Fix undated DTL and increase ALERax compatibility

.clang-format

@@ -0,0 +1,7 @@
+# see https://clang.llvm.org/docs/ClangFormatStyleOptions.html
+---
+BasedOnStyle: LLVM
+Language: Cpp
+Standard: Cpp11
+
+UseTab: Never

CMakeLists.txt

@@ -3,6 +3,12 @@ PROJECT(ale CXX)
 SET(EXECUTABLE_OUTPUT_PATH ${PROJECT_BINARY_DIR}/bin)
 add_definitions(-std=c++11)
 
+set(CMAKE_EXPORT_COMPILE_COMMANDS ON)
+
+# ignore BOOST deprecated headers
+add_definitions("-DBOOST_TIMER_ENABLE_DEPRECATED")
+# add_definitions("-DBOOST_BIND_GLOBAL_PLACEHOLDERS")
+
 IF(NOT NO_VIRTUAL_COV)
   SET(NO_VIRTUAL_COV FALSE CACHE BOOL
       "Disable covariant return type with virtual inheritance, for compilers that do not support it."

misc/ALE_compareTreeDistributions.cpp

@@ -2,97 +2,104 @@
 #include "ALE_util.h"
 using namespace std;
 
-//Compilation:  g++ -o ALE_compareTreeDistributions ALE_compareTreeDistributions.cpp ALE.h ALE.cpp ALE_util.h ALE_util.cpp exODT.h exODT.cpp model_omp.cpp -std=c++0x -I/usr/local/include  -L. -L/usr/local/lib  -lbpp-core -lbpp-seq -lbpp-phyl
-//  g++ -g -o ALE_compareTreeDistributions ALE_compareTreeDistributions.cpp ALE.h ALE.cpp ALE_util.h ALE_util.cpp exODT.h exODT.cpp model_omp.cpp -std=c++0x -I/usr/include  -I/home/ssolo/newest_bpp/include -L. -L/home/ssolo/newest_bpp/lib -L/usr/lib  -lbpp-core -lbpp-seq -lbpp-phyl
+// Compilation:  g++ -o ALE_compareTreeDistributions
+// ALE_compareTreeDistributions.cpp ALE.h ALE.cpp ALE_util.h ALE_util.cpp
+// exODT.h exODT.cpp model_omp.cpp -std=c++0x -I/usr/local/include  -L.
+// -L/usr/local/lib  -lbpp-core -lbpp-seq -lbpp-phyl
+//   g++ -g -o ALE_compareTreeDistributions ALE_compareTreeDistributions.cpp
+//   ALE.h ALE.cpp ALE_util.h ALE_util.cpp exODT.h exODT.cpp model_omp.cpp
+//   -std=c++0x -I/usr/include  -I/home/ssolo/newest_bpp/include -L.
+//   -L/home/ssolo/newest_bpp/lib -L/usr/lib  -lbpp-core -lbpp-seq -lbpp-phyl
 
-int main(int argc, char ** argv)
-{
-  if (argc == 1 ) {
-	std::cout << "\tUsage: ALE_compareTreeDistributions treeDist1.trees burnin1 treeDist2.trees burnin2\n" <<std::endl;
-  }
-else {
-  //First tree distribution
-  string ale_file=argv[1];
-  string ale_name=ale_file+".ale";
-  approx_posterior * ale;
-  vector<int> burnin;
+int main(int argc, char **argv) {
+  if (argc == 1) {
+    std::cout << "\tUsage: ALE_compareTreeDistributions treeDist1.trees "
+                 "burnin1 treeDist2.trees burnin2\n"
+              << std::endl;
+  } else {
+    // First tree distribution
+    string ale_file = argv[1];
+    string ale_name = ale_file + ".ale";
+    approx_posterior *ale;
+    vector<int> burnin;
 
-  if (argc>2) 
-    burnin.push_back(atoi(argv[2]));  
-	vector<int> every ;
-if (argc>3) 
-    every.push_back(atoi(argv[3]));
+    if (argc > 2)
+      burnin.push_back(atoi(argv[2]));
+    vector<int> every;
+    if (argc > 3)
+      every.push_back(atoi(argv[3]));
 
-  ale=observe_ALE_from_file(ale_file, burnin[0], every[0]);
+    ale = observe_ALE_from_file(ale_file, burnin[0], every[0]);
 
-  cout << "# observe "<< ale->observations << "trees from: " <<  argv[1] << endl;
-  ale->save_state(ale_name);
-  cout << "# saved in "<< ale_name<<endl;
+    cout << "# observe " << ale->observations << "trees from: " << argv[1]
+         << endl;
+    ale->save_state(ale_name);
+    cout << "# saved in " << ale_name << endl;
 
-  //Second tree distribution
-  string ale_file2=argv[4];
-  string ale_name2=ale_file+".ale";
-  approx_posterior * ale2;
+    // Second tree distribution
+    string ale_file2 = argv[4];
+    string ale_name2 = ale_file + ".ale";
+    approx_posterior *ale2;
 
-  if (argc>4) 
-    burnin.push_back(atoi(argv[5]));
-	int every2 = 0;
-  if (argc>5) 
-    every.push_back(atoi(argv[6]));
+    if (argc > 4)
+      burnin.push_back(atoi(argv[5]));
+    int every2 = 0;
+    if (argc > 5)
+      every.push_back(atoi(argv[6]));
 
-  ale2=observe_ALE_from_file(ale_file2, burnin[1], every[1]);
-  cout << "# observe "<< ale2->observations << "trees from: " <<  argv[4] << endl;
-  ale2->save_state(ale_name2);
-  cout << "# saved in "<< ale_name2<<endl;
+    ale2 = observe_ALE_from_file(ale_file2, burnin[1], every[1]);
+    cout << "# observe " << ale2->observations << "trees from: " << argv[4]
+         << endl;
+    ale2->save_state(ale_name2);
+    cout << "# saved in " << ale_name2 << endl;
 
-  //Now we want to compute the probabilities of all trees included in the files, according to the two ales.  
-  //First, we get all trees and put them in a single vector
+    // Now we want to compute the probabilities of all trees included in the
+    // files, according to the two ales. First, we get all trees and put them in
+    // a single vector
 
-  vector<string> trees;
-  std::vector< string > fnames;
-  fnames.push_back(argv[1]);
-  fnames.push_back(argv[4]);
-  size_t fileId = 0;
-  for (vector<string>::iterator it=fnames.begin();it!=fnames.end();it++)
-    {
-      string fname=(*it);
-      ifstream file_stream (fname.c_str());
-      int tree_i=0;  
-      if (file_stream.is_open())  //  ########## read trees ############
-	{
-	  while (! file_stream.eof())
-	    {
-	      string line;
-	      getline (file_stream,line);
-	      if (line.find("(")!=line.npos )
-		{
-		  tree_i++;		 
-		  if (tree_i%every[fileId]==0 ) trees.push_back(line);			     
-		}
-	    }
-	}
-    fileId++;
+    vector<string> trees;
+    std::vector<string> fnames;
+    fnames.push_back(argv[1]);
+    fnames.push_back(argv[4]);
+    size_t fileId = 0;
+    for (vector<string>::iterator it = fnames.begin(); it != fnames.end();
+         it++) {
+      string fname = (*it);
+      ifstream file_stream(fname.c_str());
+      int tree_i = 0;
+      if (file_stream.is_open()) //  ########## read trees ############
+      {
+        while (!file_stream.eof()) {
+          string line;
+          getline(file_stream, line);
+          if (line.find("(") != line.npos) {
+            tree_i++;
+            if (tree_i % every[fileId] == 0)
+              trees.push_back(line);
+          }
+        }
+      }
+      fileId++;
     }
 
-  string outFile;
-   if (argc>4) 
-    outFile=atoi(argv[5]);
-  else
-	outFile = "outFile.txt";
+    string outFile;
+    if (argc > 4)
+      outFile = atoi(argv[5]);
+    else
+      outFile = "outFile.txt";
+
+    ofstream myfile;
+    myfile.open(outFile);
+    myfile << "ALE1_proba\tALE2_proba" << std::endl;
 
-  ofstream myfile;
-  myfile.open (outFile);
-  myfile << "ALE1_proba\tALE2_proba"<<std::endl;
-
-  for (size_t i = 0; i < trees.size(); ++i) {
-  	myfile << ale->p(trees[i]) << "\t" << ale2->p(trees[i]) << std::endl;
-	cout  <<ale->p(trees[i]) << "\t" << ale2->p(trees[i]) << endl;
+    for (size_t i = 0; i < trees.size(); ++i) {
+      myfile << ale->p(trees[i]) << "\t" << ale2->p(trees[i]) << std::endl;
+      cout << ale->p(trees[i]) << "\t" << ale2->p(trees[i]) << endl;
+    }
+    myfile.flush();
+    myfile.close();
+    delete ale;
+    delete ale2;
   }
-  myfile.flush();
-  myfile.close();
-  delete ale;
-  delete ale2;
-}
   return 1;
-
 }