Revert "Proposed solution for Issue sys-bio#411"

This reverts commit ea98bb7.
kirichoi · Sep 21, 2017 · b705c8b · b705c8b
1 parent ea98bb7
commit b705c8b
Showing 1 changed file with 7 additions and 11 deletions.
diff --git a/source/rrRoadRunner.cpp b/source/rrRoadRunner.cpp
@@ -1332,8 +1332,8 @@ const DoubleMatrix* RoadRunner::simulate(const Dictionary* dict)
 
     applySimulateOptions();
 
-    const double timeEnd = self.simulateOpt.duration;
-    const double timeStart = 0;
+    const double timeEnd = self.simulateOpt.duration + self.simulateOpt.start;
+    const double timeStart = self.simulateOpt.start;
 
     // evalute the model with its current state
     self.model->getStateVectorRate(timeStart, 0, 0);
@@ -1381,8 +1381,6 @@ const DoubleMatrix* RoadRunner::simulate(const Dictionary* dict)
 
                 getSelectedValues(row, tout);
 
-                int itime = getTimeRowIndex();
-
                 // use interpolation to ensure last time point is requested end time
                 if( tout > timeEnd ) {
                     if (!getIntegrator())
@@ -1400,6 +1398,8 @@ const DoubleMatrix* RoadRunner::simulate(const Dictionary* dict)
                             row.at(n) = results.back().at(n);
                         }
 
+                        int itime = getTimeRowIndex();
+
                         if (itime >= 0)
                         {
                             row.at(itime) = timeEnd;
@@ -1419,11 +1419,6 @@ const DoubleMatrix* RoadRunner::simulate(const Dictionary* dict)
                     last_tout = tout;
                 }
 
-                // Add constant value of start time
-                if (itime >= 0)
-                {
-                    row.at(itime) = row.at(itime) + self.simulateOpt.start;
-                }
                 results.push_back(row);
 
                 ++n;
@@ -4054,9 +4049,10 @@ void RoadRunner::applySimulateOptions()
 {
     get_self();
 
-    if (self.simulateOpt.duration < 0  || self.simulateOpt.steps < 0 )
+    if (self.simulateOpt.duration < 0 || self.simulateOpt.start < 0
+            || self.simulateOpt.steps < 0 )
     {
-        throw std::invalid_argument("duration and steps must be non-negative");
+        throw std::invalid_argument("duration, startTime and steps must be non-negative");
     }
 
     // This one creates the list of what we will look at in the result