From 8065aa2185475554bac555111fa138d1c54a8630 Mon Sep 17 00:00:00 2001
From: rbouckaert <higgs.ml@gmail.com>
Date: Thu, 16 May 2024 12:28:49 +1200
Subject: [PATCH] make Alignment a StateNode -- needs testing #1150

---
 .../base/evolution/alignment/Alignment.java   | 94 +++++++++++++++++++
 src/beast/base/inference/StateNode.java       |  6 +-
 src/beast/base/inference/parameter/Map.java   |  4 +-
 3 files changed, 98 insertions(+), 6 deletions(-)

diff --git a/src/beast/base/evolution/alignment/Alignment.java b/src/beast/base/evolution/alignment/Alignment.java
index 736c696f..d1ba69c8 100644
--- a/src/beast/base/evolution/alignment/Alignment.java
+++ b/src/beast/base/evolution/alignment/Alignment.java
@@ -24,13 +24,17 @@
 */
 package beast.base.evolution.alignment;
 
+import java.io.PrintStream;
 import java.util.*;
 
+import org.w3c.dom.Node;
+
 import beast.base.core.Description;
 import beast.base.core.Input;
 import beast.base.core.Log;
 import beast.base.core.Input.Validate;
 import beast.base.evolution.datatype.DataType;
+import beast.base.inference.StateNode;
 import beast.base.inference.parameter.Map;
 import beast.pkgmgmt.BEASTClassLoader;
 import beast.pkgmgmt.PackageManager;
@@ -880,5 +884,95 @@ public String getSequenceAsString(String taxon) {
 	        } while (difference > 1E-8 && attempts < 1000);
 	        return freqs;
 	  } // calcFrequencies
+
+	@Override
+	public void init(PrintStream out) {
+		// TODO Auto-generated method stub
+		
+	}
+
+	@Override
+	public void log(long sample, PrintStream out) {
+		// TODO Auto-generated method stub
+		
+	}
+
+	@Override
+	public void close(PrintStream out) {
+		// TODO Auto-generated method stub
+		
+	}
+
+	@Override
+	public int getDimension() {
+		// TODO Auto-generated method stub
+		return 0;
+	}
+
+	@Override
+	public double getArrayValue(int dim) {
+		// TODO Auto-generated method stub
+		return 0;
+	}
+
+	@Override
+	public void setEverythingDirty(boolean isDirty) {
+		// TODO Auto-generated method stub
+		
+	}
+
+	@Override
+	public StateNode copy() {
+		// TODO Auto-generated method stub
+		return null;
+	}
+
+	@Override
+	public void assignTo(StateNode other) {
+		// TODO Auto-generated method stub
+		
+	}
+
+	@Override
+	public void assignFrom(StateNode other) {
+		// TODO Auto-generated method stub
+		
+	}
+
+	@Override
+	public void assignFromFragile(StateNode other) {
+		// TODO Auto-generated method stub
+		
+	}
+
+	@Override
+	public void fromXML(Node node) {
+		// TODO Auto-generated method stub
+		
+	}
+    
+	@Override
+	public String toXML() {
+		// TODO Auto-generated method stub
+		return null;
+	}
+
+	@Override
+	public int scale(double scale) {
+		// TODO Auto-generated method stub
+		return 0;
+	}
+
+	@Override
+	protected void store() {
+		// TODO Auto-generated method stub
+		
+	}
+
+	@Override
+	public void restore() {
+		// TODO Auto-generated method stub
+		
+	}
 	
 } // class Data
diff --git a/src/beast/base/inference/StateNode.java b/src/beast/base/inference/StateNode.java
index c3e362ba..98771039 100644
--- a/src/beast/base/inference/StateNode.java
+++ b/src/beast/base/inference/StateNode.java
@@ -117,15 +117,13 @@ public void assignFromWithoutID(StateNode other) {
      * for storing a state *
      */
     final public void toXML(PrintStream out) {
-        out.print("<statenode id='" + normalise(getID()) + "'>");
-        out.print(normalise(toString()));
-        out.print("</statenode>\n");
+    	out.println(toXML());
     }
 
     /**
      * stores a state node in XML format, to be restored by fromXML() *
      */
-    final public String toXML() {
+    public String toXML() {
         return "<statenode id='" + normalise(getID()) + "'>" +
                 normalise(toString()) +
                 "</statenode>\n";
diff --git a/src/beast/base/inference/parameter/Map.java b/src/beast/base/inference/parameter/Map.java
index f4e70ed6..28e5a710 100644
--- a/src/beast/base/inference/parameter/Map.java
+++ b/src/beast/base/inference/parameter/Map.java
@@ -6,10 +6,10 @@
 
 import beast.base.core.Description;
 import beast.base.core.Input;
-import beast.base.inference.CalculationNode;
+import beast.base.inference.StateNode;
 
 @Description("Unordered set mapping keys to values")
-abstract public class Map<T> extends CalculationNode {
+abstract public class Map<T> extends StateNode {
 
     final public Input<java.util.Map<java.lang.String, T>> defaultInput = new Input<>("*",
             "Input containing the map", new LinkedHashMap<>());