Polishing & including priors without FFTALGO

param.cpp

 /* ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
    < BioEM software for Bayesian inference of Electron Microscopy images>
-   Copyright (C) 2014 Pilar Cossio, David Rohr and Gerhard Hummer.
+   Copyright (C) 2016 Pilar Cossio, David Rohr, Fabio Baruffa, Markus Rampp, 
+        Volker Lindenstruth and Gerhard Hummer.
    Max Planck Institute of Biophysics, Frankfurt, Germany.
 
    See license statement for terms of distribution.
@@ -93,6 +94,7 @@ int bioem_param::readParameters(const char* fileinput)
   yespriorAngles=false; 
   ignorepointsout=false;
   printrotmod=false;
+  ignorePDB=false;
 
   NotUn_angles=0;
   priorMod=1; //Default
@@ -334,6 +336,11 @@ int bioem_param::readParameters(const char* fileinput)
 	  ignoreCCoff = true;
 	  cout << "Ignoring Cross-Correlation offset \n";
 	}
+      else if (strcmp(token, "IGNORE_PDB") == 0) //Ignore PDB extension
+        {
+          ignorePDB = true;
+          cout << "Ignoring PDB extension in model file \n";
+        }
       else if (strcmp(token, "NO_PROJECT_RADIUS") == 0) //If projecting CA with amino-acid radius
 	{
 	  doaaradius = false;

timer.cpp

+#include "timer.h"
+#ifdef _WIN32
+#include <windows.h>
+#include <winbase.h>
+#else
+#include <time.h>
+#endif
+
+HighResTimer::HighResTimer()
+{
+	ElapsedTime = 0;
+	running = 0;
+}
+
+HighResTimer::~HighResTimer() {}
+
+void HighResTimer::Start()
+{
+#ifdef _WIN32
+	__int64 istart;
+	QueryPerformanceCounter((LARGE_INTEGER*)&istart);
+	StartTime = (double) istart;
+#else
+	timespec tv;
+	clock_gettime(CLOCK_REALTIME, &tv);
+	StartTime = (double) tv.tv_sec * 1.0E9 + (double) tv.tv_nsec;
+#endif
+	running = 1;
+}
+
+void HighResTimer::ResetStart()
+{
+	ElapsedTime = 0;
+	Start();
+}
+
+void HighResTimer::Stop()
+{
+	if (running == 0) return;
+	running = 0;
+	double EndTime = 0;
+#ifdef _WIN32
+	__int64 iend;
+	QueryPerformanceCounter((LARGE_INTEGER*) &iend);
+	EndTime = (double) iend;
+#else
+	timespec tv;
+	clock_gettime(CLOCK_REALTIME, &tv);
+	EndTime = (double) tv.tv_sec * 1.0E9 + (double) tv.tv_nsec;
+#endif
+	ElapsedTime += EndTime - StartTime;
+}
+
+void HighResTimer::Reset()
+{
+	ElapsedTime = 0;
+	StartTime = 0;
+	running = 0;
+}
+
+double HighResTimer::GetElapsedTime()
+{
+	return ElapsedTime / Frequency;
+}
+
+double HighResTimer::GetCurrentElapsedTime()
+{
+	if (running == 0) return(GetElapsedTime());
+	double CurrentTime = 0;
+#ifdef _WIN32
+	__int64 iend;
+	QueryPerformanceCounter((LARGE_INTEGER*) &iend);
+	CurrentTime = (double) iend;
+#else
+	timespec tv;
+	clock_gettime(CLOCK_REALTIME, &tv);
+	CurrentTime = (double) tv.tv_sec * 1.0E9 + (double) tv.tv_nsec;
+#endif
+	return((CurrentTime - StartTime + ElapsedTime) / Frequency);
+}
+
+double HighResTimer::GetFrequency()
+{
+#ifdef _WIN32
+	__int64 ifreq;
+	QueryPerformanceFrequency((LARGE_INTEGER*)&ifreq);
+	return((double) ifreq);
+#else
+	return(1.0E9);
+#endif
+}
+
+double HighResTimer::Frequency = HighResTimer::GetFrequency();
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