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[Jsbml-svn] SF.net SVN: jsbml:[2385] trunk/core
|
From: <and...@us...> - 2015-10-15 20:11:18
|
Revision: 2385
http://sourceforge.net/p/jsbml/code/2385
Author: andreas-draeger
Date: 2015-10-15 20:11:15 +0000 (Thu, 15 Oct 2015)
Log Message:
-----------
Corrected several invalid JavaDoc entries.
Modified Paths:
--------------
trunk/core/src/org/sbml/jsbml/ASTNode.java
trunk/core/src/org/sbml/jsbml/CVTerm.java
trunk/core/src/org/sbml/jsbml/math/ASTArithmeticOperatorNode.java
trunk/core/src/org/sbml/jsbml/math/ASTBinaryFunctionNode.java
trunk/core/src/org/sbml/jsbml/math/ASTBoolean.java
trunk/core/src/org/sbml/jsbml/math/ASTCSymbolAvogadroNode.java
trunk/core/src/org/sbml/jsbml/math/ASTCSymbolBaseNode.java
trunk/core/src/org/sbml/jsbml/math/ASTCSymbolDelayNode.java
trunk/core/src/org/sbml/jsbml/math/ASTCSymbolTimeNode.java
trunk/core/src/org/sbml/jsbml/math/ASTCiFunctionNode.java
trunk/core/src/org/sbml/jsbml/math/ASTCiNumberNode.java
trunk/core/src/org/sbml/jsbml/math/ASTCnExponentialNode.java
trunk/core/src/org/sbml/jsbml/math/ASTCnIntegerNode.java
trunk/core/src/org/sbml/jsbml/math/ASTCnNumberNode.java
trunk/core/src/org/sbml/jsbml/math/ASTCnRationalNode.java
trunk/core/src/org/sbml/jsbml/math/ASTCnRealNode.java
trunk/core/src/org/sbml/jsbml/math/ASTConstantNumber.java
trunk/core/src/org/sbml/jsbml/math/ASTDivideNode.java
trunk/core/src/org/sbml/jsbml/math/ASTFactory.java
trunk/core/src/org/sbml/jsbml/math/ASTFunction.java
trunk/core/src/org/sbml/jsbml/math/ASTLogicalOperatorNode.java
trunk/core/src/org/sbml/jsbml/math/ASTNode2.java
trunk/core/src/org/sbml/jsbml/math/ASTPowerNode.java
trunk/core/src/org/sbml/jsbml/math/ASTQualifierNode.java
trunk/core/src/org/sbml/jsbml/math/ASTRelationalOperatorNode.java
trunk/core/src/org/sbml/jsbml/math/ASTRootNode.java
trunk/core/src/org/sbml/jsbml/math/ASTTrigonometricNode.java
trunk/core/src/org/sbml/jsbml/math/ASTUnaryFunctionNode.java
trunk/core/src/org/sbml/jsbml/math/ASTUnknown.java
trunk/core/src/org/sbml/jsbml/math/AbstractASTNode.java
trunk/core/src/org/sbml/jsbml/math/compiler/ASTNode2Compiler.java
trunk/core/src/org/sbml/jsbml/math/compiler/ASTNode2Value.java
trunk/core/src/org/sbml/jsbml/math/compiler/FindUnitsCompiler.java
trunk/core/src/org/sbml/jsbml/math/compiler/FormulaCompiler.java
trunk/core/src/org/sbml/jsbml/math/compiler/HTMLFormula.java
trunk/core/src/org/sbml/jsbml/math/compiler/LaTeXCompiler.java
trunk/core/src/org/sbml/jsbml/math/compiler/MathMLXMLStreamCompiler.java
trunk/core/src/org/sbml/jsbml/math/compiler/UnitException.java
trunk/core/src/org/sbml/jsbml/math/compiler/UnitsCompiler.java
trunk/core/src/org/sbml/jsbml/math/parser/FormulaParserLL3.java
trunk/core/src/org/sbml/jsbml/math/parser/FormulaParserLL3ASTNode2.java
trunk/core/src/org/sbml/jsbml/math/parser/IFormulaParser.java
trunk/core/src/org/sbml/jsbml/text/parser/CobraFormulaParser.java
trunk/core/src/org/sbml/jsbml/text/parser/FormulaParser.java
trunk/core/src/org/sbml/jsbml/text/parser/FormulaParserLL3.java
trunk/core/src/org/sbml/jsbml/text/parser/FormulaParserLL3ASTNode2.java
trunk/core/src/org/sbml/jsbml/validator/SBMLValidator.java
trunk/core/test/org/sbml/jsbml/math/test/ASTArithmeticOperatorNodeTest.java
trunk/core/test/org/sbml/jsbml/math/test/ASTBinaryFunctionNodeTest.java
trunk/core/test/org/sbml/jsbml/math/test/ASTBooleanTest.java
trunk/core/test/org/sbml/jsbml/math/test/ASTCiFunctionNodeTest.java
trunk/core/test/org/sbml/jsbml/math/test/ASTCiNumberNodeTest.java
trunk/core/test/org/sbml/jsbml/math/test/ASTCnExponentialNodeTest.java
trunk/core/test/org/sbml/jsbml/math/test/ASTCnNumberNodeTest.java
trunk/core/test/org/sbml/jsbml/math/test/ASTConstantNumberTest.java
trunk/core/test/org/sbml/jsbml/math/test/ASTFactoryTest.java
trunk/core/test/org/sbml/jsbml/math/test/ASTFunctionTest.java
trunk/core/test/org/sbml/jsbml/math/test/ASTLambdaFunctionTest.java
trunk/core/test/org/sbml/jsbml/math/test/ASTLogarithmNodeTest.java
trunk/core/test/org/sbml/jsbml/math/test/ASTMinusNodeTest.java
trunk/core/test/org/sbml/jsbml/math/test/ASTPowerNodeTest.java
trunk/core/test/org/sbml/jsbml/math/test/ASTQualifierNodeTest.java
trunk/core/test/org/sbml/jsbml/math/test/ASTRelationalOperatorNodeTest.java
trunk/core/test/org/sbml/jsbml/math/test/ASTRootNodeTest.java
trunk/core/test/org/sbml/jsbml/math/test/ASTTimesNodeTest.java
trunk/core/test/org/sbml/jsbml/math/test/ASTTrigonometricNodeTest.java
trunk/core/test/org/sbml/jsbml/math/test/ASTUnaryFunctionNodeTest.java
Modified: trunk/core/src/org/sbml/jsbml/ASTNode.java
===================================================================
--- trunk/core/src/org/sbml/jsbml/ASTNode.java 2015-10-14 10:24:09 UTC (rev 2384)
+++ trunk/core/src/org/sbml/jsbml/ASTNode.java 2015-10-15 20:11:15 UTC (rev 2385)
@@ -639,8 +639,8 @@
* or {@link #IMPLEMENTATION_ASTNODE2}.
*/
public static final String IMPLEMENTATION_VERSION = IMPLEMENTATION_HISTORIC;
-
-
+
+
/**
* Creates and returns an {@link ASTNode} that computes the absolute value
* of the given double value.
@@ -3797,7 +3797,6 @@
/**
* Sets the Parent of the node to the given value
*
- * @param node the orphan node
* @param parent the parent
*/
public void setParentSBMLObject(MathContainer parent) {
@@ -3829,7 +3828,7 @@
if (logger.isDebugEnabled()) {
logger.debug("ASTNode: setType(String) called: " + typeStr);
}
-
+
Type type = Type.getTypeFor(typeStr);
setType(type);
if (type != Type.UNKNOWN) {
@@ -4224,40 +4223,40 @@
return formula;
}
-
-
+
+
/**
* Returns a simple String representing the content of the ASTNode.
*
* @return a simple String representing the content of the ASTNode.
*/
public String toSimpleString() {
- StringBuffer buffer = new StringBuffer("ASTNode [type=");
+ StringBuffer buffer = new StringBuffer("ASTNode [type=");
buffer.append(type);
-
- if (isInteger())
+
+ if (isInteger())
{
buffer.append(", ").append(getInteger());
}
- else if (isReal())
+ else if (isReal())
{
buffer.append(", ").append(getReal());
-
- if (isRational())
+
+ if (isRational())
{
buffer.append(" (").append(getNumerator()).append(" / ").append(getDenominator());
}
- else if (exponent != 0)
+ else if (exponent != 0)
{
buffer.append(" (").append(getMantissa()).append("e").append(getExponent());
}
}
- else if (isName())
+ else if (isName())
{
buffer.append(", name = ").append(getName());
}
-
- if (definitionURL != null)
+
+ if (definitionURL != null)
{
buffer.append(", definitionURL = ").append(getDefinitionURL());
}
@@ -4265,19 +4264,19 @@
if (unitId != null) {
buffer.append(", units = ").append(getUnits());
}
-
+
if (getChildCount() > 0) {
buffer.append(", nb children = ").append(getChildCount());
}
-
+
if (isSetUserObjects()) {
- buffer.append(", user object keys = ").append(userObjectKeySet());
+ buffer.append(", user object keys = ").append(userObjectKeySet());
}
-
+
if (getParent() == null) {
buffer.append(", no parent defined");
}
-
+
if (id != null) {
buffer.append(", id = ").append(getId());
}
@@ -4290,7 +4289,7 @@
if (className != null) {
buffer.append(", className = ").append(getClassName());
}
-
+
return buffer.toString();
}
@@ -4342,13 +4341,13 @@
* @return a simple tree view of the ASTNode internal
*/
public static String astNodeToTree(ASTNode n, String tree, String indent) {
- tree = tree + indent + n.getType() + " " +
+ tree = tree + indent + n.getType() + " " +
(n.isInteger() ? n.getInteger() : "") + (n.isReal() ? n.getReal() : "") + "\n";
-
+
for (ASTNode child : n.getChildren()) {
tree = astNodeToTree(child, tree, indent + " ");
}
-
+
return tree;
}
Modified: trunk/core/src/org/sbml/jsbml/CVTerm.java
===================================================================
--- trunk/core/src/org/sbml/jsbml/CVTerm.java 2015-10-14 10:24:09 UTC (rev 2384)
+++ trunk/core/src/org/sbml/jsbml/CVTerm.java 2015-10-15 20:11:15 UTC (rev 2385)
@@ -375,7 +375,7 @@
* SBML level 2 version 5 (and future SBML L3V2), the annotations can be recursive.
*/
private List<CVTerm> listOfNestedCVTerms;
-
+
/**
* Represents the type of MIRIAM qualifier for this {@link CVTerm}. It
* depends on the name space in the SBML file, it can be a model qualifier
@@ -1168,8 +1168,8 @@
type = null;
}
}
-
-
+
+
/**
* Returns {@code true} if {@link #listOfNestedCVTerms} contains at least
* one element.
@@ -1192,7 +1192,7 @@
*/
public List<CVTerm> getListOfNestedCVTerms() {
if (listOfNestedCVTerms == null) {
- listOfNestedCVTerms = new ArrayList<CVTerm>();
+ listOfNestedCVTerms = new ArrayList<CVTerm>();
}
return listOfNestedCVTerms;
}
@@ -1201,12 +1201,11 @@
* Sets the given {@code ListOf<CVTerm>}.
* If {@link #listOfNestedCVTerms} was defined before and contains some
* elements, they are all unset.
- *
- * @param listOfNestedCVTerms
+ * @param listOfCVTerms
*/
public void setListOfNestedCVTerms(List<CVTerm> listOfCVTerms) {
unsetListOfNestedCVTerms();
- this.listOfNestedCVTerms = listOfCVTerms;
+ listOfNestedCVTerms = listOfCVTerms;
}
/**
@@ -1218,8 +1217,8 @@
*/
public boolean unsetListOfNestedCVTerms() {
if (isSetListOfNestedCVTerms()) {
- List<CVTerm> oldCVTerms = this.listOfNestedCVTerms;
- this.listOfNestedCVTerms = null;
+ List<CVTerm> oldCVTerms = listOfNestedCVTerms;
+ listOfNestedCVTerms = null;
// oldCVTerms.fireNodeRemovedEvent();
return true;
}
@@ -1313,7 +1312,7 @@
*
* @return the number of {@link CVTerm}s in this
* {@link CVTerm}.
- * @libsbml.deprecated same as {@link #getCVTermCount()}
+ * @libsbml.deprecated same as {@link #getNestedCVTermCount()}
*/
public int getNumNestedCVTerms() {
return getNestedCVTermCount();
Modified: trunk/core/src/org/sbml/jsbml/math/ASTArithmeticOperatorNode.java
===================================================================
--- trunk/core/src/org/sbml/jsbml/math/ASTArithmeticOperatorNode.java 2015-10-14 10:24:09 UTC (rev 2384)
+++ trunk/core/src/org/sbml/jsbml/math/ASTArithmeticOperatorNode.java 2015-10-15 20:11:15 UTC (rev 2385)
@@ -45,17 +45,17 @@
* @date May 30, 2014
*/
public class ASTArithmeticOperatorNode extends ASTFunction {
-
+
/**
*
*/
private static final long serialVersionUID = -7712374792704509306L;
-
+
/**
* A {@link Logger} for this class.
*/
private static final Logger logger = Logger.getLogger(ASTArithmeticOperatorNode.class);
-
+
/**
* Creates a new {@link ASTArithmeticOperatorNode} without a pointer
* to its containing {@link MathContainer}.
@@ -63,7 +63,7 @@
public ASTArithmeticOperatorNode() {
super();
}
-
+
/**
* Copy constructor; Creates a deep copy of the given {@link ASTArithmeticOperatorNode}.
*
@@ -73,19 +73,21 @@
public ASTArithmeticOperatorNode(ASTArithmeticOperatorNode node) {
super(node);
}
-
+
/**
* Creates a new {@link ASTArithmeticOperatorNode} with a pointer
* to the specified {@link MathContainer}..
+ * @param container
*/
public ASTArithmeticOperatorNode(MathContainer container) {
super(container);
}
-
+
/**
* Creates a new {@link ASTArithmeticOperatorNode} without a pointer
- * to its containing {@link MathContainer} but of the specified
+ * to its containing {@link MathContainer} but of the specified
* {@link Type}.
+ * @param type
*/
public ASTArithmeticOperatorNode(Type type) {
this();
@@ -95,6 +97,8 @@
/**
* Creates a new {@link ASTArithmeticOperatorNode} of type
* {@link Type} and container {@link MathContainer}.
+ * @param type
+ * @param container
*/
public ASTArithmeticOperatorNode(Type type, MathContainer container) {
this(container);
@@ -108,7 +112,7 @@
public ASTArithmeticOperatorNode clone() {
return new ASTArithmeticOperatorNode(this);
}
-
+
/* (non-Javadoc)
* @see org.sbml.jsbml.math.ASTNode2#compile(org.sbml.jsbml.util.compilers.ASTNode2Compiler)
*/
@@ -148,7 +152,7 @@
}
return processValue(value);
}
-
+
/* (non-Javadoc)
* @see org.sbml.jsbml.math.ASTFunction#isAllowableType(org.sbml.jsbml.ASTNode.Type)
*/
@@ -169,10 +173,10 @@
}
return false;
}
-
+
/**
- * Sets the value of this {@link ASTArithmeticOperatorNode} to the given character. If
- * character is one of +, -, *, / or ^, the node type will be set accordingly.
+ * Sets the value of this {@link ASTArithmeticOperatorNode} to the given character. If
+ * character is one of +, -, *, / or ^, the node type will be set accordingly.
* For all other characters, the node type will be set to UNKNOWN.
*
* @param value
Modified: trunk/core/src/org/sbml/jsbml/math/ASTBinaryFunctionNode.java
===================================================================
--- trunk/core/src/org/sbml/jsbml/math/ASTBinaryFunctionNode.java 2015-10-14 10:24:09 UTC (rev 2384)
+++ trunk/core/src/org/sbml/jsbml/math/ASTBinaryFunctionNode.java 2015-10-15 20:11:15 UTC (rev 2385)
@@ -27,8 +27,6 @@
import org.apache.log4j.Logger;
-
-
/**
* An Abstract Syntax Tree (AST) node representing a function with two
* parameters
@@ -44,7 +42,7 @@
*
*/
private static final long serialVersionUID = -4036869111918452252L;
-
+
/**
* A {@link Logger} for this class.
*/
@@ -56,7 +54,7 @@
public ASTBinaryFunctionNode() {
super();
}
-
+
/**
* Copy constructor; Creates a deep copy of the given {@link ASTBinaryFunctionNode}.
*
@@ -70,34 +68,36 @@
/**
* Creates a new {@link ASTBinaryFunctionNode} with the specified
* children.
+ * @param leftChild
+ * @param rightChild
*/
public ASTBinaryFunctionNode(ASTNode2 leftChild, ASTNode2 rightChild) {
this();
addChild(leftChild);
addChild(rightChild);
}
-
+
/**
* Adds a child to this node.
*
* @param child
* the node to add as child.
- *
+ *
* @throws NullPointerException if the child is null
* @throws IndexOutOfBoundsException if strictness is set to true
- * and max child limit has been exceeded
+ * and max child limit has been exceeded
*/
@Override
public void addChild(ASTNode2 child) {
if (! isSetList()) {
listOfNodes = new ArrayList<ASTNode2>(2);
- }
+ }
if (isStrict() && getChildCount() == 2) {
throw new IndexOutOfBoundsException("max child limit exceeded");
}
if (getChildCount() >= 2) {
logger.debug("Max child limit exceeded. To add more children " +
- "to ASTBinaryFunctionNode set strictness to false.");
+ "to ASTBinaryFunctionNode set strictness to false.");
}
listOfNodes.add(child);
ASTFactory.setParentSBMLObject(child, parentSBMLObject);
@@ -116,7 +116,7 @@
/**
* @throws IndexOutOfBoundsException if strictness is set to true
- * and max child limit has been exceeded
+ * and max child limit has been exceeded
*/
@Override
public ASTNode2 getChildAt(int childIndex) {
@@ -153,11 +153,11 @@
* long the index of the {@link ASTNode2} being added
* @param newChild
* {@link ASTNode2} to insert as the n<sup>th</sup> child
- *
+ *
* @throws NullPointerException if the child is null
* @throws IndexOutOfBoundsException if strictness is set to true
- * and max child limit has been exceeded
- *
+ * and max child limit has been exceeded
+ *
*/
@Override
public void insertChild(int n, ASTNode2 newChild) {
@@ -169,7 +169,7 @@
}
if (getChildCount() == 2) {
logger.debug("Max child limit exceeded. To add more children " +
- "to ASTBinaryFunctionNode set strictness to false.");
+ "to ASTBinaryFunctionNode set strictness to false.");
}
listOfNodes.add(n, newChild);
ASTFactory.setParentSBMLObject(newChild, parentSBMLObject);
@@ -184,7 +184,7 @@
public boolean isSetLeftChild() {
return getChildCount() > 0;
}
-
+
/**
* Return true iff right child has been set
*
@@ -193,18 +193,18 @@
public boolean isSetRightChild() {
return getChildCount() > 1;
}
-
+
/**
- * Adds the given node as a child of this {@link ASTBinaryFunctionNode}.
+ * Adds the given node as a child of this {@link ASTBinaryFunctionNode}.
* This method adds child nodes from right to left.
*
* @param child
* an {@code ASTNode2}
- *
- * @throws NullPointerException if the child is null
+ *
+ * @throws NullPointerException if the child is null
* @throws IndexOutOfBoundsException if strictness is set to true
- * and max child limit has been exceeded
- *
+ * and max child limit has been exceeded
+ *
*/
@Override
public void prependChild(ASTNode2 child) {
@@ -216,13 +216,13 @@
}
if (getChildCount() == 2) {
logger.debug("Max child limit exceeded. To add more children " +
- "to ASTBinaryFunctionNode set strictness to false.");
+ "to ASTBinaryFunctionNode set strictness to false.");
}
listOfNodes.add(0, child);
ASTFactory.setParentSBMLObject(child, parentSBMLObject);
child.setParent(this);
}
-
+
/*
* (non-Javadoc)
* @see org.sbml.jsbml.math.ASTFunction#removeChild(int)
@@ -266,7 +266,7 @@
}
addChild(child);
}
-
+
/**
* <p>
* Swaps the children of this {@link ASTFunction} with the children of that
@@ -291,10 +291,10 @@
* @param that
* the other node whose children should be used to replace this
* node's children
- *
+ *
* @throws IndexOutOfBoundsException if strictness is set to true
- * and max child limit has been exceeded
- *
+ * and max child limit has been exceeded
+ *
*/
@Override
public void swapChildren(ASTFunction that) {
@@ -303,13 +303,13 @@
}
if (that.getChildCount() > 2) {
logger.debug("Max child limit exceeded. To add more children " +
- "to ASTBinaryFunctionNode set strictness to false.");
+ "to ASTBinaryFunctionNode set strictness to false.");
}
List<ASTNode2> swap = that.listOfNodes;
that.listOfNodes = listOfNodes;
listOfNodes = swap;
}
-
+
/* (non-Javadoc)
* @see java.lang.Object#toString()
*/
Modified: trunk/core/src/org/sbml/jsbml/math/ASTBoolean.java
===================================================================
--- trunk/core/src/org/sbml/jsbml/math/ASTBoolean.java 2015-10-14 10:24:09 UTC (rev 2384)
+++ trunk/core/src/org/sbml/jsbml/math/ASTBoolean.java 2015-10-15 20:11:15 UTC (rev 2385)
@@ -1,24 +1,24 @@
/*
* $Id$
* $URL$
- * ----------------------------------------------------------------------------
- * This file is part of JSBML. Please visit <http://sbml.org/Software/JSBML>
- * for the latest version of JSBML and more information about SBML.
+ * ----------------------------------------------------------------------------
+ * This file is part of JSBML. Please visit <http://sbml.org/Software/JSBML>
+ * for the latest version of JSBML and more information about SBML.
*
- * Copyright (C) 2009-2014 jointly by the following organizations:
- * 1. The University of Tuebingen, Germany
- * 2. EMBL European Bioinformatics Institute (EBML-EBI), Hinxton, UK
- * 3. The California Institute of Technology, Pasadena, CA, USA
+ * Copyright (C) 2009-2014 jointly by the following organizations:
+ * 1. The University of Tuebingen, Germany
+ * 2. EMBL European Bioinformatics Institute (EBML-EBI), Hinxton, UK
+ * 3. The California Institute of Technology, Pasadena, CA, USA
* 4. The University of California, San Diego, La Jolla, CA, USA
* 5. The Babraham Institute, Cambridge, UK
* 6. The University of Toronto, Toronto, ON, Canada
*
- * 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. A copy of the license agreement is provided
- * in the file named "LICENSE.txt" included with this software distribution
- * and also available online as <http://sbml.org/Software/JSBML/License>.
- * ----------------------------------------------------------------------------
+ * 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. A copy of the license agreement is provided
+ * in the file named "LICENSE.txt" included with this software distribution
+ * and also available online as <http://sbml.org/Software/JSBML/License>.
+ * ----------------------------------------------------------------------------
*/
package org.sbml.jsbml.math;
@@ -51,15 +51,18 @@
* A {@link Logger} for this class.
*/
private static final Logger logger = Logger.getLogger(ASTBoolean.class);
-
+
+ /**
+ *
+ */
public ASTBoolean() {
super();
}
-
+
/**
* Copy constructor; Creates a deep copy of the given {@link ASTBoolean}.
*
- * @param node
+ * @param bool
* the {@link ASTBoolean} to be copied.
*/
public ASTBoolean(ASTBoolean bool) {
@@ -68,12 +71,13 @@
/**
* Creates a new {@link ASTBoolean}.
+ * @param type
*/
public ASTBoolean(Type type) {
this();
setType(type);
}
-
+
/* (non-Javadoc)
* @see org.sbml.jsbml.AbstractTreeNode#clone()
*/
@@ -100,7 +104,7 @@
}
return processValue(value);
}
-
+
/* (non-Javadoc)
* @see javax.swing.tree.TreeNode#getAllowsChildren()
*/
@@ -141,7 +145,7 @@
logger.warn(error);
return false;
}
-
+
/* (non-Javadoc)
* @see org.sbml.jsbml.math.ASTNode2#isAllowableType(org.sbml.jsbml.ASTNode.Type)
*/
@@ -149,7 +153,7 @@
public boolean isAllowableType(Type type) {
return type == Type.CONSTANT_TRUE || type == Type.CONSTANT_FALSE;
}
-
+
/*
* (non-Javadoc)
* @see org.sbml.jsbml.math.AbstractASTNode#isSetType()
@@ -158,7 +162,7 @@
public boolean isSetType() {
return type == Type.CONSTANT_TRUE || type == Type.CONSTANT_FALSE;
}
-
+
/**
* Set the value of this {@link ASTBoolean}
*
@@ -217,5 +221,5 @@
builder.append("]");
return builder.toString();
}
-
+
}
Modified: trunk/core/src/org/sbml/jsbml/math/ASTCSymbolAvogadroNode.java
===================================================================
--- trunk/core/src/org/sbml/jsbml/math/ASTCSymbolAvogadroNode.java 2015-10-14 10:24:09 UTC (rev 2384)
+++ trunk/core/src/org/sbml/jsbml/math/ASTCSymbolAvogadroNode.java 2015-10-15 20:11:15 UTC (rev 2385)
@@ -31,8 +31,6 @@
import org.sbml.jsbml.util.Maths;
import org.sbml.jsbml.util.TreeNodeChangeEvent;
-
-
/**
* An Abstract Syntax Tree (AST) node representing avogadro's number
*
@@ -84,7 +82,7 @@
/**
* Copy constructor; Creates a deep copy of the given {@link ASTCSymbolAvogadroNode}.
*
- * @param astFunction
+ * @param node
* the {@link ASTCSymbolAvogadroNode} to be copied.
*/
public ASTCSymbolAvogadroNode(ASTCSymbolAvogadroNode node) {
@@ -93,13 +91,13 @@
setDefinitionURL(node.getDefinitionURL());
}
if (node.isSetEncoding()) {
- setEncoding(node.getEncoding());
+ setEncoding(node.getEncoding());
}
if (node.isSetName()) {
setName(node.getName());
}
}
-
+
/*
* (non-Javadoc)
* @see org.sbml.jsbml.math.ASTConstantNumber#clone()
@@ -117,7 +115,7 @@
ASTNode2Value<?> value = null;
switch(getType()) {
case NAME_AVOGADRO:
- value = compiler.getConstantAvogadro(isSetName() ? getName() : "avogadro");
+ value = compiler.getConstantAvogadro(isSetName() ? getName() : "avogadro");
break;
default: // UNKNOWN:
value = compiler.unknownValue();
@@ -131,28 +129,37 @@
*/
@Override
public boolean equals(Object obj) {
- if (this == obj)
+ if (this == obj) {
return true;
- if (!super.equals(obj))
+ }
+ if (!super.equals(obj)) {
return false;
- if (getClass() != obj.getClass())
+ }
+ if (getClass() != obj.getClass()) {
return false;
+ }
ASTCSymbolAvogadroNode other = (ASTCSymbolAvogadroNode) obj;
if (definitionURL == null) {
- if (other.definitionURL != null)
+ if (other.definitionURL != null) {
return false;
- } else if (!definitionURL.equals(other.definitionURL))
+ }
+ } else if (!definitionURL.equals(other.definitionURL)) {
return false;
+ }
if (encoding == null) {
- if (other.encoding != null)
+ if (other.encoding != null) {
return false;
- } else if (!encoding.equals(other.encoding))
+ }
+ } else if (!encoding.equals(other.encoding)) {
return false;
+ }
if (name == null) {
- if (other.name != null)
+ if (other.name != null) {
return false;
- } else if (!name.equals(other.name))
+ }
+ } else if (!name.equals(other.name)) {
return false;
+ }
return true;
}
@@ -221,9 +228,9 @@
final int prime = 1511;
int result = super.hashCode();
result = prime * result
- + ((definitionURL == null) ? 0 : definitionURL.hashCode());
+ + ((definitionURL == null) ? 0 : definitionURL.hashCode());
result = prime * result
- + ((encoding == null) ? 0 : encoding.hashCode());
+ + ((encoding == null) ? 0 : encoding.hashCode());
result = prime * result + ((name == null) ? 0 : name.hashCode());
return result;
}
@@ -235,7 +242,7 @@
public boolean isAllowableType(Type type) {
return type == Type.NAME_AVOGADRO;
}
-
+
/*
* (non-Javadoc)
* @see org.sbml.jsbml.math.ASTCSymbolBaseNode#isSetDefinitionURL()
@@ -283,19 +290,19 @@
* Set the definitionURL of the MathML element represented by
* this {@link ASTCSymbolAvogadroNode}
*
- * @param String definitionURL
+ * @param definitionURL
*/
private void setDefinitionURL(String definitionURL) {
String old = this.definitionURL;
this.definitionURL = definitionURL;
firePropertyChange(TreeNodeChangeEvent.definitionURL, old, encoding);
}
-
+
/**
* Set the encoding of the MathML element represented by
* this {@link ASTCSymbolAvogadroNode}
*
- * @param String encoding
+ * @param encoding
*/
private void setEncoding(String encoding) {
String old = this.encoding;
Modified: trunk/core/src/org/sbml/jsbml/math/ASTCSymbolBaseNode.java
===================================================================
--- trunk/core/src/org/sbml/jsbml/math/ASTCSymbolBaseNode.java 2015-10-14 10:24:09 UTC (rev 2384)
+++ trunk/core/src/org/sbml/jsbml/math/ASTCSymbolBaseNode.java 2015-10-15 20:11:15 UTC (rev 2385)
@@ -62,7 +62,7 @@
* @return boolean
*/
public boolean isSetName();
-
+
/**
* Returns {@code true} if this node or one of its descendants contains some
* identifier with the given id. This method can be used to scan a formula
@@ -75,13 +75,13 @@
* given id.
*/
public boolean refersTo(String id);
-
+
/**
* Set the name of the MathML element represented by
* this {@link ASTCSymbolBaseNode}
*
- * @param String name
+ * @param name
*/
public void setName(String name);
-
+
}
Modified: trunk/core/src/org/sbml/jsbml/math/ASTCSymbolDelayNode.java
===================================================================
--- trunk/core/src/org/sbml/jsbml/math/ASTCSymbolDelayNode.java 2015-10-14 10:24:09 UTC (rev 2384)
+++ trunk/core/src/org/sbml/jsbml/math/ASTCSymbolDelayNode.java 2015-10-15 20:11:15 UTC (rev 2385)
@@ -84,8 +84,7 @@
/**
* Copy constructor; Creates a deep copy of the given {@link ASTCSymbolDelayNode}.
*
- * @param astFunction
- * the {@link ASTCSymbolDelayNode} to be copied.
+ * @param node the {@link ASTCSymbolDelayNode} to be copied.
*/
public ASTCSymbolDelayNode(ASTCSymbolDelayNode node) {
super(node);
@@ -99,7 +98,7 @@
setName(node.getName());
}
}
-
+
/*
* (non-Javadoc)
* @see org.sbml.jsbml.math.ASTFunction#clone()
@@ -108,15 +107,15 @@
public ASTCSymbolDelayNode clone() {
return new ASTCSymbolDelayNode(this);
}
-
+
/* (non-Javadoc)
* @see org.sbml.jsbml.math.ASTNode2#compile(org.sbml.jsbml.util.compilers.ASTNode2Compiler)
*/
@Override
public ASTNode2Value<?> compile(ASTNode2Compiler compiler) {
ASTNode2Value<?> value = null;
- value = isSetName() ? compiler.delay(getName(), getLeftChild(), getRightChild())
- : compiler.delay("delay", getLeftChild(), getRightChild());
+ value = isSetName() ? compiler.delay(getName(), getLeftChild(), getRightChild())
+ : compiler.delay("delay", getLeftChild(), getRightChild());
return processValue(value);
}
@@ -125,28 +124,37 @@
*/
@Override
public boolean equals(Object obj) {
- if (this == obj)
+ if (this == obj) {
return true;
- if (!super.equals(obj))
+ }
+ if (!super.equals(obj)) {
return false;
- if (getClass() != obj.getClass())
+ }
+ if (getClass() != obj.getClass()) {
return false;
+ }
ASTCSymbolDelayNode other = (ASTCSymbolDelayNode) obj;
if (definitionURL == null) {
- if (other.definitionURL != null)
+ if (other.definitionURL != null) {
return false;
- } else if (!definitionURL.equals(other.definitionURL))
+ }
+ } else if (!definitionURL.equals(other.definitionURL)) {
return false;
+ }
if (encoding == null) {
- if (other.encoding != null)
+ if (other.encoding != null) {
return false;
- } else if (!encoding.equals(other.encoding))
+ }
+ } else if (!encoding.equals(other.encoding)) {
return false;
+ }
if (name == null) {
- if (other.name != null)
+ if (other.name != null) {
return false;
- } else if (!name.equals(other.name))
+ }
+ } else if (!name.equals(other.name)) {
return false;
+ }
return true;
}
@@ -190,9 +198,9 @@
final int prime = 1291;
int result = super.hashCode();
result = prime * result
- + ((definitionURL == null) ? 0 : definitionURL.hashCode());
+ + ((definitionURL == null) ? 0 : definitionURL.hashCode());
result = prime * result
- + ((encoding == null) ? 0 : encoding.hashCode());
+ + ((encoding == null) ? 0 : encoding.hashCode());
result = prime * result + ((name == null) ? 0 : name.hashCode());
return result;
}
@@ -236,7 +244,7 @@
* Set the definitionURL of the MathML element represented by
* this {@link ASTCSymbolDelayNode}
*
- * @param String definitionURL
+ * @param definitionURL
*/
private void setDefinitionURL(String definitionURL) {
String old = this.definitionURL;
@@ -248,7 +256,7 @@
* Set the encoding of the MathML element represented by
* this {@link ASTCSymbolDelayNode}
*
- * @param String encoding
+ * @param encoding
*/
private void setEncoding(String encoding) {
String old = this.encoding;
Modified: trunk/core/src/org/sbml/jsbml/math/ASTCSymbolTimeNode.java
===================================================================
--- trunk/core/src/org/sbml/jsbml/math/ASTCSymbolTimeNode.java 2015-10-14 10:24:09 UTC (rev 2384)
+++ trunk/core/src/org/sbml/jsbml/math/ASTCSymbolTimeNode.java 2015-10-15 20:11:15 UTC (rev 2385)
@@ -45,266 +45,266 @@
public class ASTCSymbolTimeNode extends ASTNumber
implements ASTCSymbolNode {
- /**
- *
- */
- private static final long serialVersionUID = 3788959657360296692L;
+ /**
+ *
+ */
+ private static final long serialVersionUID = 3788959657360296692L;
- /**
- * A {@link Logger} for this class.
- */
- private static final Logger logger = Logger.getLogger(ASTCSymbolTimeNode.class);
+ /**
+ * A {@link Logger} for this class.
+ */
+ private static final Logger logger = Logger.getLogger(ASTCSymbolTimeNode.class);
- /**
- * The encoding of this csymbol element
- */
- private String encoding;
+ /**
+ * The encoding of this csymbol element
+ */
+ private String encoding;
- /**
- * definitionURL attribute for MathML element
- */
- protected String definitionURL;
+ /**
+ * definitionURL attribute for MathML element
+ */
+ protected String definitionURL;
- /**
- * The name of the MathML element represented by this
- * {@link ASTCSymbolTimeNode}.
- */
- private String name;
+ /**
+ * The name of the MathML element represented by this
+ * {@link ASTCSymbolTimeNode}.
+ */
+ private String name;
- /**
- * Creates a new {@link ASTCSymbolTimeNode}.
- */
- public ASTCSymbolTimeNode() {
- super();
- setDefinitionURL(ASTNode.URI_TIME_DEFINITION);
- setEncoding("text");
- setType(Type.NAME_TIME);
- }
+ /**
+ * Creates a new {@link ASTCSymbolTimeNode}.
+ */
+ public ASTCSymbolTimeNode() {
+ super();
+ setDefinitionURL(ASTNode.URI_TIME_DEFINITION);
+ setEncoding("text");
+ setType(Type.NAME_TIME);
+ }
- /**
- * Copy constructor; Creates a deep copy of the given {@link ASTCSymbolTimeNode}.
- *
- * @param node
- * the {@link ASTCSymbolTimeNode} to be copied.
- */
- public ASTCSymbolTimeNode(ASTCSymbolTimeNode node) {
- super(node);
- if (node.isSetDefinitionURL()) {
- setDefinitionURL(node.getDefinitionURL());
- }
- if (node.isSetEncoding()) {
- setEncoding(node.getEncoding());
- }
- if (node.isSetName()) {
- setName(node.getName());
- }
- }
+ /**
+ * Copy constructor; Creates a deep copy of the given {@link ASTCSymbolTimeNode}.
+ *
+ * @param node
+ * the {@link ASTCSymbolTimeNode} to be copied.
+ */
+ public ASTCSymbolTimeNode(ASTCSymbolTimeNode node) {
+ super(node);
+ if (node.isSetDefinitionURL()) {
+ setDefinitionURL(node.getDefinitionURL());
+ }
+ if (node.isSetEncoding()) {
+ setEncoding(node.getEncoding());
+ }
+ if (node.isSetName()) {
+ setName(node.getName());
+ }
+ }
- /*
- * (non-Javadoc)
- * @see org.sbml.jsbml.math.ASTCiNumberNode#clone()
- */
- @Override
- public ASTCSymbolTimeNode clone() {
- return new ASTCSymbolTimeNode(this);
- }
+ /*
+ * (non-Javadoc)
+ * @see org.sbml.jsbml.math.ASTCiNumberNode#clone()
+ */
+ @Override
+ public ASTCSymbolTimeNode clone() {
+ return new ASTCSymbolTimeNode(this);
+ }
- /* (non-Javadoc)
- * @see org.sbml.jsbml.math.ASTNode2#compile(org.sbml.jsbml.util.compilers.ASTNode2Compiler)
- */
- @Override
- public ASTNode2Value<?> compile(ASTNode2Compiler compiler) {
- ASTNode2Value<?> value = compiler.symbolTime(isSetName() ? getName() : "time");
+ /* (non-Javadoc)
+ * @see org.sbml.jsbml.math.ASTNode2#compile(org.sbml.jsbml.util.compilers.ASTNode2Compiler)
+ */
+ @Override
+ public ASTNode2Value<?> compile(ASTNode2Compiler compiler) {
+ ASTNode2Value<?> value = compiler.symbolTime(isSetName() ? getName() : "time");
return processValue(value);
- }
+ }
- /* (non-Javadoc)
- * @see java.lang.Object#equals(java.lang.Object)
- */
- @Override
- public boolean equals(Object obj) {
- if (this == obj) {
- return true;
- }
- if (!super.equals(obj)) {
- return false;
- }
- if (getClass() != obj.getClass()) {
- return false;
- }
- ASTCSymbolTimeNode other = (ASTCSymbolTimeNode) obj;
- if (definitionURL == null) {
- if (other.definitionURL != null) {
- return false;
- }
- } else if (!definitionURL.equals(other.definitionURL)) {
- return false;
- }
- if (encoding == null) {
- if (other.encoding != null) {
- return false;
- }
- } else if (!encoding.equals(other.encoding)) {
- return false;
- }
- return true;
- }
+ /* (non-Javadoc)
+ * @see java.lang.Object#equals(java.lang.Object)
+ */
+ @Override
+ public boolean equals(Object obj) {
+ if (this == obj) {
+ return true;
+ }
+ if (!super.equals(obj)) {
+ return false;
+ }
+ if (getClass() != obj.getClass()) {
+ return false;
+ }
+ ASTCSymbolTimeNode other = (ASTCSymbolTimeNode) obj;
+ if (definitionURL == null) {
+ if (other.definitionURL != null) {
+ return false;
+ }
+ } else if (!definitionURL.equals(other.definitionURL)) {
+ return false;
+ }
+ if (encoding == null) {
+ if (other.encoding != null) {
+ return false;
+ }
+ } else if (!encoding.equals(other.encoding)) {
+ return false;
+ }
+ return true;
+ }
- /* (non-Javadoc)
- * @see org.sbml.jsbml.math.ASTCSymbolBaseNode#getDefinitionURL()
- */
- @Override
- public String getDefinitionURL() {
- if (isSetDefinitionURL()) {
- return definitionURL;
- }
- PropertyUndefinedError error = new PropertyUndefinedError("definitionURL", this);
- if (isStrict()) {
- throw error;
- }
- logger.warn(error);
- return "";
- }
+ /* (non-Javadoc)
+ * @see org.sbml.jsbml.math.ASTCSymbolBaseNode#getDefinitionURL()
+ */
+ @Override
+ public String getDefinitionURL() {
+ if (isSetDefinitionURL()) {
+ return definitionURL;
+ }
+ PropertyUndefinedError error = new PropertyUndefinedError("definitionURL", this);
+ if (isStrict()) {
+ throw error;
+ }
+ logger.warn(error);
+ return "";
+ }
- /* (non-Javadoc)
- * @see org.sbml.jsbml.math.ASTCSymbolNode#getEncodingURL()
- */
- @Override
- public String getEncoding() {
- if (isSetEncoding()) {
- return encoding;
- }
- PropertyUndefinedError error = new PropertyUndefinedError("encodingURL", this);
- if (isStrict()) {
- throw error;
- }
- logger.warn(error);
- return "";
- }
+ /* (non-Javadoc)
+ * @see org.sbml.jsbml.math.ASTCSymbolNode#getEncodingURL()
+ */
+ @Override
+ public String getEncoding() {
+ if (isSetEncoding()) {
+ return encoding;
+ }
+ PropertyUndefinedError error = new PropertyUndefinedError("encodingURL", this);
+ if (isStrict()) {
+ throw error;
+ }
+ logger.warn(error);
+ return "";
+ }
- /* (non-Javadoc)
- * @see org.sbml.jsbml.math.ASTCSymbolBaseNode#getName()
- */
- @Override
- public String getName() {
- if (isSetName()) {
- return name;
- }
- PropertyUndefinedError error = new PropertyUndefinedError("name", this);
- if (isStrict()) {
- throw error;
- }
- logger.warn(error);
- return "";
- }
+ /* (non-Javadoc)
+ * @see org.sbml.jsbml.math.ASTCSymbolBaseNode#getName()
+ */
+ @Override
+ public String getName() {
+ if (isSetName()) {
+ return name;
+ }
+ PropertyUndefinedError error = new PropertyUndefinedError("name", this);
+ if (isStrict()) {
+ throw error;
+ }
+ logger.warn(error);
+ return "";
+ }
- /* (non-Javadoc)
- * @see java.lang.Object#hashCode()
- */
- @Override
- public int hashCode() {
- final int prime = 1277;
- int result = super.hashCode();
- result = prime * result
- + ((definitionURL == null) ? 0 : definitionURL.hashCode());
- result = prime * result
- + ((encoding == null) ? 0 : encoding.hashCode());
- return result;
- }
+ /* (non-Javadoc)
+ * @see java.lang.Object#hashCode()
+ */
+ @Override
+ public int hashCode() {
+ final int prime = 1277;
+ int result = super.hashCode();
+ result = prime * result
+ + ((definitionURL == null) ? 0 : definitionURL.hashCode());
+ result = prime * result
+ + ((encoding == null) ? 0 : encoding.hashCode());
+ return result;
+ }
- /* (non-Javadoc)
- * @see org.sbml.jsbml.math.ASTNode2#isAllowableType(org.sbml.jsbml.ASTNode.Type)
- */
- @Override
- public boolean isAllowableType(Type type) {
- return type == Type.NAME_TIME;
- }
+ /* (non-Javadoc)
+ * @see org.sbml.jsbml.math.ASTNode2#isAllowableType(org.sbml.jsbml.ASTNode.Type)
+ */
+ @Override
+ public boolean isAllowableType(Type type) {
+ return type == Type.NAME_TIME;
+ }
- /*
- * (non-Javadoc)
- * @see org.sbml.jsbml.math.ASTCSymbolBaseNode#isSetDefinitionURL()
- */
- @Override
- public boolean isSetDefinitionURL() {
- return definitionURL != null;
- }
+ /*
+ * (non-Javadoc)
+ * @see org.sbml.jsbml.math.ASTCSymbolBaseNode#isSetDefinitionURL()
+ */
+ @Override
+ public boolean isSetDefinitionURL() {
+ return definitionURL != null;
+ }
- /*
- * (non-Javadoc)
- * @see org.sbml.jsbml.math.ASTCSymbolNode#isSetEncodingURL()
- */
- @Override
- public boolean isSetEncoding() {
- return encoding != null;
- }
+ /*
+ * (non-Javadoc)
+ * @see org.sbml.jsbml.math.ASTCSymbolNode#isSetEncodingURL()
+ */
+ @Override
+ public boolean isSetEncoding() {
+ return encoding != null;
+ }
- /* (non-Javadoc)
- * @see org.sbml.jsbml.math.ASTCSymbolBaseNode#isSetName()
- */
- @Override
- public boolean isSetName() {
- return name != null;
- }
+ /* (non-Javadoc)
+ * @see org.sbml.jsbml.math.ASTCSymbolBaseNode#isSetName()
+ */
+ @Override
+ public boolean isSetName() {
+ return name != null;
+ }
- /* (non-Javadoc)
- * @see org.sbml.jsbml.math.ASTCSymbolBaseNode#refersTo(java.lang.String)
- */
- @Override
- public boolean refersTo(String id) {
- return getName().equals(id);
- }
+ /* (non-Javadoc)
+ * @see org.sbml.jsbml.math.ASTCSymbolBaseNode#refersTo(java.lang.String)
+ */
+ @Override
+ public boolean refersTo(String id) {
+ return getName().equals(id);
+ }
- /**
- * Set the definitionURL of the MathML element represented by
- * this {@link ASTCSymbolTimeNode}
- *
- * @param String definitionURL
- */
- private void setDefinitionURL(String definitionURL) {
- String old = this.definitionURL;
- this.definitionURL = definitionURL;
- firePropertyChange(TreeNodeChangeEvent.definitionURL, old, definitionURL);
- }
+ /**
+ * Set the definitionURL of the MathML element represented by
+ * this {@link ASTCSymbolTimeNode}
+ *
+ * @param definitionURL
+ */
+ private void setDefinitionURL(String definitionURL) {
+ String old = this.definitionURL;
+ this.definitionURL = definitionURL;
+ firePropertyChange(TreeNodeChangeEvent.definitionURL, old, definitionURL);
+ }
- /**
- * Set the encoding of the MathML element represented by
- * this {@link ASTCSymbolTimeNode}
- *
- * @param String encoding
- */
- private void setEncoding(String encoding) {
- String old = this.encoding;
- this.encoding = encoding;
- firePropertyChange(TreeNodeChangeEvent.encoding, old, this.encoding);
- }
+ /**
+ * Set the encoding of the MathML element represented by
+ * this {@link ASTCSymbolTimeNode}
+ *
+ * @param encoding
+ */
+ private void setEncoding(String encoding) {
+ String old = this.encoding;
+ this.encoding = encoding;
+ firePropertyChange(TreeNodeChangeEvent.encoding, old, this.encoding);
+ }
- /* (non-Javadoc)
- * @see org.sbml.jsbml.math.ASTCSymbolBaseNode#setName(java.lang.String)
- */
- @Override
- public void setName(String name) {
- String old = this.name;
- this.name = name;
- firePropertyChange(TreeNodeChangeEvent.name, old, this.name);
- }
+ /* (non-Javadoc)
+ * @see org.sbml.jsbml.math.ASTCSymbolBaseNode#setName(java.lang.String)
+ */
+ @Override
+ public void setName(String name) {
+ String old = this.name;
+ this.name = name;
+ firePropertyChange(TreeNodeChangeEvent.name, old, this.name);
+ }
- /* (non-Javadoc)
- * @see org.sbml.jsbml.math.AbstractASTNode#toFormula()
- */
- @Override
- public String toFormula() throws SBMLException {
- return compile(new FormulaCompiler()).toString();
- }
+ /* (non-Javadoc)
+ * @see org.sbml.jsbml.math.AbstractASTNode#toFormula()
+ */
+ @Override
+ public String toFormula() throws SBMLException {
+ return compile(new FormulaCompiler()).toString();
+ }
- /* (non-Javadoc)
- * @see org.sbml.jsbml.math.AbstractASTNode#toLaTeX()
- */
- @Override
- public String toLaTeX() throws SBMLException {
- return compile(new LaTeXCompiler()).toString();
- }
+ /* (non-Javadoc)
+ * @see org.sbml.jsbml.math.AbstractASTNode#toLaTeX()
+ */
+ @Override
+ public String toLaTeX() throws SBMLException {
+ return compile(new LaTeXCompiler()).toString();
+ }
- /* (non-Javadoc)
+ /* (non-Javadoc)
* @see org.sbml.jsbml.math.AbstractASTNode#toMathML()
*/
@Override
@@ -318,10 +318,10 @@
}
/* (non-Javadoc)
- * @see java.lang.Object#toString()
- */
- @Override
- public String toString() {
+ * @see java.lang.Object#toString()
+ */
+ @Override
+ public String toString() {
StringBuilder builder = new StringBuilder();
builder.append(getClass().getSimpleName());
builder.append(" [strict=");
@@ -342,6 +342,6 @@
builder.append(isSetMathMLClass() ? mathMLClass : "null");
builder.append("]");
return builder.toString();
- }
+ }
}
Modified: trunk/core/src/org/sbml/jsbml/math/ASTCiFunctionNode.java
===================================================================
--- trunk/core/src/org/sbml/jsbml/math/ASTCiFunctionNode.java 2015-10-14 10:24:09 UTC (rev 2384)
+++ trunk/core/src/org/sbml/jsbml/math/ASTCiFunctionNode.java 2015-10-15 20:11:15 UTC (rev 2385)
@@ -69,7 +69,7 @@
* The name of the MathML element represented by this
* {@link ASTCiFunctionNode}.
*/
- private String name; // TODO - remove this unused class attribute ?
+ private String name; // TODO - remove this unused class attribute ?
/**
* refId attribute for MathML element
@@ -86,7 +86,7 @@
setName(null);
setType(Type.FUNCTION);
}
-
+
/**
* Copy constructor; Creates a deep copy of the given {@link ASTCiFunctionNode}.
*
@@ -96,13 +96,13 @@
public ASTCiFunctionNode(ASTCiFunctionNode node) {
super(node);
if (node.isSetDefinitionURL()) {
- setDefinitionURL(node.getDefinitionURL());
+ setDefinitionURL(node.getDefinitionURL());
}
if (node.isSetRefId()) {
setRefId(node.getRefId());
}
}
-
+
/*
* (non-Javadoc)
* @see org.sbml.jsbml.math.ASTFunction#clone()
@@ -110,8 +110,8 @@
@Override
public ASTCiFunctionNode clone() {
return new ASTCiFunctionNode(this);
- }
-
+ }
+
/*
* (non-Javadoc)
* @see org.sbml.jsbml.math.AbstractASTNode#compile(org.sbml.jsbml.math.compiler.ASTNode2Compiler)
@@ -121,7 +121,7 @@
ASTNode2Value<?> value = null;
FunctionDefinition variable = getReferenceInstance();
if (variable instanceof FunctionDefinition) {
- value = compiler.function((FunctionDefinition) variable,
+ value = compiler.function(variable,
getChildren());
} else {
logger
@@ -132,7 +132,7 @@
+ ")");
throw new SBMLException(
"ASTNode of type FUNCTION but the variable is not a FunctionDefinition! ("
- + (isSetName() ? getName() : "null") + ", "
+ + (isSetName() ? getName() : "null") + ", "
+ (isSetParentSBMLObject() ? getParentSBMLObject().getElementName() : "null")
+ ")");
}
@@ -145,23 +145,30 @@
*/
@Override
public boolean equals(Object obj) {
- if (this == obj)
+ if (this == obj) {
return true;
- if (!super.equals(obj))
+ }
+ if (!super.equals(obj)) {
return false;
- if (getClass() != obj.getClass())
+ }
+ if (getClass() != obj.getClass()) {
return false;
+ }
ASTCiFunctionNode other = (ASTCiFunctionNode) obj;
if (definitionURL == null) {
- if (other.definitionURL != null)
+ if (other.definitionURL != null) {
return false;
- } else if (!definitionURL.equals(other.definitionURL))
+ }
+ } else if (!definitionURL.equals(other.definitionURL)) {
return false;
+ }
if (name == null) {
- if (other.name != null)
+ if (other.name != null) {
return false;
- } else if (!name.equals(other.name))
+ }
+ } else if (!name.equals(other.name)) {
return false;
+ }
return true;
}
@@ -184,7 +191,7 @@
}
/**
- * Returns the variable ({@link FunctionDefinition}) of this {@link ASTCiFunctionNode}.
+ * Returns the variable ({@link FunctionDefinition}) of this {@link ASTCiFunctionNode}.
*
* @return the variable of this node
*/
@@ -200,8 +207,8 @@
}
} else {
logger.debug(MessageFormat.format(
- "This ASTCiFunctionNode is not yet linked to a model. "
- + "No element with id \"{0}\" could be found.", isSetRefId() ? getRefId() : null));
+ "This ASTCiFunctionNode is not yet linked to a model. "
+ + "No element with id \"{0}\" could be found.", isSetRefId() ? getRefId() : null));
}
return function;
}
@@ -232,7 +239,7 @@
final int prime = 1129;
int result = super.hashCode();
result = prime * result
- + ((definitionURL == null) ? 0 : definitionURL.hashCode());
+ + ((definitionURL == null) ? 0 : definitionURL.hashCode());
result = prime * result + ((name == null) ? 0 : name.hashCode());
return result;
}
@@ -291,9 +298,9 @@
/**
* Set the definitionURL of the MathML element represented by
- * this {@link ASTCSymbolCiFunctionNode}
+ * this {@link ASTCiFunctionNode}
*
- * @param String definitionURL
+ * @param definitionURL
*/
public void setDefinitionURL(String definitionURL) {
String old = this.definitionURL;
@@ -302,11 +309,11 @@
}
/**
- * Set an instance of {@link FunctionDefinition} as the variable of this
+ * Set an instance of {@link FunctionDefinition} as the variable of this
* {@link ASTCiFunctionNode}. Note that if the given variable does not
- * have a declared {@code id} field, the pointer to this variable will
+ * have a declared {@code id} field, the pointer to this variable will
* get lost when cloning this node. Only references to identifiers are
- * permanently stored. The pointer can also not be written to an SBML
+ * permanently stored. The pointer can also not be written to an SBML
* file without a valid identifier.
*
* @param function a pointer to a {@link FunctionDefinition}.
@@ -332,7 +339,7 @@
@Override
public String toFormula() throws SBMLException {
if (isSetRefId()) {
- return compile(new FormulaCompiler()).toString();
+ return compile(new FormulaCompiler()).toString();
}
throw new SBMLException();
}
@@ -343,7 +350,7 @@
@Override
public String toLaTeX() throws SBMLException {
if (isSetRefId()) {
- return compile(new LaTeXCompiler()).toString();
+ return compile(new LaTeXCompiler()).toString();
}
throw new SBMLException();
}
@@ -355,7 +362,7 @@
public String toMathML() {
try {
if (isSetRefId()) {
- return MathMLXMLStreamCompiler.toMathML(this);
+ return MathMLXMLStreamCompiler.toMathML(this);
}
throw new SBMLException();
} catch (RuntimeException e) {
@@ -363,7 +370,7 @@
return null;
}
}
-
+
/* (non-Javadoc)
* @see java.lang.Object#toString()
*/
Modified: trunk/core/src/org/sbml/jsbml/math/ASTCiNumberNode.java
===================================================================
--- trunk/core/src/org/sbml/jsbml/math/ASTCiNumberNode.java 2015-10-14 10:24:09 UTC (rev 2384)
+++ trunk/core/src/org/sbml/jsbml/math/ASTCiNumberNode.java 2015-10-15 20:11:15 UTC (rev 2385)
@@ -33,6 +33,7 @@
import org.sbml.jsbml.PropertyUndefinedError;
import org.sbml.jsbml.QuantityWithUnit;
import org.sbml.jsbml.SBMLException;
+import org.sbml.jsbml.Variable;
import org.sbml.jsbml.math.compiler.ASTNode2Compiler;
import org.sbml.jsbml.math.compiler.ASTNode2Value;
import org.sbml.jsbml.math.compiler.FormulaCompiler;
@@ -53,359 +54,359 @@
public class ASTCiNumberNode extends ASTNumber implements
ASTCSymbolBaseNode {
- /**
- *
- */
- private static final long serialVersionUID = -6842905005458975038L;
+ /**
+ *
+ */
+ private static final long serialVersionUID = -6842905005458975038L;
- /**
- * A {@link Logger} for this class.
- */
- static final Logger logger = Logger.getLogger(ASTCiNumberNode.class);
+ /**
+ * A {@link Logger} for this class.
+ */
+ static final Logger logger = Logger.getLogger(ASTCiNumberNode.class);
- /**
- * definitionURL attribute for MathML element
- */
- protected String definitionURL;
+ /**
+ * definitionURL attribute for MathML element
+ */
+ protected String definitionURL;
- /**
- * The name of the MathML element represented by this
- * {@link ASTCiNumberNode}.
- */
- private String refId;
+ /**
+ * The name of the MathML element represented by this
+ * {@link ASTCiNumberNode}.
+ */
+ private String refId;
- /**
- * Creates a new {@link ASTCiNumberNode}.
- */
- public ASTCiNumberNode() {
- super();
- setDefinitionURL(null);
- setRefId(null);
- setType(Type.NAME);
- }
+ /**
+ * Creates a new {@link ASTCiNumberNode}.
+ */
+ public ASTCiNumberNode() {
+ super();
+ setDefinitionURL(null);
+ setRefId(null);
+ setType(Type.NAME);
+ }
- /**
- * Copy constructor; Creates a deep copy of the given {@link ASTCiNumberNode}.
- *
- * @param node
- * the {@link ASTCiNumberNode} to be copied.
- */
- public ASTCiNumberNode(ASTCiNumberNode node) {
- super(node);
- if (node.isSetDefinitionURL()) {
- setDefinitionURL(node.getDefinitionURL());
- }
- if (node.isSetRefId()) {
- setRefId(node.getRefId());
- }
- }
+ /**
+ * Copy constructor; Creates a deep copy of the given {@link ASTCiNumberNode}.
+ *
+ * @param node
+ * the {@link ASTCiNumberNode} to be copied.
+ */
+ public ASTCiNumberNode(ASTCiNumberNode node) {
+ super(node);
+ if (node.isSetDefinitionURL()) {
+ setDefinitionURL(node.getDefinitionURL());
+ }
+ if (node.isSetRefId()) {
+ setRefId(node.getRefId());
+ }
+ }
- /*(non-Javadoc)
- * @see org.sbml.jsbml.math.ASTNumber#clone()
- */
- @Override
- public ASTCiNumberNode clone() {
- return new ASTCiNumberNode(this);
- }
+ /*(non-Javadoc)
+ * @see org.sbml.jsbml.math.ASTNumber#clone()
+ */
+ @Override
+ public ASTCiNumberNode clone() {
+ return new ASTCiNumberNode(this);
+ }
- /* (non-Javadoc)
- * @see org.sbml.jsbml.math.ASTNode2#compile(org.sbml.jsbml.util.compilers.ASTNode2Compiler)
- */
- @Override
- public ASTNode2Value<?> compile(ASTNode2Compiler compiler) {
- ASTNode2Value<?> value = isSetRefId() ? compiler.compile(getRefId()) : null;
- return processValue(value);
- }
+ /* (non-Javadoc)
+ * @see org.sbml.jsbml.math.ASTNode2#compile(org.sbml.jsbml.util.compilers.ASTNode2Compiler)
+ */
+ @Override
+ public ASTNode2Value<?> compile(ASTNode2Compiler compiler) {
+ ASTNode2Value<?> value = isSetRefId() ? compiler.compile(getRefId()) : null;
+ return processValue(value);
+ }
- /**
- * Returns {@code true} or {@code false} depending on whether this
- * {@link ASTCiNumberNode} refers to elements such as parameters or
- * numbers with undeclared units.
- *
- * A return value of {@code true} indicates that the {@code UnitDefinition}
- * returned by {@link Variable#getDerivedUnitDefinition()} may not accurately
- * represent the units of the expression.
- *
- * @return {@code true} if the math expression of this {@link ASTCiNumberNode}
- * includes parameters/numbers with undeclared units,
- * {@code false} otherwise.
- */
- public boolean containsUndeclaredUnits() {
- if (isSetRefId()) {
- CallableSBase reference = getReferenceInstance();
- if (reference != null && reference instanceof QuantityWithUnit) {
- return ! ((QuantityWithUnit)reference).isSetUnits();
- } else {
- // TODO: reaction doesn't have units but may still have undeclared units
- // in kinetic law.
- // arrays or other packages
- logger.warn("??");
- return true;
- }
- }
- return false;
- }
+ /**
+ * Returns {@code true} or {@code false} depending on whether this
+ * {@link ASTCiNumberNode} refers to elements such as parameters or
+ * numbers with undeclared units.
+ *
+ * A return value of {@code true} indicates that the {@code UnitDefinition}
+ * returned by {@link Variable#getDerivedUnitDefinition()} may not accurately
+ * represent the units of the expression.
+ *
+ * @return {@code true} if the math expression of this {@link ASTCiNumberNode}
+ * includes parameters/numbers with undeclared units,
+ * {@code false} otherwise.
+ */
+ public boolean containsUndeclaredUnits() {
+ if (isSetRefId()) {
+ CallableSBase reference = getReferenceInstance();
+ if (reference != null && reference instanceof QuantityWithUnit) {
+ return ! ((QuantityWithUnit)reference).isSetUnits();
+ } else {
+ // TODO: reaction doesn't have units but may still have undeclared units
+ // in kinetic law.
+ // arrays or other packages
+ logger.warn("??");
+ return true;
+ }
+ }
+ return false;
+ }
- /* (non-Javadoc)
- * @see java.lang.Object#equals(java.lang.Object)
- */
- @Override
- public boolean equals(Object obj) {
- if (!super.equals(obj)) {
- return false;
- }
- ASTCiNumberNode other = (ASTCiNumberNode) obj;
- if (definitionURL == null) {
- if (other.definitionURL != null) {
- return false;
- }
- } else if (!definitionURL.equals(other.definitionURL)) {
- return false;
- }
- if (refId == null) {
- if (other.refId != null) {
- return false;
- }
- } else if (!refId.equals(other.refId)) {
- return false;
- }
- return true;
- }
+ /* (non-Javadoc)
+ * @see java.lang.Object#equals(java.lang.Object)
+ */
+ @Override
+ public boolean equals(Object obj) {
+ if (!super.equals(obj)) {
+ return false;
+ }
+ ASTCiNumberNode other = (ASTCiNumberNode) obj;
+ if (definitionURL == null) {
+ if (other.definitionURL != null) {
+ return false;
+ }
+ } else if (!definitionURL.equals(other.definitionURL)) {
+ return false;
+ }
+ if (refId == null) {
+ if (other.refId != null) {
+ return false;
+ }
+ } else if (!refId.equals(other.refId)) {
+ return false;
+ }
+ return true;
+ }
- /* (non-Javadoc)
- * @see org.sbml.jsbml.math.ASTCSymbolBaseNode#getDefinitionURL()
- */
- @Override
- public String getDefinitionURL() {
- if (isSetDefinitionURL()) {
- return definitionURL;
- }
- PropertyUndefinedError error = new PropertyUndefinedError("definitionURL", this);
- if (isStrict()) {
- throw error;
- }
- logger.warn(error);
- return "";
- }
+ /* (non-Javadoc)
+ * @see org.sbml.jsbml.math.ASTCSymbolBaseNode#getDefinitionURL()
+ */
+ @Override
+ public String getDefinitionURL() {
+ if (isSetDefinitionURL()) {
+ return definitionURL;
+ }
+ PropertyUndefinedError error = new PropertyUndefinedError("definitionURL", this);
+ if (isStrict()) {
+ throw error;
+ }
+ logger.warn(error);
+ return "";
+ }
- /* (non-Javadoc)
- * @see org.sbml.jsbml.math.ASTCSymbolBaseNode#getName()
- */
- @Override
- @Deprecated
- public String getName() {
- return getRefId();
- }
+ /* (non-Javadoc)
+ * @see org.sbml.jsbml.math.ASTCSymbolBaseNode#getName()
+ */
+ @Override
+ @Deprecated
+ public String getName() {
+ return getRefId();
+ }
- /**
- * Returns the variable ({@link CallableSBase}) of this {@link ASTCiNumberNode}.
- *
- * @return the variable of this node
- */
- public CallableSBase getReferenceInstance() {
- CallableSBase sbase = null;
- if (isSetParentSBMLObject()) {
- if (getParentSBMLObject() instanceof KineticLaw) {
- sbase = isSetRefId() ? ((KineticLaw) getParentSBMLObject())
- .getLocalParameter(getRefId()): null;
- }
- if (sbase == null) {
- Model m = isSetParentSBMLObject() ? getParentSBMLOb...
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