[sbml-svn] SF.net SVN: sbml:[18264] trunk/libsbml/src/sbml/packages/comp/validator/ constraints

[<sar...@us...>]

Revision: 18264
          http://sourceforge.net/p/sbml/code/18264
Author:   sarahkeating
Date:     2013-07-25 11:34:38 +0000 (Thu, 25 Jul 2013)
Log Message:
-----------
There are two places in the validation code that use the getReferencedElement function.
This function will now log errors relating to missing references.
The validation does not need these errors as they will be logged and therefore just end up as duplicates; so I added code that would remove any errors logged by the getReferencedElement function.

Modified Paths:
--------------
    trunk/libsbml/src/sbml/packages/comp/validator/constraints/UniquePortReferences.cpp
    trunk/libsbml/src/sbml/packages/comp/validator/constraints/UniqueReplacedReferences.cpp

Modified: trunk/libsbml/src/sbml/packages/comp/validator/constraints/UniquePortReferences.cpp
===================================================================
--- trunk/libsbml/src/sbml/packages/comp/validator/constraints/UniquePortReferences.cpp	2013-07-24 23:46:50 UTC (rev 18263)
+++ trunk/libsbml/src/sbml/packages/comp/validator/constraints/UniquePortReferences.cpp	2013-07-25 11:34:38 UTC (rev 18264)
@@ -94,14 +94,30 @@
 void 
 UniquePortReferences::checkReferencedElement(Port& p)
 {
-  if (mReferencedElements->find(p.getReferencedElement(), 
+  unsigned int numErrsB4 = p.getSBMLDocument()->getNumErrors();
+  
+  SBase* refElem = p.getReferencedElement();
+  
+  // if there is an issue with references the getReferencedElement
+  // code may log errors
+  // we dont want them - since we will log any  errors here
+  // so remove them
+  unsigned int numErrsAfter = p.getSBMLDocument()->getNumErrors();
+  for (unsigned int i = numErrsAfter; i > numErrsB4; i--)
+  {
+    p.getSBMLDocument()->getErrorLog()->remove(
+      p.getSBMLDocument()->getError(i-1)->getErrorId());
+  }
+  
+  if (mReferencedElements->find(refElem, 
                            (ListItemComparator) (ObjectsSame)) != NULL)
   {
     logReferenceExists (p);
   }
   else
   {
-    mReferencedElements->add(p.getReferencedElement());
+
+    mReferencedElements->add(refElem);
   }
 }
 

Modified: trunk/libsbml/src/sbml/packages/comp/validator/constraints/UniqueReplacedReferences.cpp
===================================================================
--- trunk/libsbml/src/sbml/packages/comp/validator/constraints/UniqueReplacedReferences.cpp	2013-07-24 23:46:50 UTC (rev 18263)
+++ trunk/libsbml/src/sbml/packages/comp/validator/constraints/UniqueReplacedReferences.cpp	2013-07-25 11:34:38 UTC (rev 18264)
@@ -136,7 +136,22 @@
 void 
 UniqueReplacedReferences::checkReferencedElement(ReplacedElement& repE)
 {
-  if (mReferencedElements->find(repE.getReferencedElement(), 
+  unsigned int numErrsB4 = repE.getSBMLDocument()->getNumErrors();
+  
+  SBase* refElem = repE.getReferencedElement();
+  
+  // if there is an issue with references the getReferencedElement
+  // code may log errors
+  // we dont want them - since we will log any  errors here
+  // so remove them
+  unsigned int numErrsAfter = repE.getSBMLDocument()->getNumErrors();
+  for (unsigned int i = numErrsAfter; i > numErrsB4; i--)
+  {
+    repE.getSBMLDocument()->getErrorLog()->remove(
+      repE.getSBMLDocument()->getError(i-1)->getErrorId());
+  }
+  
+  if (mReferencedElements->find(refElem, 
                            (ListItemComparator) (ObjectsSame1)) != NULL)
   {
     if (repE.getReferencedElement()->getTypeCode() != SBML_COMP_DELETION)
@@ -147,7 +162,7 @@
   else
   {
 
-    mReferencedElements->add(repE.getReferencedElement());
+    mReferencedElements->add(refElem);
   }
 }
 

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