Merge remote-tracking branch 'remotes/origin/error-output'

.gitignore

@@ -47,6 +47,7 @@ GTAGS
 .vscode
 .vscode/*
 **.vscode
+.vs/
 
 # cruft from sublime text
 *.sublime*

src/amber_netcdf.cpp

@@ -151,7 +151,8 @@ namespace loos {
 		for (AtomicGroup::iterator i = g.begin(); i != g.end(); ++i) {
 			uint idx = (*i)->index();
 			if (idx >= _natoms)
-				throw(LOOSError(**i, "Atom index into trajectory frame is out of bounds"));
+				//throw(LOOSError(_filename, **i, "Atom index into trajectory frame is out of bounds"));
+				throw(TrajectoryError("updating group coords",_filename, "Atom index into trajectory frame is out of bounds"));
 			idx *= 3;
 			(*i)->coords(GCoord(_coord_data[idx], _coord_data[idx+1], _coord_data[idx+2]));
 		}
@@ -166,7 +167,7 @@ namespace loos {
 		for (AtomicGroup::iterator i = g.begin(); i != g.end(); ++i) {
 			uint idx = (*i)->index();
 			if (idx >= _natoms)
-				throw(LOOSError(**i, "Atom index into trajectory frame is out of bounds"));
+				throw(TrajectoryError("updating group velocities", _filename, "Atom index into trajectory frame is out of bounds"));
 			idx *= 3;
 			(*i)->coords(GCoord(_velocity_data[idx], _velocity_data[idx+1], _velocity_data[idx+2]));
 		}

src/amber_rst.cpp

@@ -113,7 +113,7 @@ namespace loos {
     for (gi = g.begin(); gi != g.end(); ++gi) {
       uint i = (*gi)->index();
       if (i >= _natoms)
-        throw(LOOSError(**gi, "Atom index into trajectory is out of bounds"));
+        throw(TrajectoryError("updating group coords", _filename, "Atom index into trajectory frame is out of bounds"));
       (*gi)->coords(frame[i]);
     }
 

src/amber_traj.cpp

@@ -136,7 +136,7 @@ namespace loos {
     for (AtomicGroup::iterator i = g.begin(); i != g.end(); ++i) {
       uint idx = (*i)->index();
       if (idx >= _natoms)
-        throw(LOOSError(**i, "Atom index into trajectory is out of bounds"));
+        throw(TrajectoryError("updating group coords", _filename, "Atom index into trajectory frame is out of bounds"));
       (*i)->coords(frame[idx]);
     }
 

src/dcd.cpp

@@ -414,7 +414,7 @@ namespace loos {
     for (AtomicGroup::iterator i = g.begin(); i != g.end(); ++i) {
       uint idx = (*i)->index();
       if (idx >= _natoms)
-        throw(LOOSError(**i, "Atom index into the trajectory frame is out of bounds"));
+        throw(TrajectoryError("updating group coords", _filename, "Atom index into trajectory frame is out of bounds"));
       (*i)->coords(GCoord(xcrds[idx], ycrds[idx], zcrds[idx]));
     }
 
@@ -430,7 +430,7 @@ namespace loos {
         readHeader();
         bool b = parseFrame();
         if (!b)
-            throw(LOOSError("Cannot read first frame of DCD during initialization"));
+            throw(TrajectoryError("reading first frame of DCD during initialization"));
         cached_first = true;
     }
 

src/exceptions.hpp

@@ -48,6 +48,11 @@ namespace loos {
       ss << a << std::endl << arg;
       _msg = ss.str();
     }
+    explicit LOOSError(const std::string& fname, const Atom& a, const std::string& arg) {
+        std::stringstream ss;
+        ss << "In file: " + fname << std::endl << a << std::endl << arg;
+        _msg = ss.str();
+    }
 
     virtual ~LOOSError() throw() {};
     virtual const char* what(void) const throw() { return(_msg.c_str()); }
@@ -220,8 +225,7 @@ namespace loos {
 
   };
 
-
-
+
   //! Errors while writing to files
   class FileWriteError : public FileError {
   public:
@@ -231,6 +235,58 @@ namespace loos {
   };
 
 
+  //! Errors related to trajectory reading and writing
+  /**
+   * Most trajectory exceptions derive from this class.
+   */
+  class TrajectoryError : public LOOSError {
+  protected:
+      std::string _operation;
+      std::string _filename;
+      int _errcode;
+
+  public:
+      TrajectoryError(const std::string& op) : LOOSError("Error while " + op), _operation(op) {}
+
+      TrajectoryError(const std::string& op, const std::string& fname)
+          : LOOSError("Error while " + op + ", " + fname),
+          _operation(op), _filename(fname)
+      {}
+
+      TrajectoryError(const std::string& op,
+          const std::string& fname,
+          const std::string& msg)
+          : LOOSError("Error while " + op + ", " + fname + "\n" + msg),
+          _operation(op),
+          _filename(fname)
+      {}
+
+      TrajectoryError(const std::string& op,
+          const std::string& fname,
+          const std::string& msg,
+          const int err)
+          : LOOSError("Error while " + op + ", " + fname + "\n" + msg),
+          _operation(op),
+          _filename(fname),
+          _errcode(err)
+      {}
+
+
+      //! What operation was involved (e.g. reading, writing. etc)
+      std::string operation() const throw() { return(_operation); }
+
+      //! File that had the problem (or "stream" if not a file)
+      std::string filename() const throw() { return(_filename); }
+
+      //! The error code that may have been generated
+      int errorCode() const { return(_errcode); }
+
+      //! Sets the error code
+      void errorCode(const int i) { _errcode = i; }
+
+      ~TrajectoryError() throw() {}
+  };
+
 
 
 };

src/mdtrajtraj.cpp

@@ -123,7 +123,7 @@ namespace loos {
     for (AtomicGroup::iterator i = g.begin(); i != g.end(); ++i) {
       uint idx = (*i)->index();
       if (idx >= _natoms)
-        throw(LOOSError(**i, "Atom index into trajectory is out of bounds"));
+          throw(TrajectoryError("updating group coords", _filename, "Atom index into trajectory frame is out of bounds"));
       (*i)->coords(frame[idx]);
     }
 

src/tinker_arc.cpp

@@ -112,7 +112,7 @@ namespace loos {
     for (AtomicGroup::iterator i = g.begin(); i != g.end(); ++i) {
       uint idx = (*i)->index();
       if (idx >= _natoms)
-	throw(LOOSError(**i, "Atom index into the trajectory frame is out of bounds"));
+        throw(TrajectoryError("updating group coords", _filename, "Atom index into trajectory frame is out of bounds"));
       (*i)->coords(frame[idx]->coords());
     }
 

src/trr.cpp

@@ -163,7 +163,7 @@ namespace loos {
 		for (AtomicGroup::iterator i = g.begin(); i != g.end(); ++i) {
 			uint idx = (*i)->index();
 			if (static_cast<uint>(idx) >= natoms())
-				throw(LOOSError(**i, "atom index into trajectory frame is out of range"));
+				throw(TrajectoryError("updating group coords", _filename, "Atom index into trajectory frame is out of bounds"));
 			(*i)->coords(coords_[idx]);
 		}
 
@@ -176,7 +176,7 @@ namespace loos {
 		for (AtomicGroup::iterator i = g.begin(); i != g.end(); ++i) {
 			uint idx = (*i)->index();
 			if (static_cast<uint>(idx) >= natoms())
-				throw(LOOSError(**i, "atom index into trajectory frame is out of range"));
+				throw(TrajectoryError("updating group velocities", _filename, "Atom index into trajectory frame is out of bounds"));
 			(*i)->velocities(velo_[idx]);
 		}
 

src/xtc.cpp

@@ -362,7 +362,7 @@ namespace loos {
     for (AtomicGroup::iterator i = g.begin(); i != g.end(); ++i) {
       uint idx = (*i)->index();
       if (idx > natoms_)
-        throw(LOOSError(**i, "atom index into trajectory frame is out of range"));
+        throw(TrajectoryError("updating group coords", _filename, "Atom index into trajectory frame is out of bounds"));
       (*i)->coords(coords_[idx]);
     }