source: src/documentation/howtos/action.dox@ 936a02

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
Last change on this file since 936a02 was 750cff, checked in by Frederik Heber <heber@…>, 13 years ago

HUGE: Update on documenation.

  • a general skeleton of the documentation is now in place with all the major components of MoleCuilder explained to some extent.
  • some information has been transfered from TRAC (e.g. install procecure) into this doxygen documentation where it is general and not specific to the situation at our institute.
  • Property mode set to 100644
File size: 17.8 KB
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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
8/**
9 * \file action.dox
10 *
11 * Created on: Oct 31, 2011
12 * Author: heber
13 */
14
15/**
16 * \page howto-action Action Howto
17 *
18 * \section howto-action-introduction Introduction
19 *
20 * Actions are used in object oriented design as a replacement for callback functions.
21 * In most ways Actions can be used in the same way that callbacks were used in non
22 * OO-Systems, but can contain support for several extra mechanism such as undo/redo
23 * or progress indicators.
24 *
25 * The main purpose of an action class is to contain small procedures, that can be repeatedly
26 * called. These procedures can also be stored, passed around, so that the execution of an
27 * action can happen quite far away from the place of creation. For a detailed description of
28 * the Action pattern see GOF:1996.
29 *
30 * \subsection howto-action-usage How to use an action
31 *
32 * The process of using an action is as easy as calling the call() method of the action. The
33 * action will then do whatever it is supposed to do. If it is an action that can be undone, it
34 * will also register itself in the history to make itself available for undo. To undo the last
35 * action, you can either use the undoLast() method inside the ActionHistory class or call the
36 * UndoAction also provided by the ActionHistory. If an action was undone it will be available for
37 * redo, using the redoLast() method of the ActionHistory or the RedoAction also provided by this
38 * class. To check whether undo/redo is available at any moment you can use the hasUndo() or
39 * hasRedo() method respectively.
40 *
41 * Note that an Action always has two functions createDialog() and performCall(). The former
42 * returns a Dialog filled with query...() functions for all information that we need from the
43 * user. The latter must not contain any interaction but just uses these values (which are
44 * temporarily stored by class ValueStorage) to perform the Action.
45 *
46 * Furthermore, there is a global action function that makes the action callable with already
47 * present parameters (i.e. without user interaction and for internal use within the code only).
48 * This function is basically just a macro, that puts the parameters into the ValueStorage and
49 * calls Action::call(Action::NonInteractive).
50 *
51 * Actions can be set to be active or inactive. If an action is set to inactive it is signaling, that
52 * some condition necessary for this action to be executed is not currently met. For example the
53 * UndoAction will set itself to inactive, when there is no action at that time that can be undone.
54 * Using call() on an inactive Action results in a no-op. You can query the state of an action using
55 * the isActive() method.
56 *
57 * The undo capabilities of actions come in three types as signaled by two boolean flags (one
58 * combination of these flags is left empty as can be seen later).
59 * \li The first flag indicates if the undo mechanism for this action should be considered at all, i.e.
60 * if the state of the application changes in a way that needs to be reverted. Actions that should
61 * consider the undo mechanism are for example adding a molecule, moving atoms, changing
62 * the name of a molecule etc. Changing the View-Area on the other hand should be an action that
63 * does not consider the undo mechanism. This flag can be queried using the shouldUndo() method.
64 *
65 * \li The second flag indicates whether the changes can be undo for this action. If this flag is true
66 * the action will be made available for undo using the ActionHistory class and the actions of this
67 * class. If this flag is false while the shoudlUndo() flag is true this means that this action
68 * changes the state of the application changes in a way that cannot be undone, but might cause
69 * the undo of previous actions to fail. In this case the whole History is cleared, as to keep
70 * the state of the application intact by avoiding dangerous undos. This flag can be queried
71 * using the canUndo() method.
72 *
73 * Each action has a name, that can be used to identify it throughout the run of the application.
74 * This name can be retrieved using the getName() method. Most actions also register themselves with
75 * a global structure, called the ActionRegistry. Actions that register themselves need to have a
76 * unique name for the whole application. If the name is known these actions can be retrieved from
77 * the registry by their name and then be used as normal.
78 *
79 * \section howto-action-add Building your own actions
80 *
81 * Building actions is easy. Each specific ...Action is derived from the base class Action.
82 * In order to create all the reoccuring stuff, macros have been created which you can simply
83 * include and then don't need to worry about it.
84 * There are three major virtual functions: performCall(), performUndo(), performRedo() which
85 * you have to write, to equip your action with some actual capabilities.
86 * Each Action definition and implementation consists of of three files:
87 * -# cpp: contains performX() which you have to write, also some boilerplate functions which are
88 * constructed automatically when including your def and "Actions/action_impl_pre.hpp"
89 * -# hpp: boilerplate definitions created simply by including your def and
90 * "Actions/action_impl_header.hpp"
91 * -# def: macro definitions of all your parameters and additional variables needed for the state,
92 * also name and category and token of your action.
93 *
94 * Best thing to do is look at one of the already present triples and you should soon understand
95 * what you have to add:
96 * -# pick the right category, i.e. the right folder in src/Actions
97 * -# pick the right name
98 * -# decide which parameters your actions need and what the type, the variable name and the token
99 * to reference it from the command-line should be. Check whether already present and fitting
100 * tokens exists, e.g. "position" as token for a Vector representing a position.
101 * -# consider which additional information you need to undo your action
102 * -# don't forget to include your .def file followed by "action_impl_pre.hpp" in .cpp or
103 * "action_impl_header.hpp" in the .hpp
104 * -# continue to write the functionality of your action in performCall(), undo and redo in performUndo()
105 * and performRedo().
106 * -# You should indicate whether the action supports undo by implementing the shouldUndo() and
107 * canUndo() methods to return the appropriate flags.
108 *
109 * \subsection howto-action-add-notes Specific notes on the macros
110 *
111 * The following functions are created by the macros, i.e. you don't need to worry about it:
112 *
113 * Any user interaction should be placed into the dialog returned by fillDialog().
114 *
115 * Also, create the global function to allow for easy calling of your function internally (i.e.
116 * without user interaction). It should have the name of the Action class without the suffix Action.
117 *
118 * The constructor of your derived class also needs to call the Base constructor, passing it the
119 * name of the Action and a flag indicating whether this action should be made available in the
120 * registry. WARNING: Do not use the virtual getName() method of the derived action to provide the
121 * constructor with the name, even if you overloaded this method to return a constant. Doing this
122 * will most likely not do what you think it does (see: http://www.parashift.com/c++-faq-lite/strange-inheritance.html#faq-23.5
123 * if you want to know why this wont work)
124 *
125 * \subsection howto-action-add-undo Interfacing your Action with the Undo mechanism
126 *
127 * The performX() methods need to comply to a simple standard to allow for undo and redo. The first
128 * convention in this standard concerns the return type. All methods that handle calling, undoing
129 * or redoing return an object of Action::state_ptr. This is a smart pointer to a State object, that
130 * can be used to store state information that is needed by your action for later redo. A rename
131 * Action for example would need to store which object has been renamed and what the old name was.
132 * A move Action on the other hand would need to store the object that has been moved as well as the
133 * old position. If your Action does not need to store any kind of information for redo you can
134 * simply return Action::success and skip the rest of this paragraph. If your action has been
135 * abborted you can return Action::failure, which indicates to the history mechanism that this
136 * action should not be stored.
137 *
138 * If your Action needs any kind of information to undo its execution, you need to store this
139 * information in the state that is returned by the performCall() method. Since no assumptions
140 * can be made on the type or amount of information the ActionState base class is left empty.
141 * To use this class you need to derive a YourActionState class from the ActionState base class
142 * adding your data fields and accessor functions. Upon undo the ActionState object produced
143 * by the corresponding performCall() is then passed to the performUndo() method which should
144 * typecast the ActionState to the appropriate sub class, undo all the changes and produce
145 * a State object that can be used to redo the action if neccessary. This new state object is
146 * then used if the redo mechanism is invoked and passed to the performRedo() function, which
147 * again produces a State that can be used for performUndo().
148 *
149 * \section howto-action-implementation Outline of the implementation of Actions
150 *
151 * To sum up the actions necessary to build actions here is a brief outline of things methioned
152 * in the last paragraphs:
153 *
154 * \subsection howto-action-implementation-notes Specific notes on the macros
155 *
156 * \li create parameter tupels (type, token, reference), put into def. Access them later in
157 * the performX() via the structure params.###.
158 * \li think of name, category and token for your action, put into def
159 * \li create additional state variables tupels (type, reference) for storing extra information
160 * that you need for undo/redo in the ActionState. You can always access the parameters
161 * of your Action by state.params.### (i.e. they are copied to the state by default).
162 * \li implement performCall(), first line should be calling of getParametersfromValueStorage().
163 * \li performUndo(), performRedo()
164 * \li implement the functions that return the flags for the undo mechanism, i.e. true/false.
165 *
166 * \subsection howto-action-implementation-perform-x Implementing performX() methods
167 *
168 * \li performCall():
169 * -# first line should be calling of getParametersfromValueStorage().
170 * -# Access your parameters by the structure params.### (where ### stands for the reference/
171 * variable name chosen in the tupel).
172 * -# do whatever is needed to make the action work
173 * -# if the action was abborted return Action::failure
174 * -# if the action needs to save a state return a custom state object
175 * -# otherwise return Action::success
176 * \li performUndo():
177 * -# typecast the ActionState pointer to a Pointer to YourActionState if necessary
178 * -# undo the action using the extra information and the Action's parameters in the state
179 * -# produce a new state that can be used for redoing and return it
180 * \li performRedo():
181 * -# take the ActionState produced by performUndo and typecast it to a pointer to YourActionState if necessary
182 * -# redo the undone action using the extra information and the Action's parameters in the state
183 * -# produce a new state that can be used by performUndo() and return it
184 *
185 * \section howto-action-advanced Advanced techniques
186 *
187 * \subsection howto-action-advanced-predefined Predefined Actions
188 *
189 * To make construction of actions easy there are some predefined actions. Namely these are
190 * the MethodAction and the ErrorAction.
191 *
192 * The method action can be used to turn any function with empty arguments and return type void
193 * into an action (also works for functors with those types). Simply pass the constructor for the
194 * MethodAction a name to use for this action, the function to call inside the performCall()
195 * method and a flag indicating if this action should be made retrievable inside the registry
196 * (default is true). MethodActions always report themselves as changing the state of the
197 * application but cannot be undone. i.e. calling MethodActions will always cause the ActionHistory
198 * to be cleared.
199 *
200 * ErrorActions can be used to produce a short message using the Log() << Verbose() mechanism of
201 * the molecuilder. Simply pass the constructor a name for the action, the message to show upon
202 * calling this action and the flag for the registry (default is again true). Error action
203 * report that they do not change the state of the application and are therefore not considered
204 * for undo.
205 *
206 * \subsection howto-action-advanced-sequences Sequences of Actions and MakroActions
207 *
208 * \paragraph howto-action-advanced-sequences-add Building sequences of Actions
209 *
210 * Actions can be chained to sequences using the ActionSequence class. Once an ActionSequence is
211 * constructed it will be initially empty. Any Actions can then be added to the sequence using the
212 * addAction() method of the ActionSequence class. The last added action can be removed using the
213 * removeLastAction() method. If the construction of the sequence is done, you can use the
214 * callAll() method. Each action called this way will register itself with the History to allow
215 * separate undo of all actions in the sequence.
216 *
217 * \paragraph howto-action-advanced-sequences-build-larger Building larger Actions from simple ones
218 *
219 * Using the pre-defined class MakroAction it is possible to construct bigger actions from a sequence
220 * of smaller ones. For this you first have to build a sequence of the actions using the ActionSequence
221 * as described above. Then you can construct a MakroAction passing it a name, the sequence to use
222 * and as usual a flag for the registry. You can then simply call the complete action-sequence through
223 * this makro action using the normal interface. Other than with the direct use of the action sequence
224 * only the complete MakroAction is registered inside the history, i.e. the complete sequence can be
225 * undone at once. Also there are a few caveats you have to take care of when using the MakroAction:
226 * -# All Actions as well as the sequence should exclusively belong to the MakroAction. This
227 * especially means, that the destruction of these objects should be handled by the MakroAction.
228 * -# none of the Actions inside the MakroAction should be registered with the registry, since the
229 * registry also assumes sole ownership of the actions.
230 * -# Do not remove or add actions from the sequence once the MakroAction has been constructed, since this
231 * might brake important assumptions for the undo/redo mechanism
232 *
233 * \section howto-action-special Special kinds of Actions
234 *
235 * To make the usage of Actions more versatile there are two special kinds of actions defined,
236 * that contain special mechanisms. These are defined inside the class Process, for actions that
237 * take some time and indicate their own progress, and in the class Calculations for actions that
238 * have a retrievable result.
239 *
240 * \subsection howto-action-special-process Processes
241 *
242 * Processes are Actions that might take some time and therefore contain special mechanisms
243 * to indicate their progress to the user. If you want to implement a process you can follow the
244 * guidelines for implementing actions. In addition to the normal Action constructor parameters,
245 * you also need to define the number of steps the process takes to finish (use 0 if that number is
246 * not known upon construction). At the beginning of your process you then simply call start() to
247 * indicate that the process is taking up its work. You might also want to set the number of steps it
248 * needs to finish, if it has changed since the last invocation/construction. You can use the
249 * setMaxSteps() method for this. Then after each finished step of calulation simply call step(),
250 * to let the indicators know that it should update itself. If the number of steps is not known
251 * at the time of calculation, you should make sure the maxSteps field is set to 0, either through
252 * the constructor or by using setMaxSteps(0). Indicators are required to handle both processes that
253 * know the number of steps needed as well as processes that cannot predict when they will be finished.
254 * Once your calculation is done call stop() to let every indicator know that the process is done with
255 * the work and to let the user know.
256 *
257 * Indicators that want to know about processes need to implement the Observer class with all the
258 * methods defined there. They can then globally sign on to all processes using the static
259 * Process::AddObserver() method and remove themselves using the Process::RemoveObserver()
260 * methods. When a process starts it will take care that the notification for this process
261 * is invoked at the right time. Indicators should not try to observe a single process, but rather
262 * be ready to observe the status of any kind of process using the methods described here.
263 *
264 * \subsection howto-action-special-calculation Calculations
265 *
266 * Calculations are special Actions that also return a result when called. Calculations are
267 * always derived from Process, so that the progress of a calculation can be shown. Also
268 * Calculations should not contain side-effects and not consider the undo mechanism.
269 * When a Calculation is called using the Action mechanism this will cause it to calculate
270 * the result and make it available using the getResult() method. Another way to have a Calculation
271 * produce a result is by using the function-call operator. When this operator is used, the Calculation
272 * will try to return a previously calculated and cached result and only do any actuall calculations
273 * when no such result is available. You can delete the cached result using the reset() method.
274 *
275 *
276 * \date 2011-10-31
277 */
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