Converted almost all dangerous char buffers to std::string

Some cases were left because of the specific context they were used in. Future refactor may change that.
virtualcell · Jan 18, 2024 · 8612a09 · 8612a09
1 parent 43e7104
commit 8612a09
Show file tree

Hide file tree

Showing 10 changed files with 187 additions and 161 deletions.
diff --git a/VCell/include/VCELL/FVDataSet.h b/VCell/include/VCELL/FVDataSet.h
@@ -12,8 +12,8 @@ class Variable;
 class FVDataSet
 {
 public:
-	static void read(char *filename, Simulation *sim);
-	static void write(char *filename, SimulationExpression *sim, bool bCompress);
+	static void read(const char *filename, Simulation *sim);
+	static void write(const char *filename, SimulationExpression *sim, bool bCompress);
 	static void convolve(Simulation* sim, Variable* var, double* values);
 	static void readRandomVariables(char* filename, SimulationExpression* sim);
 };

diff --git a/VCell/include/VCELL/PostProcessingHdf5Writer.h b/VCell/include/VCELL/PostProcessingHdf5Writer.h
@@ -21,6 +21,7 @@ class PostProcessingHdf5Writer
 {
 public:
 	PostProcessingHdf5Writer(char* fileName, PostProcessingBlock* postProcessingBlock);
+	PostProcessingHdf5Writer(std::string fileName, PostProcessingBlock* postProcessingBlock);
 	virtual ~PostProcessingHdf5Writer();
 
 	void writeOutput();

diff --git a/VCell/include/VCELL/SimTool.h b/VCell/include/VCELL/SimTool.h
@@ -122,6 +122,7 @@ class SimTool {
 	void updateLog(double progress,double time,int iteration);
 	void clearLog();
 	int	getZipCount(char* zipFileName);
+	int	getZipCount(const std::string* zipFileName);
 	void start1();
 	void copyParticleCountsToConcentration();
 

diff --git a/VCell/include/VCELL/Simulation.h b/VCell/include/VCELL/Simulation.h
@@ -50,8 +50,8 @@ class Simulation
 	virtual void advanceTimeOn();
 	virtual void advanceTimeOff();
 
-	virtual void writeData(char *filename, bool bCompress)=0;
-	virtual void readData(char *filename);
+	virtual void writeData(const char *filename, bool bCompress)=0;
+	virtual void readData(const char *filename);
 
 	Variable* getVariable(int index);
 

diff --git a/VCell/include/VCELL/SimulationExpression.h b/VCell/include/VCELL/SimulationExpression.h
@@ -35,7 +35,7 @@ class SimulationExpression : public Simulation
 	void advanceTimeOn();
 	void advanceTimeOff();
 
-	void writeData(char *filename, bool bCompress);
+	void writeData(const char *filename, bool bCompress);
 
 	void addFieldData(FieldData* fd) {
 		fieldDataList.push_back(fd);

diff --git a/VCell/src/FVDataSet.cpp b/VCell/src/FVDataSet.cpp
@@ -100,7 +100,7 @@ static string extractVarNameFromQualifiedName(char* varName) {
 	return str;
 }
 
-void FVDataSet::read(char *filename, Simulation *sim)
+void FVDataSet::read(const char *filename, Simulation *sim)
 {
 	FILE *fp=NULL;
 	FileHeader fileHeader;
@@ -267,7 +267,7 @@ void FVDataSet::convolve(Simulation* sim, Variable* var, double* values) {
 	}			
 }
 
-void FVDataSet::write(char *filename, SimulationExpression *sim, bool bCompress)
+void FVDataSet::write(const char *filename, SimulationExpression *sim, bool bCompress)
 {
 	FILE *fp=NULL;
 	FileHeader fileHeader;

diff --git a/VCell/src/PostProcessingHdf5Writer.cpp b/VCell/src/PostProcessingHdf5Writer.cpp
@@ -11,6 +11,7 @@
 #include <H5Cpp.h>
 #include <iostream>
 #include <fstream>
+#include <utility>
 using std::cout;
 using std::endl;
 #include <sys/stat.h>
@@ -27,6 +28,13 @@ PostProcessingHdf5Writer::PostProcessingHdf5Writer(char* fileName, PostProcessin
 	timesDataSet = NULL;
 }
 
+PostProcessingHdf5Writer::PostProcessingHdf5Writer(std::string fileName, PostProcessingBlock* ppb) {
+	this->h5PPFileName = std::move(fileName);
+	this->postProcessingBlock = ppb;
+	h5PPFile = NULL;
+	timesDataSet = NULL;
+}
+
 PostProcessingHdf5Writer::~PostProcessingHdf5Writer() {
 	delete timesDataSet;
 	delete h5PPFile;