNcalculator idref=\"R0" + tree + "\"/>\n" +
"\t\t\t<parameter idref=\"bdss" + tree + ".origin\"/>\n");
}
w.writeText("\n" + "\t\t\t<speciationLikelihood idref=\"speciation\"/>\n");
for (int tree = 2; tree <= combiTrees; tree++) {
w.writeText("\t\t\t\t<speciationLikelihood idref=\"speciation" + tree + "\"/>\n");
}
w.writeText("\t\t</log>\n" + "\n" + // "\t\t</logTree>\n" +
"\t</mcmc>\n" + "\t<report>\n" + "\t\t<property name=\"timer\">\n" + "\t\t\t<mcmc idref=\"mcmc\"/>\n" + "\t\t</property>\n" + "\t</report>\n" + "</beast>\n");
w.flush();
w.close();
}
Also used :
XMLWriter(dr.app.beauti.util.XMLWriter)
Example 2 with XMLWriter
use of dr.app.beauti.util.XMLWriter in project beast-mcmc by beast-dev.
the class GetDateFromTree method outputExponetialXML.
private static void outputExponetialXML(String curD, int index, double[][] tips, double[] origin, Tree[] trees) throws IOException {
XMLWriter w = writeHeadAndTaxa(curD, index, tips);
w.flush();
w.writeText("\n" + "\t<exponentialGrowth id=\"exponential\" units=\"years\">\n" + "\t\t<populationSize>\n" + "\t\t\t<parameter id=\"exponential.popSize\" value=\"100.0\" lower=\"0.0\" upper=\"Infinity\"/>\n" + "\t\t</populationSize>\n" + "\t\t<growthRate>\n" + "\t\t\t<parameter id=\"exponential.growthRate\" value=\"4.50E-4\" lower=\"-Infinity\" upper=\"Infinity\"/>\n" + "\t\t</growthRate>\n" + "\t</exponentialGrowth>\n");
for (int tree = 2; tree <= combiTrees; tree++) {
w.writeText("\n" + "\t<exponentialGrowth id=\"exponential" + tree + "\" units=\"years\">\n" + "\t\t<populationSize>\n" + "\t\t\t<parameter id=\"exponential" + tree + ".popSize\" value=\"100.0\" lower=\"0.0\" upper=\"Infinity\"/>\n" + "\t\t</populationSize>\n" + "\t\t<growthRate>\n" + "\t\t\t<parameter idref=\"exponential.growthRate\"/>\n" + "\t\t</growthRate>\n" + "\t</exponentialGrowth>\n");
}
w.flush();
w.writeText("\n" + "\t<!-- Generate a random starting tree under the coalescent process -->\n" + "\t<newick id=\"startingTree\">\n");
w.write(trees[0].toString());
w.writeText("\n" + "\t</newick>\n");
w.flush();
for (int tree = 2; tree <= combiTrees; tree++) {
w.writeText("\n" + "\t<!-- Generate a random starting tree under the coalescent process -->\n" + "\t<newick id=\"startingTree" + tree + "\">\n");
w.write(insetTreeIndex(tree, trees[tree - 1].toString()));
w.writeText("\n" + "\t</newick>\n");
w.flush();
}
w.writeText("\n" + "\t<!-- Generate a tree model -->\n" + "\t<treeModel id=\"treeModel\">\n" + "\t\t<coalescentTree idref=\"startingTree\"/>\n" + "\t\t<rootHeight>\n" + "\t\t\t<parameter id=\"treeModel.rootHeight\"/>\n" + "\t\t</rootHeight>\n" + "\t\t<nodeHeights internalNodes=\"true\">\n" + "\t\t\t<parameter id=\"treeModel.internalNodeHeights\"/>\n" + "\t\t</nodeHeights>\n" + "\t\t<nodeHeights internalNodes=\"true\" rootNode=\"true\">\n" + "\t\t\t<parameter id=\"treeModel.allInternalNodeHeights\"/>\n" + "\t\t</nodeHeights>\n" + "\n" + "\t\t<!-- END Tip date sampling -->\n" + "\t</treeModel>\n");
for (int tree = 2; tree <= combiTrees; tree++) {
w.writeText("\n" + "\t<!-- Generate a tree model -->\n" + "\t<treeModel id=\"treeModel" + tree + "\">\n" + "\t\t<coalescentTree idref=\"startingTree" + tree + "\"/>\n" + "\t\t<rootHeight>\n" + "\t\t\t<parameter id=\"treeModel" + tree + ".rootHeight\"/>\n" + "\t\t</rootHeight>\n" + "\t\t<nodeHeights internalNodes=\"true\">\n" + "\t\t\t<parameter id=\"treeModel" + tree + ".internalNodeHeights\"/>\n" + "\t\t</nodeHeights>\n" + "\t\t<nodeHeights internalNodes=\"true\" rootNode=\"true\">\n" + "\t\t\t<parameter id=\"treeModel" + tree + ".allInternalNodeHeights\"/>\n" + "\t\t</nodeHeights>\n" + "\n" + "\t\t<!-- END Tip date sampling -->\n" + "\t</treeModel>\n");
}
w.flush();
w.writeText("\n" + "\t<coalescentLikelihood id=\"coalescent\">\n" + "\t\t<model>\n" + "\t\t\t<exponentialGrowth idref=\"exponential\"/>\n" + "\t\t</model>\n" + "\t\t<populationTree>\n" + "\t\t\t<treeModel idref=\"treeModel\"/>\n" + "\t\t</populationTree>\n" + "\t</coalescentLikelihood>\n");
for (int tree = 2; tree <= combiTrees; tree++) {
w.writeText("\n" + "\t<coalescentLikelihood id=\"coalescent" + tree + "\">\n" + "\t\t<model>\n" + "\t\t\t<exponentialGrowth idref=\"exponential" + tree + "\"/>\n" + "\t\t</model>\n" + "\t\t<populationTree>\n" + "\t\t\t<treeModel idref=\"treeModel" + tree + "\"/>\n" + "\t\t</populationTree>\n" + "\t</coalescentLikelihood>\n");
}
w.writeText("\n" + "\t<!-- Define operators -->\n" + "\t<operators id=\"operators\">\n" + "\t<randomWalkOperator windowSize=\"1.0\" weight=\"10\">\n" + "\t\t<parameter idref=\"exponential.growthRate\"/>\n" + "\t</randomWalkOperator>\n" + "\t<scaleOperator scaleFactor=\"0.75\" weight=\"10\">\n" + "\t\t<parameter idref=\"exponential.popSize\"/>\n" + "\t</scaleOperator>\n");
for (int tree = 2; tree <= combiTrees; tree++) {
w.writeText("\n" + "\t<scaleOperator scaleFactor=\"0.75\" weight=\"10\">\n" + "\t\t<parameter idref=\"exponential" + tree + ".popSize\"/>\n" + "\t</scaleOperator>\n");
}
w.writeText("\n" + "\t</operators>");
w.flush();
w.writeText("\n" + "\t<!-- Define MCMC -->\n" + "\t<mcmc id=\"mcmc\" chainLength=\"10000000\" autoOptimize=\"true\">\n" + "\t\t<posterior id=\"posterior\">\n" + "\t\t\t<prior id=\"prior\">\n" + "\t\t\t\t<oneOnXPrior>\n" + "\t\t\t\t\t<parameter idref=\"exponential.popSize\"/>\n");
for (int tree = 2; tree <= combiTrees; tree++) {
w.writeText("\t\t\t\t\t<parameter idref=\"exponential" + tree + ".popSize\"/>\n");
}
w.writeText("\t\t\t\t</oneOnXPrior>\n" + "\n" + "\t\t\t\t<laplacePrior mean=\"0.0010\" scale=\"2.0467423048835964E-4\">\n" + "\t\t\t\t\t<parameter idref=\"exponential.growthRate\"/>\n" + "\t\t\t\t</laplacePrior>\n" + "\t\t\t\t<coalescentLikelihood idref=\"coalescent\"\n/>");
for (int tree = 2; tree <= combiTrees; tree++) {
w.writeText("\t\t\t\t<coalescentLikelihood idref=\"coalescent" + tree + "\"/>\n");
}
w.writeText("\n" + "\t\t\t</prior>\n" + "\t\t</posterior>\n" + "\t\t<operators idref=\"operators\"/>\n");
w.flush();
w.writeText("\n" + "\t\t<!-- write log to screen -->\n" + "\t\t<log id=\"screenLog\" logEvery=\"100000\">\n" + "\t\t\t<column label=\"Posterior\" dp=\"4\" width=\"12\">\n" + "\t\t\t\t<posterior idref=\"posterior\"/>\n" + "\t\t\t</column>\n" + "\t\t\t<column label=\"Prior\" dp=\"4\" width=\"12\">\n" + "\t\t\t\t<prior idref=\"prior\"/>\n" + "\t\t\t</column>\n" + "\t\t\t<column label=\"coalescentLikelihood\" dp=\"4\" width=\"12\">\n" + "\t\t\t\t<coalescentLikelihood idref=\"coalescent\"/>\n" + "\t\t\t</column>\n" + "\t\t\t<column label=\"rootHeight\" sf=\"6\" width=\"12\">\n" + "\t\t\t\t<parameter idref=\"treeModel.rootHeight\"/>\n" + "\t\t\t</column>\n" + "\t\t\t<parameter idref=\"exponential.growthRate\"/>\n" + "\t\t\t<parameter idref=\"exponential.popSize\"/>\n");
for (int tree = 2; tree <= combiTrees; tree++) {
w.writeText("\t\t\t<parameter idref=\"treeModel" + tree + ".rootHeight\"/>\n" + "\t\t\t<parameter idref=\"exponential" + tree + ".popSize\"/>\n");
}
w.writeText("\t\t</log>\n" + "\n" + "\t\t<!-- write log to file -->\n" + "\t\t<log id=\"fileLog\" logEvery=\"1000\" fileName=\"E" + curD + "_" + Integer.toString(index) + ".log\" overwrite=\"false\">\n" + "\t\t\t<posterior idref=\"posterior\"/>\n" + "\t\t\t<prior idref=\"prior\"/>\n" + "\t\t\t<parameter idref=\"treeModel.rootHeight\"/>\n" + "\t\t\t<parameter idref=\"exponential.growthRate\"/>\n" + "\t\t\t<parameter idref=\"exponential.popSize\"/>\n");
for (int tree = 2; tree <= combiTrees; tree++) {
w.writeText("\t\t\t<parameter idref=\"treeModel" + tree + ".rootHeight\"/>\n" + "\t\t\t<parameter idref=\"exponential" + tree + ".popSize\"/>\n");
}
w.writeText("\n" + "\t\t\t<coalescentLikelihood idref=\"coalescent\"/>\n");
for (int tree = 2; tree <= combiTrees; tree++) {
w.writeText("\t\t\t\t<coalescentLikelihood idref=\"coalescent" + tree + "\"/>\n");
}
w.writeText("\t\t</log>\n" + "\n" + // "\t\t</logTree>\n" +
"\t</mcmc>\n" + "\t<report>\n" + "\t\t<property name=\"timer\">\n" + "\t\t\t<mcmc idref=\"mcmc\"/>\n" + "\t\t</property>\n" + "\t</report>\n" + "</beast>\n");
w.flush();
w.close();
}
Also used :
XMLWriter(dr.app.beauti.util.XMLWriter)
Example 3 with XMLWriter
use of dr.app.beauti.util.XMLWriter in project beast-mcmc by beast-dev.
the class BeastGenerator method generateXML.
/**
* Generate a beast xml file from these beast options
*
* @param file File
* @throws java.io.IOException IOException
* @throws dr.app.util.Arguments.ArgumentException
* ArgumentException
*/
public void generateXML(File file) throws GeneratorException, IOException, Arguments.ArgumentException {
XMLWriter writer = new XMLWriter(new BufferedWriter(new FileWriter(file)));
writer.writeText("<?xml version=\"1.0\" standalone=\"yes\"?>");
writer.writeComment("Generated by BEAUTi " + VERSION.getVersionString(), " by Alexei J. Drummond, Andrew Rambaut and Marc A. Suchard", " Department of Computer Science, University of Auckland and", " Institute of Evolutionary Biology, University of Edinburgh", " David Geffen School of Medicine, University of California, Los Angeles", " http://beast.community/");
writer.writeOpenTag("beast", new Attribute.Default<String>("version", BeautiApp.VERSION.getVersion()));
writer.writeText("");
// this gives any added implementations of the 'Component' interface a
// chance to generate XML at this point in the BEAST file.
generateInsertionPoint(ComponentGenerator.InsertionPoint.BEFORE_TAXA, writer);
if (options.originDate != null) {
// Create a dummy taxon whose job is to specify the origin date
Taxon originTaxon = new Taxon("originTaxon");
options.originDate.setUnits(options.units);
originTaxon.setDate(options.originDate);
writeTaxon(originTaxon, true, false, writer);
}
// ++++++++++++++++ Taxon List ++++++++++++++++++
try {
// write complete taxon list
writeTaxa(options.taxonList, writer);
writer.writeText("");
if (!options.hasIdenticalTaxa()) {
// write all taxa in each gene tree regarding each data partition,
for (AbstractPartitionData partition : options.dataPartitions) {
if (partition.getTaxonList() != null) {
writeDifferentTaxa(partition, writer);
}
}
} else {
// microsat
for (PartitionPattern partitionPattern : options.getPartitionPattern()) {
if (partitionPattern.getTaxonList() != null && partitionPattern.getPatterns().hasMask()) {
writeDifferentTaxa(partitionPattern, writer);
}
}
}
} catch (Exception e) {
e.printStackTrace(System.err);
throw new GeneratorException("Taxon list generation has failed:\n" + e.getMessage());
}
// ++++++++++++++++ Taxon Sets ++++++++++++++++++
List<Taxa> taxonSets = options.taxonSets;
try {
if (taxonSets != null && taxonSets.size() > 0) {
tmrcaStatisticsGenerator.writeTaxonSets(writer, taxonSets);
}
} catch (Exception e) {
e.printStackTrace();
throw new GeneratorException("Taxon sets generation has failed:\n" + e.getMessage());
}
generateInsertionPoint(ComponentGenerator.InsertionPoint.AFTER_TAXA, writer);
// ++++++++++++++++ Alignments ++++++++++++++++++
List<Alignment> alignments = new ArrayList<Alignment>();
try {
for (AbstractPartitionData partition : options.dataPartitions) {
Alignment alignment = null;
if (partition instanceof PartitionData) {
// microsat has no alignment
alignment = ((PartitionData) partition).getAlignment();
}
if (alignment != null && !alignments.contains(alignment)) {
alignments.add(alignment);
}
}
if (alignments.size() > 0) {
alignmentGenerator.writeAlignments(alignments, writer);
generateInsertionPoint(ComponentGenerator.InsertionPoint.AFTER_SEQUENCES, writer);
}
} catch (Exception e) {
e.printStackTrace();
throw new GeneratorException("Alignments generation has failed:\n" + e.getMessage());
}
// ++++++++++++++++ Pattern Lists ++++++++++++++++++
try {
// Construct pattern lists even if sampling from a null alignment
// if (!options.samplePriorOnly) {
List<Microsatellite> microsatList = new ArrayList<Microsatellite>();
for (AbstractPartitionData partition : options.dataPartitions) {
// Each PD has one TreeLikelihood
if (partition.getTaxonList() != null) {
switch(partition.getDataType().getType()) {
case DataType.NUCLEOTIDES:
case DataType.AMINO_ACIDS:
case DataType.CODONS:
case DataType.COVARION:
case DataType.TWO_STATES:
patternListGenerator.writePatternList((PartitionData) partition, writer);
break;
case DataType.GENERAL:
case DataType.CONTINUOUS:
// attribute patterns which is generated next bit of this method.
break;
case DataType.MICRO_SAT:
// microsat does not have alignment
patternListGenerator.writePatternList((PartitionPattern) partition, microsatList, writer);
break;
default:
throw new IllegalArgumentException("Unsupported data type");
}
writer.writeText("");
}
}
// }
} catch (Exception e) {
e.printStackTrace();
throw new GeneratorException("Pattern lists generation has failed:\n" + e.getMessage());
}
generateInsertionPoint(ComponentGenerator.InsertionPoint.AFTER_PATTERNS, writer);
// ++++++++++++++++ Tree Prior Model ++++++++++++++++++
try {
for (PartitionTreePrior prior : options.getPartitionTreePriors()) {
treePriorGenerator.writeTreePriorModel(prior, writer);
writer.writeText("");
}
} catch (Exception e) {
e.printStackTrace();
throw new GeneratorException("Tree prior model generation has failed:\n" + e.getMessage());
}
// ++++++++++++++++ Starting Tree ++++++++++++++++++
try {
for (PartitionTreeModel model : options.getPartitionTreeModels()) {
initialTreeGenerator.writeStartingTree(model, writer);
writer.writeText("");
}
} catch (Exception e) {
e.printStackTrace();
throw new GeneratorException("Starting tree generation has failed:\n" + e.getMessage());
}
// ++++++++++++++++ Tree Model +++++++++++++++++++
try {
for (PartitionTreeModel model : options.getPartitionTreeModels()) {
treeModelGenerator.writeTreeModel(model, writer);
writer.writeText("");
}
generateInsertionPoint(ComponentGenerator.InsertionPoint.AFTER_TREE_MODEL, writer);
} catch (Exception e) {
e.printStackTrace();
throw new GeneratorException("Tree model generation has failed:\n" + e.getMessage());
}
// ++++++++++++++++ Statistics ++++++++++++++++++
try {
if (taxonSets != null && taxonSets.size() > 0) {
tmrcaStatisticsGenerator.writeTMRCAStatistics(writer);
}
} catch (Exception e) {
e.printStackTrace();
throw new GeneratorException("TMRCA statistics generation has failed:\n" + e.getMessage());
}
// ++++++++++++++++ Tree Prior Likelihood ++++++++++++++++++
try {
for (PartitionTreeModel model : options.getPartitionTreeModels()) {
treePriorGenerator.writePriorLikelihood(model, writer);
writer.writeText("");
}
for (PartitionTreePrior prior : options.getPartitionTreePriors()) {
treePriorGenerator.writeMultiLociTreePriors(prior, writer);
}
generateInsertionPoint(ComponentGenerator.InsertionPoint.AFTER_TREE_PRIOR, writer);
} catch (Exception e) {
e.printStackTrace();
throw new GeneratorException("Tree prior likelihood generation has failed:\n" + e.getMessage());
}
// ++++++++++++++++ Branch Rates Model ++++++++++++++++++
try {
for (PartitionClockModel model : options.getPartitionClockModels()) {
clockModelGenerator.writeBranchRatesModel(model, writer);
writer.writeText("");
}
} catch (Exception e) {
e.printStackTrace();
throw new GeneratorException("Branch rates model generation has failed:\n" + e.getMessage());
}
// ++++++++++++++++ Substitution Model & Site Model ++++++++++++++++++
try {
for (PartitionSubstitutionModel model : options.getPartitionSubstitutionModels()) {
substitutionModelGenerator.writeSubstitutionSiteModel(model, writer);
writer.writeText("");
}
generateInsertionPoint(ComponentGenerator.InsertionPoint.AFTER_SUBSTITUTION_MODEL, writer);
} catch (Exception e) {
e.printStackTrace();
throw new GeneratorException("Substitution model or site model generation has failed:\n" + e.getMessage());
}
// ++++++++++++++++ AllMus parameter ++++++++++++++++++
try {
for (PartitionClockModel model : options.getPartitionClockModels()) {
clockModelGenerator.writeAllMus(model, writer);
}
} catch (Exception e) {
e.printStackTrace();
throw new GeneratorException("Clock model generation has failed:\n" + e.getMessage());
}
// ++++++++++++++++ Site Model ++++++++++++++++++
// for (PartitionSubstitutionModel model : options.getPartitionSubstitutionModels()) {
// substitutionModelGenerator.writeSiteModel(model, writer); // site model
// substitutionModelGenerator.writeAllMus(model, writer); // allMus
// writer.writeText("");
// }
generateInsertionPoint(ComponentGenerator.InsertionPoint.AFTER_SITE_MODEL, writer);
// ++++++++++++++++ Tree Likelihood ++++++++++++++++++
try {
Map<Pair<Pair<PartitionTreeModel, PartitionClockModel>, DataType>, List<PartitionData>> partitionLists = new HashMap<Pair<Pair<PartitionTreeModel, PartitionClockModel>, DataType>, List<PartitionData>>();
options.multiPartitionLists.clear();
options.otherPartitions.clear();
for (AbstractPartitionData partition : options.dataPartitions) {
// generate tree likelihoods for alignment data partitions
if (partition.getTaxonList() != null) {
if (treeLikelihoodGenerator.canUseMultiPartition(partition)) {
// all sequence partitions of the same type as the first into the list for use in a
// MultipartitionTreeDataLikelihood. Must also share the same tree, clock model and not be doing
// ancestral reconstruction or counting
Pair<Pair<PartitionTreeModel, PartitionClockModel>, DataType> key = new Pair(new Pair(partition.getPartitionTreeModel(), partition.getPartitionClockModel()), partition.getDataType());
List<PartitionData> partitions = partitionLists.get(key);
if (partitions == null) {
partitions = new ArrayList<PartitionData>();
options.multiPartitionLists.add(partitions);
}
partitions.add((PartitionData) partition);
partitionLists.put(key, partitions);
} else {
options.otherPartitions.add(partition);
}
}
}
treeLikelihoodGenerator.writeAllTreeLikelihoods(writer);
generateInsertionPoint(ComponentGenerator.InsertionPoint.AFTER_TREE_LIKELIHOOD, writer);
} catch (Exception e) {
e.printStackTrace();
throw new GeneratorException("Tree likelihood generation has failed:\n" + e.getMessage());
}
generateInsertionPoint(ComponentGenerator.InsertionPoint.AFTER_TRAITS, writer);
// ++++++++++++++++ Operators ++++++++++++++++++
try {
generateInsertionPoint(ComponentGenerator.InsertionPoint.BEFORE_OPERATORS, writer);
List<Operator> operators = options.selectOperators();
operatorsGenerator.writeOperatorSchedule(operators, writer);
writer.writeText("");
generateInsertionPoint(ComponentGenerator.InsertionPoint.AFTER_OPERATORS, writer);
} catch (Exception e) {
e.printStackTrace();
throw new GeneratorException("Operators generation has failed:\n" + e.getMessage());
}
// ++++++++++++++++ MCMC ++++++++++++++++++
try {
// XMLWriter writer, List<PartitionSubstitutionModel> models,
writeMCMC(writer);
writer.writeText("");
generateInsertionPoint(ComponentGenerator.InsertionPoint.AFTER_MCMC, writer);
} catch (Exception e) {
e.printStackTrace();
throw new GeneratorException("MCMC or log generation has failed:\n" + e.getMessage());
}
// ++++++++++++++++ ++++++++++++++++++
try {
writeTimerReport(writer);
writer.writeText("");
if (options.performTraceAnalysis) {
writeTraceAnalysis(writer);
}
if (options.generateCSV) {
for (PartitionTreePrior prior : options.getPartitionTreePriors()) {
treePriorGenerator.writeEBSPAnalysisToCSVfile(prior, writer);
}
}
} catch (Exception e) {
e.printStackTrace();
throw new GeneratorException("The last part of XML generation has failed:\n" + e.getMessage());
}
writer.writeCloseTag("beast");
writer.flush();
writer.close();
}
Also used :
Attribute(dr.util.Attribute)
FileWriter(java.io.FileWriter)
XMLWriter(dr.app.beauti.util.XMLWriter)
BufferedWriter(java.io.BufferedWriter)
Taxa(dr.evolution.util.Taxa)
Alignment(dr.evolution.alignment.Alignment)
DataType(dr.evolution.datatype.DataType)
TaxonList(dr.evolution.util.TaxonList)
Pair(dr.util.Pair)
Microsatellite(dr.evolution.datatype.Microsatellite)
Taxon(dr.evolution.util.Taxon)
IOException(java.io.IOException)
Example 4 with XMLWriter
use of dr.app.beauti.util.XMLWriter in project beast-mcmc by beast-dev.
the class XMLExporter method exportAlignment.
// END: Constructor
public String exportAlignment(SimpleAlignment alignment) throws IOException {
StringWriter sw = new StringWriter();
XMLWriter writer = new XMLWriter(sw);
// TODO: if we keep the taxa element than lets also write dates
// writer.writeOpenTag(TaxaParser.TAXA, // tagname
// new Attribute[] { // attributes[]
// new Attribute.Default<String>(XMLParser.ID, TaxaParser.TAXA) });
//
// for (int i = 0; i < alignment.getTaxonCount(); i++) {
//
// Taxon taxon = alignment.getTaxon(i);
//
// writer.writeTag(
// TaxonParser.TAXON, // tagname
// new Attribute[] { // attributes[]
// new Attribute.Default<String>(XMLParser.ID, taxon.getId()) },
// true // close
// );
//
// // System.out.println(taxon.getAttribute(Utils.ABSOLUTE_HEIGHT));
//
// // writer.writeCloseTag(TaxonParser.TAXON);
//
// }// END: taxon loop
//
// writer.writeCloseTag(TaxaParser.TAXA);
//
// writer.writeBlankLine();
// tagname
writer.writeOpenTag(// tagname
AlignmentParser.ALIGNMENT, new Attribute[] { // attributes[]
new Attribute.Default<String>(XMLParser.ID, AlignmentParser.ALIGNMENT), new Attribute.Default<String>(DataType.DATA_TYPE, alignment.getDataType().getDescription()) });
for (int i = 0; i < alignment.getSequenceCount(); i++) {
Taxon taxon = alignment.getTaxon(i);
writer.writeOpenTag(SequenceParser.SEQUENCE);
writer.writeIDref(TaxonParser.TAXON, taxon.getId());
writer.writeText(alignment.getSequence(i).getSequenceString());
writer.writeCloseTag(SequenceParser.SEQUENCE);
}
// END: sequences loop
writer.writeCloseTag(AlignmentParser.ALIGNMENT);
writer.close();
return sw.toString();
}
Also used :
StringWriter(java.io.StringWriter)
Attribute(dr.util.Attribute)
Taxon(dr.evolution.util.Taxon)
XMLWriter(dr.app.beauti.util.XMLWriter)
Example 5 with XMLWriter
use of dr.app.beauti.util.XMLWriter in project beast-mcmc by beast-dev.
the class XMLGenerator method generateXML.
// END: Constructor
public void generateXML(File file) throws IOException {
XMLWriter writer = new XMLWriter(new BufferedWriter(new FileWriter(file)));
// //////////////
// ---header---//
// //////////////
writer.writeText("<?xml version=\"1.0\" standalone=\"yes\"?>");
writer.writeComment("Generated by " + BeagleSequenceSimulatorApp.LONG_NAME + " " + BeagleSequenceSimulatorApp.VERSION);
writer.writeOpenTag("beast");
writer.writeBlankLine();
try {
int suffix = 1;
ArrayList<Taxa> taxaList = new ArrayList<Taxa>();
for (PartitionData data : dataList) {
if (data.record == null) {
throw new RuntimeException("Set Tree Model in Partitions tab for " + suffix + " partition.");
} else {
Taxa taxa = null;
if (data.demographicModelIndex == 0 && data.record.isTreeSet()) {
taxa = new Taxa(data.record.getTree().asList());
} else if (data.demographicModelIndex == 0 && data.record.isTaxaSet()) {
throw new RuntimeException("Data and demographic model incompatible for partition " + suffix);
} else if ((data.demographicModelIndex > 0 && data.demographicModelIndex <= PartitionData.lastImplementedIndex) && data.record.isTreeSet()) {
taxa = new Taxa(data.record.getTree().asList());
} else if ((data.demographicModelIndex > 0 && data.demographicModelIndex <= PartitionData.lastImplementedIndex) && data.record.isTaxaSet()) {
taxa = data.record.getTaxa();
} else {
//
}
if (taxaList.size() == 0 | !Utils.isTaxaInList(taxa, taxaList)) {
data.taxaIdref += suffix;
writeTaxa(taxa, writer, String.valueOf(suffix));
writer.writeBlankLine();
taxaList.add(taxa);
// System.out.println("NOT IN LIST");
} else {
int index = Utils.taxaIsIdenticalWith(taxa, taxaList) + 1;
data.taxaIdref += index;
// System.out.println("IDENTICAL WITH " + index);
}
}
// END: treeModel set check
suffix++;
}
// END: partition loop
} catch (Exception e) {
throw new RuntimeException("Taxa generation has failed:\n" + e.getMessage());
}
try {
int suffix = 1;
ArrayList<TreeModel> treeModelList = new ArrayList<TreeModel>();
for (PartitionData data : dataList) {
if (data.demographicModelIndex == 0) {
TreeModel treeModel = data.createTreeModel();
if (treeModelList.size() == 0 | !Utils.isTreeModelInList(treeModel, treeModelList)) {
data.treeModelIdref += suffix;
writeNewick(treeModel, writer, String.valueOf(suffix));
writer.writeBlankLine();
treeModelList.add(treeModel);
} else {
int index = Utils.treeModelIsIdenticalWith(treeModel, treeModelList) + 1;
data.treeModelIdref += index;
}
// END: list check
} else if (data.demographicModelIndex > 0 && data.demographicModelIndex <= PartitionData.lastImplementedIndex) {
data.demographicModelIdref += suffix;
data.treeModelIdref += suffix;
writeDemographicModel(data, writer, String.valueOf(suffix));
writer.writeBlankLine();
} else {
// throw exception
}
// END: demo model check
suffix++;
}
// END: partition loop
} catch (Exception e) {
throw new RuntimeException("Topology generation has failed:\n" + e.getMessage());
}
try {
int suffix = 1;
ArrayList<TreesTableRecord> recordsList = new ArrayList<TreesTableRecord>();
for (PartitionData data : dataList) {
TreesTableRecord record = data.record;
if (recordsList.size() == 0 | !Utils.isRecordInList(record, recordsList)) {
writeTreeModel(writer, String.valueOf(suffix));
writer.writeBlankLine();
recordsList.add(record);
}
suffix++;
}
// END: partition loop
} catch (Exception e) {
throw new RuntimeException("Tree model generation has failed:\n" + e.getMessage());
}
try {
int suffix = 1;
ArrayList<PartitionData> partitionList = new ArrayList<PartitionData>();
for (PartitionData data : dataList) {
if (partitionList.size() == 0 | !Utils.isElementInList(data, partitionList, Utils.BRANCH_RATE_MODEL_ELEMENT)) {
data.clockModelIdref += suffix;
writeBranchRatesModel(data, writer, String.valueOf(suffix));
writer.writeBlankLine();
partitionList.add(data);
// System.out.println("NOT IN LIST");
} else {
int index = Utils.isIdenticalWith(data, partitionList, Utils.BRANCH_RATE_MODEL_ELEMENT) + 1;
data.clockModelIdref += index;
// System.out.println("IDENTICAL WITH " + index);
}
suffix++;
}
// END: partition loop
} catch (Exception e) {
throw new RuntimeException("Clock model generation has failed:\n" + e.getMessage());
}
try {
int suffix = 1;
ArrayList<PartitionData> partitionList = new ArrayList<PartitionData>();
for (PartitionData data : dataList) {
if (partitionList.size() == 0 | !Utils.isElementInList(data, partitionList, Utils.FREQUENCY_MODEL_ELEMENT)) {
data.frequencyModelIdref += suffix;
writeFrequencyModel(data, writer);
writer.writeBlankLine();
partitionList.add(data);
// System.out.println("NOT IN LIST");
} else {
int index = Utils.isIdenticalWith(data, partitionList, Utils.FREQUENCY_MODEL_ELEMENT) + 1;
data.frequencyModelIdref += index;
// System.out.println("IDENTICAL WITH " + index);
}
suffix++;
}
// END: partition loop
} catch (Exception e) {
throw new RuntimeException("Frequency model generation has failed:\n" + e.getMessage());
}
try {
int suffix = 1;
ArrayList<PartitionData> partitionList = new ArrayList<PartitionData>();
for (PartitionData data : dataList) {
if (partitionList.size() == 0 | !Utils.isElementInList(data, partitionList, Utils.BRANCH_MODEL_ELEMENT)) {
data.substitutionModelIdref += suffix;
writeBranchModel(data, writer, String.valueOf(suffix));
writer.writeBlankLine();
partitionList.add(data);
} else {
int index = Utils.isIdenticalWith(data, partitionList, Utils.BRANCH_MODEL_ELEMENT) + 1;
data.substitutionModelIdref += index;
}
suffix++;
}
// END: partition loop
} catch (Exception e) {
throw new RuntimeException("Branch model generation has failed:\n" + e.getMessage());
}
try {
int suffix = 1;
ArrayList<PartitionData> partitionList = new ArrayList<PartitionData>();
for (PartitionData data : dataList) {
if (partitionList.size() == 0 | !Utils.isElementInList(data, partitionList, Utils.SITE_RATE_MODEL_ELEMENT)) {
data.siteRateModelIdref += suffix;
writeSiteRateModel(data, writer, suffix);
writer.writeBlankLine();
partitionList.add(data);
} else {
int index = Utils.isIdenticalWith(data, partitionList, Utils.SITE_RATE_MODEL_ELEMENT) + 1;
data.siteRateModelIdref += index;
}
suffix++;
}
// END: partition loop
} catch (Exception e) {
System.err.println(e);
throw new RuntimeException("Site rate model generation has failed:\n" + e.getMessage());
}
try {
writeBeagleSequenceSimulator(writer);
writer.writeBlankLine();
} catch (Exception e) {
throw new RuntimeException("Beagle Sequence Simulator element generation has failed:\n" + e.getMessage());
}
try {
writeReport(writer);
writer.writeBlankLine();
} catch (Exception e) {
System.err.println(e);
throw new RuntimeException("Report element generation has failed:\n" + e.getMessage());
}
// END: try-catch block
writer.writeCloseTag("beast");
writer.flush();
writer.close();
// reset all idrefs
for (PartitionData data : dataList) {
data.resetIdrefs();
}
}
Also used :
FileWriter(java.io.FileWriter)
ArrayList(java.util.ArrayList)
XMLWriter(dr.app.beauti.util.XMLWriter)
IOException(java.io.IOException)
BufferedWriter(java.io.BufferedWriter)
Taxa(dr.evolution.util.Taxa)
TreeModel(dr.evomodel.tree.TreeModel)
DefaultTreeModel(dr.evomodel.tree.DefaultTreeModel)
Aggregations
XMLWriter (dr.app.beauti.util.XMLWriter)7
Taxa (dr.evolution.util.Taxa)2
Taxon (dr.evolution.util.Taxon)2
Attribute (dr.util.Attribute)2
BufferedWriter (java.io.BufferedWriter)2
FileWriter (java.io.FileWriter)2
IOException (java.io.IOException)2
Alignment (dr.evolution.alignment.Alignment)1
DataType (dr.evolution.datatype.DataType)1
Microsatellite (dr.evolution.datatype.Microsatellite)1
TaxonList (dr.evolution.util.TaxonList)1
DefaultTreeModel (dr.evomodel.tree.DefaultTreeModel)1
TreeModel (dr.evomodel.tree.TreeModel)1
Pair (dr.util.Pair)1
StringWriter (java.io.StringWriter)1
ArrayList (java.util.ArrayList)1
