Added error detection for cases such as a read's two mates having different names...

[rsem.git] / PairedEndModel.h

diff --git a/PairedEndModel.h b/PairedEndModel.h
index f3f95fe29874881b73f3a76633d83efa1e8059e8..0d2c9b3f216db8df91fa47a85c57065123fe2331 100644 (file)
--- a/PairedEndModel.h
+++ b/PairedEndModel.h
@@ -9,6 +9,7 @@
 #include<algorithm>
 #include<sstream>
 #include<iostream>
+#include<vector>
 
 #include "utils.h"
 #include "my_assert.h"
@@ -193,12 +194,12 @@ public:
 
        const LenDist& getGLD() { return *gld; }
 
-       void startSimulation(simul*, double*);
+       void startSimulation(simul*, const std::vector<double>&);
        bool simulate(READ_INT_TYPE, PairedEndRead&, int&);
        void finishSimulation();
 
        //Use it after function 'read' or 'estimateFromReads'
-       double* getMW() { 
+       const double* getMW() { 
          assert(mw != NULL);
          return mw;
        }
@@ -349,7 +350,7 @@ void PairedEndModel::write(const char* outF) {
        fclose(fo);
 }
 
-void PairedEndModel::startSimulation(simul* sampler, double* theta) {
+void PairedEndModel::startSimulation(simul* sampler, const std::vector<double>& theta) {
        this->sampler = sampler;
 
        theta_cdf = new double[M + 1];