/dports/biology/lamarc/lamarc-2.1.8/src/ui_interface/ |
H A D | ui_strings.cpp | 19 const string uistr::TTRatio = "TT Ratio"; 27 const string uistr::allStr = "all"; 55 const string uistr::defaultStr = "default"; 56 const string uistr::disease = "Disease"; 58 const string uistr::diseaseByID2 = " from "; 67 const string uistr::divergenceEpoch = "Epoch"; 115 const string uistr::growthRate = "Growth"; 148 const string uistr::migrationByID2 = " from "; 156 const string uistr::muRate = "MuRate"; 175 const string uistr::profileByID = "Profile"; [all …]
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H A D | chainparam_interface.cpp | 26 : SetGetLong(uistr::finalChains) in uiFinalChains() 47 : SetGetLong(uistr::finalDiscard) in uiFinalDiscard() 68 : SetGetLong(uistr::finalSamples) in uiFinalSamples() 89 : SetGetLong(uistr::finalInterval) in uiFinalInterval() 110 : SetGetLong(uistr::initialChains) in uiInitialChains() 131 : SetGetLong(uistr::initialDiscard) in uiInitialDiscard() 194 : SetGetDouble(uistr::heatedChain) in uiHeatedChain() 252 : SetGetLong(uistr::tempInterval) in uiTempInterval() 273 : SetGetBool(uistr::tempAdapt) in uiAdaptiveTemp() 294 : SetGetLong(uistr::replicates) in uiNumReps() [all …]
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H A D | userparam_interface.cpp | 24 : GetString(uistr::dataFileName) in uiDataFileName() 42 : SetGetBool(uistr::plotPost) in uiPlotPost() 65 : SetGetVerbosityType(uistr::progress) in uiProgress() 88 : SetGetLong(uistr::randomSeed) in uiRandomSeed() 111 : SetGetString(uistr::resultsFileName) in uiResultsFileName() 134 : SetGetBool(uistr::systemClock) in uiSystemClock() 158 : SetGetLong(uistr::setOldSeedFromClock) in uiSetOldClockSeed() 454 : SetGetString( uistr::mapFilePrefix) in uiMapFilePrefix() 477 : SetGetString( uistr::profileprefix) in uiProfilePrefix() 570 : SetGetString( uistr::argFilePrefix) in uiArgFilePrefix() [all …]
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H A D | force_interface.cpp | 33 : GetBool(uistr::forceLegal) in uiForceLegal() 54 : SetGetBool(uistr::forceOnOff) in uiForceOnOff() 75 : SetGetLong(uistr::maxEvents) in uiMaxEvents() 245 : GetBool(uistr::coalescenceLegal) in uiCoalescenceLegal() 287 : SetGetNoval(uistr::fstSetTheta) in uiFstTheta() 335 : uiParameter(uistr::globalTheta) in uiGlobalTheta() 471 : GetBool(uistr::growthLegal) in uiGrowthLegal() 519 : uiParameter(uistr::growthByID) in uiGrowthUser() 712 : GetBool(uistr::migrationLegal) in uiMigrationLegal() 1317 : GetBool(uistr::diseaseLegal) in uiDiseaseLegal() [all …]
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H A D | datamodel_interface.cpp | 33 : GetLong(uistr::lociCount) in uiLociCount() 50 : GetString(uistr::locusName) in uiLocusName() 67 : GetString(uistr::regionName) in uiRegionName() 99 : GetDataType(uistr::dataType) in uiDataType() 127 : GetDoubleVec1d(uistr::gtrRates) in uiGTRRates() 160 : SetGetDouble(uistr::gtrRateAC) in uiGTRRateAC() 181 : SetGetDouble(uistr::gtrRateAG) in uiGTRRateAG() 202 : SetGetDouble(uistr::gtrRateAT) in uiGTRRateAT() 223 : SetGetDouble(uistr::gtrRateCG) in uiGTRRateCG() 499 : SetGetDouble(uistr::TTRatio) in uiTTRatio() [all …]
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H A D | data_interface.cpp | 28 : GetLong(uistr::crossPartitionCount) in uiCrossPartitionCount() 44 : GetLong(uistr::divmigrationPartitionCount) in uiDivMigPartitionCount() 60 : GetString(uistr::divmigrationPartitionName) in uiDivMigPartitionName() 76 : GetLong(uistr::migrationPartitionCount) in uiMigPartitionCount() 92 : GetString(uistr::migrationPartitionName) in uiMigPartitionName() 108 : GetLong(uistr::diseasePartitionCount) in uiDiseasePartitionCount() 124 : GetString(uistr::diseasePartitionName) in uiDiseasePartitionName() 146 : GetLongVec1d(uistr::lociNumbers) in uiLociNumbers() 168 : GetLongVec1d(uistr::regionNumbers) in uiRegionNumbers() 179 : SetGetDouble(uistr::effectivePopSize) in uiRegionEffectivePopSize() [all …]
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H A D | profile_interface.cpp | 29 : SetGetNoval(uistr::allProfilesOn) in uiGlobalProfileOn() 45 : SetGetNoval(uistr::allProfilesOff) in uiGlobalProfileOff() 61 : SetGetNoval(uistr::allProfilesPercentile) in uiGlobalProfilePercentile() 77 : SetGetNoval(uistr::allProfilesFixed) in uiGlobalProfileFixed() 93 : SetGetBool(uistr::profileByID) in uiProfileByID() 130 : SetGetProftype(uistr::profileByForce) in uiProfileByForce() 150 return uistr::profileByForce in Description() 180 : GetUIIdVec1d(uistr::validParamsForForce) in uiValidParamsForOneForce() 206 : GetUIIdVec1d(uistr::validForces) in uiValidForces() 224 : SetGetNoval(uistr::oneForceProfilesOff) in uiForceProfilesOff() [all …]
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H A D | traitmodel_interface.cpp | 23 : GetString(uistr::traitModelName) in uiTraitModelName() 99 : SetRangepair(uistr::addRangeForTraitModel) in uiAddRangeForTraitModel() 120 : SetRangepair(uistr::removeRangeForTraitModel) in uiRemoveRangeForTraitModel() 141 : SetGetLong(uistr::traitModelRangeToPoint) in uiSetTraitModelRangeToPoint() 178 : GetUIIdVec1d(uistr::validMovingLoci) in uiValidMovingLoci() 205 : SetGetNoval(uistr::traitAnalysisFloat) in uiTraitModelFloat() 226 : SetGetNoval(uistr::traitAnalysisJump) in uiTraitModelJump() 247 : SetGetNoval(uistr::traitAnalysisData) in uiTraitModelData() 268 : SetGetNoval(uistr::traitAnalysisPartition) in uiTraitModelPartition()
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H A D | constraint_interface.cpp | 27 : SetGetIndividualParamstatus(uistr::constraintType) in uiParameterStatus() 54 : SetGetNoval(uistr::addParamToGroup) in uiAddParamToGroup() 70 : SetGetNoval(uistr::addParamToNewGroup) in uiAddParamToNewGroup() 86 : SetGetNoval(uistr::removeParamFromGroup) in uiRemoveParamFromGroup() 102 : SetGetGroupParamstatus(uistr::groupConstraintType) in uiGroupParameterStatus() 131 : SetGetLongVec1d(uistr::groupParamList) in uiGroupParameterList() 152 : GetUIIdVec1d(uistr::ungroupedParamsForForce) in uiUngroupedParamsForOneForce() 182 : GetUIIdVec2d(uistr::groupedParamsForForce) in uiGroupedParamsForOneForce()
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/dports/biology/lamarc/lamarc-2.1.8/src/lamarcmenus/ |
H A D | forcesmenus.cpp | 71 uistr::growth, in ForcesMenu() 76 uistr::migration, in ForcesMenu() 100 uistr::disease, in ForcesMenu() 147 return ui.doGetBool(uistr::migration); in IsVisible() 150 return ui.doGetBool(uistr::disease); in IsVisible() 153 return ui.doGetBool(uistr::recombination); in IsVisible() 156 return ui.doGetBool(uistr::growth); in IsVisible() 162 return ui.doGetBool(uistr::regionGamma); in IsVisible() 165 return ui.doGetBool(uistr::expGrowStick); in IsVisible() 171 return ui.doGetBool(uistr::divergence); in IsVisible() [all …]
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H A D | overviewmenus.cpp | 103 uistr::coalescence, in forceName() 104 uistr::disease, in forceName() 105 uistr::growth, in forceName() 106 uistr::migration, in forceName() 107 uistr::recombination, in forceName() 108 uistr::logisticSelection in forceName() 119 uistr::diseaseMaxEvents, in forceMaxEvents() 120 uistr::growthMaxEvents, in forceMaxEvents() 121 uistr::migrationMaxEvents, in forceMaxEvents() 605 uistr::recombinationRate,uistr::recombination, in ForceOverviewMenu() [all …]
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H A D | lamarcmenuitems.cpp | 42 : SetMenuItemNoId(k,myui,uistr::tempInterval) in SetMenuItemTempInterval() 59 : SetMenuItemNoId(k,myui,uistr::hapArranger) in SetMenuItemHapArranger() 69 return ui.doGetBool(uistr::canHapArrange); in IsVisible() 119 return ui.doGetBool(uistr::bayesian); in IsVisible() 170 return (ui.doGetBool(uistr::bayesian) && ui.doGetBool(uistr::useCurveFiles)); in IsVisible() 223 return (ui.doGetBool(uistr::useReclocFiles) && ui.doGetBool(uistr::recombination)); in IsVisible() 292 return ui.doGetBool(uistr::bayesian); in IsVisible() 390 return ui.doGetBool(uistr::bayesian); in IsVisible() 496 return ui.doGetBool(uistr::bayesian); in IsVisible() 526 if (menuKey == uistr::initialSamples) in GetText() [all …]
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H A D | datamodelmenu.cpp | 55 : SetMenuItemId(myKey,myui,uistr::TTRatio,myid) in TTRatioMenuItem() 65 model_type mt = ui.doGetModelType(uistr::dataModel,id); in IsVisible() 86 data_type dt = ui.doGetDataType(uistr::dataType,id); in IsVisible() 96 : SetMenuItemId(myKey,myui,uistr::alpha,myid) in AlphaMenuItem() 157 return title + ui.doGetString(uistr::regionName,id); in Title() 177 return uistr::gtrRates; in GetText() 182 return ui.doGetPrintString(uistr::gtrRates,id); in GetVariableText() 241 return !(ui.doGetBool(uistr::freqsFromData,id)); in IsVisible() 292 return uistr::baseFrequencies; in GetText() 495 long numLoci = ui.doGetLong(uistr::lociCount,id); in MakeOneHandler() [all …]
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H A D | migmenus.cpp | 32 : SetMenuItemId(myKey,myui,uistr::globalMigration, UIId(force_MIG, uiconst::GLOBAL_ID)) in SetAllMigrationsMenuItem() 42 return ui.doGetBool(uistr::migration); in IsVisible() 53 : ToggleMenuItemNoId(key,ui,uistr::fstSetMigration) in SetMigrationsFstMenuItem() 63 return ui.doGetBool(uistr::migration); in IsVisible() 69 : SetMenuItemNoId(myKey,myui,uistr::migrationMaxEvents) in MigrationMaxEventsMenuItem() 79 return ui.doGetBool(uistr::migration); in IsVisible() 87 AddMenuItem(new DisplayOnlyMenuItem(uistr::migration, ui)); in MigrationMenu() 95 uistr::migrationInto, in MigrationMenu() 96 uistr::migrationUser, in MigrationMenu() 97 uistr::migrationPartitionCount, in MigrationMenu() [all …]
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H A D | diseasemenus.cpp | 32 : SetMenuItemId(myKey,myui,uistr::globalDisease, UIId(force_DISEASE, uiconst::GLOBAL_ID)) in SetAllDiseaseRatesMenuItem() 42 return ui.doGetBool(uistr::disease); in IsVisible() 53 : SetMenuItemNoId(myKey,myui,uistr::diseaseMaxEvents) in DiseaseMaxEventsMenuItem() 63 return ui.doGetBool(uistr::disease); in IsVisible() 69 : SetMenuItemNoId(myKey,myui,uistr::diseaseLocation) in DiseaseLocationMenuItem() 79 return ui.doGetBool(uistr::disease); in IsVisible() 90 AddMenuItem(new DisplayOnlyMenuItem(uistr::disease,ui)); in DiseaseMenu() 98 uistr::diseaseInto, in DiseaseMenu() 99 uistr::diseaseByID, in DiseaseMenu() 100 uistr::diseasePartitionCount, in DiseaseMenu() [all …]
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H A D | treesummenus.cpp | 23 : SetMenuItemNoId(myKey,myui,uistr::treeSumInFileName) in SetMenuItemTreeSumInFileName() 32 : SetMenuItemNoId(myKey,myui,uistr::treeSumOutFileName) in SetMenuItemTreeSumOutFileName() 42 return ui.doGetBool(uistr::treeSumInFileEnabled); in IsVisible() 47 return ui.doGetBool(uistr::treeSumOutFileEnabled); in IsVisible() 51 : NewMenu(myui,uistr::treeSumInFileEnabled,menustr::emptyString) in TreeSumInMenu() 53 AddMenuItem(new ToggleMenuItemNoId("X",ui,uistr::treeSumInFileEnabled)); in TreeSumInMenu() 62 : NewMenu(myui,uistr::treeSumOutFileEnabled,menustr::emptyString) in TreeSumOutMenu() 64 AddMenuItem(new ToggleMenuItemNoId("X",ui,uistr::treeSumOutFileEnabled)); in TreeSumOutMenu() 84 return ui.doGetPrintString(uistr::treeSumInFileEnabled,GetId()); in GetVariableText() 89 return ui.doGetPrintString(uistr::treeSumOutFileEnabled,GetId()); in GetVariableText()
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H A D | profilemenus.cpp | 26 AddMenuItem(new ToggleMenuItemNoId("A",ui,uistr::allProfilesOn)); in ProfileMenu() 27 AddMenuItem(new ToggleMenuItemNoId("X",ui,uistr::allProfilesOff)); in ProfileMenu() 28 AddMenuItem(new ToggleMenuItemNoId("P",ui,uistr::allProfilesPercentile)); in ProfileMenu() 29 AddMenuItem(new ToggleMenuItemNoId("F",ui,uistr::allProfilesFixed)); in ProfileMenu() 38 : MenuDisplayGroupBaseImplementation(ui,uistr::profileByForce) in ProfileByForceMenuItemGroup() 55 return ui.doGetUIIdVec1d(uistr::validForces); in GetVisibleIds() 100 AddMenuItem(new ToggleMenuItemId("A",ui,uistr::oneForceProfilesOn,id)); in ProfileMenuForOneForce() 101 AddMenuItem(new ToggleMenuItemId("X",ui,uistr::oneForceProfilesOff,id)); in ProfileMenuForOneForce() 102 AddMenuItem(new ToggleMenuItemId("P",ui,uistr::oneForceProfileType,id)); in ProfileMenuForOneForce() 120 : ToggleMenuItemGroup(ui,uistr::profileByID), m_id(id) in ToggleMenuItemGroupProfiles() [all …]
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H A D | divmigmenus.cpp | 32 : SetMenuItemId(myKey,myui,uistr::globalDivMigration, UIId(force_DIVMIG, uiconst::GLOBAL_ID)) in SetAllDivMigsMenuItem() 42 return ui.doGetBool(uistr::divmigration); in IsVisible() 69 : SetMenuItemNoId(myKey,myui,uistr::divmigrationMaxEvents) in DivMigMaxEventsMenuItem() 79 return ui.doGetBool(uistr::divmigration); in IsVisible() 87 AddMenuItem(new DisplayOnlyMenuItem(uistr::divmigration, ui)); in DivMigMenu() 97 uistr::divmigrationInto, in DivMigMenu() 98 uistr::divmigrationUser, in DivMigMenu() 99 uistr::divmigrationPartitionCount, in DivMigMenu() 100 uistr::divmigration, in DivMigMenu()
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H A D | growthmenus.cpp | 29 : SetMenuItemId(myKey,ui,uistr::globalGrowth, UIId(force_GROW, uiconst::GLOBAL_ID)) in SetAllGrowthMenuItem() 39 return ui.doGetBool(uistr::growth); in IsVisible() 50 : ToggleMenuItemNoId(k,myui,uistr::growthScheme) in ToggleMenuItemGrowthScheme() 63 return ui.doGetBool(uistr::growth); in IsVisible() 70 : ToggleMenuItemNoId(k,myui,uistr::growthType) in ToggleMenuItemGrowthType() 83 return ui.doGetBool(uistr::growth); in IsVisible() 90 : SetMenuItemGroup(myui,uistr::growthByID) in SetMenuItemGrowths() 100 return ui.doGetUIIdVec1d(uistr::validParamsForForce,UIId(force_GROW)); in GetVisibleIds() 108 AddMenuItem(new ToggleMenuItemNoId("X",ui,uistr::growth)); in GrowthMenu()
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H A D | traitmodelmenu.cpp | 66 return ui.doGetUIIdVec1d(uistr::validMovingLoci,UIId()); in GetVisibleIds() 71 vector<UIId> ids = ui.doGetUIIdVec1d(uistr::validMovingLoci, UIId()); in GetHandler() 85 return lamarcmenu::traitModel1 + ui.doGetString(uistr::regionName, id); in GetText() 90 return ui.doGetString(uistr::traitModelName, id); in GetVariableText() 95 vector<UIId> ids = ui.doGetUIIdVec1d(uistr::validMovingLoci, UIId()); in GetKey() 110 AddMenuItem(new DisplayOnlyMenuItem(uistr::traitModelName, ui, m_id)); in SingleTraitModelMenu() 113 AddMenuItem(new ToggleMenuItemId("J", ui, uistr::traitAnalysisJump, m_id)); in SingleTraitModelMenu() 136 return lamarcmenu::traitModel1 + ui.doGetString(uistr::locusName, m_id); in Title() 198 : SetMenuItemId(key, ui, uistr::addRangeForTraitModel, id) in AddRangeToTraitModel() 236 : SetMenuItemId(key, ui, uistr::removeRangeForTraitModel, id) in RemoveRangeFromTraitModel() [all …]
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H A D | priormenus.cpp | 39 : MenuDisplayGroupBaseImplementation(ui,uistr::priorByForce) in PriorByForceMenuItemGroup() 56 return ui.doGetUIIdVec1d(uistr::validForces); in GetVisibleIds() 101 AddMenuItem(new ToggleMenuItemId("U",ui,uistr::useDefaultPriorsForForce,id)); in PriorMenuForOneForce() 121 return (ForceSubMenuItem::IsVisible() && ui.doGetBool(uistr::bayesian)); in IsVisible() 125 : MenuDisplayGroupBaseImplementation(ui,uistr::priorByID), in PriorByParameterMenuItemGroup() 137 return ui.doGetUIIdVec1d(uistr::validParamsForForce,m_id); in GetVisibleIds() 170 AddMenuItem( new ToggleMenuItemId("D",ui,uistr::priorUseDefault,id)); in PriorMenuForOneParameter() 172 AddMenuItem(new ToggleMenuItemId("S",ui,uistr::priorType,id)); in PriorMenuForOneParameter() 173 AddMenuItem(new SetMenuItemId("U",ui,uistr::priorUpperBound,id)); in PriorMenuForOneParameter() 174 AddMenuItem(new SetMenuItemId("L",ui,uistr::priorLowerBound,id)); in PriorMenuForOneParameter() [all …]
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H A D | coalmenus.cpp | 29 : SetMenuItemId(myKey,ui,uistr::globalTheta, UIId(force_COAL, uiconst::GLOBAL_ID)) in SetAllThetasMenuItem() 39 return (ui.doGetLong(uistr::crossPartitionCount) > 1); in IsVisible() 50 : ToggleMenuItemNoId(key,ui,uistr::fstSetTheta) in SetThetasFstMenuItem() 60 return (ui.doGetLong(uistr::crossPartitionCount) > 1); in IsVisible() 66 : SetMenuItemGroup(myui,uistr::userSetTheta) in SetMenuItemThetas() 76 return ui.doGetUIIdVec1d(uistr::validParamsForForce,UIId(force_COAL)); in GetVisibleIds() 90 AddMenuItem(new ToggleMenuItemNoId("W",ui,uistr::wattersonSetTheta)); in CoalescenceMenu()
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H A D | divmenus.cpp | 32 : SetMenuItemGroup(myui,uistr::divergenceEpochBoundaryTime) in SetMenuItemEpochs() 42 return ui.doGetUIIdVec1d(uistr::validParamsForForce,UIId(force_DIVERGENCE)); in GetVisibleIds() 49 ancestor += ui.doGetDescription(uistr::divergenceEpochAncestor,id); in GetExtraText() 52 decendents += ui.doGetDescription(uistr::divergenceEpochDescendents,id); in GetExtraText() 60 s.push_back(ui.doGetPrintString(uistr::divergenceEpochAncestor,id)); in GetExtraVariableText() 61 s.push_back(ui.doGetPrintString(uistr::divergenceEpochDescendents,id)); in GetExtraVariableText() 71 AddMenuItem(new DisplayOnlyMenuItem(uistr::divergence, ui)); in DivergenceMenu()
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H A D | recmenus.cpp | 25 : SetMenuItemNoId(myKey,myui,uistr::recombinationMaxEvents) in RecombineMaxEventsMenuItem() 35 return ui.doGetBool(uistr::recombination); in IsVisible() 39 : SetMenuItemId(myKey,myui,uistr::recombinationRate, UIId(force_REC, uiconst::GLOBAL_ID)) in RecombineRateMenuItem() 49 return ui.doGetBool(uistr::recombination); in IsVisible() 55 AddMenuItem(new ToggleMenuItemNoId("X",ui,uistr::recombination)); in RecombinationMenu()
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/dports/biology/lamarc/lamarc-2.1.8/src/xml/ |
H A D | parsetreetosettings.cpp | 213 uiInterface.doSet(uistr::dataModel,modelName,locusUIId); in DoDLModel() 326 uiInterface.doSet(uistr::freqsFromData,"true",thisId); in DoBaseFrequencies() 364 uiInterface.doSet(uistr::gtrRateAC,strings[0],thisId); in DoGTR() 365 uiInterface.doSet(uistr::gtrRateAG,strings[1],thisId); in DoGTR() 600 uiInterface.doSet(uistr::forceOnOff,"on",forceId); in DoForce() 608 uiInterface.doSet(uistr::growthType,growthType); in DoForce() 615 uiInterface.doSet(uistr::selectType,stype); in DoForce() 797 if(!uiInterface.doGetBool(uistr::bayesian)) in DoForce() 800 uiInterface.doSet(uistr::bayesian,"true"); in DoForce() 834 if(uiInterface.doGetBool(uistr::forceLegal,forceId)) in DoForce() [all …]
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