Changeset ca331c

Timestamp:

Jun 18, 2012, 10:53:30 AM (13 years ago)

Author:

Frederik Heber <heber@…>

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:

345883

Parents:

5b0581

git-author:

Frederik Heber <heber@…> (06/14/12 13:24:13)

git-committer:

Frederik Heber <heber@…> (06/18/12 10:53:30)

Message:

Added Undo/Redo capability to SetTremoloAtomdataAction.

• SetTremoloAtomdataAction may either set/append or reset the AtomData line.
• TremoloParser has new functions getAtomData() and resetAtomData() along with setAtomData(), added unit test function on the triple.
• TEST: Added undo and redo test to Parser/Tremolo-SetAtomData, also new reset test.

Files:

• src/Actions/ParserAction/SetTremoloAtomdataAction.cpp (modified) (1 diff)
• src/Actions/ParserAction/SetTremoloAtomdataAction.def (modified) (2 diffs)
• src/Parser/TremoloParser.cpp (modified) (4 diffs)
• src/Parser/TremoloParser.hpp (modified) (1 diff)
• src/Parser/unittests/ParserTremoloUnitTest.cpp (modified) (1 diff)
• src/Parser/unittests/ParserTremoloUnitTest.hpp (modified) (2 diffs)
• tests/Python/AllActions/options.dat (modified) (1 diff)
• tests/regression/Makefile.am (modified) (1 diff)
• tests/regression/Parser/Tremolo-SetAtomdata/post/output.data (added)
• tests/regression/Parser/Tremolo-SetAtomdata/post/undo.data (added)
• tests/regression/Parser/Tremolo-SetAtomdata/testsuite-parser-tremolo-resetatomdata.at (added)
• tests/regression/Parser/Tremolo-SetAtomdata/testsuite-parser-tremolo-setatomdata.at (modified) (2 diffs)
• tests/regression/Parser/Tremolo/post/water-neighbors.data (added)
• tests/regression/Parser/testsuite-parser.at (modified) (1 diff)

src/Actions/ParserAction/SetTremoloAtomdataAction.cpp

@@ -43 +43 @@
   LOG(1, "Setting Tremolo's ATOMDATA to: '" << params.atomdata_string.get() << "'");
 
-  parser.setAtomData(params.atomdata_string.get());
+  const std::string old_atomdata = parser.getAtomData();
 
-  return Action::success;
+  if (params.atomdata_reset.get())
+    parser.resetAtomData(params.atomdata_string.get());
+  else
+    parser.setAtomData(params.atomdata_string.get());
+
+  return Action::state_ptr(new ParserSetTremoloAtomdataState(old_atomdata, params));
 }
 
 Action::state_ptr ParserSetTremoloAtomdataAction::performUndo(Action::state_ptr _state) {
-//  ParserLoadXyzState *state = assert_cast<ParserLoadXyzState*>(_state.get());
+  ParserSetTremoloAtomdataState *state = assert_cast<ParserSetTremoloAtomdataState*>(_state.get());
 
-  return Action::failure;
-//  string newName = state->mol->getName();
-//  state->mol->setName(state->lastName);
-//
-//  return Action::state_ptr(new ParserLoadXyzState(state->mol,newName));
+  FormatParser<tremolo> &parser = FormatParserStorage::getInstance().getParser<tremolo>();
+  LOG(1, "INFO: Reverting to 'ATOMDATA " << state->old_atomdata << "'.");
+  parser.resetAtomData(state->old_atomdata);
+
+  return Action::state_ptr(_state);
 }
 
 Action::state_ptr ParserSetTremoloAtomdataAction::performRedo(Action::state_ptr _state){
-  return Action::failure;
+  ParserSetTremoloAtomdataState *state = assert_cast<ParserSetTremoloAtomdataState*>(_state.get());
+
+  FormatParser<tremolo> &parser = FormatParserStorage::getInstance().getParser<tremolo>();
+
+  if (state->params.atomdata_reset.get())
+    parser.resetAtomData(state->params.atomdata_string.get());
+  else
+    parser.setAtomData(state->params.atomdata_string.get());
+
+  return Action::state_ptr(_state);
 }
 
 bool ParserSetTremoloAtomdataAction::canUndo() {
-  return false;
+  return true;
 }
 
 bool ParserSetTremoloAtomdataAction::shouldUndo() {
-  return false;
+  return true;
 }
 /** =========== end of function ====================== */

src/Actions/ParserAction/SetTremoloAtomdataAction.def

@@ -9 +9 @@
 #include <boost/filesystem.hpp>
 
+#include "Parameters/Validators/DummyValidator.hpp"
 #include "Parameters/Validators/Specific/AtomDataValidator.hpp"
 
@@ -14 +15 @@
 // ValueStorage by the token "Z" -> first column: int, Z, "Z"
 // "undefine" if no parameters are required, use (NOPARAM_DEFAULT) for each (undefined) default value
-#define paramtypes (std::string)
-#define paramtokens ("set-tremolo-atomdata")
-#define paramdescriptions ("properties to set, space-separated")
-#undef paramdefaults
-#define paramreferences (atomdata_string)
+#define paramtypes (std::string)(bool)
+#define paramtokens ("set-tremolo-atomdata")("reset")
+#define paramdescriptions ("properties to set, space-separated")("whether to append (false) or overwrite (true) with given atomdata")
+#define paramdefaults (NOPARAM_DEFAULT)(PARAM_DEFAULT(true))
+#define paramreferences (atomdata_string)(atomdata_reset)
 #define paramvalids \
-(AtomDataValidator())
+(AtomDataValidator()) \
+(DummyValidator<bool>())
 
-#undef statetypes
-#undef statereferences
+#define statetypes (std::string)
+#define statereferences (old_atomdata)
 
 // some defines for all the names, you may use ACTION, STATE and PARAMS

src/Parser/TremoloParser.cpp

@@ -41 +41 @@
 
 #include <algorithm>
+#include <boost/lambda/lambda.hpp>
 #include <boost/lexical_cast.hpp>
 #include <boost/tokenizer.hpp>
@@ -47 +48 @@
 #include <map>
 #include <sstream>
+#include <string>
 #include <vector>
 
@@ -531 +533 @@
 }
 
+std::string FormatParser< tremolo >::getAtomData() const
+{
+  std::stringstream output;
+  std::for_each(usedFields_save.begin(), usedFields_save.end(),
+      output << boost::lambda::_1 << " ");
+  const std::string returnstring(output.str());
+  return returnstring.substr(0, returnstring.find_last_of(" "));
+}
+
+/** Appends the properties per atom to print to .data file by parsing line from
+ *  \a atomdata_string.
+ *
+ *  We just call \sa  FormatParser< tremolo >::parseAtomDataKeysLine().
+ *
+ * @param atomdata_string line to parse with space-separated values
+ */
+void FormatParser< tremolo >::setAtomData(const std::string &atomdata_string)
+{
+  parseAtomDataKeysLine(atomdata_string, 0, usedFields_save);
+}
+
 /** Sets the properties per atom to print to .data file by parsing line from
  *  \a atomdata_string.
@@ -539 +562 @@
  * @param atomdata_string line to parse with space-separated values
  */
-void FormatParser< tremolo >::setAtomData(const std::string &atomdata_string)
+void FormatParser< tremolo >::resetAtomData(const std::string &atomdata_string)
 {
   usedFields_save.clear();

src/Parser/TremoloParser.hpp

@@ -53 +53 @@
   void load(std::istream* file);
   void save(std::ostream* file, const std::vector<atom *> &atoms);
+  std::string getAtomData() const;
   void setAtomData(const std::string &atomdata_string);
+  void resetAtomData(const std::string &atomdata_string);
 
 private:

src/Parser/unittests/ParserTremoloUnitTest.cpp

@@ -148 +148 @@
 }
 
+void ParserTremoloUnitTest::getsetAtomDataTest() {
+  stringstream input;
+  input << Tremolo_Atomdata1;
+  parser->load(&input);
+
+  CPPUNIT_ASSERT_EQUAL( std::string("Id name type x=3"), parser->getAtomData() );
+
+  // overwrite keys
+  const std::string fewkeys("Id type x=3 neighbors=2");
+  parser->resetAtomData(fewkeys);
+  CPPUNIT_ASSERT_EQUAL( fewkeys, parser->getAtomData() );
+
+  // add some keys
+  const std::string morekeys("charge");
+  parser->setAtomData(morekeys);
+  CPPUNIT_ASSERT_EQUAL( fewkeys+std::string(" ")+morekeys, parser->getAtomData() );
+
+  // add similar key
+  const std::string otherkey("neighbors=4");
+  parser->setAtomData(otherkey);
+  CPPUNIT_ASSERT( fewkeys+std::string(" ")+morekeys != parser->getAtomData() );
+}
+
 void ParserTremoloUnitTest::readTremoloCoordinatesTest() {
   stringstream input;

src/Parser/unittests/ParserTremoloUnitTest.hpp

@@ -22 +22 @@
   CPPUNIT_TEST_SUITE( ParserTremoloUnitTest ) ;
   CPPUNIT_TEST ( readTremoloPreliminaryCommentsTest );
+  CPPUNIT_TEST ( getsetAtomDataTest );
   CPPUNIT_TEST ( readTremoloCoordinatesTest );
   CPPUNIT_TEST ( readTremoloVelocityTest );
@@ -35 +36 @@
 
   void readTremoloPreliminaryCommentsTest();
+  void getsetAtomDataTest();
   void readTremoloCoordinatesTest();
   void readTremoloVelocityTest();

tests/Python/AllActions/options.dat

@@ -123 +123 @@
 random-number-engine-parameters "seed=2;"
 repeat-box      "1 1 1"
+reset   1
 rotate-around-origin    "180."
 rotate-around-origin    "20."

tests/regression/Makefile.am

@@ -140 +140 @@
         $(srcdir)/Parser/Tremolo-Potentials/testsuite-parser-tremolo-potentials-load.at \
         $(srcdir)/Parser/Tremolo-Potentials/testsuite-parser-tremolo-potentials-save.at \
+        $(srcdir)/Parser/Tremolo-SetAtomdata/testsuite-parser-tremolo-resetatomdata.at \
         $(srcdir)/Parser/Tremolo-SetAtomdata/testsuite-parser-tremolo-setatomdata.at \
         $(srcdir)/Parser/Xyz/testsuite-parser-xyz-empty.at \

tests/regression/Parser/Tremolo-SetAtomdata/testsuite-parser-tremolo-setatomdata.at

@@ -1 +1 @@
 ### parsing tremolo
 
-AT_SETUP([Parser - set tremolo's atomdata])
+AT_SETUP([Parser - reset tremolo's atomdata])
 AT_KEYWORDS([parser tremolo set-tremolo-atomdata])
 
@@ -8 +8 @@
 AT_CHECK([chmod u+w $file], 0, [ignore], [ignore])
 AT_CHECK([../../molecuilder -i argon.data --set-tremolo-atomdata "type x=3"], 0, [stdout], [ignore])
-AT_CHECK([file=argon.data; diff -I '%.*' $file ${abs_top_srcdir}/tests/regression/Parser/Tremolo-SetAtomdata/post/argon.data], 0, [ignore], [ignore])
+AT_CHECK([diff -I '%.*' $file ${abs_top_srcdir}/tests/regression/Parser/Tremolo-SetAtomdata/post/argon.data], 0, [ignore], [ignore])
 
 AT_CLEANUP
+
+AT_SETUP([Parser - reset tremolo's atomdata with Undo])
+AT_KEYWORDS([parser tremolo set-tremolo-atomdata undo])
+
+file=argon.data
+AT_CHECK([/bin/cp ${abs_top_srcdir}/tests/regression/Parser/Tremolo-SetAtomdata/pre/argon.data $file], 0, [ignore], [ignore])
+AT_CHECK([chmod u+w $file], 0, [ignore], [ignore])
+AT_CHECK([../../molecuilder -i argon.data --set-tremolo-atomdata "type x=3" --undo], 0, [stdout], [ignore])
+AT_CHECK([diff -I '%.*' $file ${abs_top_srcdir}/tests/regression/Parser/Tremolo-SetAtomdata/post/undo.data], 0, [ignore], [ignore])
+
+AT_CLEANUP
+
+AT_SETUP([Parser - reset tremolo's atomdata with Redo])
+AT_KEYWORDS([parser tremolo set-tremolo-atomdata redo])
+
+file=argon.data
+AT_CHECK([/bin/cp ${abs_top_srcdir}/tests/regression/Parser/Tremolo-SetAtomdata/pre/argon.data $file], 0, [ignore], [ignore])
+AT_CHECK([chmod u+w $file], 0, [ignore], [ignore])
+AT_CHECK([../../molecuilder -i argon.data --set-tremolo-atomdata "type x=3" --undo --redo], 0, [stdout], [ignore])
+AT_CHECK([diff -I '%.*' $file ${abs_top_srcdir}/tests/regression/Parser/Tremolo-SetAtomdata/post/argon.data], 0, [ignore], [ignore])
+
+AT_CLEANUP

tests/regression/Parser/testsuite-parser.at

@@ -59 +59 @@
 # setting tremolo's atomdata line
 m4_include([Parser/Tremolo-SetAtomdata/testsuite-parser-tremolo-setatomdata.at])
+m4_include([Parser/Tremolo-SetAtomdata/testsuite-parser-tremolo-resetatomdata.at])
 
 # writing and exttypes file