--- trunk/src/applications/dump2Xyz/Dump2XYZ.cpp	2005/02/04 22:46:10	294
+++ trunk/src/applications/dump2Xyz/Dump2XYZ.cpp	2005/03/09 17:30:29	413
@@ -55,6 +55,9 @@
 #include "visitors/OtherVisitor.hpp"
 #include "visitors/ZconsVisitor.hpp"
 #include "selection/SelectionEvaluator.hpp"
+#include "selection/SelectionManager.hpp"
+#include "visitors/LipidTransVisitor.hpp"
+
 using namespace oopse;
 
 int main(int argc, char* argv[]){
@@ -98,51 +101,13 @@ int main(int argc, char* argv[]){
   
   //creat visitor list
   CompositeVisitor* compositeVisitor = new CompositeVisitor();
-  
-  //creat ignore visitor
-  if(args_info.ignore_given ||args_info.water_flag){
     
-    IgnoreVisitor* ignoreVisitor = new IgnoreVisitor(info);
-    
-    for(int i = 0; i < args_info.ignore_given; i++)
-      ignoreVisitor->addIgnoreType(args_info.ignore_arg[i]);
-    
-    //ignore water 
-    if(args_info.water_flag){
-      ignoreVisitor->addIgnoreType("SSD");
-      ignoreVisitor->addIgnoreType("SSD1");
-      ignoreVisitor->addIgnoreType("SSD_E");
-      ignoreVisitor->addIgnoreType("SSD_RF");
-      ignoreVisitor->addIgnoreType("TIP3P_RB_0");
-      ignoreVisitor->addIgnoreType("TIP4P_RB_0");
-      ignoreVisitor->addIgnoreType("TIP5P_RB_0");
-      ignoreVisitor->addIgnoreType("SPCE_RB_0");      
-      ignoreVisitor->addIgnoreType("DPD_RB_0");
-    }
-    
-    compositeVisitor->addVisitor(ignoreVisitor, 1000);
-  }
-  
   //creat RigidBody Visitor
   if(args_info.rigidbody_flag){
     RBCOMVisitor* rbCOMVisitor = new RBCOMVisitor(info);
     compositeVisitor->addVisitor(rbCOMVisitor, 900);
   }
   
-  //create selection visitor
-  //if (args_info.selection_given){
-  //  SelectionVisitor* selectionVisitor = new SelectionVisitor(info, args_info.selection_arg);
-  //  compositeVisitor->addVisitor(selectionVisitor, 850);
-  //}
-
-  SelectionEvaluator* evaluator = NULL;
-  if (args_info.selection_given) {
-    evaluator = new SelectionEvaluator(info);
-    assert(evaluator);
-    evaluator->loadScriptString( args_info.selection_arg);
-          
-  }
-  
   //creat SSD atom visitor
   SSDAtomVisitor* ssdVisitor = new SSDAtomVisitor(info);
   compositeVisitor->addVisitor(ssdVisitor, 800);
@@ -178,16 +143,30 @@ int main(int argc, char* argv[]){
     WrappingVisitor* wrappingVisitor = new WrappingVisitor(info);
     compositeVisitor->addVisitor(wrappingVisitor, 400);
   }
-  
+
   //creat replicate visitor
   if(args_info.repeatX_given > 0 || args_info.repeatY_given > 0 ||args_info.repeatY_given > 0){
     Vector3i replicateOpt(args_info.repeatX_arg, args_info.repeatY_arg, args_info.repeatZ_arg);
     ReplicateVisitor* replicateVisitor = new ReplicateVisitor(info, replicateOpt);
     compositeVisitor->addVisitor(replicateVisitor, 300);
   }
-  
+
+
+  //create rotation visitor
+  if (args_info.refsele_given&& args_info.originsele_given) {
+    compositeVisitor->addVisitor(new LipidTransVisitor(info, args_info.originsele_arg, args_info.refsele_arg), 250); 
+  } else if (args_info.refsele_given || args_info.originsele_given) {
+    std::cerr << "Both of --refsele and --originsele should appear by pair" << std::endl;
+    exit(1);
+  }
+    
   //creat xyzVisitor
-  XYZVisitor* xyzVisitor = new XYZVisitor(info);
+  XYZVisitor* xyzVisitor;
+  if (args_info.selection_given) {
+    xyzVisitor = new XYZVisitor(info, args_info.selection_arg);
+  } else {
+    xyzVisitor = new XYZVisitor(info);
+  }
   compositeVisitor->addVisitor(xyzVisitor, 200);
   
   std::cout << compositeVisitor->toString();
@@ -210,11 +189,7 @@ int main(int argc, char* argv[]){
   Molecule* mol;
   StuntDouble* integrableObject;
   RigidBody* rb;
-
-  if (evaluator && !evaluator->isDynamic()) {
-    info->getSelectionManager()->setSelectionSet(evaluator->evaluate());
-  }
-  
+       
   for (int i = 0; i < nframes; i += args_info.frame_arg){
     dumpReader->readFrame(i);
     
@@ -238,11 +213,7 @@ int main(int argc, char* argv[]){
     //update visitor
     compositeVisitor->update();
 
-    //if dynamic, we need to re-evaluate the selection
-    if (evaluator && evaluator->isDynamic()) {
-      info->getSelectionManager()->setSelectionSet(evaluator->evaluate());
-    }
-    
+
     //visit stuntdouble
     for (mol = info->beginMolecule(miter); mol != NULL; mol = info->nextMolecule(miter)) {
       for (integrableObject = mol->beginIntegrableObject(iiter); integrableObject != NULL;