Skip to content

Commit

Permalink
replace arguments at the same time instead of sequentially
Browse files Browse the repository at this point in the history 
- add `ASTNode::replaceArguments` to replace all arguments at the same time
- refactor shared functionality into `copyNode`
- modify `SBMLTransforms::replaceBvars` to use this instead of replacing arguments sequentially
  • Loading branch information
@lkeegan @fbergmann
lkeegan authored and fbergmann committed Mar 14, 2023
1 parent 14bef1f commit a664e47
Show file tree
Hide file tree
Showing 3 changed files with 100 additions and 128 deletions.
59 changes: 7 additions & 52 deletions src/sbml/SBMLTransforms.cpp
View file
Original file line number Diff line number Diff line change
Expand Up @@ -146,59 +146,14 @@ SBMLTransforms::replaceBvars(ASTNode * node, const FunctionDefinition *fd)
noBvars = fd->getMath()->getNumBvars();
fdMath = *fd->getBody();

// get names of all bvars
std::vector<std::string> allBVars;
for (unsigned int i = 0; i < noBvars; ++i)
allBVars.push_back(fd->getArgument(i)->getName());

// get all names in the node
List* names = node->getListOfNodes((ASTNodePredicate)ASTNode_isName);

// convert to std::vector
std::vector<std::string> currentChildNames;
for (unsigned int j = 0 ; j < names->getSize(); ++j)
{
ASTNode* name = (ASTNode*)names->get(j);
currentChildNames.push_back(name->getName());
}
delete names;

// establish order in which to replace bvars, we want to ensure that
// no bvars are replaced before they are used
std::vector<unsigned int> replaceOrder;
for (unsigned int i = 0; i < noBvars; ++i)
{
std::string currentArg = fd->getArgument(i)->getName();
bool added = false;
for (unsigned int j = 0; j < currentChildNames.size(); ++j)
{
if (currentArg == currentChildNames[j])
{
replaceOrder.insert(replaceOrder.begin(), i);
added = true;
break;
}
}
if (!added)
{
replaceOrder.push_back(i);
}
}

unsigned int nodeCount = 0;

// now replace in the order established above
std::vector<unsigned int>::iterator it = replaceOrder.begin();
for (; it != replaceOrder.end(); ++it)
{
unsigned int i = *it;
if (nodeCount < node->getNumChildren())
{
fdMath.replaceArgument(fd->getArgument(i)->getName(),
node->getChild(nodeCount));
}
++nodeCount;
// get names of bvars and AST node to substitute for each
std::vector<std::string> bVars;
std::vector<ASTNode*> astNodes;
for (unsigned int i = 0; i < noBvars; ++i){
bVars.push_back(fd->getArgument(i)->getName());
astNodes.push_back(node->getChild(i));
}
fdMath.replaceArguments(bVars, astNodes);
(*node) = fdMath;
}

Expand Down
151 changes: 77 additions & 74 deletions src/sbml/math/ASTNode.cpp
View file
Original file line number Diff line number Diff line change
Expand Up @@ -2759,100 +2759,103 @@ ASTNode::isWellFormedASTNode() const

/** @endcond */


LIBSBML_EXTERN
void
ASTNode::replaceArgument(const std::string& bvar, ASTNode * arg)
static void copyNode(const ASTNode * source, ASTNode * dest)
{
if (arg == NULL)
return;
else if (getNumChildren() == 0)
{
if (this->isName() && this->getName() == bvar)
if (source == NULL)
{
if (arg->isName())
{
this->setType(arg->getType());
this->setName(arg->getName());
}
else if (arg->isReal())
{
this->setValue(arg->getReal());
if (arg->isSetUnits())
return;
}
if (source->isName())
{
dest->setType(source->getType());
dest->setName(source->getName());
}
else if (source->isReal())
{
dest->setValue(source->getReal());
if (source->isSetUnits())
{
this->setUnits(arg->getUnits());
dest->setUnits(source->getUnits());
}
}
else if (arg->isInteger())
{
this->setValue(arg->getInteger());
if (arg->isSetUnits())
}
else if (source->isInteger())
{
dest->setValue(source->getInteger());
if (source->isSetUnits())
{
this->setUnits(arg->getUnits());
dest->setUnits(source->getUnits());
}
}
else if (arg->isConstant())
{
this->setType(arg->getType());
}
else
{
this->setType(arg->getType());
this->setName(arg->getName());
for (unsigned int c = 0; c < arg->getNumChildren(); c++)
}
else if (source->isConstant())
{
dest->setType(source->getType());
}
else
{
dest->setType(source->getType());
dest->setName(source->getName());
for (unsigned int c = 0; c < source->getNumChildren(); c++)
{
this->addChild(arg->getChild(c)->deepCopy());
dest->addChild(source->getChild(c)->deepCopy());
}
}
}
}

LIBSBML_EXTERN
void
ASTNode::replaceArgument(const std::string& bvar, ASTNode * arg)
{
if (getNumChildren() == 0 && this->isName() && this->getName() == bvar)
{
copyNode(arg, this);
return;
}
for (unsigned int i = 0; i < getNumChildren(); i++)
{
if (getChild(i)->isName())
if (getChild(i)->isName() && getChild(i)->getName() == bvar)
{
if (getChild(i)->getName() == bvar)
{
if (arg->isName())
{
getChild(i)->setType(arg->getType());
getChild(i)->setName(arg->getName());
}
else if (arg->isReal())
{
getChild(i)->setValue(arg->getReal());
if (arg->isSetUnits())
{
getChild(i)->setUnits(arg->getUnits());
}
}
else if (arg->isInteger())
copyNode(arg, getChild(i));
}
else
{
getChild(i)->replaceArgument(bvar, arg);
}
}
}

LIBSBML_EXTERN
void
ASTNode::replaceArguments(const std::vector<std::string>& bvars, std::vector<ASTNode *>& args)
{
std::size_t n = bvars.size();
if (getNumChildren() == 0)
{
for(std::size_t j=0; j<n; ++j)
{
getChild(i)->setValue(arg->getInteger());
if (arg->isSetUnits())
{
getChild(i)->setUnits(arg->getUnits());
}
if (this->isName() && this->getName() == bvars[j])
{
copyNode(args[j], this);
return;
}
}
else if (arg->isConstant())
}
for (unsigned int i = 0; i < getNumChildren(); i++)
{
bool child_replaced = false;
for(std::size_t j=0; j<n; ++j)
{
getChild(i)->setType(arg->getType());
if (getChild(i)->isName() && getChild(i)->getName() == bvars[j])
{
copyNode(args[j], getChild(i));
child_replaced = true;
break;
}
}
else
if (!child_replaced)
{
getChild(i)->setType(arg->getType());
getChild(i)->setName(arg->getName());
for (unsigned int c = 0; c < arg->getNumChildren(); c++)
{
getChild(i)->addChild(arg->getChild(c)->deepCopy());
}
getChild(i)->replaceArguments(bvars, args);
}
}
}
else
{
getChild(i)->replaceArgument(bvar, arg);
}
}
}

LIBSBML_EXTERN
Expand Down
18 changes: 16 additions & 2 deletions src/sbml/math/ASTNode.h
View file
Original file line number Diff line number Diff line change
Expand Up @@ -1796,7 +1796,7 @@ setValue(value, 0);
* For example, if the formula in this ASTNode is <code>x + y</code>,
* and the function is called with @c bvar = @c "x" and @c arg = an ASTNode
* representing the real value @c 3. This method would substitute @c 3 for
* @c x within this ASTNode object, resulting in the forula <code>3 + y</code>.
* @c x within this ASTNode object, resulting in the formula <code>3 + y</code>.
*
* @param bvar a string representing the variable name to be substituted.
* @param arg an ASTNode representing the name/value/formula to use as
Expand All @@ -1805,8 +1805,22 @@ setValue(value, 0);
LIBSBML_EXTERN
void replaceArgument(const std::string& bvar, ASTNode * arg);

/**
* Replaces occurrences of each given name with the corresponding ASTNode.
*
* For example, if the formula in this ASTNode is <code>x - y</code>,
* and the function is called with bvars = {"x", "y"} and args = ASTNodes
* representing objects with names {"y", "x"}, the result would be <code>y - x</code>.
*
* @param bvars a vector of strings representing the variable names to be substituted.
* @param args a vector of ASTNodes representing the name/value/formula to use as
* a replacement for each variable name
*/
LIBSBML_EXTERN
void replaceArguments(const std::vector<std::string>& bvars, std::vector<ASTNode *>& args);

/** @cond doxygenLibsbmlInternal */

/** @cond doxygenLibsbmlInternal */

/**
* Sets the parent SBML object of this node. Is not recursive, and will not set the parent SBML object of any children of this node.
Expand Down

0 comments on commit a664e47

Please sign in to comment.