src/ui_interface/ui_strings.cpp

// $Id: ui_strings.cpp,v 1.102 2012/03/23 20:33:37 ewalkup Exp $

/*
  Copyright 2002  Mary Kuhner, Jon Yamato, and Joseph Felsenstein

  This software is distributed free of charge for non-commercial use
  and is copyrighted.  Of course, we do not guarantee that the software
  works, and are not responsible for any damage you may cause or have.
*/

#include "ui_strings.h"
#include <string>

using std::string;

// Strings assigned here should be defined in ui_strings.h as
// public static const string members of class uistr.

const string uistr::TTRatio         = "TT Ratio";
const string uistr::addParamToGroup = "Add a parameter to an existing or new group";
const string uistr::addParamToNewGroup = "Add a parameter to a new group";
const string uistr::addRangeForTraitModel = "Allow a range of sites for this trait";
const string uistr::allProfilesOff  = "Turn OFF Profiling for ALL parameters";
const string uistr::allProfilesOn   = "Turn ON  Profiling for ALL parameters";
const string uistr::allProfilesPercentile = "Set all profiling to Percentile";
const string uistr::allProfilesFixed      = "Set all profiling to Fixed";
const string uistr::allStr          = "all";
const string uistr::alpha           = "Percentage stepwise mutations";
const string uistr::argFilePrefix   = "Prefix to use for all ARG output files";
const string uistr::autoCorrelation = "Auto-Correlation";
const string uistr::baseFrequencies = "Base Frequencies (A C G T)";
const string uistr::baseFrequencyA  = "Relative Base Frequency of Adenine ";
const string uistr::baseFrequencyC  = "Relative Base Frequency of Cytosine";
const string uistr::baseFrequencyG  = "Relative Base Frequency of Guanine ";
const string uistr::baseFrequencyT  = "Relative Base Frequency of Thymine ";
const string uistr::bayesArranger   = "Bayesian rearranger frequency";
const string uistr::bayesian        = "Perform Bayesian or Likelihood analysis";
const string uistr::canHapArrange   = "Haplotype Arrangement allowed";
const string uistr::categoryCount   = "Number of Categories";
const string uistr::categoryPair    = "Category (Probability, Rate)";
const string uistr::categoryProbability     = "Relative Category Probability";
const string uistr::categoryRate    = "Relative Category Rate";
const string uistr::coalescence     = "Coalescence";
const string uistr::coalescenceLegal  = "Coalescence legal for this data set ";
const string uistr::coalescenceMaxEvents = "Maximum number of coalescence events";
const string uistr::coalescenceStartMethodByID= "Method for calcualting starting coalescence for";
const string uistr::constraintByForce = "Constraint tables for ";
const string uistr::constraintType = "Constraint for this parameter";
const string uistr::crossPartitionCount= "Number of cross partitions";
const string uistr::curveFilePrefix = "Prefix to use for all Bayesian curvefiles";
const string uistr::dataFileName    = "Input data file name";
const string uistr::dataModel       = "Data Model";
const string uistr::dataModelReport = "Data Model Report";
const string uistr::dataType        = "Datatype for this region";
const string uistr::defaultStr      = "default";
const string uistr::disease         = "Disease";
const string uistr::diseaseByID     = "Disease mutation rate to ";
const string uistr::diseaseByID2    = " from ";
const string uistr::diseaseInto     = "Disease mutation rate into ";
const string uistr::diseaseLegal    = "Disease legal for this data set ";
const string uistr::diseaseLocation = "Disease site ";
const string uistr::diseaseMaxEvents= "Maximum number of disease events";
const string uistr::diseasePartitionCount= "Number of disease partitions ";
const string uistr::diseasePartitionName= "Name of disease partition ";
const string uistr::diseasePartitionNames= "Names of disease partitions ";
const string uistr::divergence      = "Divergence";
const string uistr::divergenceEpoch = "Epoch";
const string uistr::divergenceEpochAncestor = "Ancestor";
const string uistr::divergenceEpochDescendent = "Descendent";
const string uistr::divergenceEpochDescendents = "Descendents";
const string uistr::divergenceEpochCount= "Number of divergence epochs";
const string uistr::divergenceEpochName= "Name of divergence epoch";
const string uistr::divergenceEpochNames= "Names of divergence epochs";
const string uistr::divergenceEpochBoundaryTime= "Boundary Time";
const string uistr::divergenceLegal = "Divergence legal using this data set ";
const string uistr::divmigration       = "Migration (in the presence of divergence)";
const string uistr::divmigrationByID   = "Rate of migrants into ";
const string uistr::divmigrationByID2  = " originating from ";
const string uistr::divmigrationInto   = "Migrating into ";
const string uistr::divmigrationLegal  = "Migration legal using this data set ";
const string uistr::divmigrationMaxEvents = "Maximum number of migration event";
const string uistr::divmigrationPartitionCount= "Number of migration groups";
const string uistr::divmigrationPartitionName= "Name of migration group ";
const string uistr::divmigrationPartitionNames= "Names of migration groups ";
const string uistr::divmigrationUser="User never sees: uistr::divmigrationUser string";
const string uistr::dropArranger    = "Topology rearranger frequency";
const string uistr::effectivePopSize= "Effective population size";
const string uistr::epochSizeArranger= "Epoch size rearranger frequency";
const string uistr::expGrowStick    = "Exponential Growth via stick";
const string uistr::finalChains     = "Number of chains (final)";
const string uistr::finalDiscard    = "Number of samples to discard (final burn-in)";
const string uistr::finalInterval   = "Interval between recorded items (final)";
const string uistr::finalSamples    = "Number of recorded genealogies (final)";
const string uistr::finalSamplesBayes = "Number of recorded parameter sets (final)";
const string uistr::forceLegal      = "Is a force legal";
const string uistr::forceName       = "Name of force";
const string uistr::forceOnOff      = "Force turned on?";
const string uistr::forceVector     = "Force vector";
const string uistr::freqsFromData   = "Base frequencies computed from data";
const string uistr::fstSetMigration = "Use FST estimate for migration rates";
const string uistr::fstSetTheta     = "Use FST estimate for thetas";
const string uistr::globalDisease   = "Single disease starting estimate for all data";
const string uistr::globalGrowth    = "Single growth starting estimate for all data";
const string uistr::globalLogisticSelectionCoefficient = "Single log. sel. coeff. starting estimate for all data";
const string uistr::globalMigration = "Single migration starting estimate for all data";
const string uistr::globalDivMigration = "Single migration starting value for all data";
const string uistr::globalTheta     = "Single theta starting estimate for all data";
const string uistr::groupConstraintType = "Constraint type for this group.";
const string uistr::groupParamList  = "List of parameters to constrain together.";
const string uistr::groupedParamsForForce = "Ids of valid grouped params for force.";
const string uistr::growth          = "Growth estimation";
const string uistr::growthByID      = "Growth rate for";
const string uistr::growthLegal     = "Growth legal for this data set ";
const string uistr::growthMaxEvents = "Maximum number of growth events";
const string uistr::growthRate      = "Growth";
const string uistr::growthScheme    = "Type of Growth";
const string uistr::growthType      = "Growth implemented via";
const string uistr::gtrRateAC       = "GTR rates AC";
const string uistr::gtrRateAG       = "GTR rates AG";
const string uistr::gtrRateAT       = "GTR rates AT";
const string uistr::gtrRateCG       = "GTR rates CG";
const string uistr::gtrRateCT       = "GTR rates CT";
const string uistr::gtrRateGT       = "GTR rates GT";
const string uistr::gtrRates        = "GTR rates [AC AG AT CG CT GT]";
const string uistr::hapArranger     = "Haplotype rearranger frequency";
const string uistr::heatedChain     = "Relative temperature for search ";
const string uistr::heatedChainCount= "Number of Simultaneous Searches (Heating)";
const string uistr::heatedChains    = "Relative Temperatures of Simultaneous Searches (Heating)";
const string uistr::initialChains   = "Number of chains (initial)";
const string uistr::initialDiscard  = "Number of samples to discard (initial burn-in) ";
const string uistr::initialInterval = "Interval between recorded items (initial)";
const string uistr::initialSamples  = "Number of recorded genealogies (initial)";
const string uistr::initialSamplesBayes  = "Number of recorded parameter sets (initial)";
const string uistr::lociCount       = "Number of segments for region";
const string uistr::lociNumbers     = "List of segment numbers";
const string uistr::locusArranger   = "Trait Location rearranger frequency (for mapping)";
const string uistr::locusName       = "Segment name";
const string uistr::logSelectStick  = "Stochastic selection.";
const string uistr::logisticSelection = "Est. of logistic selection coeff.";
const string uistr::logisticSelectionCoefficient = "Starting selection coeff. (\"s\")";
const string uistr::logisticSelectionLegal = "Logistic selection legal for this data set";
const string uistr::logisticSelectionMaxEvents = "Maximum number of logistic selection events";
const string uistr::manyArgFiles    = "Write out ALL sampled ARGs from last chain";
const string uistr::mapFilePrefix   = "Prefix to use for all Mapping information files";
const string uistr::maxEvents       = "Maximum number of events";
const string uistr::migration       = "Migration";
const string uistr::migrationByID   = "Migration rate into ";
const string uistr::migrationByID2  = " from ";
const string uistr::migrationInto   = "Migration into ";
const string uistr::migrationLegal  = "Migration legal for this data set ";
const string uistr::migrationMaxEvents = "Maximum number of migration events";
const string uistr::migrationPartitionCount= "Number of migration partitions";
const string uistr::migrationPartitionName= "Name of migration partition ";
const string uistr::migrationPartitionNames= "Names of migration partitions";
const string uistr::migrationUser="User never sees: uistr::migrationUser string";
const string uistr::muRate          = "MuRate";
const string uistr::newickTreeFilePrefix = "Prefix to use for all Newick Tree files";
const string uistr::normalization   = "Normalization";
const string uistr::oneForceProfileType = "Profile type for ";
const string uistr::oneForceProfilesOff = "Turn OFF profiles for ";
const string uistr::oneForceProfilesOn  = "Turn ON  profiles for ";
const string uistr::optimizeAlpha   = "Optimize the multi-step:single-step ratio after each chain";
const string uistr::paramName       = "Name of parameter";
const string uistr::paramVector     = "Parameter vector";
const string uistr::perBaseErrorRate= "Per-base error rate";
const string uistr::plotPost        = "Show plots";
const string uistr::priorByForce    = "Bayesian priors for ";
const string uistr::priorByID       = "Prior settings for ";
const string uistr::priorLowerBound = "Lower bound of the prior";
const string uistr::priorType       = "Shape of the prior";
const string uistr::priorUpperBound = "Upper bound of the prior";
const string uistr::priorUseDefault = "Use the default prior for this force";
const string uistr::probhapArranger = "Trait haplotypes rearranger frequency";
const string uistr::profileByForce  = "Profile tables for ";
const string uistr::profileByID     = "Profile";
const string uistr::profileprefix   = "prefix for profile output (beta test)";
const string uistr::profiles        = "Calculate profile tables";
const string uistr::progress        = "Verbosity of progress reports";
const string uistr::randomSeed      = "Random seed (closest 4n+1)";
const string uistr::rateCategories  = "Rate Categories";
const string uistr::recRate         = "RecRate";
const string uistr::reclocFilePrefix= "Prefix to use for all Recloc files";
const string uistr::recombination   = "Recombination";
const string uistr::recombinationLegal     = "Recombination legal for this data set ";
const string uistr::recombinationMaxEvents = "Maximum number of recombination events";
const string uistr::recombinationRate   = "Starting recombination rate";
const string uistr::regGammaShape = "Scaled shape parameter (\"alpha\")";
const string uistr::regionCount     = "Number of regions";
const string uistr::regionGamma     = "Gamma (mu rate varies over regions)";
const string uistr::regionGammaLegal = "Gamma over regions legal for this data set ";
const string uistr::regionGammaShape= "Starting scaled shape parameter (\"alpha\")";
const string uistr::regionName      = "Region name";
const string uistr::regionNumbers   = "List of region numbers";
const string uistr::relativeMuRate  = "Relative mutation rate";
#ifdef LAMARC_NEW_FEATURE_RELATIVE_SAMPLING
const string uistr::relativeSampleRate  = "Relative parameter change proposal rate";
#endif
const string uistr::removeParamFromGroup = "Remove a parameter from its group";
const string uistr::removeRangeForTraitModel = "Disallow a range of sites for this trait";
const string uistr::replicates      = "Number of replicates";
const string uistr::resultsFileName = "Name of output results file";
const string uistr::selectType      = "Selection implemented via";
const string uistr::setOldSeedFromClock= "Random seed from earlier run";
const string uistr::simulateData    = "Simulate new data for this segment (destroying provided data!)";
const string uistr::sizeArranger    = "Tree-size rearranger frequency";
const string uistr::startValue      = "Initial starting value";
const string uistr::startValueMethod = "Method for calculating starting value";
const string uistr::stairArranger    = "Stair arranger frequency";
const string uistr::systemClock     = "Use system clock to set random seed";
const string uistr::tempAdapt       = "Adjust temperatures automatically during run";
const string uistr::tempInterval    = "Swap interval for different temperatures";
const string uistr::theta           = "Theta";
const string uistr::traceFilePrefix = "Prefix to use for all Tracer files";
const string uistr::traitAnalysisData = "Use this trait as data only";
const string uistr::traitAnalysisFloat = "Map this trait after collecting trees ('float')";
const string uistr::traitAnalysisJump = "Map this trait while collecting trees ('jump')";
const string uistr::traitAnalysisPartition = "Partition your data into sub-populations using this trait";
const string uistr::traitModelName  = "Trait name";
const string uistr::traitModelRangeToPoint  = "Place this trait at a single site";
const string uistr::treeSumInFileEnabled  = "Reading of tree summary file";
const string uistr::treeSumInFileName     = "Name of input tree summary file";
const string uistr::treeSumOutFileEnabled = "Writing of tree summary file";
const string uistr::treeSumOutFileName    = "Name of output tree summary file";
const string uistr::trueValue       = "The TRUTH, string never seen by users";
const string uistr::ungroupedParamsForForce = "Ids of valid ungrouped params for force.";
const string uistr::useArgFiles     = "Write out ARG at end of last chain";
const string uistr::useCurveFiles   = "Write Bayesian results to individual files";
const string uistr::useDefaultPriorsForForce = "Use default priors for all parameters for ";
const string uistr::useGlobalDataModelForAll = "Use default data model for all regions/segments";
const string uistr::useGlobalDataModelForOne = "Use default data model for this region/segment";
const string uistr::useNewickTreeFiles = "Write the best Newick Trees to files";
const string uistr::useOldSeedFromClock= "Restore random seed from earlier run";
const string uistr::useReclocFiles  = "Write recombination locations to files";
const string uistr::useTraceFiles   = "Write Tracer output to files";
const string uistr::userSetTheta    = "Theta value for";
const string uistr::validForces     = "Ids of valid forces";
const string uistr::validMovingLoci = "Ids of valid moving segments";
const string uistr::validParamsForForce  = "Ids of valid parameters for force ";
const string uistr::verbosity       = "Verbosity level of output file";
const string uistr::wattersonSetTheta = "Use Watterson's estimate for thetas";
const string uistr::xmlOutFileName  = "Name of menu-modified version of input file";
const string uistr::xmlReportFileName="Name for XML output file. (Beta test)";
const string uistr::zilchArranger   = "Do-nothing rearranger frequency";

//____________________________________________________________________________________