update to BEAST v2.6.0

build.xml

@@ -17,7 +17,7 @@
 	<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="1.8.2" />
+	<property name="version" value="1.9.0" />
 
     <import file="${beast2path}/build.xml" />
 

src/beast/app/beauti/FileInputEditor.java

@@ -55,7 +55,7 @@ public void actionPerformed(ActionEvent arg0) {
 						m_entry.setText(file.getName());
 						m_input.setValue(newFile(file), m_beastObject);
 						String path = file.getPath();
-						Beauti.g_sDir = path;
+						Beauti.setCurrentDir(path);
 					}
 				} catch (Exception e) {
 					// TODO Auto-generated catch block

src/beast/app/beauti/OutFileInputEditor.java

@@ -51,7 +51,7 @@ public void actionPerformed(ActionEvent arg0) {
 					m_entry.setText(file.getName());
 					m_input.setValue(new OutFile(file.getPath()), m_beastObject);
 					String path = file.getPath();
-					Beauti.g_sDir = path;
+					Beauti.setCurrentDir(path);
 				} catch (Exception e) {
 					// TODO Auto-generated catch block
 					e.printStackTrace();

src/beast/app/draw/SpreadSheet.java

@@ -88,6 +88,7 @@
 import beast.core.BEASTObject;
 import beast.evolution.alignment.Alignment;
 import beast.evolution.alignment.Sequence;
+import beast.util.BEASTClassLoader;
 import beast.util.PackageManager;
 import beast.util.XMLParser;
 import beast.util.XMLProducer;
@@ -236,7 +237,7 @@ public void mouseClicked(MouseEvent e) {
                             "select", JOptionPane.PLAIN_MESSAGE,  null, m_sPlugInNames, null);
                     if (sClassName != null) {
                     	try {
-                    		BEASTObject plugin = (beast.core.BEASTObject) Class.forName(sClassName).newInstance();
+                    		BEASTObject plugin = (beast.core.BEASTObject) BEASTClassLoader.forName(sClassName).newInstance();
                     		m_objects[iRow][iCol] = plugin;
                 			m_pluginLocation.put(plugin, iRow + iCol * MAX_ROW);
                 			m_plugins.add(plugin);
@@ -701,7 +702,7 @@ void parsePlugin(String sStr, int iRow, int iCol) {
 			}
 			BEASTObject plugin = null;
 			if (m_objects[iRow][iCol]==null || !m_objects[iRow][iCol].getClass().getName().equals(sClass)) {
-				plugin = (BEASTObject) Class.forName(sClass).newInstance();
+				plugin = (BEASTObject) BEASTClassLoader.forName(sClass).newInstance();
 			} else {
 				plugin = (BEASTObject) m_objects[iRow][iCol];
 			}

src/beast/app/util/Application.java

@@ -12,6 +12,7 @@
 
 import org.json.JSONObject;
 
+import beast.app.beauti.Beauti;
 import beast.app.beauti.BeautiConfig;
 import beast.app.beauti.BeautiDoc;
 import beast.app.draw.BEASTObjectDialog;
@@ -20,6 +21,7 @@
 import beast.core.Description;
 import beast.core.Input;
 import beast.core.util.Log;
+import beast.util.BEASTClassLoader;
 
 @Description("BEAST application that handles argument parsing by introspection "
 		+ "using Inputs declared in the class.")
@@ -155,6 +157,10 @@ public void parseArgs(String[] args, boolean sloppy) throws Exception {
 					Log.info.println(getUsage());
 					// CLI usage only
 					System.exit(0);
+				} else if (name.equals("wd")) {
+					// set working directory
+					Beauti.g_sDir = value;
+					i++;
 				}
 				if (matchingInput == null) {
 
@@ -195,6 +201,7 @@ public String getUsage() {
 		try {
 			List<Input<?>> inputs = myBeastObject.listInputs();
 			buf.append("Usage: " + myBeastObject.getClass().getName() + "\n");
+			buf.append(myBeastObject.getDescription() + "\n");
 			for (Input<?> input : inputs) {
 				buf.append("-" + input.getName() + " ");
 				try {
@@ -225,7 +232,7 @@ public void run() throws Exception {
 	public static void main(final String[] args) throws Exception {
 		Application main = null;
 		try {
-			BEASTObject myBeastObject = (BEASTObject) Class.forName(args[0])
+			BEASTObject myBeastObject = (BEASTObject) BEASTClassLoader.forName(args[0])
 					.newInstance();
 			main = new Application(myBeastObject);
 			String[] args2 = new String[args.length - 1];

src/beast/inference/ParticleFilter.java

@@ -28,6 +28,7 @@
 import beast.core.BEASTObject;
 import beast.core.Input.Validate;
 import beast.math.statistic.DiscreteStatistics;
+import beast.util.BEASTClassLoader;
 import beast.util.Randomizer;
 import beast.util.XMLProducer;
 
@@ -375,7 +376,7 @@ public void run() throws Exception {
 		m_nCountDown = new CountDownLatch(m_nParticles);
 
 		for (int i = 0; i < m_nParticles; i++) {
-	    	Object o = Class.forName(m_sParticleLauncher.get()).newInstance();
+	    	Object o = BEASTClassLoader.forName(m_sParticleLauncher.get()).newInstance();
 	    	if (!(o instanceof ParticleLauncher)) {
 	    		throw new Exception(m_sParticleLauncher.get() + " is not a particle launcher.");
 	    	}

src/beast/math/distributions/MultiMRCAPriors.java

@@ -16,10 +16,10 @@ public class MultiMRCAPriors extends MultiMonophyleticConstraint {
     public Input<List<MRCAPrior>> calibrationsInput =
                 new Input<List<MRCAPrior>>("distribution", "Set of calibrated nodes", new ArrayList<MRCAPrior>());
 
-    private int[] nodeToCladeGroup = null;
-    private int prevNodeCount = -1;
-    private int[] ctops = null;
-    private boolean[] ctopParent = null;
+    protected int[] nodeToCladeGroup = null;
+    protected int prevNodeCount = -1;
+    protected int[] ctops = null;
+    protected boolean[] ctopParent = null;
 
     @Override
     public void initAndValidate() {

version.xml

@@ -1,5 +1,5 @@
-<package name='BEASTLabs' version='1.8.2'>
-	<depends on='beast2' atleast='2.5.0'/>
+<package name='BEASTLabs' version='1.9.0'>
+	<depends on='beast2' atleast='2.6.0' atmost="2.6.9"/>
     <packageapp description="BEAST model spreadsheet"
               class="beast.app.draw.SpreadSheet"
               args=""