Lines Matching refs:uistr
213 uiInterface.doSet(uistr::dataModel,modelName,locusUIId); in DoDLModel()
225 DoOptionalElement(modelElement,xmlstr::XML_TAG_TTRATIO,uistr::TTRatio,locusUIId); in DoDLModel()
227 DoOptionalElement(modelElement,xmlstr::XML_TAG_NORMALIZE,uistr::normalization,locusUIId); in DoDLModel()
236 …DoOptionalElement(modelElement,xmlstr::XML_TAG_PER_BASE_ERROR_RATE,uistr::perBaseErrorRate,locusUI… in DoDLModel()
238 DoOptionalElement(modelElement,xmlstr::XML_TAG_ALPHA,uistr::alpha,locusUIId); in DoDLModel()
240 DoOptionalElement(modelElement,xmlstr::XML_TAG_ISOPT,uistr::optimizeAlpha,locusUIId); in DoDLModel()
251 DoOptionalElement(modelElement,xmlstr::XML_TAG_RELATIVE_MURATE,uistr::relativeMuRate,locusUIId); in DoDLModel()
257 …DoOptionalElement(categoriesElement,xmlstr::XML_TAG_NUM_CATEGORIES,uistr::categoryCount,locusUIId); in DoCategories()
258 …DoOptionalElement(categoriesElement,xmlstr::XML_TAG_AUTOCORRELATION,uistr::autoCorrelation,locusUI… in DoCategories()
266 long catCount = uiInterface.doGetLong(uistr::categoryCount,locusUIId); in DoCategories()
284 uiInterface.doSet(uistr::categoryRate,strings[index],innerId); in DoCategories()
290 long catCount = uiInterface.doGetLong(uistr::categoryCount,locusUIId); in DoCategories()
308 uiInterface.doSet(uistr::categoryProbability,strings[index],innerId); in DoCategories()
326 uiInterface.doSet(uistr::freqsFromData,"true",thisId); in DoBaseFrequencies()
336 uiInterface.doSet(uistr::baseFrequencyA,strings[0],thisId); in DoBaseFrequencies()
337 uiInterface.doSet(uistr::baseFrequencyC,strings[1],thisId); in DoBaseFrequencies()
338 uiInterface.doSet(uistr::baseFrequencyG,strings[2],thisId); in DoBaseFrequencies()
339 uiInterface.doSet(uistr::baseFrequencyT,strings[3],thisId); in DoBaseFrequencies()
364 uiInterface.doSet(uistr::gtrRateAC,strings[0],thisId); in DoGTR()
365 uiInterface.doSet(uistr::gtrRateAG,strings[1],thisId); in DoGTR()
366 uiInterface.doSet(uistr::gtrRateAT,strings[2],thisId); in DoGTR()
367 uiInterface.doSet(uistr::gtrRateCG,strings[3],thisId); in DoGTR()
368 uiInterface.doSet(uistr::gtrRateCT,strings[4],thisId); in DoGTR()
369 uiInterface.doSet(uistr::gtrRateGT,strings[5],thisId); in DoGTR()
384 DoOptionalElement(chainsElement,xmlstr::XML_TAG_REPLICATES,uistr::replicates); in DoChainParams()
390 DoOptionalElement(initialChainElement,xmlstr::XML_TAG_NUMBER,uistr::initialChains); in DoChainParams()
391 DoOptionalElement(initialChainElement,xmlstr::XML_TAG_SAMPLES,uistr::initialSamples); in DoChainParams()
392 DoOptionalElement(initialChainElement,xmlstr::XML_TAG_INTERVAL,uistr::initialInterval); in DoChainParams()
393 DoOptionalElement(initialChainElement,xmlstr::XML_TAG_DISCARD,uistr::initialDiscard); in DoChainParams()
400 DoOptionalElement(finalChainElement,xmlstr::XML_TAG_NUMBER,uistr::finalChains); in DoChainParams()
401 DoOptionalElement(finalChainElement,xmlstr::XML_TAG_SAMPLES,uistr::finalSamples); in DoChainParams()
402 DoOptionalElement(finalChainElement,xmlstr::XML_TAG_INTERVAL,uistr::finalInterval); in DoChainParams()
403 DoOptionalElement(finalChainElement,xmlstr::XML_TAG_DISCARD,uistr::finalDiscard); in DoChainParams()
418 DoOptionalElement(heatingElement,xmlstr::XML_TAG_HEATING_STRATEGY,uistr::tempAdapt); in DoChainParams()
424 DoOptionalElement(chainsElement,xmlstr::XML_TAG_BAYESIAN_ANALYSIS,uistr::bayesian); in DoChainParams()
429 DoOptionalElement(strategyElement,xmlstr::XML_TAG_RESIMULATING,uistr::dropArranger); in DoChainParams()
431 DoOptionalElement(strategyElement,xmlstr::XML_TAG_TREESIZE,uistr::sizeArranger); in DoChainParams()
432 DoOptionalElement(strategyElement,xmlstr::XML_TAG_STAIRARRANGER,uistr::stairArranger); in DoChainParams()
433 DoOptionalElement(strategyElement,xmlstr::XML_TAG_HAPLOTYPING,uistr::hapArranger); in DoChainParams()
434 DoOptionalElement(strategyElement,xmlstr::XML_TAG_BAYESIAN,uistr::bayesArranger); in DoChainParams()
435 … DoOptionalElement(strategyElement,xmlstr::XML_TAG_EPOCHSIZEARRANGER,uistr::epochSizeArranger); in DoChainParams()
452 uiInterface.doSet(uistr::heatedChainCount,ToString(temperatures.size())); in DoTemperatures()
455 uiInterface.doSet(uistr::heatedChain,temperatures[index],UIId(index)); in DoTemperatures()
468 uiInterface.doSet(uistr::tempInterval,values[values.size()-1]); in DoSwapInterval()
496 DoOptionalElement(formatElement,xmlstr::XML_TAG_SEED,uistr::randomSeed); in DoSeedParams()
497 DoOptionalElement(formatElement,xmlstr::XML_TAG_SEED_FROM_CLOCK,uistr::setOldSeedFromClock); in DoSeedParams()
503 DoOptionalElement(formatElement,xmlstr::XML_TAG_VERBOSITY,uistr::verbosity); in DoUserParams()
504 DoOptionalElement(formatElement,xmlstr::XML_TAG_PROGRESS_REPORTS,uistr::progress); in DoUserParams()
510 DoOptionalElement(plottingElement,xmlstr::XML_TAG_POSTERIOR,uistr::plotPost); in DoUserParams()
514 DoOptionalElement(formatElement,xmlstr::XML_TAG_RESULTS_FILE,uistr::resultsFileName); in DoUserParams()
517 DoOptionalElement(formatElement,xmlstr::XML_TAG_OLD_SUMMARY_FILE,uistr::treeSumInFileName); in DoUserParams()
518 DoOptionalElement(formatElement,xmlstr::XML_TAG_IN_SUMMARY_FILE,uistr::treeSumInFileName); in DoUserParams()
519 DoOptionalElement(formatElement,xmlstr::XML_TAG_OUT_SUMMARY_FILE,uistr::treeSumOutFileName); in DoUserParams()
520 DoOptionalElement(formatElement,xmlstr::XML_TAG_USE_IN_SUMMARY,uistr::treeSumInFileEnabled); in DoUserParams()
521 DoOptionalElement(formatElement,xmlstr::XML_TAG_USE_OUT_SUMMARY,uistr::treeSumOutFileEnabled); in DoUserParams()
523 DoOptionalElement(formatElement,xmlstr::XML_TAG_ARGFILE_PREFIX,uistr::argFilePrefix); in DoUserParams()
524 DoOptionalElement(formatElement,xmlstr::XML_TAG_USE_ARGFILES,uistr::useArgFiles); in DoUserParams()
525 DoOptionalElement(formatElement,xmlstr::XML_TAG_MANY_ARGFILES,uistr::manyArgFiles); in DoUserParams()
527 …DoOptionalElement(formatElement,xmlstr::XML_TAG_NEWICKTREEFILE_PREFIX,uistr::newickTreeFilePrefix); in DoUserParams()
528 DoOptionalElement(formatElement,xmlstr::XML_TAG_USE_NEWICKTREEFILE,uistr::useNewickTreeFiles); in DoUserParams()
531 DoOptionalElement(formatElement,xmlstr::XML_TAG_USE_CURVEFILES,uistr::useCurveFiles); in DoUserParams()
532 DoOptionalElement(formatElement,xmlstr::XML_TAG_CURVEFILE_PREFIX,uistr::curveFilePrefix); in DoUserParams()
533 DoOptionalElement(formatElement,xmlstr::XML_TAG_PROFILE_PREFIX,uistr::profileprefix); in DoUserParams()
534 DoOptionalElement(formatElement,xmlstr::XML_TAG_USE_RECLOCFILE,uistr::useReclocFiles); in DoUserParams()
535 DoOptionalElement(formatElement,xmlstr::XML_TAG_RECLOCFILE_PREFIX,uistr::reclocFilePrefix); in DoUserParams()
536 DoOptionalElement(formatElement,xmlstr::XML_TAG_USE_TRACEFILE,uistr::useTraceFiles); in DoUserParams()
537 DoOptionalElement(formatElement,xmlstr::XML_TAG_TRACEFILE_PREFIX,uistr::traceFilePrefix); in DoUserParams()
540 DoOptionalElement(formatElement,xmlstr::XML_TAG_OUT_XML_FILE,uistr::xmlOutFileName); in DoUserParams()
541 DoOptionalElement(formatElement,xmlstr::XML_TAG_REPORT_XML_FILE,uistr::xmlReportFileName); in DoUserParams()
596 uiInterface.doSet(uistr::forceOnOff,forceOnOff,forceId); in DoForce()
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()
802 double bayesFreq = uiInterface.doGetDouble(uistr::bayesArranger); in DoForce()
803 double resimFreq = uiInterface.doGetDouble(uistr::dropArranger); in DoForce()
805 uiInterface.doSet(uistr::epochSizeArranger,ToString(epochFreq)); in DoForce()
834 if(uiInterface.doGetBool(uistr::forceLegal,forceId)) in DoForce()
836 DoOptionalElement(forceElement,xmlstr::XML_TAG_MAX_EVENTS,uistr::maxEvents,forceId); in DoForce()
837 … DoOptionalElement(forceElement,xmlstr::XML_TAG_DISEASELOCATION,uistr::diseaseLocation,forceId); in DoForce()
937 uiInterface.doSet(uistr::startValue,values[index],id); in DoStartValuesAndMethods()
938 uiInterface.doSet(uistr::startValueMethod,ToString(method_USER),id); in DoStartValuesAndMethods()
949 uiInterface.doSet(uistr::startValueMethod,methods[index],id); in DoStartValuesAndMethods()
972 uiInterface.doSet(uistr::startValue,values[index],id); in DoStartValuesAndMethods()
979 uiInterface.doSet(uistr::startValueMethod,methods[index],id); in DoStartValuesAndMethods()
994 = uiInterface.doGetMethodType(uistr::startValueMethod,UIId(thisForce,index)); in DoStartValuesAndMethods()
1015 uiInterface.doSet(uistr::startValue,values[index],id); in DoStartValuesAndMethods()
1036 uiInterface.doSet(uistr::startValueMethod,methods[index],id); in DoStartValuesAndMethods()
1051 …method_type culprit = uiInterface.doGetMethodType(uistr::startValueMethod,UIId(forceId.GetForceTyp… in DoStartValuesAndMethods()
1079 uiInterface.doSet(uistr::trueValue,values[index],id); in DoTrueValues()
1110 uiInterface.doSet(uistr::profileByID,"true",localId); in DoProfiles()
1114 uiInterface.doSet(uistr::profileByID,"true",localId); in DoProfiles()
1117 uiInterface.doSet(uistr::profileByID,"false",localId); in DoProfiles()
1123 uiInterface.doSet(uistr::profileByForce,"fixed",forceId); in DoProfiles()
1127 uiInterface.doSet(uistr::profileByForce,"percentile",forceId); in DoProfiles()
1157 uiInterface.doSet(uistr::constraintType,ToString(constraints[index].Status()) ,localID); in DoConstraints()
1184 uiInterface.doSet(uistr::groupParamList, indicesString, localID); in DoGroup()
1185 uiInterface.doSet(uistr::groupConstraintType, constraintType, localID); in DoGroup()
1217 …if ((!CaselessStrCmp(paramName, uistr::defaultStr)) && (!CaselessStrCmp(paramName, uistr::allStr))) in DoPrior()
1228 uiInterface.doSet(uistr::priorType, priorTypeString, localId); in DoPrior()
1235 uiInterface.doSet(uistr::priorLowerBound, lowerString, localId); in DoPrior()
1240 uiInterface.doSet(uistr::priorUpperBound, upperString, localId); in DoPrior()
1249 uiInterface.doSet(uistr::priorUpperBound, upperString, localId); in DoPrior()
1254 uiInterface.doSet(uistr::priorLowerBound, lowerString, localId); in DoPrior()
1264 uiInterface.doSet(uistr::relativeSampleRate,rateString,localId); in DoPrior()