Changeset e6317b for src/UIElements

Timestamp:

Jun 16, 2010, 12:24:21 PM (15 years ago)

Author:

Tillmann Crueger <crueger@…>

Branches:

Action_Thermostats, Add_AtomRandomPerturbation, Add_FitFragmentPartialChargesAction, Add_RotateAroundBondAction, Add_SelectAtomByNameAction, Added_ParseSaveFragmentResults, AddingActions_SaveParseParticleParameters, Adding_Graph_to_ChangeBondActions, Adding_MD_integration_tests, Adding_ParticleName_to_Atom, Adding_StructOpt_integration_tests, AtomFragments, Automaking_mpqc_open, AutomationFragmentation_failures, Candidate_v1.5.4, Candidate_v1.6.0, Candidate_v1.6.1, ChangeBugEmailaddress, ChangingTestPorts, ChemicalSpaceEvaluator, CombiningParticlePotentialParsing, Combining_Subpackages, Debian_Package_split, Debian_package_split_molecuildergui_only, Disabling_MemDebug, Docu_Python_wait, EmpiricalPotential_contain_HomologyGraph, EmpiricalPotential_contain_HomologyGraph_documentation, Enable_parallel_make_install, Enhance_userguide, Enhanced_StructuralOptimization, Enhanced_StructuralOptimization_continued, Example_ManyWaysToTranslateAtom, Exclude_Hydrogens_annealWithBondGraph, FitPartialCharges_GlobalError, Fix_BoundInBox_CenterInBox_MoleculeActions, Fix_ChargeSampling_PBC, Fix_ChronosMutex, Fix_FitPartialCharges, Fix_FitPotential_needs_atomicnumbers, Fix_ForceAnnealing, Fix_IndependentFragmentGrids, Fix_ParseParticles, Fix_ParseParticles_split_forward_backward_Actions, Fix_PopActions, Fix_QtFragmentList_sorted_selection, Fix_Restrictedkeyset_FragmentMolecule, Fix_StatusMsg, Fix_StepWorldTime_single_argument, Fix_Verbose_Codepatterns, Fix_fitting_potentials, Fixes, ForceAnnealing_goodresults, ForceAnnealing_oldresults, ForceAnnealing_tocheck, ForceAnnealing_with_BondGraph, ForceAnnealing_with_BondGraph_continued, ForceAnnealing_with_BondGraph_continued_betteresults, ForceAnnealing_with_BondGraph_contraction-expansion, FragmentAction_writes_AtomFragments, FragmentMolecule_checks_bonddegrees, GeometryObjects, Gui_Fixes, Gui_displays_atomic_force_velocity, ImplicitCharges, IndependentFragmentGrids, IndependentFragmentGrids_IndividualZeroInstances, IndependentFragmentGrids_IntegrationTest, IndependentFragmentGrids_Sole_NN_Calculation, JobMarket_RobustOnKillsSegFaults, JobMarket_StableWorkerPool, JobMarket_unresolvable_hostname_fix, MoreRobust_FragmentAutomation, ODR_violation_mpqc_open, PartialCharges_OrthogonalSummation, PdbParser_setsAtomName, PythonUI_with_named_parameters, QtGui_reactivate_TimeChanged_changes, Recreated_GuiChecks, Rewrite_FitPartialCharges, RotateToPrincipalAxisSystem_UndoRedo, SaturateAtoms_findBestMatching, SaturateAtoms_singleDegree, StoppableMakroAction, Subpackage_CodePatterns, Subpackage_JobMarket, Subpackage_LinearAlgebra, Subpackage_levmar, Subpackage_mpqc_open, Subpackage_vmg, Switchable_LogView, ThirdParty_MPQC_rebuilt_buildsystem, TrajectoryDependenant_MaxOrder, TremoloParser_IncreasedPrecision, TremoloParser_MultipleTimesteps, TremoloParser_setsAtomName, Ubuntu_1604_changes, stable

Children:

492279

Parents:

f8e486 (diff), 980dd6 (diff)
Note: this is a merge changeset, the changes displayed below correspond to the merge itself.
Use the (diff) links above to see all the changes relative to each parent.

Message:

Broken: Merge commit 'Gitosis/stable' into stable

Conflicts:

molecuilder/src/Actions/AnalysisAction/PairCorrelationToPointAction.cpp
molecuilder/src/Actions/AnalysisAction/PairCorrelationToSurfaceAction.cpp
molecuilder/src/Makefile.am

Location:

src/UIElements

Files:

• CommandLineUI/CommandLineDialog.cpp (modified) (12 diffs)
• CommandLineUI/CommandLineDialog.hpp (modified) (2 diffs)
• CommandLineUI/CommandLineWindow.cpp (modified) (8 diffs)
• Dialog.cpp (modified) (3 diffs)
• Dialog.hpp (modified) (4 diffs)
• TextUI/TextDialog.cpp (modified) (5 diffs)
• TextUI/TextDialog.hpp (modified) (2 diffs)

src/UIElements/CommandLineUI/CommandLineDialog.cpp

@@ -8 +8 @@
 #include "Helpers/MemDebug.hpp"
 
-#include <cassert>
 #include <iostream>
+#include <vector>
 
 #include <Descriptors/AtomDescriptor.hpp>
@@ -16 +16 @@
 #include <Descriptors/MoleculeIdDescriptor.hpp>
 #include "CommandLineUI/CommandLineDialog.hpp"
+
+#include "Actions/Values.hpp"
 
 #include "element.hpp"
@@ -79 +81 @@
 }
 
-void CommandLineDialog::queryElement(const char* title, const element **target, string _description){
+void CommandLineDialog::queryElement(const char* title, std::vector<element *> *target, string _description){
   registerQuery(new ElementCommandLineQuery(title,target, _description));
 }
@@ -106 +108 @@
     tmp = CommandLineParser::getInstance().vm[getTitle()].as<int>();
     return true;
-  } else
-    return false;
+  } else {
+    DoeLog(1) && (eLog() << Verbose(1) << "CommandLineUI parsing error: Missing integer for " << getTitle() << "." << endl);
+    return false;
+  }
 }
 
@@ -117 +121 @@
 
 bool CommandLineDialog::BooleanCommandLineQuery::handle() {
-  bool badInput = false;
-  char input = ' ';
-  do{
-    badInput = false;
-    Log() << Verbose(0) << getTitle();
-    cin >> input;
-    if ((input == 'y' ) || (input == 'Y')) {
-      tmp = true;
-    } else if ((input == 'n' ) || (input == 'N')) {
-      tmp = false;
-    } else {
-      badInput=true;
-      cin.clear();
-      cin.ignore(std::numeric_limits<streamsize>::max(),'\n');
-      Log() << Verbose(0) << "Input was not of [yYnN]!" << endl;
-    }
-  } while(badInput);
-  // clear the input buffer of anything still in the line
-  cin.ignore(std::numeric_limits<streamsize>::max(),'\n');
-  return true;
+  if (CommandLineParser::getInstance().vm.count(getTitle())) {
+    tmp = CommandLineParser::getInstance().vm[getTitle()].as<bool>();
+    return true;
+  } else {
+    DoeLog(1) && (eLog() << Verbose(1) << "CommandLineUI parsing error: Missing boolean for " << getTitle() << "." << endl);
+    return false;
+  }
 }
 
@@ -149 +140 @@
     tmp = CommandLineParser::getInstance().vm[getTitle()].as<string>();
     return true;
-  } else
-    return false;
+  } else {
+    DoeLog(1) && (eLog() << Verbose(1) << "CommandLineUI parsing error: Missing string for " << getTitle() << "." << endl);
+    return false;
+  }
 }
 
@@ -163 +156 @@
     tmp = CommandLineParser::getInstance().vm[getTitle()].as<double>();
     return true;
-  } else
-    return false;
+  } else {
+    DoeLog(1) && (eLog() << Verbose(1) << "CommandLineUI parsing error: Missing double for " << getTitle() << "." << endl);
+    return false;
+  }
 }
 
@@ -179 +174 @@
     tmp = World::getInstance().getAtom(AtomById(IdxOfAtom));
     return true;
-  } else
-    return false;
+  } else {
+    DoeLog(1) && (eLog() << Verbose(1) << "CommandLineUI parsing error: Missing atom for " << getTitle() << "." << endl);
+    return false;
+  }
 }
 
@@ -199 +196 @@
       tmp = NULL;
     return true;
-  } else
-    return false;
+  } else {
+    DoeLog(1) && (eLog() << Verbose(1) << "CommandLineUI parsing error: Missing molecule for " << getTitle() << "." << endl);
+    return false;
+  }
 }
 
@@ -211 +210 @@
 
 bool CommandLineDialog::VectorCommandLineQuery::handle() {
-  vector<double> temp;
-  if (CommandLineParser::getInstance().vm.count(getTitle())) {
-    temp = CommandLineParser::getInstance().vm[getTitle()].as<vector<double> >();
-    assert((temp.size() == 3) && "Vector from command line does not have three components.");
-    for (int i=0;i<NDIM;i++)
-      tmp->at(i) = temp[i];
-    return true;
-  } else
-    return false;
+  VectorValue temp;
+  if (CommandLineParser::getInstance().vm.count(getTitle())) {
+    temp = CommandLineParser::getInstance().vm[getTitle()].as< VectorValue >();
+    tmp->at(0) = temp.x;
+    tmp->at(1) = temp.y;
+    tmp->at(2) = temp.z;
+    return true;
+  } else {
+    DoeLog(1) && (eLog() << Verbose(1) << "CommandLineUI parsing error: Missing vector for " << getTitle() << "." << endl);
+    return false;
+  }
 }
 
@@ -231 +232 @@
 
 bool CommandLineDialog::BoxCommandLineQuery::handle() {
-  vector<double> temp;
-  if (CommandLineParser::getInstance().vm.count(getTitle())) {
-    temp = CommandLineParser::getInstance().vm[getTitle()].as<vector<double> >();
-    assert((temp.size() == 6) && "Symmetric box matrix from command line does not have six components.");
-    for (int i=0;i<6;i++) {
-      tmp[i] = temp[i];
-    }
-    return true;
-  } else
-    return false;
-}
-
-CommandLineDialog::ElementCommandLineQuery::ElementCommandLineQuery(string title, const element **target, string _description) :
+  BoxValue temp;
+  if (CommandLineParser::getInstance().vm.count(getTitle())) {
+    temp = CommandLineParser::getInstance().vm[getTitle()].as< BoxValue >();
+    tmp[0] = temp.xx;
+    tmp[1] = temp.xy;
+    tmp[2] = temp.xz;
+    tmp[3] = temp.yy;
+    tmp[4] = temp.yz;
+    tmp[5] = temp.zz;
+    return true;
+  } else {
+    DoeLog(1) && (eLog() << Verbose(1) << "CommandLineUI parsing error: Missing symmetric box matrix for " << getTitle() << "." << endl);
+    return false;
+  }
+}
+
+CommandLineDialog::ElementCommandLineQuery::ElementCommandLineQuery(string title, std::vector<element *> *target, string _description) :
     Dialog::ElementQuery(title,target, _description)
 {}
@@ -252 +257 @@
 bool CommandLineDialog::ElementCommandLineQuery::handle() {
   // TODO: vector of ints and removing first is not correctly implemented yet. How to remove from a vector?
-  int Z;
+  periodentafel *periode = World::getInstance().getPeriode();
+  element *elemental = NULL;
   if (CommandLineParser::getInstance().vm.count(getTitle())) {
     vector<int> AllElements = CommandLineParser::getInstance().vm[getTitle()].as< vector<int> >();
-    vector<int>::iterator ElementRunner = AllElements.begin();
-    Z = *ElementRunner;
-    // TODO: So far, this does not really erase the element in the parsed list.
-    AllElements.erase(ElementRunner);
-    tmp = World::getInstance().getPeriode()->FindElement(Z);
-    return true;
-  } else
-    return false;
-}
+    for (vector<int>::iterator ZRunner = AllElements.begin(); ZRunner != AllElements.end(); ++ZRunner) {
+      elemental = periode->FindElement(*ZRunner);
+      ASSERT(elemental != NULL, "Invalid element specified in ElementCommandLineQuery");
+      elements.push_back(elemental);
+    }
+    return true;
+  } else {
+    DoeLog(1) && (eLog() << Verbose(1) << "CommandLineUI parsing error: Missing element for " << getTitle() << "." << endl);
+    return false;
+  }
+}

src/UIElements/CommandLineUI/CommandLineDialog.hpp

@@ -36 +36 @@
   virtual void queryVector(const char*,Vector *,const double * const,bool, std::string = "");
   virtual void queryBox(const char*,double ** const, std::string = "");
-  virtual void queryElement(const char*,const element **, std::string = "");
+  virtual void queryElement(const char*, std::vector<element *> *, std::string = "");
 
 protected:
@@ -105 +105 @@
   class ElementCommandLineQuery : public Dialog::ElementQuery {
   public:
-    ElementCommandLineQuery(std::string title, const element **_target, std::string _description = "");
+    ElementCommandLineQuery(std::string title, std::vector<element *> *_target, std::string _description = "");
     virtual ~ElementCommandLineQuery();
     virtual bool handle();

src/UIElements/CommandLineUI/CommandLineWindow.cpp

@@ -14 +14 @@
 
 #include "Actions/ActionRegistry.hpp"
+#include "Actions/AnalysisAction/MolecularVolumeAction.hpp"
 #include "Actions/AnalysisAction/PairCorrelationAction.hpp"
-#include "Actions/AnalysisAction/PairCorrelationToPointAction.hpp"
-#include "Actions/AnalysisAction/PairCorrelationToSurfaceAction.hpp"
+#include "Actions/AnalysisAction/PrincipalAxisSystemAction.hpp"
 #include "Actions/AtomAction/AddAction.hpp"
 #include "Actions/AtomAction/ChangeElementAction.hpp"
@@ -28 +28 @@
 #include "Actions/FragmentationAction/DepthFirstSearchAction.hpp"
 #include "Actions/FragmentationAction/SubgraphDissectionAction.hpp"
+#include "Actions/FragmentationAction/FragmentationAction.hpp"
 #include "Actions/MoleculeAction/BondFileAction.hpp"
 #include "Actions/MoleculeAction/ChangeNameAction.hpp"
@@ -35 +36 @@
 #include "Actions/MoleculeAction/SaveBondsAction.hpp"
 #include "Actions/MoleculeAction/SaveTemperatureAction.hpp"
+#include "Actions/MoleculeAction/TranslateAction.hpp"
 #include "Actions/MoleculeAction/VerletIntegrationAction.hpp"
 #include "Actions/ParserAction/LoadXyzAction.hpp"
@@ -75 +77 @@
 CommandLineWindow::~CommandLineWindow()
 {
-//  // go through all possible actions
-//  for(std::map<const std::string,Action*>::iterator ActionRunner = ActionRegistry::getInstance().getBeginIter(); ActionRegistry::getInstance().getBeginIter() != ActionRegistry::getInstance().getEndIter(); ActionRunner = ActionRegistry::getInstance().getBeginIter()) {
-//    ActionRegistry::getInstance().unregisterAction(ActionRunner->second);
-//    delete(ActionRunner->second);
-//  }
-
   delete statusIndicator;
 }
@@ -86 +82 @@
 void CommandLineWindow::display() {
   // go through all possible actions
-  for(std::map<const std::string,Action*>::iterator ActionRunner = ActionRegistry::getInstance().getBeginIter(); ActionRunner != ActionRegistry::getInstance().getEndIter(); ActionRunner++) {
-    // check whether action is present in command line
-    if (CommandLineParser::getInstance().vm.count(ActionRunner->first)) {
-      ActionRunner->second->call();
-    }
+  for (std::list<std::string>::iterator CommandRunner = CommandLineParser::getInstance().SequenceOfActions.begin(); CommandRunner != CommandLineParser::getInstance().SequenceOfActions.end(); ++CommandRunner) {
+    cout << "Checking presence of " << *CommandRunner << endl;
+    if (ActionRegistry::getInstance().isActionByNamePresent(*CommandRunner))
+      ActionRegistry::getInstance().getActionByName(*CommandRunner)->call();
   }
 }
@@ -96 +91 @@
 void CommandLineWindow::populateAnalysisActions()
 {
+  new AnalysisMolecularVolumeAction();
   new AnalysisPairCorrelationAction();
-  new AnalysisPairCorrelationToPointAction();
-  new AnalysisPairCorrelationToSurfaceAction();
+  new AnalysisPrincipalAxisSystemAction();
 }
 
@@ -121 +116 @@
 {
   new FragmentationDepthFirstSearchAction();
+  new FragmentationFragmentationAction();
+  new FragmentationSubgraphDissectionAction();
 }
 
@@ -132 +129 @@
   new MoleculeSaveBondsAction();
   new MoleculeSaveTemperatureAction();
+  new MoleculeTranslateAction();
   new MoleculeVerletIntegrationAction();
 }

src/UIElements/Dialog.cpp

@@ -41 +41 @@
     retval &= (*iter)->handle();
     // if any query fails (is canceled), we can end the handling process
-    if(!retval)
+    if(!retval) {
+      DoeLog(1) && (eLog() << Verbose(1) << "The following query failed: " << (**iter).getTitle() << "." << endl);
       break;
+    }
   }
   if (retval){
@@ -201 +203 @@
 
 // Element Queries
-Dialog::ElementQuery::ElementQuery(std::string title, const element **_target, std::string _description) :
+Dialog::ElementQuery::ElementQuery(std::string title, std::vector<element *> *_target, std::string _description) :
   Query(title, _description),
-  tmp(0),
   target(_target)
   {}
@@ -210 +211 @@
 
 void Dialog::ElementQuery::setResult(){
-  *target=tmp;
-}
+  *target=elements;
+}

src/UIElements/Dialog.hpp

@@ -11 +11 @@
 #include<string>
 #include<list>
+#include<vector>
 
 class atom;
@@ -32 +33 @@
   virtual void queryVector(const char*,Vector *,const double *const,bool, std::string = "")=0;
   virtual void queryBox(const char*,double ** const, std::string = "")=0;
-  virtual void queryElement(const char*,const element **, std::string = "")=0;
+  virtual void queryElement(const char*, std::vector<element *> *, std::string = "")=0;
 
   virtual bool display();
@@ -49 +50 @@
   //base class for all queries
   class Query {
+    friend class Dialog;
   public:
     Query(std::string _title, std::string _description = "");
@@ -172 +174 @@
   class ElementQuery : public Query {
   public:
-    ElementQuery(std::string title, const element**_target, std::string _description = "");
+    ElementQuery(std::string title, std::vector<element *> *_target, std::string _description = "");
     virtual ~ElementQuery();
     virtual bool handle()=0;
     virtual void setResult();
   protected:
-    const element *tmp;
+    std::vector<element *> elements;
   private:
-    const element **target;
+    std::vector<element *> * const target;
   };
 

src/UIElements/TextUI/TextDialog.cpp

@@ -74 +74 @@
 }
 
-void TextDialog::queryElement(const char* title, const element **target, string description){
+void TextDialog::queryElement(const char* title, std::vector<element *> *target, string description){
   registerQuery(new ElementTextQuery(title,target,description));
 }
@@ -283 +283 @@
 }
 
-TextDialog::ElementTextQuery::ElementTextQuery(std::string title, const element **target, std::string _description) :
-    Dialog::ElementQuery(title,target,_description)
+TextDialog::ElementTextQuery::ElementTextQuery(std::string title, std::vector<element *> *_target, std::string _description) :
+    Dialog::ElementQuery(title,_target,_description)
 {}
 
@@ -293 +293 @@
   bool badInput=false;
   bool aborted = false;
+  element * tmp = NULL;
   do{
     badInput = false;
@@ -309 +310 @@
           Log() << Verbose(0) << "No element with this atomic number!" << endl;
           badInput = true;
+        } else {
+          elements.push_back(tmp);
         }
       }
@@ -331 +334 @@
           Log() << Verbose(0) << "No element with this shorthand!" << endl;
           badInput = true;
+        } else {
+          elements.push_back(tmp);
         }
       }

src/UIElements/TextUI/TextDialog.hpp

@@ -33 +33 @@
   virtual void queryVector(const char*,Vector *,const double * const,bool, std::string = "");
   virtual void queryBox(const char*,double ** const, std::string = "");
-  virtual void queryElement(const char*,const element **, std::string = "");
+  virtual void queryElement(const char*, std::vector<element *> *, std::string = "");
 
 protected:
@@ -102 +102 @@
   class ElementTextQuery : public Dialog::ElementQuery {
   public:
-    ElementTextQuery(std::string title, const element **_target, std::string _description = NULL);
+    ElementTextQuery(std::string title, std::vector<element *> *_target, std::string _description = NULL);
     virtual ~ElementTextQuery();
     virtual bool handle();