- import supported distributions

 - when the distrib package is enabled on libsbml, convert distrib to annotations and import the supported ones: normal / gamma / uniform / poisson

Author: fbergmann

copasi/sbml/SBMLImporter.cpp

@@ -1152,6 +1152,17 @@ bool addToKnownFunctionToMap(std::map<std::string, std::string>& map, const Func
       return true;
     }
 
+  id = isKnownCustomFunctionDefinition(sbmlFunction,
+                                       "http://sbml.org/annotations/distribution",
+                                       "distribution",
+                                       "http://en.wikipedia.org/wiki/Normal_distribution");
+
+  if (!id.empty())
+    {
+      map[id] = "RNORMAL";
+      return true;
+    }
+
   id = isKnownCustomFunctionDefinition(sbmlFunction,
                                        "http://sbml.org/annotations/distribution",
                                        "distribution",
@@ -1163,6 +1174,28 @@ bool addToKnownFunctionToMap(std::map<std::string, std::string>& map, const Func
       return true;
     }
 
+  id = isKnownCustomFunctionDefinition(sbmlFunction,
+                                       "http://sbml.org/annotations/distribution",
+                                       "distribution",
+                                       "http://en.wikipedia.org/wiki/Uniform_distribution_(continuous)");
+
+  if (!id.empty())
+    {
+      map[id] = "RUNIFORM";
+      return true;
+    }
+
+  id = isKnownCustomFunctionDefinition(sbmlFunction,
+                                       "http://sbml.org/annotations/distribution",
+                                       "distribution",
+                                       "http://en.wikipedia.org/wiki/Uniform_distribution");
+
+  if (!id.empty())
+    {
+      map[id] = "RUNIFORM";
+      return true;
+    }
+
   id = isKnownCustomFunctionDefinition(sbmlFunction,
                                        "http://sbml.org/annotations/distribution",
                                        "distribution",
@@ -1174,6 +1207,17 @@ bool addToKnownFunctionToMap(std::map<std::string, std::string>& map, const Func
       return true;
     }
 
+  id = isKnownCustomFunctionDefinition(sbmlFunction,
+                                       "http://sbml.org/annotations/distribution",
+                                       "distribution",
+                                       "http://en.wikipedia.org/wiki/Gamma_distribution");
+
+  if (!id.empty())
+    {
+      map[id] = "RGAMMA";
+      return true;
+    }
+
   id = isKnownCustomFunctionDefinition(sbmlFunction,
                                        "http://sbml.org/annotations/distribution",
                                        "distribution",
@@ -1185,6 +1229,17 @@ bool addToKnownFunctionToMap(std::map<std::string, std::string>& map, const Func
       return true;
     }
 
+  id = isKnownCustomFunctionDefinition(sbmlFunction,
+                                       "http://sbml.org/annotations/distribution",
+                                       "distribution",
+                                       "http://en.wikipedia.org/wiki/Poisson_distribution");
+
+  if (!id.empty())
+    {
+      map[id] = "RPOISSON";
+      return true;
+    }
+
   return false;
 }
 
@@ -3074,6 +3129,27 @@ bool SBMLImporter::checkValidityOfSourceDocument(SBMLDocument* sbmlDoc)
         }
     }
 
+  if (sbmlDoc->getPlugin("distrib") != NULL && sbmlDoc->isSetPackageRequired("distrib"))
+  {
+    ConversionProperties props;
+    props.addOption("convert distrib to annotations", true, "convert distrib to annotations");
+    props.addOption("writeMeans", true, "Created functions return means of distributions instead of NaN");
+
+    if (sbmlDoc->convert(props) != LIBSBML_OPERATION_SUCCESS)
+      {
+        std::string message =
+          "The SBML model you are trying to import uses the Distrib extension. "
+          "In order to import this model in COPASI, it has to be converted, however conversion failed";
+
+        if (sbmlDoc->getNumErrors() == 0)
+          message += ".";
+        else
+          message += " with the following errors:\n" + sbmlDoc->getErrorLog()->toString();
+
+        CCopasiMessage(CCopasiMessage::ERROR, message.c_str());
+      }
+  }
+
   if (sbmlDoc->getPlugin("comp") != NULL && sbmlDoc->isSetPackageRequired("comp"))
     {