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Searched refs:uistr (Results 1 – 25 of 338) sorted by relevance

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/dports/biology/lamarc/lamarc-2.1.8/src/ui_interface/
H A Dui_strings.cpp19 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";
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H A Dchainparam_interface.cpp26 : 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()
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H A Duserparam_interface.cpp24 : 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()
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H A Dforce_interface.cpp33 : 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()
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H A Ddatamodel_interface.cpp33 : 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()
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H A Ddata_interface.cpp28 : 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()
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H A Dprofile_interface.cpp29 : 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()
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H A Dtraitmodel_interface.cpp23 : 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()
H A Dconstraint_interface.cpp27 : 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()
/dports/biology/lamarc/lamarc-2.1.8/src/lamarcmenus/
H A Dforcesmenus.cpp71 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()
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H A Doverviewmenus.cpp103 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()
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H A Dlamarcmenuitems.cpp42 : 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()
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H A Ddatamodelmenu.cpp55 : 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()
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H A Dmigmenus.cpp32 : 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()
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H A Ddiseasemenus.cpp32 : 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()
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H A Dtreesummenus.cpp23 : 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()
H A Dprofilemenus.cpp26 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()
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H A Ddivmigmenus.cpp32 : 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()
H A Dgrowthmenus.cpp29 : 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()
H A Dtraitmodelmenu.cpp66 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()
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H A Dpriormenus.cpp39 : 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()
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H A Dcoalmenus.cpp29 : 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()
H A Ddivmenus.cpp32 : 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()
H A Drecmenus.cpp25 : 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()
/dports/biology/lamarc/lamarc-2.1.8/src/xml/
H A Dparsetreetosettings.cpp213 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()
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