udpate to beast 2.3.0

BEAST2-Dev · May 20, 2015 · ac2ab0d · ac2ab0d
1 parent db9eb17
commit ac2ab0d
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Showing 4 changed files with 15 additions and 12 deletions.
diff --git a/src/beast/app/beauti/FossilCalibrationInputEditor.java b/src/beast/app/beauti/FossilCalibrationInputEditor.java
@@ -3,13 +3,14 @@
 
 
 
+
 import java.awt.Dimension;
 
 import beast.app.beauti.BeautiDoc;
 import beast.app.ca.CAPanel;
 import beast.app.ca.CAPanelListener;
 import beast.app.draw.BEASTObjectInputEditor;
-import beast.core.BEASTObject;
+import beast.core.BEASTInterface;
 import beast.core.Input;
 import beast.core.parameter.RealParameter;
 import beast.math.distributions.FossilCalibration;
@@ -33,7 +34,7 @@ public Class<?> type() {
 	FossilCalibration calibration;
 
 	@Override
-	public void init(Input<?> input, BEASTObject plugin, int itemNr, ExpandOption bExpandOption, boolean bAddButtons) {
+	public void init(Input<?> input, BEASTInterface plugin, int itemNr, ExpandOption bExpandOption, boolean bAddButtons) {
         m_input = input;
         m_plugin = plugin;
         calibration = (FossilCalibration) m_input.get();

diff --git a/src/beast/app/beauti/FossilPriorInputEditor.java b/src/beast/app/beauti/FossilPriorInputEditor.java
@@ -14,6 +14,7 @@
 import beast.app.beauti.MRCAPriorInputEditor;
 import beast.app.beauti.PriorInputEditor;
 import beast.app.beauti.TaxonSetDialog;
+import beast.core.BEASTInterface;
 import beast.core.BEASTObject;
 import beast.core.Input;
 import beast.evolution.alignment.Taxon;
@@ -35,7 +36,7 @@ public Class<?> type() {
 	}
 
 	@Override
-	public void init(Input<?> input, BEASTObject plugin, final int listItemNr, ExpandOption bExpandOption, boolean bAddButtons) {
+	public void init(Input<?> input, BEASTInterface plugin, final int listItemNr, ExpandOption bExpandOption, boolean bAddButtons) {
 		doc.beautiConfig.suppressPlugins.add("beast.math.distributions.FossilPrior.tree");
 		doc.beautiConfig.suppressPlugins.add("beast.math.distributions.FossilPrior.distr");
 		doc.beautiConfig.suppressPlugins.add("beast.math.distributions.FossilPrior.monophyletic");
@@ -106,7 +107,7 @@ Set<Taxon> getTaxonCandidates(FossilPrior prior) {
         Set<Taxon> candidates = new HashSet<Taxon>();
         for (String sTaxon : prior.treeInput.get().getTaxaNames()) {
             Taxon taxon = null;
-            for (Taxon taxon2 : doc.taxaset) {
+            for (Taxon taxon2 : doc.taxaset.values()) {
                 if (taxon2.getID().equals(sTaxon)) {
                     taxon = taxon2;
                     break;
@@ -115,7 +116,7 @@ Set<Taxon> getTaxonCandidates(FossilPrior prior) {
             if (taxon == null) {
                 taxon = new Taxon();
                 taxon.setID(sTaxon);
-                doc.taxaset.add(taxon);
+                doc.taxaset.put(sTaxon, taxon);
             }
             candidates.add(taxon);
         }

diff --git a/src/beast/app/beauti/FossilPriorListInputEditor.java b/src/beast/app/beauti/FossilPriorListInputEditor.java
@@ -15,6 +15,7 @@
 import beast.app.ca.CAPanel;
 import beast.app.ca.CAPanelListener;
 import beast.app.draw.BEASTObjectPanel;
+import beast.core.BEASTInterface;
 import beast.core.BEASTObject;
 import beast.core.Input;
 import beast.core.Logger;
@@ -50,7 +51,7 @@ public Class<?> baseType() {
 	    FossilCalibration calibration;
 
 	    @Override
-	    public void init(Input<?> input, BEASTObject plugin, int itemNr, ExpandOption bExpandOption, boolean bAddButtons) {
+	    public void init(Input<?> input, BEASTInterface plugin, int itemNr, ExpandOption bExpandOption, boolean bAddButtons) {
 	    	List<?> list = (List) input.get();
 	    	if (list.size() > 0) {
 	    		calibration = ((FossilPrior) list.get(0)).calibrationDistr.get();
@@ -71,7 +72,7 @@ public void init(Input<?> input, BEASTObject plugin, int itemNr, ExpandOption bE
 	    }
 
 	    @Override
-	    public List<BEASTObject> pluginSelector(Input<?> input, BEASTObject parent, List<String> sTabuList) {
+	    public List<BEASTInterface> pluginSelector(Input<?> input, BEASTInterface parent, List<String> sTabuList) {
 	        FossilPrior prior = new FossilPrior();
 	        try {
 
@@ -132,7 +133,7 @@ public List<BEASTObject> pluginSelector(Input<?> input, BEASTObject parent, List
 //				fossilCallibration.setInputValue("maxSamplingGap", new RealParameter("0.0"));
 //				fossilCallibration.setInputValue("minSamplingGap", new RealParameter("0.0"));
 
-				List<BeautiSubTemplate> availablePlugins = doc.getInpuEditorFactory().getAvailableTemplates(
+				List<BeautiSubTemplate> availablePlugins = doc.getInputEditorFactory().getAvailableTemplates(
 						new Input<FossilCalibration>("fossil","",FossilCalibration.class), doc, null, doc);
 				FossilCalibration fossilCallibration = (FossilCalibration) availablePlugins.get(0).createSubNet(new PartitionContext(), false);
 	        	fossilCallibration.setID("FossilCallibration.0");
@@ -144,7 +145,7 @@ public List<BEASTObject> pluginSelector(Input<?> input, BEASTObject parent, List
 	        	e.printStackTrace();
 	            // TODO: handle exception
 	        }
-	        List<BEASTObject> selectedPlugins = new ArrayList<BEASTObject>();
+	        List<BEASTInterface> selectedPlugins = new ArrayList<BEASTInterface>();
 	        selectedPlugins.add(prior);
 	        g_collapsedIDs.add(prior.getID());	        
 	        return selectedPlugins;

diff --git a/src/beast/app/ca/CAPanel.java b/src/beast/app/ca/CAPanel.java
@@ -629,7 +629,7 @@ public void actionPerformed(ActionEvent e) {
 		JPanel panel2b = new JPanel();
 		panel2b.setLayout(new BorderLayout());
 
-		JLabel lblIcon = new MyJLabel(BeautiPanel.getIcon(CA_ICON));
+		JLabel lblIcon = new MyJLabel(Utils.getIcon(CA_ICON));
 		if (mode == MODE_BEAUTI_BOTTOM) {
 			lblIcon.setMinimumSize(new Dimension(84,84));
 			lblIcon.setPreferredSize(new Dimension(84,84));
@@ -1471,7 +1471,7 @@ static void showHelp(String text) {
 		    String title = text.substring(0, text.indexOf(":"));
 		    title = title.replaceAll("<html>", "");
 			//JOptionPane.showMessageDialog(null, pane, title, JOptionPane.PLAIN_MESSAGE);
-			JOptionPane.showMessageDialog(null, pane, title, JOptionPane.PLAIN_MESSAGE, BeautiPanel.getIcon(CA_ICON2));
+			JOptionPane.showMessageDialog(null, pane, title, JOptionPane.PLAIN_MESSAGE, Utils.getIcon(CA_ICON2));
 
 	}
 
@@ -1720,7 +1720,7 @@ public DocumentFrame doNew() {
 
 		frame.setSize(1024, 728);
 
-        ImageIcon icon = BeautiPanel.getIcon(CA_ICON);
+        ImageIcon icon = Utils.getIcon(CA_ICON);
         if (icon != null) {
             frame.setIconImage(icon.getImage());
         }