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[sbml-svn] SF.net SVN: sbml:[22270] trunk/libsbml/src/sbml
|
From: <fbe...@us...> - 2015-05-28 08:09:02
|
Revision: 22270
http://sourceforge.net/p/sbml/code/22270
Author: fbergmann
Date: 2015-05-28 08:08:59 +0000 (Thu, 28 May 2015)
Log Message:
-----------
- first batch of NULL reference checks (and tests) removed
Modified Paths:
--------------
trunk/libsbml/src/sbml/Compartment.cpp
trunk/libsbml/src/sbml/CompartmentType.cpp
trunk/libsbml/src/sbml/Constraint.cpp
trunk/libsbml/src/sbml/Delay.cpp
trunk/libsbml/src/sbml/Event.cpp
trunk/libsbml/src/sbml/EventAssignment.cpp
trunk/libsbml/src/sbml/FunctionDefinition.cpp
trunk/libsbml/src/sbml/InitialAssignment.cpp
trunk/libsbml/src/sbml/KineticLaw.cpp
trunk/libsbml/src/sbml/LocalParameter.cpp
trunk/libsbml/src/sbml/Model.cpp
trunk/libsbml/src/sbml/Parameter.cpp
trunk/libsbml/src/sbml/Priority.cpp
trunk/libsbml/src/sbml/Reaction.cpp
trunk/libsbml/src/sbml/Rule.cpp
trunk/libsbml/src/sbml/SBMLDocument.cpp
trunk/libsbml/src/sbml/SBMLNamespaces.cpp
trunk/libsbml/src/sbml/SBMLReader.cpp
trunk/libsbml/src/sbml/SBMLWriter.cpp
trunk/libsbml/src/sbml/SBase.cpp
trunk/libsbml/src/sbml/SimpleSpeciesReference.cpp
trunk/libsbml/src/sbml/Species.cpp
trunk/libsbml/src/sbml/SpeciesReference.cpp
trunk/libsbml/src/sbml/SpeciesType.cpp
trunk/libsbml/src/sbml/StoichiometryMath.cpp
trunk/libsbml/src/sbml/Trigger.cpp
trunk/libsbml/src/sbml/Unit.cpp
trunk/libsbml/src/sbml/UnitDefinition.cpp
trunk/libsbml/src/sbml/annotation/CVTerm.cpp
trunk/libsbml/src/sbml/annotation/Date.cpp
trunk/libsbml/src/sbml/annotation/ModelCreator.cpp
trunk/libsbml/src/sbml/annotation/ModelHistory.cpp
trunk/libsbml/src/sbml/annotation/RDFAnnotationParser.cpp
trunk/libsbml/src/sbml/annotation/test/TestCopyAndClone.cpp
trunk/libsbml/src/sbml/conversion/ConversionOption.cpp
trunk/libsbml/src/sbml/conversion/ConversionProperties.cpp
trunk/libsbml/src/sbml/conversion/SBMLConverter.cpp
trunk/libsbml/src/sbml/conversion/SBMLFunctionDefinitionConverter.cpp
trunk/libsbml/src/sbml/conversion/SBMLIdConverter.cpp
trunk/libsbml/src/sbml/conversion/SBMLInferUnitsConverter.cpp
trunk/libsbml/src/sbml/conversion/SBMLInitialAssignmentConverter.cpp
trunk/libsbml/src/sbml/conversion/SBMLLevel1Version1Converter.cpp
trunk/libsbml/src/sbml/conversion/SBMLLevelVersionConverter.cpp
trunk/libsbml/src/sbml/conversion/SBMLLocalParameterConverter.cpp
trunk/libsbml/src/sbml/conversion/SBMLReactionConverter.cpp
trunk/libsbml/src/sbml/conversion/SBMLRuleConverter.cpp
trunk/libsbml/src/sbml/conversion/SBMLStripPackageConverter.cpp
trunk/libsbml/src/sbml/conversion/SBMLUnitsConverter.cpp
trunk/libsbml/src/sbml/conversion/test/TestConversionOption.cpp
trunk/libsbml/src/sbml/conversion/test/TestConversionProperties.cpp
trunk/libsbml/src/sbml/extension/SBMLDocumentPlugin.cpp
trunk/libsbml/src/sbml/extension/SBMLDocumentPluginNotRequired.cpp
trunk/libsbml/src/sbml/extension/SBMLExtension.cpp
trunk/libsbml/src/sbml/extension/SBMLExtensionRegistry.cpp
trunk/libsbml/src/sbml/extension/SBaseExtensionPoint.cpp
trunk/libsbml/src/sbml/extension/SBasePlugin.cpp
trunk/libsbml/src/sbml/extension/SBasePluginCreatorBase.cpp
trunk/libsbml/src/sbml/extension/test/TestSBMLExtension.cpp
trunk/libsbml/src/sbml/extension/test/TestSBMLExtensionRegistry.cpp
trunk/libsbml/src/sbml/math/ASTBase.cpp
trunk/libsbml/src/sbml/math/ASTBinaryFunctionNode.cpp
trunk/libsbml/src/sbml/math/ASTCSymbolAvogadroNode.cpp
trunk/libsbml/src/sbml/math/ASTCSymbolDelayNode.cpp
trunk/libsbml/src/sbml/math/ASTCSymbolTimeNode.cpp
trunk/libsbml/src/sbml/math/ASTCiFunctionNode.cpp
trunk/libsbml/src/sbml/math/ASTCiNumberNode.cpp
trunk/libsbml/src/sbml/math/ASTCnBase.cpp
trunk/libsbml/src/sbml/math/ASTConstantNumberNode.cpp
trunk/libsbml/src/sbml/math/ASTFunction.cpp
trunk/libsbml/src/sbml/math/ASTFunctionBase.cpp
trunk/libsbml/src/sbml/math/ASTLambdaFunctionNode.cpp
trunk/libsbml/src/sbml/math/ASTNaryFunctionNode.cpp
trunk/libsbml/src/sbml/math/ASTPiecewiseFunctionNode.cpp
trunk/libsbml/src/sbml/math/ASTQualifierNode.cpp
trunk/libsbml/src/sbml/math/ASTSemanticsNode.cpp
trunk/libsbml/src/sbml/math/ASTTypes.cpp
trunk/libsbml/src/sbml/math/ASTUnaryFunctionNode.cpp
trunk/libsbml/src/sbml/math/MathML.cpp
trunk/libsbml/src/sbml/math-legacy/MathML.cpp
trunk/libsbml/src/sbml/packages/comp/extension/CompSBasePlugin.cpp
trunk/libsbml/src/sbml/packages/comp/sbml/CompBase.cpp
trunk/libsbml/src/sbml/packages/comp/sbml/ListOfDeletions.cpp
trunk/libsbml/src/sbml/packages/comp/sbml/ListOfPorts.cpp
trunk/libsbml/src/sbml/packages/comp/sbml/ListOfSubmodels.cpp
trunk/libsbml/src/sbml/packages/comp/util/CompFlatteningConverter.cpp
trunk/libsbml/src/sbml/packages/comp/util/SBMLFileResolver.cpp
trunk/libsbml/src/sbml/packages/comp/util/SBMLResolver.cpp
trunk/libsbml/src/sbml/packages/comp/util/SBMLUri.cpp
trunk/libsbml/src/sbml/packages/comp/validator/CompValidator.cpp
trunk/libsbml/src/sbml/packages/fbc/util/CobraToFbcConverter.cpp
trunk/libsbml/src/sbml/packages/fbc/util/FbcToCobraConverter.cpp
trunk/libsbml/src/sbml/packages/fbc/validator/FbcValidator.cpp
trunk/libsbml/src/sbml/packages/layout/sbml/GraphicalObject.cpp
trunk/libsbml/src/sbml/packages/layout/sbml/Layout.cpp
trunk/libsbml/src/sbml/packages/layout/validator/LayoutValidator.cpp
trunk/libsbml/src/sbml/packages/qual/sbml/DefaultTerm.cpp
trunk/libsbml/src/sbml/packages/qual/sbml/FunctionTerm.cpp
trunk/libsbml/src/sbml/packages/qual/sbml/Input.cpp
trunk/libsbml/src/sbml/packages/qual/sbml/Output.cpp
trunk/libsbml/src/sbml/packages/qual/sbml/QualitativeSpecies.cpp
trunk/libsbml/src/sbml/packages/qual/sbml/Transition.cpp
trunk/libsbml/src/sbml/packages/qual/validator/QualValidator.cpp
trunk/libsbml/src/sbml/packages/qual/validator/constraints/QualCSymbolMathCheck.cpp
trunk/libsbml/src/sbml/test/TestSBMLConstructorException.cpp
trunk/libsbml/src/sbml/units/FormulaUnitsData.cpp
trunk/libsbml/src/sbml/util/ElementFilter.h
trunk/libsbml/src/sbml/util/IdList.cpp
trunk/libsbml/src/sbml/validator/SBMLValidator.cpp
trunk/libsbml/src/sbml/validator/VConstraint.cpp
trunk/libsbml/src/sbml/validator/Validator.cpp
trunk/libsbml/src/sbml/validator/constraints/CiElementMathCheck.cpp
trunk/libsbml/src/sbml/validator/constraints/CiElementNot0DComp.cpp
trunk/libsbml/src/sbml/validator/constraints/EqualityArgsMathCheck.cpp
trunk/libsbml/src/sbml/validator/constraints/FunctionApplyMathCheck.cpp
trunk/libsbml/src/sbml/validator/constraints/FunctionNoArgsMathCheck.cpp
trunk/libsbml/src/sbml/validator/constraints/LambdaMathCheck.cpp
trunk/libsbml/src/sbml/validator/constraints/LocalParameterMathCheck.cpp
trunk/libsbml/src/sbml/validator/constraints/LogicalArgsMathCheck.cpp
trunk/libsbml/src/sbml/validator/constraints/NumberArgsMathCheck.cpp
trunk/libsbml/src/sbml/validator/constraints/NumericArgsMathCheck.cpp
trunk/libsbml/src/sbml/validator/constraints/NumericReturnMathCheck.cpp
trunk/libsbml/src/sbml/validator/constraints/PieceBooleanMathCheck.cpp
trunk/libsbml/src/sbml/validator/constraints/PiecewiseValueMathCheck.cpp
trunk/libsbml/src/sbml/validator/constraints/ValidCnUnitsValue.cpp
trunk/libsbml/src/sbml/xml/XMLAttributes.cpp
trunk/libsbml/src/sbml/xml/XMLError.cpp
trunk/libsbml/src/sbml/xml/XMLErrorLog.cpp
trunk/libsbml/src/sbml/xml/XMLFileBuffer.cpp
trunk/libsbml/src/sbml/xml/XMLNamespaces.cpp
trunk/libsbml/src/sbml/xml/XMLNode.cpp
trunk/libsbml/src/sbml/xml/XMLNode.h
trunk/libsbml/src/sbml/xml/XMLOutputStream.cpp
trunk/libsbml/src/sbml/xml/XMLToken.cpp
trunk/libsbml/src/sbml/xml/XMLTokenizer.cpp
trunk/libsbml/src/sbml/xml/XMLTriple.cpp
trunk/libsbml/src/sbml/xml/test/TestXMLExceptions.cpp
Modified: trunk/libsbml/src/sbml/Compartment.cpp
===================================================================
--- trunk/libsbml/src/sbml/Compartment.cpp 2015-05-20 10:21:59 UTC (rev 22269)
+++ trunk/libsbml/src/sbml/Compartment.cpp 2015-05-28 08:08:59 UTC (rev 22270)
@@ -143,12 +143,7 @@
Compartment::Compartment(const Compartment& orig) :
SBase ( orig )
{
- if (&orig == NULL)
{
- throw SBMLConstructorException("Null argument to copy constructor");
- }
- else
- {
mSpatialDimensions = orig.mSpatialDimensions;
mSpatialDimensionsDouble = orig.mSpatialDimensionsDouble;
mSize = orig.mSize;
@@ -172,12 +167,8 @@
*/
Compartment& Compartment::operator=(const Compartment& rhs)
{
- if (&rhs == NULL)
+ if(&rhs!=this)
{
- throw SBMLConstructorException("Null argument to assignment operator");
- }
- else if(&rhs!=this)
- {
this->SBase::operator =(rhs);
mSpatialDimensions= rhs.mSpatialDimensions ;
mSpatialDimensionsDouble= rhs.mSpatialDimensionsDouble ;
@@ -497,14 +488,10 @@
return LIBSBML_UNEXPECTED_ATTRIBUTE;
}
*/
- if (&(sid) == NULL)
+ if (!(SyntaxChecker::isValidInternalSId(sid)))
{
return LIBSBML_INVALID_ATTRIBUTE_VALUE;
}
- else if (!(SyntaxChecker::isValidInternalSId(sid)))
- {
- return LIBSBML_INVALID_ATTRIBUTE_VALUE;
- }
else
{
mId = sid;
@@ -522,12 +509,8 @@
/* if this is setting an L2 name the type is string
* whereas if it is setting an L1 name its type is SId
*/
- if (&(name) == NULL)
+ if (getLevel() == 1)
{
- return LIBSBML_INVALID_ATTRIBUTE_VALUE;
- }
- else if (getLevel() == 1)
- {
if (!(SyntaxChecker::isValidInternalSId(name)))
{
return LIBSBML_INVALID_ATTRIBUTE_VALUE;
@@ -552,11 +535,7 @@
int
Compartment::setCompartmentType (const std::string& sid)
{
- if (&(sid) == NULL)
- {
- return LIBSBML_INVALID_ATTRIBUTE_VALUE;
- }
- else if ( (getLevel() < 2)
+ if ( (getLevel() < 2)
|| (getLevel() == 2 && getVersion() == 1))
{
return LIBSBML_UNEXPECTED_ATTRIBUTE;
@@ -674,14 +653,10 @@
int
Compartment::setUnits (const std::string& sid)
{
- if (&(sid) == NULL)
+ if (!(SyntaxChecker::isValidInternalUnitSId(sid)))
{
return LIBSBML_INVALID_ATTRIBUTE_VALUE;
}
- else if (!(SyntaxChecker::isValidInternalUnitSId(sid)))
- {
- return LIBSBML_INVALID_ATTRIBUTE_VALUE;
- }
else
{
mUnits = sid;
@@ -696,14 +671,10 @@
int
Compartment::setOutside (const std::string& sid)
{
- if (&(sid) == NULL)
+ if (!(SyntaxChecker::isValidInternalSId(sid)))
{
return LIBSBML_INVALID_ATTRIBUTE_VALUE;
}
- else if (!(SyntaxChecker::isValidInternalSId(sid)))
- {
- return LIBSBML_INVALID_ATTRIBUTE_VALUE;
- }
else
{
mOutside = sid;
@@ -1570,12 +1541,7 @@
{
vector<SBase*>::const_iterator result;
- if (&(sid) == NULL)
{
- return NULL;
- }
- else
- {
result = find_if( mItems.begin(), mItems.end(), IdEq<Compartment>(sid) );
return (result == mItems.end()) ? NULL :
static_cast <Compartment*> (*result);
@@ -1598,15 +1564,12 @@
SBase* item = NULL;
vector<SBase*>::iterator result;
- if (&(sid) != NULL)
+ result = find_if( mItems.begin(), mItems.end(), IdEq<Compartment>(sid) );
+
+ if (result != mItems.end())
{
- result = find_if( mItems.begin(), mItems.end(), IdEq<Compartment>(sid) );
-
- if (result != mItems.end())
- {
- item = *result;
- mItems.erase(result);
- }
+ item = *result;
+ mItems.erase(result);
}
return static_cast <Compartment*> (item);
Modified: trunk/libsbml/src/sbml/CompartmentType.cpp
===================================================================
--- trunk/libsbml/src/sbml/CompartmentType.cpp 2015-05-20 10:21:59 UTC (rev 22269)
+++ trunk/libsbml/src/sbml/CompartmentType.cpp 2015-05-28 08:08:59 UTC (rev 22270)
@@ -86,19 +86,11 @@
/*
* Copy constructor. Creates a copy of this CompartmentType.
*/
-CompartmentType::CompartmentType(const CompartmentType& orig) :
- SBase ( orig )
+CompartmentType::CompartmentType(const CompartmentType& orig)
+ : SBase ( orig )
+ , mId (orig.mId)
+ , mName (orig.mName)
{
- if (&orig == NULL)
- {
- throw SBMLConstructorException("Null argument to copy constructor");
- }
- else
- {
- mId = orig.mId;
- mName = orig.mName;
- }
-
}
@@ -107,12 +99,8 @@
*/
CompartmentType& CompartmentType::operator=(const CompartmentType& rhs)
{
- if (&rhs == NULL)
+ if(&rhs!=this)
{
- throw SBMLConstructorException("Null argument to assignment operator");
- }
- else if(&rhs!=this)
- {
this->SBase::operator =(rhs);
mId = rhs.mId;
mName = rhs.mName;
@@ -204,14 +192,10 @@
return LIBSBML_UNEXPECTED_ATTRIBUTE;
}
*/
- if (&(sid) == NULL)
+ if (!(SyntaxChecker::isValidInternalSId(sid)))
{
return LIBSBML_INVALID_ATTRIBUTE_VALUE;
}
- else if (!(SyntaxChecker::isValidInternalSId(sid)))
- {
- return LIBSBML_INVALID_ATTRIBUTE_VALUE;
- }
else
{
mId = sid;
@@ -229,12 +213,8 @@
/* if this is setting an L2 name the type is string
* whereas if it is setting an L1 name its type is SId
*/
- if (&(name) == NULL)
+ if (getLevel() == 1)
{
- return LIBSBML_INVALID_ATTRIBUTE_VALUE;
- }
- else if (getLevel() == 1)
- {
if (!(SyntaxChecker::isValidInternalSId(name)))
{
return LIBSBML_INVALID_ATTRIBUTE_VALUE;
@@ -566,16 +546,9 @@
{
vector<SBase*>::const_iterator result;
- if (&(sid) == NULL)
- {
- return NULL;
- }
- else
- {
- result = find_if( mItems.begin(), mItems.end(), IdEqCT(sid) );
- return (result == mItems.end()) ? NULL :
- static_cast <CompartmentType*> (*result);
- }
+ result = find_if( mItems.begin(), mItems.end(), IdEqCT(sid) );
+ return (result == mItems.end()) ? NULL :
+ static_cast <CompartmentType*> (*result);
}
@@ -594,15 +567,12 @@
SBase* item = NULL;
vector<SBase*>::iterator result;
- if (&(sid) != NULL)
+ result = find_if( mItems.begin(), mItems.end(), IdEqCT(sid) );
+
+ if (result != mItems.end())
{
- result = find_if( mItems.begin(), mItems.end(), IdEqCT(sid) );
-
- if (result != mItems.end())
- {
- item = *result;
- mItems.erase(result);
- }
+ item = *result;
+ mItems.erase(result);
}
return static_cast <CompartmentType*> (item);
Modified: trunk/libsbml/src/sbml/Constraint.cpp
===================================================================
--- trunk/libsbml/src/sbml/Constraint.cpp 2015-05-20 10:21:59 UTC (rev 22269)
+++ trunk/libsbml/src/sbml/Constraint.cpp 2015-05-28 08:08:59 UTC (rev 22270)
@@ -98,19 +98,13 @@
, mMath ( NULL )
, mMessage( NULL )
{
- if (&orig == NULL)
+ if (orig.mMath != NULL)
{
- throw SBMLConstructorException("Null argument to copy constructor");
+ mMath = orig.mMath->deepCopy();
+ mMath->setParentSBMLObject(this);
}
- else
- {
- if (orig.mMath != NULL)
- {
- mMath = orig.mMath->deepCopy();
- mMath->setParentSBMLObject(this);
- }
- if (orig.mMessage != NULL) mMessage = new XMLNode(*orig.mMessage);
- }
+ if (orig.mMessage != NULL) mMessage = new XMLNode(*orig.mMessage);
+
}
@@ -119,12 +113,8 @@
*/
Constraint& Constraint::operator=(const Constraint& rhs)
{
- if (&rhs == NULL)
+ if(&rhs!=this)
{
- throw SBMLConstructorException("Null argument to assignment operator");
- }
- else if(&rhs!=this)
- {
this->SBase::operator =(rhs);
delete mMath;
@@ -297,12 +287,8 @@
bool addXHTMLMarkup)
{
int success = LIBSBML_OPERATION_FAILED;
- if (&(message) == NULL)
+ if (message.empty())
{
- success = LIBSBML_INVALID_ATTRIBUTE_VALUE;
- }
- else if (message.empty())
- {
success = unsetMessage();
}
else
Modified: trunk/libsbml/src/sbml/Delay.cpp
===================================================================
--- trunk/libsbml/src/sbml/Delay.cpp 2015-05-20 10:21:59 UTC (rev 22269)
+++ trunk/libsbml/src/sbml/Delay.cpp 2015-05-28 08:08:59 UTC (rev 22270)
@@ -93,24 +93,18 @@
/*
* Copy constructor. Creates a copy of this Delay.
*/
-Delay::Delay (const Delay& orig) :
- SBase ( orig )
- , mMath ( NULL )
+Delay::Delay (const Delay& orig)
+ : SBase ( orig )
+ , mMath ( NULL )
+ , mInternalId ( orig.mInternalId )
{
- if (&orig == NULL)
+
+ if (orig.mMath != NULL)
{
- throw SBMLConstructorException("Null argument to copy constructor");
+ mMath = orig.mMath->deepCopy();
+ mMath->setParentSBMLObject(this);
}
- else
- {
- mInternalId = orig.mInternalId;
-
- if (orig.mMath != NULL)
- {
- mMath = orig.mMath->deepCopy();
- mMath->setParentSBMLObject(this);
- }
- }
+
}
@@ -119,12 +113,8 @@
*/
Delay& Delay::operator=(const Delay& rhs)
{
- if (&rhs == NULL)
+ if(&rhs!=this)
{
- throw SBMLConstructorException("Null argument to assignment operator");
- }
- else if(&rhs!=this)
- {
this->SBase::operator =(rhs);
this->mInternalId = rhs.mInternalId;
Modified: trunk/libsbml/src/sbml/Event.cpp
===================================================================
--- trunk/libsbml/src/sbml/Event.cpp 2015-05-20 10:21:59 UTC (rev 22269)
+++ trunk/libsbml/src/sbml/Event.cpp 2015-05-28 08:08:59 UTC (rev 22270)
@@ -125,40 +125,36 @@
* Copy constructor. Creates a copy of this Event.
*/
Event::Event (const Event& orig) :
- SBase ( orig )
- , mTrigger ( NULL )
- , mDelay ( NULL )
- , mPriority ( NULL )
- , mEventAssignments ( orig.mEventAssignments )
+ SBase ( orig )
+ , mId ( orig.mId )
+ , mName ( orig.mName )
+ , mTrigger ( NULL )
+ , mDelay ( NULL )
+ , mPriority ( NULL )
+ , mTimeUnits ( orig.mTimeUnits )
+ , mUseValuesFromTriggerTime ( orig.mUseValuesFromTriggerTime )
+ , mIsSetUseValuesFromTriggerTime ( orig.mIsSetUseValuesFromTriggerTime )
+ , mInternalIdOnly ( orig.mInternalIdOnly )
+ , mExplicitlySetUVFTT ( orig.mExplicitlySetUVFTT )
+ , mEventAssignments ( orig.mEventAssignments )
{
- if (&orig == NULL)
+
+ if (orig.mTrigger != NULL)
{
- throw SBMLConstructorException("Null argument to copy constructor");
+ mTrigger = new Trigger(*orig.getTrigger());
}
- else
+
+ if (orig.mDelay != NULL)
{
- mId = orig.mId;
- mName = orig.mName;
- mTimeUnits = orig.mTimeUnits;
- mUseValuesFromTriggerTime = orig.mUseValuesFromTriggerTime ;
- mIsSetUseValuesFromTriggerTime = orig.mIsSetUseValuesFromTriggerTime ;
- mExplicitlySetUVFTT = orig.mExplicitlySetUVFTT;
- mInternalIdOnly = orig.mInternalIdOnly;
-
- if (orig.mTrigger != NULL)
- {
- mTrigger = new Trigger(*orig.getTrigger());
- }
- if (orig.mDelay != NULL)
- {
- mDelay = new Delay(*orig.getDelay());
- }
- if (orig.mPriority != NULL)
- {
- mPriority = new Priority(*orig.getPriority());
- }
+ mDelay = new Delay(*orig.getDelay());
}
+ if (orig.mPriority != NULL)
+ {
+ mPriority = new Priority(*orig.getPriority());
+ }
+
+
connectToChild();
}
@@ -168,12 +164,8 @@
*/
Event& Event::operator=(const Event& rhs)
{
- if (&rhs == NULL)
+ if(&rhs!=this)
{
- throw SBMLConstructorException("Null argument to assignment operator");
- }
- else if(&rhs!=this)
- {
this->SBase::operator =(rhs);
mId = rhs.mId;
@@ -535,14 +527,10 @@
return LIBSBML_UNEXPECTED_ATTRIBUTE;
}
*/
- if (&(sid) == NULL)
+ if (!(SyntaxChecker::isValidInternalSId(sid)))
{
return LIBSBML_INVALID_ATTRIBUTE_VALUE;
}
- else if (!(SyntaxChecker::isValidInternalSId(sid)))
- {
- return LIBSBML_INVALID_ATTRIBUTE_VALUE;
- }
else
{
mId = sid;
@@ -561,12 +549,8 @@
/* if this is setting an L2 name the type is string
* whereas if it is setting an L1 name its type is SId
*/
- if (&(name) == NULL)
+ if (getLevel() == 1)
{
- return LIBSBML_INVALID_ATTRIBUTE_VALUE;
- }
- else if (getLevel() == 1)
- {
if (!(SyntaxChecker::isValidInternalSId(name)))
{
return LIBSBML_INVALID_ATTRIBUTE_VALUE;
@@ -709,12 +693,8 @@
int
Event::setTimeUnits (const std::string& sid)
{
- if (&(sid) == NULL)
+ if (getLevel() == 2 && getVersion() > 2)
{
- return LIBSBML_INVALID_ATTRIBUTE_VALUE;
- }
- else if (getLevel() == 2 && getVersion() > 2)
- {
return LIBSBML_UNEXPECTED_ATTRIBUTE;
}
else if (!(SyntaxChecker::isValidInternalSId(sid)))
@@ -1108,8 +1088,7 @@
const EventAssignment*
Event::getEventAssignment (const std::string& variable) const
{
- return (&variable != NULL ) ?
- static_cast<const EventAssignment*>( mEventAssignments.get(variable) ) : NULL;
+ return static_cast<const EventAssignment*>( mEventAssignments.get(variable) );
}
@@ -1120,8 +1099,7 @@
EventAssignment*
Event::getEventAssignment (const std::string& variable)
{
- return (&variable != NULL ) ?
- static_cast<EventAssignment*>( mEventAssignments.get(variable) ) : NULL;
+ return static_cast<EventAssignment*>( mEventAssignments.get(variable) );
}
@@ -1153,7 +1131,7 @@
EventAssignment*
Event::removeEventAssignment (const std::string& variable)
{
- return (&variable != NULL) ? mEventAssignments.remove(variable) : NULL;
+ return mEventAssignments.remove(variable);
}
@@ -1786,8 +1764,8 @@
Event*
ListOfEvents::get (const std::string& sid)
{
- return (&sid != NULL) ? const_cast<Event*>(
- static_cast<const ListOfEvents&>(*this).get(sid) ) : NULL;
+ return const_cast<Event*>(
+ static_cast<const ListOfEvents&>(*this).get(sid) );
}
@@ -1795,7 +1773,6 @@
const Event*
ListOfEvents::get (const std::string& sid) const
{
- if (&sid == NULL) return NULL;
vector<SBase*>::const_iterator result;
result = find_if( mItems.begin(), mItems.end(), IdEqE(sid) );
@@ -1818,15 +1795,12 @@
SBase* item = NULL;
vector<SBase*>::iterator result;
- if (&(sid) != NULL)
+ result = find_if( mItems.begin(), mItems.end(), IdEqE(sid) );
+
+ if (result != mItems.end())
{
- result = find_if( mItems.begin(), mItems.end(), IdEqE(sid) );
-
- if (result != mItems.end())
- {
- item = *result;
- mItems.erase(result);
- }
+ item = *result;
+ mItems.erase(result);
}
return static_cast <Event*> (item);
Modified: trunk/libsbml/src/sbml/EventAssignment.cpp
===================================================================
--- trunk/libsbml/src/sbml/EventAssignment.cpp 2015-05-20 10:21:59 UTC (rev 22269)
+++ trunk/libsbml/src/sbml/EventAssignment.cpp 2015-05-28 08:08:59 UTC (rev 22270)
@@ -94,23 +94,16 @@
* Copy constructor. Creates a copy of this EventAssignment.
*/
EventAssignment::EventAssignment (const EventAssignment& orig) :
- SBase ( orig )
- , mMath ( NULL )
+ SBase ( orig )
+ , mVariable ( orig.mVariable )
+ , mMath ( NULL )
{
- if (&orig == NULL)
+ if (orig.mMath != NULL)
{
- throw SBMLConstructorException("Null argument to copy constructor");
+ mMath = orig.mMath->deepCopy();
+ mMath->setParentSBMLObject(this);
}
- else
- {
- mVariable = orig.mVariable;
-
- if (orig.mMath != NULL)
- {
- mMath = orig.mMath->deepCopy();
- mMath->setParentSBMLObject(this);
- }
- }
+
}
@@ -119,12 +112,8 @@
*/
EventAssignment& EventAssignment::operator=(const EventAssignment& rhs)
{
- if (&rhs == NULL)
+ if(&rhs!=this)
{
- throw SBMLConstructorException("Null argument to assignment operator");
- }
- else if(&rhs!=this)
- {
this->SBase::operator =(rhs);
this->mVariable = rhs.mVariable;
@@ -216,14 +205,10 @@
int
EventAssignment::setVariable (const std::string& sid)
{
- if (&(sid) == NULL)
+ if (!(SyntaxChecker::isValidInternalSId(sid)))
{
return LIBSBML_INVALID_ATTRIBUTE_VALUE;
}
- else if (!(SyntaxChecker::isValidInternalSId(sid)))
- {
- return LIBSBML_INVALID_ATTRIBUTE_VALUE;
- }
else
{
mVariable = sid;
@@ -885,16 +870,9 @@
{
vector<SBase*>::const_iterator result;
- if (&(sid) == NULL)
- {
- return NULL;
- }
- else
- {
- result = find_if( mItems.begin(), mItems.end(), IdEqEA(sid) );
- return (result == mItems.end()) ? NULL :
- static_cast <EventAssignment*> (*result);
- }
+ result = find_if( mItems.begin(), mItems.end(), IdEqEA(sid) );
+ return (result == mItems.end()) ? NULL :
+ static_cast <EventAssignment*> (*result);
}
@@ -913,15 +891,12 @@
SBase* item = NULL;
vector<SBase*>::iterator result;
- if (&(sid) != NULL)
+ result = find_if( mItems.begin(), mItems.end(), IdEqEA(sid) );
+
+ if (result != mItems.end())
{
- result = find_if( mItems.begin(), mItems.end(), IdEqEA(sid) );
-
- if (result != mItems.end())
- {
- item = *result;
- mItems.erase(result);
- }
+ item = *result;
+ mItems.erase(result);
}
return static_cast <EventAssignment*> (item);
Modified: trunk/libsbml/src/sbml/FunctionDefinition.cpp
===================================================================
--- trunk/libsbml/src/sbml/FunctionDefinition.cpp 2015-05-20 10:21:59 UTC (rev 22269)
+++ trunk/libsbml/src/sbml/FunctionDefinition.cpp 2015-05-28 08:08:59 UTC (rev 22270)
@@ -97,23 +97,17 @@
*/
FunctionDefinition::FunctionDefinition (const FunctionDefinition& orig) :
SBase ( orig )
- , mMath ( NULL )
+ , mId ( orig.mId )
+ , mName ( orig.mName )
+ , mMath ( NULL )
{
- if (&orig == NULL)
+
+ if (orig.mMath != NULL)
{
- throw SBMLConstructorException("Null argument to copy constructor");
+ mMath = orig.mMath->deepCopy();
+ mMath->setParentSBMLObject(this);
}
- else
- {
- mId = orig.mId;
- mName = orig.mName;
- if (orig.mMath != NULL)
- {
- mMath = orig.mMath->deepCopy();
- mMath->setParentSBMLObject(this);
- }
- }
}
@@ -122,12 +116,8 @@
*/
FunctionDefinition& FunctionDefinition::operator=(const FunctionDefinition& rhs)
{
- if (&rhs == NULL)
+ if(&rhs!=this)
{
- throw SBMLConstructorException("Null argument to assignment operator");
- }
- else if(&rhs!=this)
- {
this->SBase::operator =(rhs);
mId = rhs.mId;
mName = rhs.mName;
@@ -250,14 +240,10 @@
return LIBSBML_UNEXPECTED_ATTRIBUTE;
}
*/
- if (&(sid) == NULL)
+ if (!(SyntaxChecker::isValidInternalSId(sid)))
{
return LIBSBML_INVALID_ATTRIBUTE_VALUE;
}
- else if (!(SyntaxChecker::isValidInternalSId(sid)))
- {
- return LIBSBML_INVALID_ATTRIBUTE_VALUE;
- }
else
{
mId = sid;
@@ -275,12 +261,8 @@
/* if this is setting an L2 name the type is string
* whereas if it is setting an L1 name its type is SId
*/
- if (&(name) == NULL)
+ if (getLevel() == 1)
{
- return LIBSBML_INVALID_ATTRIBUTE_VALUE;
- }
- else if (getLevel() == 1)
- {
if (!(SyntaxChecker::isValidInternalSId(name)))
{
return LIBSBML_INVALID_ATTRIBUTE_VALUE;
@@ -1020,16 +1002,10 @@
{
vector<SBase*>::const_iterator result;
- if (&(sid) == NULL)
- {
- return NULL;
- }
- else
- {
- result = find_if( mItems.begin(), mItems.end(), IdEqFD(sid) );
- return (result == mItems.end()) ? NULL :
- static_cast <FunctionDefinition*> (*result);
- }
+ result = find_if( mItems.begin(), mItems.end(), IdEqFD(sid) );
+ return (result == mItems.end()) ? NULL :
+ static_cast <FunctionDefinition*> (*result);
+
}
@@ -1048,15 +1024,12 @@
SBase* item = NULL;
vector<SBase*>::iterator result;
- if (&(sid) != NULL)
+ result = find_if( mItems.begin(), mItems.end(), IdEqFD(sid) );
+
+ if (result != mItems.end())
{
- result = find_if( mItems.begin(), mItems.end(), IdEqFD(sid) );
-
- if (result != mItems.end())
- {
- item = *result;
- mItems.erase(result);
- }
+ item = *result;
+ mItems.erase(result);
}
return static_cast <FunctionDefinition*> (item);
Modified: trunk/libsbml/src/sbml/InitialAssignment.cpp
===================================================================
--- trunk/libsbml/src/sbml/InitialAssignment.cpp 2015-05-20 10:21:59 UTC (rev 22269)
+++ trunk/libsbml/src/sbml/InitialAssignment.cpp 2015-05-28 08:08:59 UTC (rev 22270)
@@ -92,22 +92,15 @@
*/
InitialAssignment::InitialAssignment (const InitialAssignment& orig) :
SBase ( orig )
+ , mSymbol ( orig.mSymbol)
, mMath ( NULL )
{
- if (&orig == NULL)
+ if (orig.mMath != NULL)
{
- throw SBMLConstructorException("Null argument to copy constructor");
+ mMath = orig.mMath->deepCopy();
+ mMath->setParentSBMLObject(this);
}
- else
- {
- mSymbol = orig.mSymbol;
-
- if (orig.mMath != NULL)
- {
- mMath = orig.mMath->deepCopy();
- mMath->setParentSBMLObject(this);
- }
- }
+
}
@@ -116,15 +109,10 @@
*/
InitialAssignment& InitialAssignment::operator=(const InitialAssignment& rhs)
{
- if (&rhs == NULL)
+ if(&rhs!=this)
{
- throw SBMLConstructorException("Null argument to assignment operator");
- }
- else if(&rhs!=this)
- {
this->SBase::operator =(rhs);
this->mSymbol = rhs.mSymbol;
-
delete mMath;
if (rhs.mMath != NULL)
{
@@ -229,14 +217,10 @@
int
InitialAssignment::setSymbol (const std::string& sid)
{
- if (&(sid) == NULL)
+ if (!(SyntaxChecker::isValidInternalSId(sid)))
{
return LIBSBML_INVALID_ATTRIBUTE_VALUE;
}
- else if (!(SyntaxChecker::isValidInternalSId(sid)))
- {
- return LIBSBML_INVALID_ATTRIBUTE_VALUE;
- }
else
{
mSymbol = sid;
@@ -883,16 +867,10 @@
{
vector<SBase*>::const_iterator result;
- if (&(sid) == NULL)
- {
- return NULL;
- }
- else
- {
- result = find_if( mItems.begin(), mItems.end(), IdEqIA(sid) );
- return (result == mItems.end()) ? NULL :
- static_cast <InitialAssignment*> (*result);
- }
+ result = find_if( mItems.begin(), mItems.end(), IdEqIA(sid) );
+ return (result == mItems.end()) ? NULL :
+ static_cast <InitialAssignment*> (*result);
+
}
@@ -911,15 +889,12 @@
SBase* item = NULL;
vector<SBase*>::iterator result;
- if (&(sid) != NULL)
+ result = find_if( mItems.begin(), mItems.end(), IdEqIA(sid) );
+
+ if (result != mItems.end())
{
- result = find_if( mItems.begin(), mItems.end(), IdEqIA(sid) );
-
- if (result != mItems.end())
- {
- item = *result;
- mItems.erase(result);
- }
+ item = *result;
+ mItems.erase(result);
}
return static_cast <InitialAssignment*> (item);
Modified: trunk/libsbml/src/sbml/KineticLaw.cpp
===================================================================
--- trunk/libsbml/src/sbml/KineticLaw.cpp 2015-05-20 10:21:59 UTC (rev 22269)
+++ trunk/libsbml/src/sbml/KineticLaw.cpp 2015-05-28 08:08:59 UTC (rev 22270)
@@ -109,28 +109,22 @@
* Copy constructor. Creates a copy of this KineticLaw.
*/
KineticLaw::KineticLaw (const KineticLaw& orig) :
- SBase ( orig )
- , mMath ( NULL )
- , mParameters ( orig.mParameters )
- , mLocalParameters ( orig.mLocalParameters )
+ SBase ( orig )
+ , mFormula ( orig.mFormula )
+ , mMath ( NULL )
+ , mParameters ( orig.mParameters )
+ , mLocalParameters ( orig.mLocalParameters )
+ , mTimeUnits ( orig.mTimeUnits )
+ , mSubstanceUnits ( orig.mSubstanceUnits )
+ , mInternalId ( orig.mInternalId )
{
- if (&orig == NULL)
+
+ if (orig.mMath != NULL)
{
- throw SBMLConstructorException("Null argument to copy constructor");
+ mMath = orig.mMath->deepCopy();
+ mMath->setParentSBMLObject(this);
}
- else
- {
- mFormula = orig.mFormula;
- mTimeUnits = orig.mTimeUnits;
- mSubstanceUnits = orig.mSubstanceUnits;
- mInternalId = orig.mInternalId;
-
- if (orig.mMath != NULL)
- {
- mMath = orig.mMath->deepCopy();
- mMath->setParentSBMLObject(this);
- }
- }
+
connectToChild();
}
@@ -140,12 +134,8 @@
*/
KineticLaw& KineticLaw::operator=(const KineticLaw& rhs)
{
- if (&rhs == NULL)
+ if(&rhs!=this)
{
- throw SBMLConstructorException("Null argument to assignment operator");
- }
- else if(&rhs!=this)
- {
this->SBase::operator =(rhs);
mFormula = rhs.mFormula ;
mTimeUnits = rhs.mTimeUnits ;
@@ -360,38 +350,32 @@
int
KineticLaw::setFormula (const std::string& formula)
{
- if (&(formula) == NULL)
+ if (formula == "")
{
- return LIBSBML_INVALID_ATTRIBUTE_VALUE;
+ mFormula.erase();
+ delete mMath;
+ mMath = NULL;
+ return LIBSBML_OPERATION_SUCCESS;
}
+ ASTNode * math = SBML_parseFormula(formula.c_str());
+ if (math == NULL || !(math->isWellFormedASTNode()))
+ {
+ delete math;
+ return LIBSBML_INVALID_OBJECT;
+ }
else
{
- if (formula == "")
+ mFormula = formula;
+
+ if (mMath != NULL)
{
- mFormula.erase();
delete mMath;
mMath = NULL;
- return LIBSBML_OPERATION_SUCCESS;
}
- ASTNode * math = SBML_parseFormula(formula.c_str());
- if (math == NULL || !(math->isWellFormedASTNode()))
- {
- delete math;
- return LIBSBML_INVALID_OBJECT;
- }
- else
- {
- mFormula = formula;
-
- if (mMath != NULL)
- {
- delete mMath;
- mMath = NULL;
- }
- delete math;
- return LIBSBML_OPERATION_SUCCESS;
- }
+ delete math;
+ return LIBSBML_OPERATION_SUCCESS;
}
+
}
@@ -434,11 +418,7 @@
KineticLaw::setTimeUnits (const std::string& sid)
{
/* only in L1 and L2V1 */
- if (&(sid) == NULL)
- {
- return LIBSBML_INVALID_ATTRIBUTE_VALUE;
- }
- else if ((getLevel() == 2 && getVersion() > 1)
+ if ((getLevel() == 2 && getVersion() > 1)
|| getLevel() > 2)
{
return LIBSBML_UNEXPECTED_ATTRIBUTE;
@@ -462,11 +442,7 @@
KineticLaw::setSubstanceUnits (const std::string& sid)
{
/* only in L1 and L2V1 */
- if (&(sid) == NULL)
- {
- return LIBSBML_INVALID_ATTRIBUTE_VALUE;
- }
- else if ((getLevel() == 2 && getVersion() > 1)
+ if ((getLevel() == 2 && getVersion() > 1)
|| getLevel() > 2)
{
return LIBSBML_UNEXPECTED_ATTRIBUTE;
@@ -1031,7 +1007,7 @@
Parameter*
KineticLaw::removeParameter (const std::string& sid)
{
- return (&sid != NULL) ? mParameters.remove(sid) : NULL;
+ return mParameters.remove(sid);
}
@@ -1042,7 +1018,7 @@
LocalParameter*
KineticLaw::removeLocalParameter (const std::string& sid)
{
- return (&sid != NULL) ? mLocalParameters.remove(sid) : NULL;
+ return mLocalParameters.remove(sid);
}
Modified: trunk/libsbml/src/sbml/LocalParameter.cpp
===================================================================
--- trunk/libsbml/src/sbml/LocalParameter.cpp 2015-05-20 10:21:59 UTC (rev 22269)
+++ trunk/libsbml/src/sbml/LocalParameter.cpp 2015-05-28 08:08:59 UTC (rev 22270)
@@ -100,10 +100,6 @@
LocalParameter::LocalParameter(const LocalParameter& orig) :
Parameter ( orig )
{
- if (&orig == NULL)
- {
- throw SBMLConstructorException("Null argument to copy constructor");
- }
}
@@ -112,23 +108,15 @@
*/
LocalParameter::LocalParameter(const Parameter& orig) :
Parameter ( orig )
-{
- if (&orig == NULL)
- {
- throw SBMLConstructorException("Null argument to copy constructor");
- }
+{
}
/*
* Assignment operator.
*/
LocalParameter& LocalParameter::operator=(const LocalParameter& rhs)
{
- if (&rhs == NULL)
+ if(&rhs!=this)
{
- throw SBMLConstructorException("Null argument to assignment operator");
- }
- else if(&rhs!=this)
- {
this->Parameter::operator =(rhs);
}
@@ -415,16 +403,10 @@
{
vector<SBase*>::const_iterator result;
- if (&(sid) == NULL)
- {
- return NULL;
- }
- else
- {
- result = find_if( mItems.begin(), mItems.end(), IdEqP(sid) );
- return (result == mItems.end()) ? NULL :
- static_cast <LocalParameter*> (*result);
- }
+ result = find_if( mItems.begin(), mItems.end(), IdEqP(sid) );
+ return (result == mItems.end()) ? NULL :
+ static_cast <LocalParameter*> (*result);
+
}
@@ -457,15 +439,12 @@
SBase* item = NULL;
vector<SBase*>::iterator result;
- if (&(sid) != NULL)
+ result = find_if( mItems.begin(), mItems.end(), IdEqP(sid) );
+
+ if (result != mItems.end())
{
- result = find_if( mItems.begin(), mItems.end(), IdEqP(sid) );
-
- if (result != mItems.end())
- {
- item = *result;
- mItems.erase(result);
- }
+ item = *result;
+ mItems.erase(result);
}
return static_cast <LocalParameter*> (item);
Modified: trunk/libsbml/src/sbml/Model.cpp
===================================================================
--- trunk/libsbml/src/sbml/Model.cpp 2015-05-20 10:21:59 UTC (rev 22269)
+++ trunk/libsbml/src/sbml/Model.cpp 2015-05-28 08:08:59 UTC (rev 22270)
@@ -157,53 +157,44 @@
/*
* Copy constructor.
*/
-Model::Model(const Model& orig) :
- SBase (orig )
- , mFunctionDefinitions (orig.mFunctionDefinitions)
- , mUnitDefinitions (orig.mUnitDefinitions)
- , mCompartmentTypes (orig.mCompartmentTypes)
- , mSpeciesTypes (orig.mSpeciesTypes)
- , mCompartments (orig.mCompartments)
- , mSpecies (orig.mSpecies)
- , mParameters (orig.mParameters)
- , mInitialAssignments (orig.mInitialAssignments)
- , mRules (orig.mRules)
- , mConstraints (orig.mConstraints)
- , mReactions (orig.mReactions)
- , mEvents (orig.mEvents)
+Model::Model(const Model& orig)
+ : SBase (orig)
+ , mId (orig.mId)
+ , mName (orig.mName)
+ , mSubstanceUnits (orig.mSubstanceUnits)
+ , mTimeUnits (orig.mTimeUnits)
+ , mVolumeUnits (orig.mVolumeUnits)
+ , mAreaUnits (orig.mAreaUnits)
+ , mLengthUnits (orig.mLengthUnits)
+ , mExtentUnits (orig.mExtentUnits)
+ , mConversionFactor (orig.mConversionFactor)
+ , mFunctionDefinitions (orig.mFunctionDefinitions)
+ , mUnitDefinitions (orig.mUnitDefinitions)
+ , mCompartmentTypes (orig.mCompartmentTypes)
+ , mSpeciesTypes (orig.mSpeciesTypes)
+ , mCompartments (orig.mCompartments)
+ , mSpecies (orig.mSpecies)
+ , mParameters (orig.mParameters)
+ , mInitialAssignments (orig.mInitialAssignments)
+ , mRules (orig.mRules)
+ , mConstraints (orig.mConstraints)
+ , mReactions (orig.mReactions)
+ , mEvents (orig.mEvents)
+ , mFormulaUnitsData (NULL)
{
- if (&orig == NULL)
+
+ if(orig.mFormulaUnitsData != NULL)
{
- throw SBMLConstructorException("Null argument to copy constructor");
- }
- else
- {
- mId = orig.mId;
- mName = orig.mName;
- mSubstanceUnits = orig.mSubstanceUnits ;
- mTimeUnits = orig.mTimeUnits ;
- mVolumeUnits = orig.mVolumeUnits ;
- mAreaUnits = orig.mAreaUnits ;
- mLengthUnits = orig.mLengthUnits ;
- mExtentUnits = orig.mExtentUnits ;
- mConversionFactor = orig.mConversionFactor ;
-
- if(orig.mFormulaUnitsData != NULL)
+ this->mFormulaUnitsData = new List();
+ unsigned int i,iMax = orig.mFormulaUnitsData->getSize();
+ for(i = 0; i < iMax; ++i)
{
- this->mFormulaUnitsData = new List();
- unsigned int i,iMax = orig.mFormulaUnitsData->getSize();
- for(i = 0; i < iMax; ++i)
- {
- this->mFormulaUnitsData
- ->add(static_cast<FormulaUnitsData*>
- (orig.mFormulaUnitsData->get(i))->clone());
- }
+ this->mFormulaUnitsData
+ ->add(static_cast<FormulaUnitsData*>
+ (orig.mFormulaUnitsData->get(i))->clone());
}
- else
- {
- this->mFormulaUnitsData = NULL;
- }
}
+
connectToChild();
}
@@ -213,12 +204,8 @@
*/
Model& Model::operator=(const Model& rhs)
{
- if (&rhs == NULL)
+ if(&rhs!=this)
{
- throw SBMLConstructorException("Null argument to assignment operator");
- }
- else if(&rhs!=this)
- {
this->SBase::operator = (rhs);
mId = rhs.mId;
mName = rhs.mName;
@@ -715,14 +702,10 @@
return LIBSBML_UNEXPECTED_ATTRIBUTE;
}
*/
- if (&(sid) == NULL)
+ if (!(SyntaxChecker::isValidInternalSId(sid)))
{
return LIBSBML_INVALID_ATTRIBUTE_VALUE;
}
- else if (!(SyntaxChecker::isValidInternalSId(sid)))
- {
- return LIBSBML_INVALID_ATTRIBUTE_VALUE;
- }
else
{
mId = sid;
@@ -740,12 +723,8 @@
/* if this is setting an L2 name the type is string
* whereas if it is setting an L1 name its type is SId
*/
- if (&(name) == NULL)
+ if (getLevel() == 1)
{
- return LIBSBML_INVALID_ATTRIBUTE_VALUE;
- }
- else if (getLevel() == 1)
- {
if (!(SyntaxChecker::isValidInternalSId(name)))
{
return LIBSBML_INVALID_ATTRIBUTE_VALUE;
@@ -770,12 +749,8 @@
int
Model::setSubstanceUnits (const std::string& units)
{
- if (&(units) == NULL)
+ if (getLevel() < 3)
{
- return LIBSBML_INVALID_ATTRIBUTE_VALUE;
- }
- else if (getLevel() < 3)
- {
return LIBSBML_UNEXPECTED_ATTRIBUTE;
}
else if (!(SyntaxChecker::isValidInternalUnitSId(units)))
@@ -796,12 +771,8 @@
int
Model::setTimeUnits (const std::string& units)
{
- if (&(units) == NULL)
+ if (getLevel() < 3)
{
- return LIBSBML_INVALID_ATTRIBUTE_VALUE;
- }
- else if (getLevel() < 3)
- {
return LIBSBML_UNEXPECTED_ATTRIBUTE;
}
else if (!(SyntaxChecker::isValidInternalUnitSId(units)))
@@ -822,12 +793,8 @@
int
Model::setVolumeUnits (const std::string& units)
{
- if (&(units) == NULL)
+ if (getLevel() < 3)
{
- return LIBSBML_INVALID_ATTRIBUTE_VALUE;
- }
- else if (getLevel() < 3)
- {
return LIBSBML_UNEXPECTED_ATTRIBUTE;
}
else if (!(SyntaxChecker::isValidInternalUnitSId(units)))
@@ -848,12 +815,8 @@
int
Model::setAreaUnits (const std::string& units)
{
- if (&(units) == NULL)
+ if (getLevel() < 3)
{
- return LIBSBML_INVALID_ATTRIBUTE_VALUE;
- }
- else if (getLevel() < 3)
- {
return LIBSBML_UNEXPECTED_ATTRIBUTE;
}
else if (!(SyntaxChecker::isValidInternalUnitSId(units)))
@@ -874,12 +837,8 @@
int
Model::setLengthUnits (const std::string& units)
{
- if (&(units) == NULL)
+ if (getLevel() < 3)
{
- return LIBSBML_INVALID_ATTRIBUTE_VALUE;
- }
- else if (getLevel() < 3)
- {
return LIBSBML_UNEXPECTED_ATTRIBUTE;
}
else if (!(SyntaxChecker::isValidInternalUnitSId(units)))
@@ -900,12 +859,8 @@
int
Model::setExtentUnits (const std::string& units)
{
- if (&(units) == NULL)
+ if (getLevel() < 3)
{
- return LIBSBML_INVALID_ATTRIBUTE_VALUE;
- }
- else if (getLevel() < 3)
- {
return LIBSBML_UNEXPECTED_ATTRIBUTE;
}
else if (!(SyntaxChecker::isValidInternalUnitSId(units)))
@@ -926,12 +881,8 @@
int
Model::setConversionFactor (const std::string& id)
{
- if (&(id) == NULL)
+ if (getLevel() < 3)
{
- return LIBSBML_INVALID_ATTRIBUTE_VALUE;
- }
- else if (getLevel() < 3)
- {
return LIBSBML_UNEXPECTED_ATTRIBUTE;
}
else if (!(SyntaxChecker::isValidInternalSId(id)))
Modified: trunk/libsbml/src/sbml/Parameter.cpp
===================================================================
--- trunk/libsbml/src/sbml/Parameter.cpp 2015-05-20 10:21:59 UTC (rev 22269)
+++ trunk/libsbml/src/sbml/Parameter.cpp 2015-05-28 08:08:59 UTC (rev 22270)
@@ -149,25 +149,19 @@
/*
* Copy constructor. Creates a copy of this Parameter.
*/
-Parameter::Parameter(const Parameter& orig) :
- SBase ( orig )
+Parameter::Parameter(const Parameter& orig)
+ : SBase ( orig )
+ , mId (orig.mId)
+ , mName (orig.mName)
+ , mValue (orig.mValue)
+ , mUnits (orig.mUnits)
+ , mConstant (orig.mConstant)
+ , mIsSetValue (orig.mIsSetValue)
+ , mIsSetConstant (orig.mIsSetConstant)
+ , mExplicitlySetConstant (orig.mExplicitlySetConstant)
+ , mCalculatingUnits (false) // only set by units converter
+
{
- if (&orig == NULL)
- {
- throw SBMLConstructorException("Null argument to copy constructor");
- }
- else
- {
- mValue = orig.mValue ;
- mUnits = orig.mUnits ;
- mConstant = orig.mConstant ;
- mIsSetValue = orig.mIsSetValue;
- mId = orig.mId;
- mName = orig.mName;
- mIsSetConstant = orig.mIsSetConstant;
- mExplicitlySetConstant = orig.mExplicitlySetConstant;
- mCalculatingUnits = false; // only set by units converter
- }
}
@@ -176,12 +170,8 @@
*/
Parameter& Parameter::operator=(const Parameter& rhs)
{
- if (&rhs == NULL)
+ if(&rhs!=this)
{
- throw SBMLConstructorException("Null argument to assignment operator");
- }
- else if(&rhs!=this)
- {
this->SBase::operator =(rhs);
mValue = rhs.mValue ;
mUnits = rhs.mUnits ;
@@ -361,14 +351,10 @@
return LIBSBML_UNEXPECTED_ATTRIBUTE;
}
*/
- if (&(sid) == NULL)
+ if (!(SyntaxChecker::isValidInternalSId(sid)))
{
return LIBSBML_INVALID_ATTRIBUTE_VALUE;
}
- else if (!(SyntaxChecker::isValidInternalSId(sid)))
- {
- return LIBSBML_INVALID_ATTRIBUTE_VALUE;
- }
else
{
mId = sid;
@@ -386,12 +372,8 @@
/* if this is setting an L2 name the type is string
* whereas if it is setting an L1 name its type is SId
*/
- if (&(name) == NULL)
+ if (getLevel() == 1)
{
- return LIBSBML_INVALID_ATTRIBUTE_VALUE;
- }
- else if (getLevel() == 1)
- {
if (!(SyntaxChecker::isValidInternalSId(name)))
{
return LIBSBML_INVALID_ATTRIBUTE_VALUE;
@@ -428,14 +410,10 @@
int
Parameter::setUnits (const std::string& units)
{
- if (&(units) == NULL)
+ if (!(SyntaxChecker::isValidInternalUnitSId(units)))
{
return LIBSBML_INVALID_ATTRIBUTE_VALUE;
}
- else if (!(SyntaxChecker::isValidInternalUnitSId(units)))
- {
- return LIBSBML_INVALID_ATTRIBUTE_VALUE;
- }
else
{
mUnits = units;
@@ -1578,15 +1556,8 @@
{
vector<SBase*>::const_iterator result;
- if (&(sid) == NULL)
- {
- return NULL;
- }
- else
- {
- result = find_if( mItems.begin(), mItems.end(), IdEqP(sid) );
- return (result == mItems.end()) ? NULL : static_cast <Parameter*> (*result);
- }
+ result = find_if( mItems.begin(), mItems.end(), IdEqP(sid) );
+ return (result == mItems.end()) ? NULL : static_cast <Parameter*> (*result);
}
@@ -1605,15 +1576,12 @@
SBase* item = NULL;
vector<SBase*>::iterator result;
- if (&(sid) != NULL)
+ result = find_if( mItems.begin(), mItems.end(), IdEqP(sid) );
+
+ if (result != mItems.end())
{
- result = find_if( mItems.begin(), mItems.end(), IdEqP(sid) );
-
- if (result != mItems.end())
- {
- item = *result;
- mItems.erase(result);
- }
+ item = *result;
+ mItems.erase(result);
}
return static_cast <Parameter*> (item);
Modified: trunk/libsbml/src/sbml/Priority.cpp
===================================================================
--- trunk/libsbml/src/sbml/Priority.cpp 2015-05-20 10:21:59 UTC (rev 22269)
+++ trunk/libsbml/src/sbml/Priority.cpp 2015-05-28 08:08:59 UTC (rev 22270)
@@ -94,23 +94,15 @@
* Copy constructor. Creates a copy of this Priority.
*/
Priority::Priority (const Priority& orig) :
- SBase ( orig )
- , mMath ( NULL )
+ SBase ( orig )
+ , mMath ( NULL )
+ , mInternalId ( orig.mInternalId )
{
- if (&orig == NULL)
+ if (orig.mMath != NULL)
{
- throw SBMLConstructorException("Null argument to copy constructor");
+ mMath = orig.mMath->deepCopy();
+ mMath->setParentSBMLObject(this);
}
- else
- {
- mInternalId = orig.mInternalId;
-
- if (orig.mMath != NULL)
- {
- mMath = orig.mMath->deepCopy();
- mMath->setParentSBMLObject(this);
- }
- }
}
@@ -119,12 +111,8 @@
*/
Priority& Priority::operator=(const Priority& rhs)
{
- if (&rhs == NULL)
+ if(&rhs!=this)
{
- throw SBMLConstructorException("Null argument to assignment operator");
- }
- else if(&rhs!=this)
- {
this->SBase::operator =(rhs);
this->mInternalId = rhs.mInternalId;
Modified: trunk/libsbml/src/sbml/Reaction.cpp
===================================================================
--- trunk/libsbml/src/sbml/Reaction.cpp 2015-05-20 10:21:59 UTC (rev 22269)
+++ trunk/libsbml/src/sbml/Reaction.cpp 2015-05-28 08:08:59 UTC (rev 22270)
@@ -175,34 +175,26 @@
/*
* Copy constructor. Creates a copy of this Reaction.
*/
-Reaction::Reaction (const Reaction& orig) :
- SBase ( orig )
+Reaction::Reaction (const Reaction& orig)
+ : SBase ( orig )
+ , mId ( orig.mId )
+ , mName ( orig.mName )
, mReactants ( orig.mReactants )
, mProducts ( orig.mProducts )
, mModifiers ( orig.mModifiers )
, mKineticLaw( NULL )
-{
- if (&orig == NULL)
+ , mReversible( orig.mReversible )
+ , mFast ( orig.mFast )
+ , mIsSetFast ( orig.mIsSetFast )
+ , mCompartment ( orig.mCompartment )
+ , mIsSetReversible ( orig.mIsSetReversible )
+ , mExplicitlySetReversible ( orig.mExplicitlySetReversible )
+ , mExplicitlySetFast ( orig.mExplicitlySetFast )
+{
+ if (orig.mKineticLaw != NULL)
{
- throw SBMLConstructorException("Null argument to copy constructor");
+ mKineticLaw = static_cast<KineticLaw*>( orig.mKineticLaw->clone() );
}
- else
- {
- mReversible = orig.mReversible ;
- mFast = orig.mFast ;
- mIsSetFast = orig.mIsSetFast ;
- mId = orig.mId;
- mName = orig.mName;
- mCompartment = orig.mCompartment;
- mIsSetReversible = orig.mIsSetReversible;
- mExplicitlySetReversible = orig.mExplicitlySetReversible;
- mExplicitlySetFast = orig.mExplicitlySetFast;
-
- if (orig.mKineticLaw != NULL)
- {
- mKineticLaw = static_cast<KineticLaw*>( orig.mKineticLaw->clone() );
- }
- }
connectToChild();
}
@@ -212,12 +204,8 @@
*/
Reaction& Reaction::operator=(const Reaction& rhs)
{
- if (&rhs == NULL)
+ if(&rhs!=this)
{
- throw SBMLConstructorException("Null argument to assignment operator");
- }
- else if(&rhs!=this)
- {
this->SBase::operator =(rhs);
mReversible = rhs.mReversible ;
mFast = rhs.mFast ;
@@ -546,14 +534,10 @@
return LIBSBML_UNEXPECTED_ATTRIBUTE;
}
*/
- if (&(sid) == NULL)
+ if (!(SyntaxChecker::isValidInternalSId(sid)))
{
return LIBSBML_INVALID_ATTRIBUTE_VALUE;
}
- else if (!(SyntaxChecker::isValidInternalSId(sid)))
- {
- return LIBSBML_INVALID_ATTRIBUTE_VALUE;
- }
else
{
mId = sid;
@@ -571,12 +555,8 @@
/* if this is setting an L2 name the type is string
* whereas if it is setting an L1 name its type is SId
*/
- if (&(name) == NULL)
+ if (getLevel() == 1)
{
- return LIBSBML_INVALID_ATTRIBUTE_VALUE;
- }
- else if (getLevel() == 1)
- {
if (!(SyntaxChecker::isValidInternalSId(name)))
{
return LIBSBML_INVALID_ATTRIBUTE_VALUE;
@@ -662,12 +642,8 @@
int
Reaction::setCompartment (const std::string& sid)
{
- if (&(sid) == NULL)
+ if (getLevel() < 3)
{
- return LIBSBML_INVALID_ATTRIBUTE_VALUE;
- }
- else if (getLevel() < 3)
- {
return LIBSBML_UNEXPECTED_ATTRIBUTE;
}
@@ -1930,15 +1906,8 @@
{
vector<SBase*>::const_iterator result;
- if (&(sid) == NULL)
- {
- return NULL;
- }
- else
- {
- result = find_if( mItems.begin(), mItems.end(), IdEq<Reaction>(sid) );
- return (result == mItems.end()) ? NULL : static_cast <Reaction*> (*result);
- }
+ result = find_if( mItems.begin(), mItems.end(), IdEq<Reaction>(sid) );
+ return (result == mItems.end()) ? NULL : static_cast <Reaction*> (*result);
}
@@ -1957,17 +1926,15 @@
SBase* item = NULL;
vector<SBase*>::iterator result;
- if (&(sid) != NULL)
+ result = find_if( mItems.begin(), mItems.end(), IdEq<Reaction>(sid) );
+
+ if (result != mItems.end())
{
- result = find_if( mItems.begin(), mItems.end(), IdEq<Reaction>(sid) );
-
- if (result != mItems.end())
- {
- item = *result;
- mItems.erase(result);
- }
+ item = *result;
+ mItems.erase(result);
}
+
return static_cast <Reaction*> (item);
}
Modified: trunk/libsbml/src/sbml/Rule.cpp
===================================================================
--- trunk/libsbml/src/sbml/Rule.cpp 2015-05-20 10:21:59 UTC (rev 22269)
+++ trunk/libsbml/src/sbml/Rule.cpp 2015-05-28 08:08:59 UTC (rev 22270)
@@ -103,29 +103,21 @@
/*
* Copy constructor. Creates a copy of this Rule.
*/
-Rule::Rule (const Rule& orig) :
- SBase ( orig )
- , mMath ( NULL )
+Rule::Rule (const Rule& orig)
+ : SBase ( orig )
+ , mVariable ( orig.mVariable )
+ , mFormula ( orig.mFormula )
+ , mMath ( NULL )
+ , mUnits ( orig.mUnits )
+ , mType ( orig.mType )
+ , mL1Type ( orig.mL1Type )
+ , mInternalId ( orig.mInternalId )
{
- if (&orig == NULL)
+ if (orig.mMath != NULL)
{
- throw SBMLConstructorException("Null argument to copy constructor");
+ mMath = orig.mMath->deepCopy();
+ mMath->setParentSBMLObject(this);
}
- else
- {
- mVariable = orig.mVariable;
- mFormula = orig.mFormula ;
- mUnits = orig.mUnits ;
- mType = orig.mType ;
- mL1Type = orig.mL1Type ;
- mInternalId = orig.mInternalId;
-
- if (orig.mMath != NULL)
- {
- mMath = orig.mMath->deepCopy();
- mMath->setParentSBMLObject(this);
- }
- }
}
@@ -134,12 +126,8 @@
*/
Rule& Rule::operator=(const Rule& rhs)
{
- if (&rhs == NULL)
+ if(&rhs!=this)
{
- throw SBMLConstructorException("Null argument to assignment operator");
- }
- else if(&rhs!=this)
- {
this->SBase::operator =(rhs);
mVariable = rhs.mVariable;
mFormula = rhs.mFormula ;
@@ -323,38 +311,34 @@
int
Rule::setFormula (const std::string& formula)
{
- if (&(formula) == NULL)
+
+
+ if (formula == "")
{
- return LIBSBML_INVALID_ATTRIBUTE_VALUE;
+ mFormula.erase();
+ delete mMath;
+ mMath = NULL;
+ return LIBSBML_OPERATION_SUCCESS;
}
- else
+ ASTNode * math = SBML_parseFormula(formula.c_str());
+ if (math == NULL || !(math->isWellFormedASTNode()))
{
- if (formula == "")
+ delete math;
+ return LIBSBML_INVALID_OBJECT;
+ }
+ else
+ {
+ delete math;
+ mFormula = formula;
+
+ if (mMath != NULL)
{
- mFormula.erase();
delete mMath;
mMath = NULL;
- return LIBSBML_OPERATION_SUCCESS;
}
- ASTNode * math = SBML_parseFormula(formula.c_str());
- if (math == NULL || !(math->isWellFormedASTNode()))
- {
- delete math;
- return LIBSBML_INVALID_OBJECT;
- }
- else
- {
- delete math;
- mFormula = formula;
-
- if (mMath != NULL)
- {
- delete mMath;
- mMath = NULL;
- }
- return LIBSBML_OPERATION_SUCCESS;
- }
+ return LIBSBML_OPERATION_SUCCESS;
}
+
}
@@ -396,12 +380,8 @@
int
Rule::setVariable (const std::string& sid)
{
- if (&(sid) == NULL)
+ if (isAlgebraic())
{
- return LIBSBML_INVALID_ATTRIBUTE_VALUE;
- }
- else if (isAlgebraic())
- {
return LIBSBML_UNEXPECTED_ATTRIBUTE;
}
else if (!(SyntaxChecker::isValidInternalSId(sid)))
@@ -424,12 +404,8 @@
Rule::setUnits (const std::string& sname)
{
/* only in L1 ParameterRule */
- if (&(sname) == NULL)
+ if (getLevel() > 1)
{
- return LIBSBML_INVALID_ATTRIBUTE_VALUE;
- }
- else if (getLevel() > 1)
- {
return LIBSBML_UNEXPECTED_ATTRIBUTE;
}
else if ( !isParameter())
@@ -1478,15 +1454,8 @@
{
vector<SBase*>::const_iterator result;
- if (&(sid) == NULL)
- {
- return NULL;
- }
- else
- {
- result = find_if( mItems.begin(), mItems.end(), IdEqRule(sid) );
- return (result == mItems.end()) ? NULL : static_cast <Rule*> (*result);
- }
+ result = find_if( mItems.begin(), mItems.end(), IdEqRule(sid) );
+ return (result == mItems.end()) ? NULL : static_cast <Rule*> (*result);
}
@@ -1519,15 +1488,12 @@
SBase* item = NULL;
vector<SBase*>::iterator result;
- if (&(sid) != NULL)
+ result = find_if( mItems.begin(), mItems.end(), IdEqRule(sid) );
+
+ if (result != mItems.end())
{
- result = find_if( mItems.begin(), mItems.end(), IdEqRule(sid) );
-
- if (result != mItems.end())
- {
- item = *result;
- mItems.erase(result);
- }
+ item = *result;
+ mItems.erase(result);
}
return static_cast <Rule*> (item);
Modified: trunk/libsbml/src/sbml/SBMLDocument.cpp
===================================================================
--- trunk/libsbml/src/sbml/SBMLDocument.cpp 2015-05-20 10:21:59 UTC (rev 22269)
+++ trunk/libsbml/src/sbml/SBMLDocument.cpp 2015-05-28 08:08:59 UTC (rev 22270)
@@ -251,37 +251,33 @@
/*
* Creates a copy of this SBMLDocument.
*/
-SBMLDocument::SBMLDocument (const SBMLDocument& orig) :
- SBase ( orig )
+SBMLDocument::SBMLDocument (const SBMLDocument& orig)
+ : SBase ( orig )
+ , mLevel ( orig.mLevel )
+ , mVersion ( orig.mVersion )
, mModel ( NULL )
, mLocationURI (orig.mLocationURI )
+ , mErrorLog()
+ , mValidators ()
+ , mInternalValidator(new SBMLInternalValidator())
+ , mRequiredAttrOfUnknownPkg(orig.mRequiredAttrOfUnknownPkg)
+ , mRequiredAttrOfUnknownDisabledPkg(orig.mRequiredAttrOfUnknownDisabledPkg)
+ , mPkgUseDefaultNSMap()
{
- if (&orig == NULL)
+
+
+ setSBMLDocument(this);
+
+ mInternalValidator->setDocument(this);
+ mInternalValidator->setApplicableValidators(orig.getApplicableValidators());
+ mInternalValidator->setConversionValidators(orig.getConversionValidators());
+
+ if (orig.mModel != NULL)
{
- throw SBMLConstructorException("Null argument to copy constructor");
+ mModel = static_cast<Model*>( orig.mModel->clone() );
+ mModel->setSBMLDocument(this);
}
- else
- {
- mLevel = orig.mLevel;
- mVersion = orig.mVersion;
-
- setSBMLDocument(this);
-
- mInternalValidator = new SBMLInternalValidator();
- mInternalValidator->setDocument(this);
- mInternalValidator->setApplicableValidators(orig.getApplicableValidators());
- mInternalValidator->setConversionValidators(orig.getConversionValidators());
- mRequiredAttrOfUnknownPkg = orig.mRequiredAttrOfUnknownPkg;
- mRequiredAttrOfUnknownDisabledPkg = orig.mRequiredAttrOfUnknownDisabledPkg;
-
- if (orig.mModel != NULL)
- {
- mModel = static_cast<Model*>( orig.mModel->clone() );
- mModel->setSBMLDocument(this);
- }
-
- }
-
+
connectToChild();
//if(orig.mNamespaces)
// this->mNamespaces =
@@ -297,12 +293,8 @@
*/
SBMLDocument& SBMLDocument::operator=(const SBMLDocument& rhs)
{
- if (&rhs == NULL)
+ if(&rhs!=this)
{
- throw SBMLConstructorException("Null argument to assignment operator");
- }
- else if(&rhs!=this)
- {
this->SBase::operator =(rhs);
setSBMLDocument(this);
Modified: trunk/libsbml/src/sbml/SBMLNamespaces.cpp
===================================================================
--- trunk/libsbml/src/sbml/SBMLNamespaces.cpp 2015-05-20 10:21:59 UTC (rev 22269)
+++ trunk/libsbml/src/sbml/SBMLNamespaces.cpp 2015-05-28 08:08:59 UTC (rev 22270)
@@ -174,22 +174,13 @@
* Copy constructor; creates a copy of a SBMLNamespaces.
*/
SBMLNamespaces::SBMLNamespaces(const SBMLNamespaces& orig)
+ : mLevel(orig.mLevel)
+ , mVersion...
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