removed dead code

sys-bio · Aug 24, 2014 · d2c27a3 · d2c27a3
1 parent f5d87e4
commit d2c27a3
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Showing 7 changed files with 12 additions and 113 deletions.
diff --git a/apps/rr-sbml-benchmark/main.cpp b/apps/rr-sbml-benchmark/main.cpp
@@ -22,6 +22,7 @@
 #include <stdlib.h>
 
 using namespace rr;
+using namespace std;
 
 // copasi test suite called like
 // ./sbml-testsuite ~/src/sbml_test/cases/semantic 00221 ~/tmp/copasi 2 4

diff --git a/examples/one_rr/main.cpp b/examples/one_rr/main.cpp
@@ -31,7 +31,7 @@ int main(int argc, char** argv)
         Log(lInfo)<<" ---------- SIMULATE ---------------------";
 
         rr1.simulate();
-        Log(lInfo)<<"Data:"<<*(rr1.getSimulationResult());
+        Log(lInfo)<<"Data:"<<*(rr1.getSimulationData());
     }
     catch(const Exception& ex)
     {

diff --git a/source/llvm_testing/src/ConfigurableTest.cpp b/source/llvm_testing/src/ConfigurableTest.cpp
@@ -8,6 +8,9 @@
 #include "ConfigurableTest.h"
 #include "rrRoadRunner.h"
 #include <iostream>
+#include <fstream>
+#include <sstream>
+
 
 using namespace std;
 

diff --git a/source/rrRoadRunner.cpp b/source/rrRoadRunner.cpp
@@ -500,7 +500,7 @@ string RoadRunner::getExtendedVersionInfo()
 
 
 
-LibStructural* RoadRunner::getLibStruct()
+ls::LibStructural* RoadRunner::getLibStruct()
 {
     Mutex::ScopedLock lock(roadRunnerMutex);
 
@@ -665,14 +665,6 @@ void RoadRunner::updateIntegrator()
     }
 }
 
-RoadRunnerData *RoadRunner::getSimulationResult()
-{
-    // set the data into the RoadRunnerData struct
-    populateResult();
-
-    return &impl->mRoadRunnerData;
-}
-
 
 double RoadRunner::getValue(const SelectionRecord& record)
 {

diff --git a/source/rrRoadRunner.h b/source/rrRoadRunner.h
@@ -4,7 +4,6 @@
 #include "rrOSSpecifics.h"
 #include "rr-libstruct/lsMatrix.h"
 #include "rrSelectionRecord.h"
-#include "rrRoadRunnerData.h"
 #include "rrRoadRunnerOptions.h"
 #include "Configurable.h"
 
@@ -25,6 +24,11 @@ class SBMLModelSimulation;
 class ExecutableModel;
 class Integrator;
 
+using ls::Matrix;
+using ls::DoubleMatrix;
+using ls::Complex;
+using ls::ComplexMatrix;
+
 /**
  * The main RoadRunner class.
  *
@@ -163,12 +167,6 @@ class RR_DECLSPEC RoadRunner : public Configurable
 
     #ifndef SWIG // deprecated methods not SWIG'ed
 
-    /**
-     * Use getSimulationData() instead.
-     * Also, can use the RoadRunnerData::RoadRunnerData(const RoadRunner*) ctor
-     */
-    RR_DEPRECATED(rr::RoadRunnerData *getSimulationResult());
-
     #endif
 
     void setSimulateOptions(const SimulateOptions& settings);
@@ -834,7 +832,7 @@ class RR_DECLSPEC RoadRunner : public Configurable
     /**
      * the LibStruct is normally null, only created on demand here.
      */
-    LibStructural* getLibStruct();
+    ls::LibStructural* getLibStruct();
 
     /**
      * If the specified integrator does not exist, create it, and point the

diff --git a/wrappers/C/rrc_cpp_support.cpp b/wrappers/C/rrc_cpp_support.cpp
@@ -315,96 +315,7 @@ RRList* createArrayList(const rrc::ArrayList& aList)
     return theList;
 }
 
-//RRParameterHandle createParameter(const rr::BaseParameter& para)
-//{
-//    if(para.getType() == "bool")
-//    {
-//        Parameter<bool> *thePara = dynamic_cast< Parameter<bool>* >(const_cast< BaseParameter* >(&para));
-//
-//        RRParameter* aPara     = new RRParameter;
-//        aPara->ParaType     = ptBool;
-//        aPara->data.bValue     = thePara->getValue();
-//        aPara->mName        = rr::createText(thePara->getName());
-//        aPara->mHint        = rr::createText(thePara->getHint());
-//        return aPara;
-//    }
-//
-//    if(para.getType() == "integer")
-//    {
-//        Parameter<int> *thePara = dynamic_cast< Parameter<int>* >(const_cast< BaseParameter* >(&para));
-//
-//        RRParameter* aPara     = new RRParameter;
-//        aPara->ParaType     = ptInteger;
-//        aPara->data.iValue     = thePara->getValue();
-//        aPara->mName        = rr::createText(thePara->getName());
-//        aPara->mHint        = rr::createText(thePara->getHint());
-//        return aPara;
-//    }
-//
-//    if(para.getType() == "double")
-//    {
-//        Parameter<double> *thePara = dynamic_cast< Parameter<double>* >(const_cast< BaseParameter* >(&para));
-//
-//        RRParameter* aPara     = new RRParameter;
-//        aPara->ParaType     = ptInteger;
-//        aPara->data.iValue     = thePara->getValue();
-//        aPara->mName        = rr::createText(thePara->getName());
-//        aPara->mHint        = rr::createText(thePara->getHint());
-//        return aPara;
-//    }
-//
-//    if(para.getType() == "vector")
-//    {
-//        Parameter<RRVector*> *thePara = dynamic_cast< Parameter<RRVector*>* >(const_cast< BaseParameter* >(&para));
-//
-//        RRParameter* aPara     = new RRParameter;
-//        aPara->ParaType     = ptVector;
-//        aPara->data.vValue     = thePara->getValue();
-//        aPara->mName        = rr::createText(thePara->getName());
-//        aPara->mHint        = rr::createText(thePara->getHint());
-//        return aPara;
-//    }
-//    return NULL;
-//}
-
-
-RRCDataPtr createRRCData(const RoadRunnerData& result)
-{
-    RRCData* rrCData  = new RRCData;
-    memset(rrCData, 0, sizeof(RRCData));
-
-    rrCData->ColumnHeaders = new char*[result.cSize()];
-    for(int i = 0; i < result.cSize(); i++)
-    {
-        rrCData->ColumnHeaders[i] = rr::createText(result.getColumnNames()[i]);
-    }
 
-    rrCData->RSize = result.rSize();
-    rrCData->CSize = result.cSize();
-    int size = rrCData->RSize*rrCData->CSize;
-    rrCData->Data = new double[size];
-
-    if(result.hasWeights())
-    {
-        rrCData->Weights = new double[size];
-    }
-
-    int index = 0;
-    //The data layout is simple row after row, in one single long row...
-    for(int row = 0; row < rrCData->RSize; row++)
-    {
-        for(int col = 0; col < rrCData->CSize; col++)
-        {
-            rrCData->Data[index] = result(row, col);
-            if(result.hasWeights())
-            {
-                rrCData->Weights[index] = result.getWeight(row, col);
-            }
-            ++index;
-        }
-    }
-    return rrCData;
-}
 
 RRCDataPtr createRRCData(const RoadRunner& tmp)
 {

diff --git a/wrappers/C/rrc_cpp_support.h b/wrappers/C/rrc_cpp_support.h
@@ -153,12 +153,6 @@ C_DECL_SPEC RRStringArrayPtr               createList(const rrc::StringList& lis
 */
 C_DECL_SPEC RRListPtr                      createArrayList(const ArrayList& list);
 
-/**
- * @deprecated
- *
- * RoadRunnerData is going away.
- */
-C_DECL_SPEC RRCDataPtr    createRRCData(const rr::RoadRunnerData& data);
 
 /**
  * Creates an RRCDataPtr from the current state of a RoadRunner object.