add model analyser app -- introduce dependency on BEASTlabs

build.xml

@@ -13,12 +13,13 @@
 	<property name="libbModelTest" location="lib" />
 	<property name="release_dir" value="release" />
 	<property name="distbModelTest" location="${buildbModelTest}/dist" />
+	<property name="BEASTLabsclasspath" location="../BEASTLabs/build" />
 	<property name="beast2path" location="../beast2" />
 	<property name="libBeast2" location="${beast2path}/lib" />
 	<property name="srcBeast2" location="${beast2path}/src" />
 	<property name="beast2classpath" location="${beast2path}/build" />
 	<property name="Add_on_dir" value="${release_dir}/add-on" />
-	<property name="version" value="0.2.0" />
+	<property name="version" value="0.3.0" />
 
     <import file="${beast2path}/build.xml" />
 
@@ -34,6 +35,7 @@
         <fileset dir="${libBeast2}" includes="jam.jar"/>
         <fileset dir="${libBeast2}" includes="colt.jar"/>
         <pathelement path="${beast2classpath}"/>
+        <pathelement path="${BEASTLabsclasspath}"/>
 	</path>
 
 	<!-- start -->

src/beast/app/tools/BModelAnalyser.java

@@ -0,0 +1,139 @@
+package beast.app.tools;
+
+import java.io.File;
+import java.text.DecimalFormat;
+import java.text.NumberFormat;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import beast.app.beauti.BeautiConfig;
+import beast.app.beauti.BeautiDoc;
+import beast.app.draw.BEASTObjectDialog;
+import beast.app.draw.BEASTObjectPanel;
+import beast.app.util.Application;
+import beast.app.util.ConsoleApp;
+import beast.app.util.LogFile;
+import beast.core.Description;
+import beast.core.Input;
+import beast.core.Input.Validate;
+import beast.core.Runnable;
+import beast.util.LogAnalyser;
+
+@Description("Analyses bModelTest log and list useful stats such as 95% HPDs of model indicators")
+public class BModelAnalyser extends Runnable {
+	public Input<LogFile> traceFileInput = new Input<>("file","trace log file containing output of a bModelTest analysis", Validate.REQUIRED);
+	public Input<String> prefixInput = new Input<>("prefix", "prefix of the entry in the log file containing the substitution model trace (default 'substmodel')" , "substmodel");
+	public Input<Integer> burninInput = new Input<>("burnin", "percentage of the log file to disregard as burn-in (default 10)" , 10);
+
+
+	@Override
+	public void initAndValidate() {
+		int burnin = burninInput.get();
+		if (burnin >= 100) {
+			throw new IllegalArgumentException("burnin is a percentage and should not be larger than 100");
+		}
+
+	}
+
+	@Override
+	public void run() throws Exception {
+		File file = traceFileInput.get();
+		String prefix = prefixInput.get();
+		int burnin = burninInput.get();
+		if (burnin < 0) {
+			burnin = 0;
+		}
+
+		LogAnalyser analyser = new LogAnalyser(file.getAbsolutePath(), burnin);
+		for (String label : analyser.getLabels()) {
+			if (label.startsWith(prefix)) {
+				Double [] trace = analyser.getTrace(label);
+				processTrace(label, trace);
+			}
+		}
+	}
+
+	private void processTrace(String label, Double[] trace) {
+		System.out.println(label);
+		int [] model = new int[trace.length];
+		for (int i = 0; i < trace.length; i++) {
+			model[i] = (int) (double) (trace[i] + 0.5);
+		}
+
+		Map<Integer, Integer> countMap = new HashMap<>();
+		for (int i : model) {
+			if (!countMap.containsKey(i)) {
+				countMap.put(i, 0);
+			}
+			countMap.put(i, countMap.get(i) + 1);
+		}
+
+		List<Integer> models = new ArrayList<>();
+		for (Integer i : countMap.keySet().toArray(new Integer[]{})) {
+			models.add(i);
+		}
+
+		Collections.sort(models, (i1,i2)-> {
+			return countMap.get(i1).compareTo(countMap.get(i2));
+		});
+
+		int treshold = 95 * trace.length / 100;
+		int sum = 0;
+		NumberFormat formatter = new DecimalFormat("##0.00");     
+		for (int i = models.size() - 1; i > 0 && sum < treshold; i--) {
+			int current = models.get(i);
+			int contribution = countMap.get(current);
+			sum += contribution;
+			double con = 100*(contribution + 0.0)/trace.length;
+			if (con < 10) {
+				System.out.print(" ");
+			}
+			System.out.print(formatter.format(con) + "% " );
+			System.out.print(formatter.format(100*(sum + 0.0)/trace.length) + "% " );
+			System.out.println(current);
+		}
+		System.out.println();
+	}
+
+	static ConsoleApp app;
+	public static void main(String[] args) throws Exception {
+		BModelAnalyser analyser = new BModelAnalyser();
+		analyser.setID("Analyses bModelTest trace logs");
+		analyser.traceFileInput.setValue(new LogFile("someTrace.log"), analyser);
+
+		if (args.length == 0) {
+			// create BeautiDoc and beauti configuration
+			BeautiDoc doc = new BeautiDoc();
+			doc.beautiConfig = new BeautiConfig();
+			doc.beautiConfig.initAndValidate();
+
+			// create panel with entries for the application
+			BEASTObjectPanel panel = new BEASTObjectPanel(analyser, analyser.getClass(), doc);
+
+			// wrap panel in a dialog
+			BEASTObjectDialog dialog = new BEASTObjectDialog(panel, null);
+
+			// show the dialog
+			if (dialog.showDialog()) {
+				dialog.accept(analyser, doc);
+				// create a console to show standard error and standard output
+				app = new ConsoleApp("BModelAnalyser", 
+						"BModelAnalyser: " + analyser.traceFileInput.get().getPath(),
+						null
+						);
+				analyser.initAndValidate();
+				analyser.run();
+			}
+			return;
+		}
+
+		Application main = new Application(analyser);
+		main.parseArgs(args, false);
+		analyser.initAndValidate();
+		analyser.run();
+	}
+
+}

version.xml

@@ -1,3 +1,9 @@
-<addon name='bModelTest' version='0.2.0'>
+<addon name='bModelTest' version='0.3.0'>
 	<depends on='beast2' atleast='2.4.0'/>
+	<depends on='BEASTLabs' atleast='1.5.0'/>
+
+<addonapp description="BModelAnalyser"
+              class="beast.app.tools.BModelAnalyser"
+              args=""
+            />
 </addon>