Changes in / [e971c4:533838]

Location:

src

Files:

• Actions/Makefile.am (modified) (3 diffs)
• Actions/MapOfActions.cpp (modified) (9 diffs)
• Actions/SelectionAction/AtomByIdAction.cpp (added)
• Actions/SelectionAction/AtomByIdAction.hpp (added)
• Actions/SelectionAction/MoleculeByIdAction.cpp (added)
• Actions/SelectionAction/MoleculeByIdAction.hpp (added)
• Actions/SelectionAction/NotAtomByIdAction.cpp (added)
• Actions/SelectionAction/NotAtomByIdAction.hpp (added)
• Actions/SelectionAction/NotMoleculeByIdAction.cpp (added)
• Actions/SelectionAction/NotMoleculeByIdAction.hpp (added)
• CommandLineParser.cpp (modified) (1 diff)
• World.cpp (modified) (2 diffs)
• World.hpp (modified) (2 diffs)

src/Actions/Makefile.am

@@ -17 +17 @@
   ${MOLECULEACTIONSOURCE} \
   ${PARSERACTIONSOURCE} \
+  ${SELECTIONACTIONSOURCE} \
   ${TESSELATIONACTIONSOURCE} \
   ${WORLDACTIONSOURCE} \
@@ -28 +29 @@
   ${MOLECULEACTIONHEADER} \
   ${PARSERACTIONHEADER} \
+  ${SELECTIONACTIONHEADER} \
   ${TESSELATIONACTIONHEADER} \
   ${WORLDACTIONHEADER} \
@@ -111 +113 @@
   ParserAction/SaveXyzAction.hpp
 
+SELECTIONACTIONSOURCE = \
+        SelectionAction/AtomByIdAction.cpp \
+        SelectionAction/MoleculeByIdAction.cpp \
+        SelectionAction/NotAtomByIdAction.cpp \
+        SelectionAction/NotMoleculeByIdAction.cpp
+SELECTIONACTIONHEADER = \
+        SelectionAction/AtomByIdAction.hpp \
+        SelectionAction/MoleculeByIdAction.hpp \
+        SelectionAction/NotAtomByIdAction.hpp \
+        SelectionAction/NotMoleculeByIdAction.hpp
+
 TESSELATIONACTIONSOURCE = \
   TesselationAction/ConvexEnvelopeAction.cpp \

src/Actions/MapOfActions.cpp

@@ -64 +64 @@
 #include "Actions/ParserAction/LoadXyzAction.hpp"
 #include "Actions/ParserAction/SaveXyzAction.hpp"
+#include "Actions/SelectionAction/AtomByIdAction.hpp"
+#include "Actions/SelectionAction/MoleculeByIdAction.hpp"
+#include "Actions/SelectionAction/NotAtomByIdAction.hpp"
+#include "Actions/SelectionAction/NotMoleculeByIdAction.hpp"
 #include "Actions/TesselationAction/ConvexEnvelopeAction.hpp"
 #include "Actions/TesselationAction/NonConvexEnvelopeAction.hpp"
@@ -209 +213 @@
   DescriptionMap["version"] = "show version";
   // keys for values
-  DescriptionMap["atom-by-id"] = "index of an atom";
   DescriptionMap["bin-output-file"] = "name of the bin output file";
   DescriptionMap["bin-end"] = "start of the last bin";
@@ -233 +236 @@
   DescriptionMap["periodic"] = "system is constraint to periodic boundary conditions (y/n)";
   DescriptionMap["position"] = "position in R^3 space";
+  DescriptionMap["select-atom-by-id"] = "select an atom by index";
+  DescriptionMap["select-molecule-by-id"] = "select a molecule by index";
   DescriptionMap["sphere-radius"] = "radius of tesselation sphere";
   DescriptionMap["start-step"] = "first or start step";
+  DescriptionMap["unselect-atom-by-id"] = "unselect an atom by index";
+  DescriptionMap["unselect-molecule-by-id"] = "unselect a molecule by index";
 
   // short forms for the actions
@@ -317 +324 @@
 
   // value types for the values
-  TypeMap["atom-by-id"] = &typeid(atom);
   TypeMap["bin-output-file"] = &typeid(std::string);
   TypeMap["bin-end"] = &typeid(double);
@@ -340 +346 @@
   TypeMap["periodic"] = &typeid(bool);
   TypeMap["position"] = &typeid(VectorValue);
+  TypeMap["select-atom-by-id"] = &typeid(atom);
+  TypeMap["select-molecule-by-id"] = &typeid(molecule);
   TypeMap["sphere-radius"] = &typeid(double);
   TypeMap["start-step"] = &typeid(int);
+  TypeMap["unselect-atom-by-id"] = &typeid(atom);
+  TypeMap["unselect-molecule-by-id"] = &typeid(molecule);
 
   TypeEnumMap[&typeid(void)] = None;
@@ -474 +484 @@
     // positional arguments
   generic.insert("input");
-  inputfile.insert("input");
 
     // hidden arguments
-  generic.insert("atom-by-id");
-  generic.insert("bin-end");
-  generic.insert("bin-output-file");
-  generic.insert("bin-start");
-  generic.insert("bin-width");
-  generic.insert("convex-file");
-  generic.insert("distance");
-  generic.insert("DoRotate");
-  generic.insert("distances");
-  generic.insert("element");
-  generic.insert("elements");
-  generic.insert("end-step");
-  generic.insert("id-mapping");
-  generic.insert("lengths");
-  generic.insert("MaxDistance");
-  generic.insert("molecule-by-id");
-  generic.insert("molecule-by-name");
-  generic.insert("nonconvex-file");
-  generic.insert("order");
-  generic.insert("output-file");
-  generic.insert("periodic");
-  generic.insert("position");
-  generic.insert("sphere-radius");
-  generic.insert("start-step");
+  hidden.insert("bin-end");
+  hidden.insert("bin-output-file");
+  hidden.insert("bin-start");
+  hidden.insert("bin-width");
+  hidden.insert("convex-file");
+  hidden.insert("distance");
+  hidden.insert("DoRotate");
+  hidden.insert("distances");
+  hidden.insert("element");
+  hidden.insert("elements");
+  hidden.insert("end-step");
+  hidden.insert("id-mapping");
+  hidden.insert("lengths");
+  hidden.insert("MaxDistance");
+  hidden.insert("molecule-by-id");
+  hidden.insert("molecule-by-name");
+  hidden.insert("nonconvex-file");
+  hidden.insert("order");
+  hidden.insert("output-file");
+  hidden.insert("periodic");
+  hidden.insert("position");
+  hidden.insert("select-atom-by-id");
+  hidden.insert("select-molecule-by-id");
+  hidden.insert("sphere-radius");
+  hidden.insert("start-step");
+  hidden.insert("unselect-atom-by-id");
+  hidden.insert("unselect-molecule-by-id");
 }
 
@@ -779 +791 @@
   new ParserSaveXyzAction();
 
+  new SelectionAtomByIdAction();
+  new SelectionMoleculeByIdAction();
+  new SelectionNotAtomByIdAction();
+  new SelectionNotMoleculeByIdAction();
+
   new TesselationConvexEnvelopeAction();
   new TesselationNonConvexEnvelopeAction();
@@ -806 +823 @@
     for (set<string>::iterator OptionRunner = ListRunner->first->begin(); OptionRunner != ListRunner->first->end(); ++OptionRunner) {
       if (hasValue(*OptionRunner)) {
-        DoLog(3) && (Log() << Verbose(3) << "Adding option " << *OptionRunner << " with type " << TypeMap[*OptionRunner]->name() << " to CommandLineParser." << endl);
+        DoLog(0) && (Log() << Verbose(0) << "Adding option " << *OptionRunner << " with type " << TypeMap[*OptionRunner]->name() << " to CommandLineParser." << endl);
            switch(TypeEnumMap[TypeMap[*OptionRunner]]) {
           default:
@@ -947 +964 @@
     }
   }
-  // add positional arguments
-  for (set<string>::iterator OptionRunner = inputfile.begin(); OptionRunner != inputfile.end(); ++OptionRunner) {
-    DoLog(3) && (Log() << Verbose(3) << "Adding option " << *OptionRunner << " to positional CommandLineParser." << endl);
-    CommandLineParser::getInstance().inputfile.add((*OptionRunner).c_str(), -1);
-  }
-  cout << "Name for position 1: " << CommandLineParser::getInstance().inputfile.name_for_position(1) << endl;
 }
 

src/CommandLineParser.cpp

@@ -41 +41 @@
 void CommandLineParser::Parse()
 {
-  po::store(po::command_line_parser(argc,argv).options(cmdline_options).options(visible).run(), vm);
+  po::store(po::command_line_parser(argc,argv).options(cmdline_options).run(), vm);
   ifstream input;
   input.open("example.cfg");

src/World.cpp

@@ -565 +565 @@
 }
 
+bool World::isSelected(atom *atom) {
+  return selectedAtoms.find(atom->getId()) != selectedAtoms.end();
+}
+
 // Molecules
 
@@ -638 +642 @@
     count++;
   return count;
+}
+
+bool World::isSelected(molecule *mol) {
+  return selectedMolecules.find(mol->getId()) != selectedMolecules.end();
 }
 

src/World.hpp

@@ -265 +265 @@
   void unselectAtomsOfMolecule(moleculeId_t);
   size_t countSelectedAtoms();
+  bool isSelected(atom *_atom);
 
   void clearMoleculeSelection();
@@ -278 +279 @@
   void unselectMoleculeOfAtom(atomId_t);
   size_t countSelectedMolecules();
+  bool isSelected(molecule *_mol);
 
   /******************** Iterators to selections *****************/