Author: mes
Date: 2011-11-23 16:54:00 -0800 (Wed, 23 Nov 2011)
New Revision: 27598

Added:
   
core3/api/trunk/equations-api/src/main/java/org/cytoscape/equations/AbstractNode.java
   
core3/api/trunk/equations-api/src/main/java/org/cytoscape/equations/TreeNode.java
Removed:
   core3/api/trunk/equations-api/src/main/java/org/cytoscape/equations/Node.java
Modified:
   
core3/api/trunk/equations-api/src/main/java/org/cytoscape/equations/EquationParser.java
   
core3/api/trunk/equations-api/src/test/java/org/cytoscape/equations/SimpleNode.java
   
core3/impl/trunk/equations-impl/src/main/java/org/cytoscape/equations/internal/EquationCompilerImpl.java
   
core3/impl/trunk/equations-impl/src/main/java/org/cytoscape/equations/internal/EquationParserImpl.java
   
core3/impl/trunk/equations-impl/src/main/java/org/cytoscape/equations/internal/parse_tree/BinOpNode.java
   
core3/impl/trunk/equations-impl/src/main/java/org/cytoscape/equations/internal/parse_tree/BooleanConstantNode.java
   
core3/impl/trunk/equations-impl/src/main/java/org/cytoscape/equations/internal/parse_tree/FConvNode.java
   
core3/impl/trunk/equations-impl/src/main/java/org/cytoscape/equations/internal/parse_tree/FloatConstantNode.java
   
core3/impl/trunk/equations-impl/src/main/java/org/cytoscape/equations/internal/parse_tree/FuncCallNode.java
   
core3/impl/trunk/equations-impl/src/main/java/org/cytoscape/equations/internal/parse_tree/IdentNode.java
   
core3/impl/trunk/equations-impl/src/main/java/org/cytoscape/equations/internal/parse_tree/SConvNode.java
   
core3/impl/trunk/equations-impl/src/main/java/org/cytoscape/equations/internal/parse_tree/StringConstantNode.java
   
core3/impl/trunk/equations-impl/src/main/java/org/cytoscape/equations/internal/parse_tree/UnaryOpNode.java
Log:
Extracted interface and renamed Node to AbstractNode

Copied: 
core3/api/trunk/equations-api/src/main/java/org/cytoscape/equations/AbstractNode.java
 (from rev 27587, 
core3/api/trunk/equations-api/src/main/java/org/cytoscape/equations/Node.java)
===================================================================
--- 
core3/api/trunk/equations-api/src/main/java/org/cytoscape/equations/AbstractNode.java
                               (rev 0)
+++ 
core3/api/trunk/equations-api/src/main/java/org/cytoscape/equations/AbstractNode.java
       2011-11-24 00:54:00 UTC (rev 27598)
@@ -0,0 +1,88 @@
+/*
+  File: Node.java
+
+  Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+  This library is free software; you can redistribute it and/or modify it
+  under the terms of the GNU Lesser General Public License as published
+  by the Free Software Foundation; either version 2.1 of the License, or
+  any later version.
+
+  This library is distributed in the hope that it will be useful, but
+  WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+  MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE.  The software and
+  documentation provided hereunder is on an "as is" basis, and the
+  Institute for Systems Biology and the Whitehead Institute
+  have no obligations to provide maintenance, support,
+  updates, enhancements or modifications.  In no event shall the
+  Institute for Systems Biology and the Whitehead Institute
+  be liable to any party for direct, indirect, special,
+  incidental or consequential damages, including lost profits, arising
+  out of the use of this software and its documentation, even if the
+  Institute for Systems Biology and the Whitehead Institute
+  have been advised of the possibility of such damage.  See
+  the GNU Lesser General Public License for more details.
+
+  You should have received a copy of the GNU Lesser General Public License
+  along with this library; if not, write to the Free Software Foundation,
+  Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations;
+
+
+import java.util.Stack;
+
+
+/**
+ *  A node in the parse tree.
+ *  @CyAPI.Abstract.Class
+ */
+public abstract class AbstractNode implements TreeNode {
+       private final int sourceLocation; // What location the "source code" is 
this associated with.
+
+       /** Base class constructor for any <code>Node</code> type.
+        *  @param sourceLocation  start of the location in the equation where 
the code was found
+        *                         that was turned into a node in the parse tree
+        */
+       public AbstractNode(final int sourceLocation) {
+               this.sourceLocation = sourceLocation;
+       }
+
+       /* (non-Javadoc)
+        * @see org.cytoscape.equations.TreeNode#getSourceLocation()
+        */
+       @Override
+       public final int getSourceLocation() {
+               return sourceLocation;
+       }
+
+       /** Returns s <code>String</code> representation of this node.
+        *  @return a textual representation of this node
+        *  Note: This is typically only used for debugging.
+        */
+       public abstract String toString();
+
+       /* (non-Javadoc)
+        * @see org.cytoscape.equations.TreeNode#getType()
+        */
+       @Override
+       public abstract Class getType(); // The type of this node.
+
+       /* (non-Javadoc)
+        * @see org.cytoscape.equations.TreeNode#getLeftChild()
+        */
+       @Override
+       public abstract TreeNode getLeftChild();
+
+       /* (non-Javadoc)
+        * @see org.cytoscape.equations.TreeNode#getRightChild()
+        */
+       @Override
+       public abstract TreeNode getRightChild();
+
+       /* (non-Javadoc)
+        * @see org.cytoscape.equations.TreeNode#genCode(java.util.Stack)
+        */
+       @Override
+       public abstract void genCode(final Stack<CodeAndSourceLocation> 
codeStack);
+}

Modified: 
core3/api/trunk/equations-api/src/main/java/org/cytoscape/equations/EquationParser.java
===================================================================
--- 
core3/api/trunk/equations-api/src/main/java/org/cytoscape/equations/EquationParser.java
     2011-11-24 00:47:09 UTC (rev 27597)
+++ 
core3/api/trunk/equations-api/src/main/java/org/cytoscape/equations/EquationParser.java
     2011-11-24 00:54:00 UTC (rev 27598)
@@ -94,5 +94,5 @@
         * Returns the parse tree. Must only be called if parse() returns true!
         *  @return the parse tree.
         */
-       Node getParseTree();
+       TreeNode getParseTree();
 }

Deleted: 
core3/api/trunk/equations-api/src/main/java/org/cytoscape/equations/Node.java
===================================================================
--- 
core3/api/trunk/equations-api/src/main/java/org/cytoscape/equations/Node.java   
    2011-11-24 00:47:09 UTC (rev 27597)
+++ 
core3/api/trunk/equations-api/src/main/java/org/cytoscape/equations/Node.java   
    2011-11-24 00:54:00 UTC (rev 27598)
@@ -1,84 +0,0 @@
-/*
-  File: Node.java
-
-  Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
-
-  This library is free software; you can redistribute it and/or modify it
-  under the terms of the GNU Lesser General Public License as published
-  by the Free Software Foundation; either version 2.1 of the License, or
-  any later version.
-
-  This library is distributed in the hope that it will be useful, but
-  WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
-  MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE.  The software and
-  documentation provided hereunder is on an "as is" basis, and the
-  Institute for Systems Biology and the Whitehead Institute
-  have no obligations to provide maintenance, support,
-  updates, enhancements or modifications.  In no event shall the
-  Institute for Systems Biology and the Whitehead Institute
-  be liable to any party for direct, indirect, special,
-  incidental or consequential damages, including lost profits, arising
-  out of the use of this software and its documentation, even if the
-  Institute for Systems Biology and the Whitehead Institute
-  have been advised of the possibility of such damage.  See
-  the GNU Lesser General Public License for more details.
-
-  You should have received a copy of the GNU Lesser General Public License
-  along with this library; if not, write to the Free Software Foundation,
-  Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
-*/
-package org.cytoscape.equations;
-
-
-import java.util.Stack;
-
-
-/**
- *  A node in the parse tree.
- *  @CyAPI.Abstract.Class
- */
-public abstract class Node {
-       private final int sourceLocation; // What location the "source code" is 
this associated with.
-
-       /** Base class constructor for any <code>Node</code> type.
-        *  @param sourceLocation  start of the location in the equation where 
the code was found
-        *                         that was turned into a node in the parse tree
-        */
-       public Node(final int sourceLocation) {
-               this.sourceLocation = sourceLocation;
-       }
-
-       /** Returns the start of the location in the equation where the code 
was found that was
-        *  turned into a node in the parse tree.
-        *  @return the location in the source code that resulted in this node
-        */
-       public final int getSourceLocation() {
-               return sourceLocation;
-       }
-
-       /** Returns s <code>String</code> representation of this node.
-        *  @return a textual representation of this node
-        *  Note: This is typically only used for debugging.
-        */
-       public abstract String toString();
-
-       /** Returns the type of this node.
-        *  @return the type of the result of the code generated from this node 
will result in 
-        */
-       public abstract Class getType(); // The type of this node.
-
-       /** Returns the left child if it exists or null if it doesn't.
-        *  @return the left child, if any, of this node in the parse tree
-        */
-       public abstract Node getLeftChild();
-
-       /** Returns the right child if it exists or null if it doesn't.
-        *  @return the right child, if any, of this node in the parse tree
-        */
-       public abstract Node getRightChild();
-
-       /** Generated code for this node and pushes it onto the execution 
stack. 
-        * @param codeStack the execution stack to push the generated code for 
this node.
-        */
-       public abstract void genCode(final Stack<CodeAndSourceLocation> 
codeStack);
-}

Added: 
core3/api/trunk/equations-api/src/main/java/org/cytoscape/equations/TreeNode.java
===================================================================
--- 
core3/api/trunk/equations-api/src/main/java/org/cytoscape/equations/TreeNode.java
                           (rev 0)
+++ 
core3/api/trunk/equations-api/src/main/java/org/cytoscape/equations/TreeNode.java
   2011-11-24 00:54:00 UTC (rev 27598)
@@ -0,0 +1,33 @@
+package org.cytoscape.equations;
+
+import java.util.Stack;
+
+public interface TreeNode {
+
+       /** Returns the start of the location in the equation where the code 
was found that was
+        *  turned into a node in the parse tree.
+        *  @return the location in the source code that resulted in this node
+        */
+       int getSourceLocation();
+
+       /** Returns the type of this node.
+        *  @return the type of the result of the code generated from this node 
will result in 
+        */
+       Class getType(); // The type of this node.
+
+       /** Returns the left child if it exists or null if it doesn't.
+        *  @return the left child, if any, of this node in the parse tree
+        */
+       TreeNode getLeftChild();
+
+       /** Returns the right child if it exists or null if it doesn't.
+        *  @return the right child, if any, of this node in the parse tree
+        */
+       TreeNode getRightChild();
+
+       /** Generated code for this node and pushes it onto the execution 
stack. 
+        * @param codeStack the execution stack to push the generated code for 
this node.
+        */
+       void genCode(final Stack<CodeAndSourceLocation> codeStack);
+
+}
\ No newline at end of file

Modified: 
core3/api/trunk/equations-api/src/test/java/org/cytoscape/equations/SimpleNode.java
===================================================================
--- 
core3/api/trunk/equations-api/src/test/java/org/cytoscape/equations/SimpleNode.java
 2011-11-24 00:47:09 UTC (rev 27597)
+++ 
core3/api/trunk/equations-api/src/test/java/org/cytoscape/equations/SimpleNode.java
 2011-11-24 00:54:00 UTC (rev 27598)
@@ -4,7 +4,7 @@
 import java.util.Stack;
 
 
-class SimpleNode extends Node {
+class SimpleNode extends AbstractNode {
        SimpleNode(final int sourceLocation) {
                super(sourceLocation);
        }
@@ -16,10 +16,10 @@
        public Class getType() { return null; }
 
        @Override
-       public Node getLeftChild() { return null; }
+       public TreeNode getLeftChild() { return null; }
 
        @Override
-       public Node getRightChild() { return null; }
+       public TreeNode getRightChild() { return null; }
 
        @Override
        public void genCode(final Stack<CodeAndSourceLocation> codeStack) { }

Modified: 
core3/impl/trunk/equations-impl/src/main/java/org/cytoscape/equations/internal/EquationCompilerImpl.java
===================================================================
--- 
core3/impl/trunk/equations-impl/src/main/java/org/cytoscape/equations/internal/EquationCompilerImpl.java
    2011-11-24 00:47:09 UTC (rev 27597)
+++ 
core3/impl/trunk/equations-impl/src/main/java/org/cytoscape/equations/internal/EquationCompilerImpl.java
    2011-11-24 00:54:00 UTC (rev 27598)
@@ -38,7 +38,7 @@
 import org.cytoscape.equations.EquationCompiler;
 import org.cytoscape.equations.EquationParser;
 import org.cytoscape.equations.Equation;
-import org.cytoscape.equations.Node;
+import org.cytoscape.equations.TreeNode;
 
 
 public class EquationCompilerImpl implements EquationCompiler {
@@ -59,7 +59,7 @@
                        return false;
                }
 
-               final Node parseTree = parser.getParseTree();
+               final TreeNode parseTree = parser.getParseTree();
 
                final Stack<CodeAndSourceLocation> codeStack = new 
Stack<CodeAndSourceLocation>();
                try {

Modified: 
core3/impl/trunk/equations-impl/src/main/java/org/cytoscape/equations/internal/EquationParserImpl.java
===================================================================
--- 
core3/impl/trunk/equations-impl/src/main/java/org/cytoscape/equations/internal/EquationParserImpl.java
      2011-11-24 00:47:09 UTC (rev 27597)
+++ 
core3/impl/trunk/equations-impl/src/main/java/org/cytoscape/equations/internal/EquationParserImpl.java
      2011-11-24 00:54:00 UTC (rev 27598)
@@ -41,7 +41,8 @@
 import org.cytoscape.equations.EquationParser;
 import org.cytoscape.equations.Function;
 import org.cytoscape.equations.FunctionUtil;
-import org.cytoscape.equations.Node;
+import org.cytoscape.equations.AbstractNode;
+import org.cytoscape.equations.TreeNode;
 import org.cytoscape.equations.internal.builtins.*;
 import org.cytoscape.equations.internal.parse_tree.*;
 
@@ -51,7 +52,7 @@
        private Tokeniser tokeniser;
        private Map<String, Function> nameToFunctionMap;
        private String lastErrorMessage;
-       private Node parseTree;
+       private TreeNode parseTree;
        private Map<String, Class<?>> variableNameToTypeMap;
        private Set<String> variableReferences;
        private Map<String, Object> defaultVariableValues;
@@ -147,7 +148,7 @@
        /**
         *  @return the parse tree.  Must only be called if parse() returns 
true!
         */
-       public Node getParseTree() { return parseTree; }
+       public TreeNode getParseTree() { return parseTree; }
 
        //
        // The actual parsing takes place here.
@@ -156,21 +157,21 @@
        /**
         *   Implements expr --> term | term {+ term } | term {- term} | term 
{&amp; term} | term compOp term.
         */
-       private Node parseExpr() {
-               Node exprNode = parseTerm();
+       private AbstractNode parseExpr() {
+               AbstractNode exprNode = parseTerm();
 
                for (;;) {
                        final Token token = tokeniser.getToken();
                        final int sourceLocation = tokeniser.getStartPos();
                        if (token == Token.PLUS || token == Token.MINUS || 
token == Token.AMPERSAND) {
-                               final Node term = parseTerm();
+                               final TreeNode term = parseTerm();
                                if (token == Token.PLUS || token == Token.MINUS)
                                        exprNode = 
handleBinaryArithmeticOp(token, sourceLocation, exprNode, term);
                                else // String concatenation.
                                        exprNode = new 
BinOpNode(sourceLocation, Token.AMPERSAND, exprNode, term);
                        }
                        else if (token.isComparisonOperator()) {
-                               final Node term = parseTerm();
+                               final TreeNode term = parseTerm();
                                return handleComparisonOp(token, 
sourceLocation, exprNode, term); // No chaining for comparison operators!
                        } else {
                                tokeniser.ungetToken(token);
@@ -182,14 +183,14 @@
        /**
         *  Implements term --> power {* power} | power {/ power}
         */
-       private Node parseTerm() {
-               Node termNode = parsePower();
+       private AbstractNode parseTerm() {
+               AbstractNode termNode = parsePower();
 
                for (;;) {
                        final Token token = tokeniser.getToken();
                        final int sourceLocation = tokeniser.getStartPos();
                        if (token == Token.MUL || token == Token.DIV) {
-                               final Node powerNode = parsePower();
+                               final TreeNode powerNode = parsePower();
                                termNode = handleBinaryArithmeticOp(token, 
sourceLocation, termNode, powerNode);
                        }
                        else {
@@ -202,13 +203,13 @@
        /**
         *  Implements power --> factor | factor ^ power
         */
-       private Node parsePower() {
-               Node powerNode = parseFactor();
+       private AbstractNode parsePower() {
+               AbstractNode powerNode = parseFactor();
 
                final Token token = tokeniser.getToken();
                final int sourceLocation = tokeniser.getStartPos();
                if (token == Token.CARET) {
-                       final Node rhs = parsePower();
+                       final TreeNode rhs = parsePower();
                        powerNode = handleBinaryArithmeticOp(token, 
sourceLocation, powerNode, rhs);
                }
                else
@@ -220,7 +221,7 @@
        /**
         *  Implements factor --> constant | variable_ref | "(" expr ")" | 
("-"|"+") factor  | func_call
         */
-       private Node parseFactor() {
+       private AbstractNode parseFactor() {
                Token token = tokeniser.getToken();
                int sourceLocation = tokeniser.getStartPos();
 
@@ -288,7 +289,7 @@
 
                // 3. a parenthesised expression
                if (token == Token.OPEN_PAREN) {
-                       final Node exprNode = parseExpr();
+                       final AbstractNode exprNode = parseExpr();
                        token = tokeniser.getToken();
                        if (token != Token.CLOSE_PAREN)
                                throw new IllegalStateException(sourceLocation 
+ ": '(' expected!");
@@ -298,7 +299,7 @@
 
                // 4. a unary operator
                if (token == Token.PLUS || token == Token.MINUS) {
-                       final Node factor = parseFactor();
+                       final TreeNode factor = parseFactor();
                        return handleUnaryOp(sourceLocation, token, factor);
                }
 
@@ -314,7 +315,7 @@
                throw new IllegalStateException(sourceLocation + ": unexpected 
input token: " + token + "!");
        }
 
-       private Node handleUnaryOp(final int sourceLocation, final Token 
operator, final Node operand) {
+       private AbstractNode handleUnaryOp(final int sourceLocation, final 
Token operator, final TreeNode operand) {
                final Class<?> operandType = operand.getType();
                if (operandType == Boolean.class || operandType == String.class
                    || FunctionUtil.isSomeKindOfList(operandType))
@@ -329,7 +330,7 @@
        /**
         *   Implements func_call --> ident "(" ")" | ident "(" expr {"," expr} 
")".
         */
-       private Node parseFunctionCall() {
+       private AbstractNode parseFunctionCall() {
                Token token = tokeniser.getToken();
                final int functionNameStartPos = tokeniser.getStartPos();
                if (token != Token.IDENTIFIER)
@@ -358,7 +359,7 @@
 
                // Parse the comma-separated argument list.
                final ArrayList<Class<?>> argTypes = new ArrayList<Class<?>>();
-               ArrayList<Node> args = new ArrayList<Node>();
+               ArrayList<AbstractNode> args = new ArrayList<AbstractNode>();
                int sourceLocation;
                for (;;) {
                        token = tokeniser.getToken();
@@ -367,7 +368,7 @@
                                break;
 
                        tokeniser.ungetToken(token);
-                       final Node exprNode = parseExpr();
+                       final AbstractNode exprNode = parseExpr();
                        argTypes.add(exprNode.getType());
                        args.add(exprNode);
 
@@ -386,7 +387,7 @@
                        throw new IllegalStateException(sourceLocation + ": 
expected the closing parenthesis of a call to "
                                                        + functionNameCandidate 
+ "!");
 
-               Node[] nodeArray = new Node[args.size()];
+               AbstractNode[] nodeArray = new AbstractNode[args.size()];
                return new FuncCallNode(functionNameStartPos, func, returnType, 
args.toArray(nodeArray));
        }
 
@@ -394,7 +395,7 @@
        /**
         *  Implements --> "DEFINED" "(" ident ")".  If the opening brace is 
found a closing brace is also required.
         */
-       private Node parseDefined() {
+       private AbstractNode parseDefined() {
                Token token = tokeniser.getToken();
                final int definedStart = tokeniser.getStartPos();
                if (token != Token.OPEN_PAREN)
@@ -442,7 +443,7 @@
        /**
         *  Deals w/ any necessary type conversions for any binary arithmetic 
operation on numbers.
         */
-       private Node handleBinaryArithmeticOp(final Token operator, final int 
sourceLocation, final Node lhs, final Node rhs) {
+       private AbstractNode handleBinaryArithmeticOp(final Token operator, 
final int sourceLocation, final TreeNode lhs, final TreeNode rhs) {
                // First operand is Double:
                if (lhs.getType() == Double.class && rhs.getType() == 
Double.class)
                        return new BinOpNode(sourceLocation, operator, lhs, 
rhs);
@@ -480,7 +481,7 @@
        /**
         *  Deals w/ any necessary type conversions for any binary comparison 
operation.
         */
-       private Node handleComparisonOp(final Token operator, final int 
sourceLocation, final Node lhs, final Node rhs) {
+       private AbstractNode handleComparisonOp(final Token operator, final int 
sourceLocation, final TreeNode lhs, final TreeNode rhs) {
                // First operand is Double:
                if (lhs.getType() == Double.class && rhs.getType() == 
Double.class)
                        return new BinOpNode(sourceLocation, operator, lhs, 
rhs);

Modified: 
core3/impl/trunk/equations-impl/src/main/java/org/cytoscape/equations/internal/parse_tree/BinOpNode.java
===================================================================
--- 
core3/impl/trunk/equations-impl/src/main/java/org/cytoscape/equations/internal/parse_tree/BinOpNode.java
    2011-11-24 00:47:09 UTC (rev 27597)
+++ 
core3/impl/trunk/equations-impl/src/main/java/org/cytoscape/equations/internal/parse_tree/BinOpNode.java
    2011-11-24 00:54:00 UTC (rev 27598)
@@ -33,7 +33,8 @@
 import java.util.Stack;
 
 import org.cytoscape.equations.CodeAndSourceLocation;
-import org.cytoscape.equations.Node;
+import org.cytoscape.equations.AbstractNode;
+import org.cytoscape.equations.TreeNode;
 import org.cytoscape.equations.internal.Token;
 import org.cytoscape.equations.internal.interpreter.Instruction;
 
@@ -41,11 +42,11 @@
 /**
  *  A node in the parse tree representing a binary operator.
  */
-public class BinOpNode extends Node {
+public class BinOpNode extends AbstractNode {
        private final Token operator;
-       private final Node lhs, rhs;
+       private final TreeNode lhs, rhs;
 
-       public BinOpNode(final int sourceLocation, final Token operator, final 
Node lhs, final Node rhs) {
+       public BinOpNode(final int sourceLocation, final Token operator, final 
TreeNode lhs, final TreeNode rhs) {
                super(sourceLocation);
 
                if (lhs == null)
@@ -65,12 +66,12 @@
        /**
         *  @return the left operand
         */
-       public Node getLeftChild() { return lhs; }
+       public TreeNode getLeftChild() { return lhs; }
 
        /**
         *  @return the right operand
         */
-       public Node getRightChild() { return rhs; }
+       public TreeNode getRightChild() { return rhs; }
 
        public Token getOperator() { return operator; }
 

Modified: 
core3/impl/trunk/equations-impl/src/main/java/org/cytoscape/equations/internal/parse_tree/BooleanConstantNode.java
===================================================================
--- 
core3/impl/trunk/equations-impl/src/main/java/org/cytoscape/equations/internal/parse_tree/BooleanConstantNode.java
  2011-11-24 00:47:09 UTC (rev 27597)
+++ 
core3/impl/trunk/equations-impl/src/main/java/org/cytoscape/equations/internal/parse_tree/BooleanConstantNode.java
  2011-11-24 00:54:00 UTC (rev 27598)
@@ -33,13 +33,14 @@
 import java.util.Stack;
 
 import org.cytoscape.equations.CodeAndSourceLocation;
-import org.cytoscape.equations.Node;
+import org.cytoscape.equations.AbstractNode;
+import org.cytoscape.equations.TreeNode;
 
 
 /**
  *  A node in the parse tree representing an integer constant.
  */
-public class BooleanConstantNode extends Node {
+public class BooleanConstantNode extends AbstractNode {
        private final boolean value;
 
        public BooleanConstantNode(final int sourceLocation, final boolean 
value) {
@@ -55,12 +56,12 @@
        /**
         *  @return null, This type of node never has any children!
         */
-       public Node getLeftChild() { return null; }
+       public TreeNode getLeftChild() { return null; }
 
        /**
         *  @return null, This type of node never has any children!
         */
-       public Node getRightChild() { return null; }
+       public TreeNode getRightChild() { return null; }
 
        public boolean getValue() { return value; }
 

Modified: 
core3/impl/trunk/equations-impl/src/main/java/org/cytoscape/equations/internal/parse_tree/FConvNode.java
===================================================================
--- 
core3/impl/trunk/equations-impl/src/main/java/org/cytoscape/equations/internal/parse_tree/FConvNode.java
    2011-11-24 00:47:09 UTC (rev 27597)
+++ 
core3/impl/trunk/equations-impl/src/main/java/org/cytoscape/equations/internal/parse_tree/FConvNode.java
    2011-11-24 00:54:00 UTC (rev 27598)
@@ -33,17 +33,18 @@
 import java.util.Stack;
 
 import org.cytoscape.equations.CodeAndSourceLocation;
-import org.cytoscape.equations.Node;
+import org.cytoscape.equations.AbstractNode;
+import org.cytoscape.equations.TreeNode;
 import org.cytoscape.equations.internal.interpreter.Instruction;
 
 
 /**
  *  A node in the parse tree representing a conversion to a floating point 
number
  */
-public class FConvNode extends Node {
-       private final Node convertee;
+public class FConvNode extends AbstractNode {
+       private final TreeNode convertee;
 
-       public FConvNode(final Node convertee) {
+       public FConvNode(final TreeNode convertee) {
                super(-1); // Type conversions are generated by the compiler 
and do not correspond to actual source locations!
 
                if (convertee == null)
@@ -65,12 +66,12 @@
        /**
         *  @return the only child of this node
         */
-       public Node getLeftChild() { return convertee; }
+       public TreeNode getLeftChild() { return convertee; }
 
        /**
         *  @return null, This type of node never has any right children!
         */
-       public Node getRightChild() { return null; }
+       public TreeNode getRightChild() { return null; }
 
        public void genCode(final Stack<CodeAndSourceLocation> codeStack) {
                convertee.genCode(codeStack);

Modified: 
core3/impl/trunk/equations-impl/src/main/java/org/cytoscape/equations/internal/parse_tree/FloatConstantNode.java
===================================================================
--- 
core3/impl/trunk/equations-impl/src/main/java/org/cytoscape/equations/internal/parse_tree/FloatConstantNode.java
    2011-11-24 00:47:09 UTC (rev 27597)
+++ 
core3/impl/trunk/equations-impl/src/main/java/org/cytoscape/equations/internal/parse_tree/FloatConstantNode.java
    2011-11-24 00:54:00 UTC (rev 27598)
@@ -33,13 +33,14 @@
 import java.util.Stack;
 
 import org.cytoscape.equations.CodeAndSourceLocation;
-import org.cytoscape.equations.Node;
+import org.cytoscape.equations.AbstractNode;
+import org.cytoscape.equations.TreeNode;
 
 
 /**
  *  A node in the parse tree representing an integer constant.
  */
-public class FloatConstantNode extends Node {
+public class FloatConstantNode extends AbstractNode {
        private final double value;
 
        public FloatConstantNode(final int sourceLocation, final double value) {
@@ -55,12 +56,12 @@
        /**
         *  @return null, This type of node never has any children!
         */
-       public Node getLeftChild() { return null; }
+       public TreeNode getLeftChild() { return null; }
 
        /**
         *  @return null, This type of node never has any children!
         */
-       public Node getRightChild() { return null; }
+       public TreeNode getRightChild() { return null; }
 
        public double getValue() { return value; }
 

Modified: 
core3/impl/trunk/equations-impl/src/main/java/org/cytoscape/equations/internal/parse_tree/FuncCallNode.java
===================================================================
--- 
core3/impl/trunk/equations-impl/src/main/java/org/cytoscape/equations/internal/parse_tree/FuncCallNode.java
 2011-11-24 00:47:09 UTC (rev 27597)
+++ 
core3/impl/trunk/equations-impl/src/main/java/org/cytoscape/equations/internal/parse_tree/FuncCallNode.java
 2011-11-24 00:54:00 UTC (rev 27598)
@@ -34,19 +34,20 @@
 
 import org.cytoscape.equations.CodeAndSourceLocation;
 import org.cytoscape.equations.Function;
-import org.cytoscape.equations.Node;
+import org.cytoscape.equations.AbstractNode;
+import org.cytoscape.equations.TreeNode;
 import org.cytoscape.equations.internal.interpreter.Instruction;
 
 
 /**
  *  A node in the parse tree representing a function call.
  */
-public class FuncCallNode extends Node {
+public class FuncCallNode extends AbstractNode {
        private final Function func;
        final Class returnType;
-       private final Node[] args;
+       private final TreeNode[] args;
 
-       public FuncCallNode(final int sourceLocation, final Function func, 
final Class returnType, final Node[] args) {
+       public FuncCallNode(final int sourceLocation, final Function func, 
final Class returnType, final TreeNode[] args) {
                super(sourceLocation);
 
                if (func == null)
@@ -68,12 +69,12 @@
        /**
         *  @return null, This type of node never has any children!
         */
-       public Node getLeftChild() { return null; }
+       public TreeNode getLeftChild() { return null; }
 
        /**
         *  @return null, This type of node never has any children!
         */
-       public Node getRightChild() { return null; }
+       public TreeNode getRightChild() { return null; }
 
        /**
         *  @return null, The return value for this node is only known at 
runtime!

Modified: 
core3/impl/trunk/equations-impl/src/main/java/org/cytoscape/equations/internal/parse_tree/IdentNode.java
===================================================================
--- 
core3/impl/trunk/equations-impl/src/main/java/org/cytoscape/equations/internal/parse_tree/IdentNode.java
    2011-11-24 00:47:09 UTC (rev 27597)
+++ 
core3/impl/trunk/equations-impl/src/main/java/org/cytoscape/equations/internal/parse_tree/IdentNode.java
    2011-11-24 00:54:00 UTC (rev 27598)
@@ -33,14 +33,15 @@
 import java.util.Stack;
 
 import org.cytoscape.equations.CodeAndSourceLocation;
-import org.cytoscape.equations.Node;
+import org.cytoscape.equations.AbstractNode;
+import org.cytoscape.equations.TreeNode;
 import org.cytoscape.equations.internal.interpreter.Instruction;
 
 
 /**
  *  A node in the parse tree representing an attribute reference.
  */
-public class IdentNode extends Node {
+public class IdentNode extends AbstractNode {
        private final String attribName;
        private final Object defaultValue;
        private final Class type;
@@ -66,12 +67,12 @@
        /**
         *  @return null, This type of node never has any children!
         */
-       public Node getLeftChild() { return null; }
+       public TreeNode getLeftChild() { return null; }
 
        /**
         *  @return null, This type of node never has any children!
         */
-       public Node getRightChild() { return null; }
+       public TreeNode getRightChild() { return null; }
 
        public String getAttribName() { return attribName; }
        public Object getDefaultValue() { return defaultValue; }

Modified: 
core3/impl/trunk/equations-impl/src/main/java/org/cytoscape/equations/internal/parse_tree/SConvNode.java
===================================================================
--- 
core3/impl/trunk/equations-impl/src/main/java/org/cytoscape/equations/internal/parse_tree/SConvNode.java
    2011-11-24 00:47:09 UTC (rev 27597)
+++ 
core3/impl/trunk/equations-impl/src/main/java/org/cytoscape/equations/internal/parse_tree/SConvNode.java
    2011-11-24 00:54:00 UTC (rev 27598)
@@ -33,17 +33,18 @@
 import java.util.Stack;
 
 import org.cytoscape.equations.CodeAndSourceLocation;
-import org.cytoscape.equations.Node;
+import org.cytoscape.equations.AbstractNode;
+import org.cytoscape.equations.TreeNode;
 import org.cytoscape.equations.internal.interpreter.Instruction;
 
 
 /**
  *  A node in the parse tree representing an conversion to a string
  */
-public class SConvNode extends Node {
-       private final Node convertee;
+public class SConvNode extends AbstractNode {
+       private final TreeNode convertee;
 
-       public SConvNode(final Node convertee) {
+       public SConvNode(final TreeNode convertee) {
                super(-1); // Type conversions are generated by the compiler 
and do not correspond to actual source locations!
 
                if (convertee == null)
@@ -65,12 +66,12 @@
        /**
         *  @return the only child of this node
         */
-       public Node getLeftChild() { return convertee; }
+       public TreeNode getLeftChild() { return convertee; }
 
        /**
         *  @return null, This type of node never has any right children!
         */
-       public Node getRightChild() { return null; }
+       public TreeNode getRightChild() { return null; }
 
        public void genCode(final Stack<CodeAndSourceLocation> codeStack) {
                convertee.genCode(codeStack);

Modified: 
core3/impl/trunk/equations-impl/src/main/java/org/cytoscape/equations/internal/parse_tree/StringConstantNode.java
===================================================================
--- 
core3/impl/trunk/equations-impl/src/main/java/org/cytoscape/equations/internal/parse_tree/StringConstantNode.java
   2011-11-24 00:47:09 UTC (rev 27597)
+++ 
core3/impl/trunk/equations-impl/src/main/java/org/cytoscape/equations/internal/parse_tree/StringConstantNode.java
   2011-11-24 00:54:00 UTC (rev 27598)
@@ -33,13 +33,14 @@
 import java.util.Stack;
 
 import org.cytoscape.equations.CodeAndSourceLocation;
-import org.cytoscape.equations.Node;
+import org.cytoscape.equations.AbstractNode;
+import org.cytoscape.equations.TreeNode;
 
 
 /**
  *  A node in the parse tree representing an integer constant.
  */
-public class StringConstantNode extends Node {
+public class StringConstantNode extends AbstractNode {
        private final String value;
 
        public StringConstantNode(final int sourceLocation, final String value) 
{
@@ -55,12 +56,12 @@
        /**
         *  @return null, This type of node never has any children!
         */
-       public Node getLeftChild() { return null; }
+       public TreeNode getLeftChild() { return null; }
 
        /**
         *  @return null, This type of node never has any children!
         */
-       public Node getRightChild() { return null; }
+       public TreeNode getRightChild() { return null; }
 
        public String getValue() { return value; }
 

Modified: 
core3/impl/trunk/equations-impl/src/main/java/org/cytoscape/equations/internal/parse_tree/UnaryOpNode.java
===================================================================
--- 
core3/impl/trunk/equations-impl/src/main/java/org/cytoscape/equations/internal/parse_tree/UnaryOpNode.java
  2011-11-24 00:47:09 UTC (rev 27597)
+++ 
core3/impl/trunk/equations-impl/src/main/java/org/cytoscape/equations/internal/parse_tree/UnaryOpNode.java
  2011-11-24 00:54:00 UTC (rev 27598)
@@ -33,7 +33,8 @@
 import java.util.Stack;
 
 import org.cytoscape.equations.CodeAndSourceLocation;
-import org.cytoscape.equations.Node;
+import org.cytoscape.equations.AbstractNode;
+import org.cytoscape.equations.TreeNode;
 import org.cytoscape.equations.internal.Token;
 import org.cytoscape.equations.internal.interpreter.Instruction;
 
@@ -41,11 +42,11 @@
 /**
  *  A node in the parse tree representing a unary operator application.
  */
-public class UnaryOpNode extends Node {
+public class UnaryOpNode extends AbstractNode {
        private final Token operator;
-       private final Node operand;
+       private final TreeNode operand;
 
-       public UnaryOpNode(final int sourceLocation, final Token operator, 
final Node operand) {
+       public UnaryOpNode(final int sourceLocation, final Token operator, 
final TreeNode operand) {
                super(sourceLocation);
 
                if (operand == null)
@@ -62,12 +63,12 @@
        /**
         *  @return the operand
         */
-       public Node getLeftChild() { return operand; }
+       public TreeNode getLeftChild() { return operand; }
 
        /**
         *  @return null, This type of node never has any left children!
         */
-       public Node getRightChild() { return null; }
+       public TreeNode getRightChild() { return null; }
 
        public Token getOperator() { return operator; }
 

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