source: src/Actions/FragmentationAction/DepthFirstSearchAction.cpp@ 7cb450

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Last change on this file since 7cb450 was e4afb4, checked in by Frederik Heber <heber@…>, 15 years ago

Huge refactoring: Introduction of Traits to Actions.

This change is really big but the introduction of the Trait concept (at least
in its current light form) is so fundamental that lots of pieces had to be
changed in order to get everything working.

The main point why it was necessary to add these traits in the first place was
to comfortably allow for adding extension of Actions information-wise, i.e.
with stuff that is only important for the QtUI, such as icons, or tooltips, ...
This extra information should not be stored with Action itself, as it has
nothing to do with the workings of the Action. And neither should it get
stored with some blown-out-of-proportions MapOfActions class ...

The gist of the change is as follows:

  • OptionTrait contains the token, description, shortform and type of an option, such as ("position", "position in space, none, typeid(Vector)).
  • ActionTrait is the derived form for actions where additionally MenuPosition and MenuName are stored (and probably more to come for the GUI), also we have a set of OptionTrait instances, one for each option of the Action.
  • Action then contains this ActionTrait, specialized for each Action.
  • the preprocessor macros have been enhanced to gather all this information from the .def files.
  • MapOfActions is gone. Completely. Most of its use was to store this extra information and the ValueStorage part now is just in class ValueStorage.
  • ValueStorage is no more an interface to MapOfActions but as the name says a (type-safe) ValueStorage.

Listing the (remaining) changes in alphabetical order of the class:

  • Action
    • member value ::name dropped, ::getName() uses ActionTraits::getName()
    • new define NODEFAULT which is used in paramdefaults in .def files
    • all derived actions classes such as Process, Calculations, MakroAction,... have been adapated to use the ActionTrait concept as well.
  • ActionHistory
    • extraced RedoAction and UndoAction, shifted implementation into their own object files and they use .def files as well (i.e. streamlined with method used for other actions)
  • MenuDescription
    • contain information on Menus such as name, ...
    • new unit test checks for consistency
  • molecule
    • const member functions: Copy(), Output() and OutputBonds()
  • OptionRegistry
    • new registry class for options only
    • we want the same type throughout the code for each token, e.g. "position"
    • the registry containts checks for consistency
  • OptionTrait
    • default values are specified in paramdefaults, none are given by NODEFAULT
    • introduced default for translate-atoms, point-correlation, pair-correlation
  • Registry pattern
    • new unit test, but only sceleton code so far
  • ...Query, also ...Pipe
    • atoms, molecule and elements are now all const
    • also ValueStorage's signatures all have const therein
  • ValueStorage
    • set/queryCurrentValue from MapOfActions
    • at times VectorValue has been in .def files where Vector was in the signature. This is cleared. Such stuff is only present for e.g. BoxVector being queried as a Vector. But this is a feature and intended.
  • World
    • most of the (un)selection functions now work on const atoms and molecules
    • in one case we need a const_cast to remove this, but this is intentional, as the vector of selected atoms stores non-const pointers and this is ok.

There is only one test which had to be changed slightly because a specific
option token as "position" must now have the same type everywhere, e.g. always
Vector.

  • TESTFIX: Simple_configuration/2: --position -> --domain-position (and associated to BoxVector)
  • Property mode set to 100644
File size: 2.9 KB
RevLine 
[bcf653]1/*
2 * Project: MoleCuilder
3 * Description: creates and alters molecular systems
4 * Copyright (C) 2010 University of Bonn. All rights reserved.
5 * Please see the LICENSE file or "Copyright notice" in builder.cpp for details.
6 */
7
[97ebf8]8/*
9 * DepthFirstSearchAction.cpp
10 *
11 * Created on: May 9, 2010
12 * Author: heber
13 */
14
[bf3817]15// include config.h
16#ifdef HAVE_CONFIG_H
17#include <config.h>
18#endif
19
[112b09]20#include "Helpers/MemDebug.hpp"
21
[97ebf8]22#include "atom.hpp"
[a3fded]23#include "bondgraph.hpp"
[97ebf8]24#include "config.hpp"
[952f38]25#include "Helpers/Log.hpp"
[97ebf8]26#include "molecule.hpp"
27#include "Descriptors/MoleculeDescriptor.hpp"
28#include "Descriptors/MoleculeIdDescriptor.hpp"
29#include "stackclass.hpp"
[952f38]30#include "Helpers/Verbose.hpp"
[97ebf8]31#include "World.hpp"
32
33#include <iostream>
34#include <string>
35
36using namespace std;
37
[1fd675]38#include "Actions/FragmentationAction/DepthFirstSearchAction.hpp"
[f394a6]39
[1fd675]40// and construct the stuff
41#include "DepthFirstSearchAction.def"
42#include "Action_impl_pre.hpp"
43/** =========== define the function ====================== */
[f394a6]44Action::state_ptr FragmentationDepthFirstSearchAction::performCall() {
[1fd675]45 // obtain information
46 getParametersfromValueStorage();
[f394a6]47
48 DoLog(1) && (Log() << Verbose(1) << "Depth-First-Search Analysis." << endl);
49 molecule * const mol = World::getInstance().getMolecule(MoleculeById(0));
50 MoleculeLeafClass *Subgraphs = NULL; // list of subgraphs from DFS analysis
51 int *MinimumRingSize = new int[mol->getAtomCount()];
52 atom **ListOfAtoms = NULL;
53 class StackClass<bond *> *BackEdgeStack = NULL;
54 class StackClass<bond *> *LocalBackEdgeStack = NULL;
[1fd675]55 mol->CreateAdjacencyList(params.distance, World::getInstance().getConfig()->GetIsAngstroem(), &BondGraph::CovalentMinMaxDistance, NULL);
[f394a6]56 Subgraphs = mol->DepthFirstSearchAnalysis(BackEdgeStack);
57 if (Subgraphs != NULL) {
58 int FragmentCounter = 0;
59 while (Subgraphs->next != NULL) {
60 Subgraphs = Subgraphs->next;
61 ListOfAtoms = NULL;
62 Subgraphs->FillBondStructureFromReference(mol, ListOfAtoms, false); // we want to keep the created ListOfLocalAtoms
63 LocalBackEdgeStack = new StackClass<bond *> (Subgraphs->Leaf->BondCount);
64 Subgraphs->Leaf->PickLocalBackEdges(ListOfAtoms, BackEdgeStack, LocalBackEdgeStack);
65 Subgraphs->Leaf->CyclicStructureAnalysis(LocalBackEdgeStack, MinimumRingSize);
66 delete(LocalBackEdgeStack);
67 delete(Subgraphs->previous);
68 delete[](ListOfAtoms); // and here we remove it
69 FragmentCounter++;
[97ebf8]70 }
[f394a6]71 delete(Subgraphs);
[97ebf8]72 }
[f394a6]73 delete(BackEdgeStack);
74 delete[](MinimumRingSize);
75 return Action::success;
[97ebf8]76}
77
78Action::state_ptr FragmentationDepthFirstSearchAction::performUndo(Action::state_ptr _state) {
[f394a6]79 return Action::success;
[97ebf8]80}
81
82Action::state_ptr FragmentationDepthFirstSearchAction::performRedo(Action::state_ptr _state){
[f394a6]83 return Action::success;
[97ebf8]84}
85
86bool FragmentationDepthFirstSearchAction::canUndo() {
[f394a6]87 return true;
[97ebf8]88}
89
90bool FragmentationDepthFirstSearchAction::shouldUndo() {
[f394a6]91 return true;
[97ebf8]92}
[1fd675]93/** =========== end of function ====================== */
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