 sortie | |
  data | |
   funcgroups | |
    analysis | |
     BoleVolumeCalculator | Corresponds to the clBoleVolumeCalculator class |
     CarbonValueCalculator | Corresponds to the clCarbonValueCalculator class |
     ConditOmegaCalculator | Corresponds to the clConditOmegaCalculator class |
     DimensionAnalysis | Corresponds to the clDimensionAnalysis class |
     FoliarChemistry | Corresponds to the clFoliarChemistry class |
     MerchValueCalculator | Corresponds to the clMerchValueCalculator class |
     PartitionedDBHBiomass | Corresponds to the clPartitionedBiomass class |
     PartitionedHeightBiomass | Corresponds to the clPartitionedBiomass class |
     RipleysKCalculator | Corresponds to the clRipleysKCalculator class |
     StateReporter | Corresponds to the clStateReporter class |
     StormKilledPartitionedDBHBiomass | Corresponds to the clStormKilledPartitionedBiomass class |
     StormKilledPartitionedHeightBiomass | Corresponds to the clStormKilledPartitionedBiomass class |
     TreeAgeCalculator | Corresponds to the clTreeAgeCalculator class |
     VolumeCalculator | Corresponds to the clVolumeCalculator class |
    disperse | |
     DisperseBase | |
     GapSpatialDisperse | Corresponds to the clSpatialDispersal class |
     MastingNonSpatialDisperse | Corresponds to the clMastingNonSpatialDisperse class |
     MastingSpatialDisperse | Corresponds to the clMastingSpatialDisperse class |
     NonGapSpatialDisperse | Corresponds to the clSpatialDispersal class |
     NonSpatialDisperse | Corresponds to the clNonSpatialDispersal class |
     SpatialDisperseBase | Corresponds to the clSpatialDispersal class |
     StochDoubleLogTempDepNeighDisperse | Corresponds to the clStochDoubleLogTempDepNeighDisperse class |
     TemperatureDependentNeighborhoodDisperse | Corresponds to the clTemperatureDependentNeighborhoodDisperse class |
    disturbance | |
     CompetitionHarvest | Corresponds to the clCompetitionHarvest class |
     DensDepInfestation | Corresponds to the clDensDepInfestation class |
     EpisodicMortality | Corresponds to the clDisturbance class |
     GeneralizedHarvestRegime | Corresponds to the clGeneralizedHarvestRegime class |
     Harvest | Corresponds to the clDisturbance class |
     HarvestData | This class encapsulates the data for a single harvest event - being for one timestep, for one cut type |
     HarvestInterface | Corresponds to the clHarvestInterface class |
     InsectInfestation | Corresponds to the clInsectInfestation class |
     RandomBrowse | Corresponds to the clRandomBrowse class |
     SelectionHarvest | Corresponds to the clSelectionHarvest class |
     Storm | Corresponds to the clStorm class |
     StormDamageApplier | Corresponds to the clStormDamageApplier class |
     StormDamageKiller | Corresponds to the clStormKiller class |
     StormDirectKiller | Corresponds to the clStormDirectKiller class |
     Windstorm | Corresponds to the clWindstorm class |
    epiphyticestablishment | |
     EpiphyticEstablishment | Corresponds to the clEpiphyticEstablishment class |
    establishment | |
     ConspecificTreeDensitySeedSurvival | Corresponds to the clDensitySeedSurvival class |
     DensityDependentSeedSurvival | Corresponds to the clDensitySeedSurvival class |
     Establishment | Corresponds to the clEstablishment class |
     GapSubstrateSeedSurvival | Corresponds to the clSubstrateDepSeedSurvival class |
     LightDependentSeedSurvival | Corresponds to the clLightDepSeedSurvival class |
     MicroEstablishment | Corresponds to the clMicroEstablishment class |
     MicrotopographicSubstrateSeedSurvival | Corresponds to the clSubstrateDepSeedSurvival class |
     NoGapSubstrateSeedSurvival | Corresponds to the clSubstrateDepSeedSurvival class |
     ProportionalSeedSurvival | Corresponds to the clGermination class |
     StormLightDependentSeedSurvival | Corresponds to the clLightDepSeedSurvival class |
     SubstrateDepEstablishmentBase | |
    growth | |
     AbsoluteGrowthBALimited | Corresponds to the clAbsoluteGrowth class |
     AbsoluteGrowthRadialLimited | Corresponds to the clAbsoluteGrowth class |
     AbsoluteUnlimited | Corresponds to the clAbsoluteGrowth class |
     AllometricDiam | Corresponds to the clAllometricGrowthIncrementer class |
     AllometricHeight | Corresponds to the clAllometricGrowthIncrementer class |
     BrowsedRelativeGrowth | Corresponds to the clBrowsedRelativeGrowth class |
     ConstantBA | Corresponds to the clConstantBAGrowth class |
     ConstantRadial | Corresponds to the clConstantBAGrowth class |
     DoubleMMRel | Corresponds to the clDoubleMMRelGrowth class |
     LaggedPostHarvestGrowth | Corresponds to the clLaggedPostHarvestGrowth class |
     LinearBiLevel | Corresponds to the clLinearBiLevelGrowth class |
     LogBiLevel | Corresponds to the clLogBiLevelGrowth class |
     Logistic | Corresponds to the clLogisticGrowth class |
     LogisticHeightOnly | Corresponds to the clLogisticGrowth class |
     Lognormal | Corresponds to the clLognormalGrowth class |
     LognormalHeightOnly | Corresponds to the clLognormalGrowth class |
     MichMenNeg | Corresponds to the clMichMenNegGrowth class |
     MichMenPhotoinhibition | Corresponds to the clMichMenPhotoinhibition class |
     PowerHeight | Corresponds to the clPowerHeightGrowth class |
     PRSemiStochDiamOnly | Corresponds to the clPRSemiStochGrowth class |
     PRStormBiLevel | Corresponds to the clPRStormBiLevelGrowth class |
     RelativeGrowthBALimited | Corresponds to the clRelativeGrowth class |
     RelativeGrowthRadialLimited | Corresponds to the clRelativeGrowth class |
     RelativeHeight | Corresponds to the clRelativeGrowth class |
     RelativeUnlimited | Corresponds to the clRelativeGrowth class |
     ShadedLinearGrowth | Corresponds to the clShadedLinearGrowth class |
     ShadedLinearGrowthHeightOnly | Corresponds to the clShadedLinearGrowth class |
     SimpleLinear | Corresponds to the clSimpleLinearGrowth class |
     SimpleLinearHeightOnly | Corresponds to the clSimpleLinearGrowth class |
     SizeDepLogistic | Corresponds to the clSizeDepLogisticGrowth class |
     SizeDepLogisticHeightOnly | Corresponds to the clSizeDepLogisticGrowth class |
     StochasticGap | Corresponds to the clStochasticGapGrowth class |
    light | |
     AverageLight | Corresponds to the clAverageLight class |
     BasalAreaLight | Corresponds to the clBasalAreaLight class |
     ConstantGLI | Corresponds to the clConstantGLI class |
     GapLight | Corresponds to the clGapLight class |
     GLIBase | Corresponds to the class |
     GLILight | Corresponds to the clGLILight class |
     GLIMap | Corresponds to the clGLIMap class |
     GLIPoints | Corresponds to the clGLIPoints class |
     LightFilter | Corresponds to the clLightFilter class |
     QuadratGLILight | Corresponds to the clQuadratGLILight class |
     SailLight | Corresponds to the clSailLight class |
     StormLight | Corresponds to the clStormLight class |
    management | |
     QualityVigorClassifier | Corresponds to the clQualityVigorClassifier class |
    mortality | |
     AggregatedMortality | Corresponds to the clAggregatedMortality class |
     BCMort | Corresponds to the clBCMort class |
     BrowsedStochasticMortality | Corresponds to the clBrowsedStochasticMortality class |
     ClimateCompDepNeighborhoodSurvival | Corresponds to the clClimateCompDepNeighborhoodSurvival class |
     CompetitionMortality | Corresponds to the clCompetitionMort class |
     DensitySelfThinning | Corresponds to the clDensitySelfThinning class |
     DensitySelfThinningGompertz | Corresponds to the clDensitySelfThinningGompertz class |
     ExpResourceMortality | Corresponds to the clExpResourceMortality class |
     GMFMort | Corresponds to the clGMFMort class |
     GrowthResourceMortality | Corresponds to the clResourceMortality class |
     HeightGLIWeibullMortality | Corresponds to the clHeightGLIWeibullMortality class |
     InsectInfestationMortality | Corresponds to the clInsectInfestationMortality class |
     LogisticBiLevelMortality | Corresponds to the clLogisticBiLevelMortality class |
     PostHarvestSkiddingMort | Corresponds to the clPostHarvestSkiddingMort class |
     SelfThinMort | Corresponds to the clSelfThinMort class |
     SenescenceMort | Corresponds to the clSenescenceMort class |
     SizeDependentLogisticMortality | Corresponds to the clSizeDependentLogisticMortality class |
     StochasticBiLevelLightMortality | Corresponds to the clStochasticBiLevelMortality class |
     StochasticMort | Corresponds to the clStochasticMort class |
     SuppressionDurationMort | Corresponds to the clSuppressionDurationMort class |
     TempDepNeighborhoodSurvival | Corresponds to the clTempDependentNeighborhoodSurvival class |
     WeibullSnagMort | Corresponds to the clWeibullSnagMort class |
    mortalityutilities | |
     DeadTreeRemover | Corresponds to the clTreeRemover class |
    nci | |
     CrowdingEffectDefault | This class calculates a crowding effect |
     CrowdingEffectNoSize | This class calculates a crowding effect with no size term |
     CrowdingEffectTempDep | This class calculates a crowding effect using the function: |
     DamageEffectDefault | This returns the damage effect due to storms |
     InfectionEffect | This class calculates an infection effect according to the term:
Pest Effect = a * ln(T) + b
where T is the time in years that an individual tree has been infested, and a and b are parameters |
     InfectionEffectSizeDependent | This class calculates an infection effect according to the term:
Infection Effect = [a * ln(T) + b] * exp(-0.5*[( ((DBH-Xp)/X0) / Xb)^2]
where |
     NCIEffect | This class provides a class for NCI effects with organizing information |
      crowding_effect | Flag values for which crowding effect term is desired |
      damage_effect | Flag values for which damage effect term is desired |
      effectType | Identifier for different types of effects |
      infection_effect | Flag values for which infection effect term is desired |
      nci_term | Flag values for which NCI term is desired |
      nitrogen_effect | Flag values for which nitrogen effect term is desired |
      precipitation_effect | Flag values for which precipitation effect term is desired |
      shading_effect | Flag values for which shading effect term is desired |
      size_effect | Flag values for which size effect term is desired |
      temperature_effect | Flag values for which temperature effect term is desired |
     NCILargerNeighbors | The NCI term is simply a count of sapling and adult neighbors with a larger DBH than the target within a certain radius, subject to a minimum value |
     NCIMasterBase | The base for behaviors using the flexible NCI system allowing the user to choose any combination of multiplicative effects |
     NCIMasterGrowth | Corresponds to the clNCIMasterGrowth class |
     NCIMasterMortality | Corresponds to the clNCIGrowth class |
     NCIMasterQuadratGrowth | Corresponds to the clNCIMasterQuadratGrowth class |
     NCINeighborBA | The NCI term is the sum of BA of neighbors |
     NCITermBARatio | NCIi is calculated using basal area ratio |
     NCITermBARatioDBHDefault | NCIi is calculated using basal area ratio, using a single default value for target tree size |
     NCITermDefault | NCIi is calculated as follows (simplifying the notation):
NCIi = Σ λk((DBHk/q)α/distanceβ)
where:
- we're summing over k = 0 to N neighbors greater than the minimum
neighbor DBH
- α is the neighbor DBH effect parameter
- β is the neighbor distance effect parameter
- DBH is of the target tree, in cm
- q is the DBH divisor parameter
- DBHk is the DBH of the kth neighbor, in meters
- γ is the size sensitivity to NCI parameter
- λk is the NCI lambda parameter for the species
of the kth neighbor
- distance is distance from target to neighbor, in meters
|
     NCITermNCIBARatio | NCIi is calculated as follows (simplifying the notation):
NCIi = Σ λk((DBHk)α/distanceβ)
where:
- we're summing over k = 0 to N neighbors greater than the minimum
neighbor DBH
- α is the neighbor DBH effect parameter
- β is the neighbor distance effect parameter
- DBH is of the target tree, in cm
- DBHk is the DBH of the kth neighbor, in meters
- γ is the size sensitivity to NCI parameter
- λk is the NCI lambda parameter for the species
of the kth neighbor
- distance is distance from target to neighbor, in meters
|
     NCITermNCIBARatioDBHDefault | NCIi is calculated as follows (simplifying the notation):
NCIi = Σ λk((DBHk)α/distanceβ)
where:
- we're summing over k = 0 to N neighbors greater than the minimum
neighbor DBH
- α is the neighbor DBH effect parameter
- β is the neighbor distance effect parameter
- DBH is of the target tree, in cm
- DBHk is the DBH of the kth neighbor, in meters
- γ is the size sensitivity to NCI parameter
- λk is the NCI lambda parameter for the species
of the kth neighbor
- distance is distance from target to neighbor, in meters
|
     NCITermNCITempDepBARatio | NCIi is calculated as follows (simplifying the notation):
NCIi = Σ λk((DBHk)α/distanceβ)
where:
- we're summing over k = 0 to N neighbors greater than the minimum
neighbor DBH
- α is the neighbor DBH effect parameter
- β is the neighbor distance effect parameter
- DBH is of the target tree, in cm
- DBHk is the DBH of the kth neighbor, in meters
- γ is the size sensitivity to NCI parameter
- λk is the NCI lambda parameter for the species
of the kth neighbor
- distance is distance from target to neighbor, in meters
|
     NCITermNCITempDepBARatioDBHDefault | NCIi is calculated as follows (simplifying the notation):
NCIi = Σ λk((DBHk)α/distanceβ)
where:
- we're summing over k = 0 to N neighbors greater than the minimum
neighbor DBH
- α is the neighbor DBH effect parameter
- β is the neighbor distance effect parameter
- DBH is of the target tree, in cm
- DBHk is the DBH of the kth neighbor, in meters
- γ is the size sensitivity to NCI parameter
- λk is the NCI lambda parameter for the species
of the kth neighbor
- distance is distance from target to neighbor, in meters
|
     NCITermWithNeighborDamage | NCIi is calculated as follows (simplifying the notation):
NCIi = Σ η λk((DBHk/q)α/distanceβ)
where:
- we're summing over k = 0 to N neighbors greater than the minimum
neighbor DBH
- η is the storm damage parameter of the target,
depending on the damage status. It’s 1 if the neighbor is undamaged.
- α is the neighbor DBH effect parameter
- β is the neighbor distance effect parameter
- DBH is of the target tree, in cm
- q is the DBH divisor parameter
- DBHk is the DBH of the kth neighbor, in meters
- γ is the size sensitivity to NCI parameter
- λk is the NCI lambda parameter for the species
of the kth neighbor
- distance is distance from target to neighbor, in meters
Note that eta is per target species, not per neighbor (like lambda) |
     NCIWithSeedlings | This is an NCI term which allows seedlings to compete |
     NitrogenEffectGaussian | This class calculates a nitrogen effect according to the term:
Nitrogen Effect = exp(-0.5*((NDEP - X0) / Xb)2)
where: |
     PrecipitationEffectDoubleLogistic | This represents precipitation effect in NCI behaviors calculated with a double logistic function |
     PrecipitationEffectWeibull | This represents the default Weibull precipitation effect in NCI growth |
     ShadingDefault | This represents the default shading effect in NCI growth |
     SizeEffectCompoundExpInf | This represents the default size effect in NCI growth |
     SizeEffectCompoundExponential | This represents the default size effect in NCI growth |
     SizeEffectDefault | This represents the default size effect in NCI growth |
     SizeEffectLowerBounded | This represents the default size effect in NCI growth |
     SizeEffectPowerFunction | This represents the default size effect in NCI growth |
     SizeEffectShiftedLogInf | This represents a size effect in NCI growth that uses a shifted lognormal function |
     SizeEffectShiftedLognormal | This represents a size effect in NCI growth that uses a shifted lognormal function |
     TemperatureEffectDoubleLogistic | This represents temperature effect in NCI behaviors calculated with a double logistic function |
     TemperatureEffectWeibull | This represents the default Weibull temperature effect in NCI behaviors |
    output | |
     DetailedOutput | Corresponds to detailed output |
     ShortOutput | Corresponds to short output |
    planting | |
     Planting | Corresponds to the clPlant class |
     PlantingData | This class encapsulates the data for a single planting event - being for one species, for one timestep |
    seedpredation | |
     FuncResponseSeedPredation | Corresponds to the clFuncResponseSeedPredation class |
     FuncResponseSeedPredationLnk | Corresponds to the clFuncResponseSeedPredation class |
     NeighborhoodSeedPredation | Corresponds to the clNeighborhoodSeedPredation class |
     NeighborhoodSeedPredationLnk | Corresponds to the clNeighborhoodSeedPredation class |
    snagdynamics | |
     SnagDecayClassDynamics | Corresponds to the clSnagDecomp class |
    statechange | |
     PrecipitationClimateChange | Corresponds to the clClimateChange class |
     SeasonalWaterDeficit | Corresponds to the clSeasonalWaterDeficit class |
     TemperatureClimateChange | Corresponds to the clClimateChange class |
    substrate | |
     DetailedSubstrate | Corresponds to the clDetailedSubstrate class |
     Substrate | Corresponds to the clSubstrate class |
    Allometry | This holds all data relating to allometry |
    AnalysisBehaviors | Manages analysis behaviors and data |
    Behavior | Represents a single behavior in the core |
     setupType | How this behavior's setup interface is handled |
    BehaviorInstantiator | Contains information for behavior instantiation |
    BehaviorTypeBase | This class functions as an organizer for model-level behaviors |
    DisperseBehaviors | This is the organizer class for all disperse behaviors |
    DisturbanceBehaviors | This class manages data for disturbance behaviors |
    EpiphyticEstablishmentBehaviors | Manages treefern establishment |
    EstablishmentBehaviors | This is the organizer class for all establishment behaviors |
    Grid | This class represents grids in the core model |
    GridValue | Class for holding the data for a single grid cell |
    GrowthBehaviors | Controls the data relating to growth behaviors |
    LightBehaviors | Manages data for the light behaviors |
    ManagementBehaviors | Manages management behaviors and data |
    MortalityBehaviors | Manages mortality behaviors and data |
    MortalityUtilitiesBehaviors | This is the organizer class for the dead remover behavor |
    OutputBehaviors | Manages output behaviors and data |
    PackageGridValue | Class for holding the data for a single package |
    PlantingBehaviors | Manages planting behaviors and data |
    Plot | Holds clPlot data |
    PlotBehaviors | Plot object |
    SeedPredationBehaviors | This class organizes the seed predation behaviors |
    SnagDynamicsBehaviors | Manages snag dynamics data and behaviors |
    SpeciesSpecific | This class will package together a data member and an array of booleans on which species uses it |
    StateChangeBehaviors | Manages state change behaviors |
    Subplot | This rolls up a set of cell coordinates into a defined subplot |
    SubstrateBehaviors | Manages substrate data and behaviors |
    Tree | Represents a single tree's data |
    TreeBehavior | Holds clTreePopulation data |
    TreeOutputSaveInfo | This collects tree saving information for short output for one tree type |
    TreePopulation | This holds all data relating to the tree population |
    ValidationHelpers | |
   simpletypes | |
    Cell | This class holds a set of grid cell coordinates |
    ComboDisplay | Combines a text description of species/type combos with the actual data, for display in lists |
    DataMember | An object of this class represents a data member from a grid or tree |
    DataMemberData | Abstract class holding data member-based data, such as trees or grid values |
    DetailedGridSettings | Captures the output settings for a single grid |
    DetailedOutputSettings | Base class for detailed output settings |
    DetailedTreeSettings | This class packages together a set of tree settings |
    ModelData | This is a base class for packaging data values with additional information |
    ModelEnum | Packages a data value with other information |
    ModelException | Model exception class |
    ModelFloat | This class packages float values with additional information |
    ModelInt | This class packages integer values with additional data |
    ModelMessage | Structure for message passing |
    ModelString | Packages a String value together with additional data |
    ModelVector | This class packages vector data with other pieces of information important to the model |
    SpeciesTypeCombo | This class allows you to group together a species number and a type number into one object that can be placed in an array or vector or passed as an argument |
  datavisualizer | |
   CarbonValueDataRequest | Produces a table of carbon value results |
   DataFileManager | This class manages a single data file for the data visualizer |
   DataGrapher | Objects of this class can create graphs of various kinds, given data |
   DataRequest | This class is used by the DetailedOutputFileManager class to manage open requests for data |
   DataVisualizerManager | This class takes care of managing data visualization |
   DesktopListener | This class listens for the movement of desktop frames and resizes the desktop as necessary to make sure every part of it is reachable by scrolling |
   DetailedOutputFileManager | Controls the data visualization for a single detailed output file |
   DetailedOutputFileSetupParseHandler | Plugs into the Xerces SAX parser to handle the incoming data when the detailed output setup XML file is parsed |
   DetailedOutputLegend | This extends the legend class and adds some features specific to the viewing of detailed output files - specifically the ability to step through timesteps |
   DetailedOutputTimestepParseHandler | An object of this class will parse detailed output timestep files and pass the data to a DetailedOutputFileManager object |
   FoliarChemistryLineGraphDataRequest | Produces a line graph of foliar chemistry results (one component - i.e |
   FoliarChemistryTableDataRequest | Produces a table of foliar chemistry results |
   GridAllSpeciesHistogramDataRequest | This controls the drawing of a histogram for all species at once for a grid for those grids that display values by species |
   GridDataRequest | Draws a map for a single grid's data member |
   GridHistogramDataRequest | This controls the drawing of a histogram for a single piece of grid information |
   HarvestDataRequest | Produces a table of harvest or mortality episode results |
   HistogramBin | Copied from HistogramBin in JFreeChart by Jelai Wang with some modifications |
   HistogramDataRequest | This controls the drawing of a histogram for a single piece of information |
   Legend | This is an internal frame which displays a color legend for species-based charts |
   LineGraphDataRequest | Creates different types of line graphs for detailed output files |
   MerchValueDataRequest | Produces a table of merchantable timber value results |
   ModelHistogramDataset | This is a hack of the HistogramDataset in JFreeChart |
   ModelInternalFrame | Ensures consistent behavior across graph windows |
   OverviewTableDataRequest | Writes an overview table for a detailed output file (basal area and density for each life history stage) |
   PartitionedBiomassLineGraphDataRequest | Produces a line graph of partitioned biomass results (one component - i.e |
   PartitionedBiomassTableDataRequest | Produces a table of partitioned biomass results |
   RelativeNeighborhoodDensityDataRequest | Produces a line graph of Relative Neighborhood Density grid results |
   RipleysKDataRequest | Produces a line graph of Ripley's K results |
   SeedTableDataRequest | Produces a table of dispersed seeds |
   ShortOutputFileManager | Manages all the data visualization for a single short output file |
   StandTableDataRequest | Writes a stand table for a detailed output file (basal area or density for each life history stage throughout the run) |
   StateVariableTableDataRequest | Produces a table of state variable results |
   StockTableDataRequest | Writes a stock table for a detailed output file |
   StormDataRequest | Produces a table of storm results |
   StormKilledPartitionedBiomassDataRequest | Produces a table of partitioned biomass results |
   TreeListWriter | This class will write a complete tree list for any desired time step |
   TreeMapCrownRadDataRequest | This class manages the data for, and draws, tree maps |
   TreeMapDataRequest | This class manages the data for, and draws, tree maps |
   WindstormDataRequest | Produces a table of windstorm results |
   XYCellRenderer | This class fills in map cell rectangles on a plot |
    CellTooltipGenerator | Provides a more informative tooltip string for cell values |
   XYSimpleCellRenderer | This class fills in map cell rectangles on a plot |
   XYTreeRenderer | A renderer that draws a circle at each data point |
    TreeTooltipGenerator | Provides a more informative tooltip string for cell values |
   XYZDataItem | Represents one (x, y, z) data item for an xyz-series |
   XYZSimpleDataset | A simple implementation of the jorg.jfree.data.xyXYZDataset interface that stores data values in arrays of bool primitives |
  fileops | |
   ModelFileFunctions | This provides common file-reading functions for reading tab-delimited files |
   TarArchive | The TarArchive class implements the concept of a tar archive |
   Tarball | Functions for working with tarballs (.gz.tar files) |
  gui | |
   behaviorsetup | |
    AllometryFunctionEditor | Makes a window for editing tree allometry functions |
    AllometryParameterEdit | This class displays the dialog for editing Allometry parameters, with a button for editing the function choices |
    BehaviorParameterDisplay | Packages all the information needed for displaying a behavior's parameters |
    DefaultBehaviorParameterEdit | This class displays the default dialog for editing the parameters for a single behavior |
    EnhancedTable | Provides extensions and customizations for JTable |
    EnhancedTableWindow | Interface for classes wishing to use the EnhancedTable class |
    HarvestInterfaceSetup | This is a window allowing setup of the Harvest Interface behavior |
     FileColumnsChooser | Dialog for choosing new file columns |
    NCIEffectsEditor | Makes a window for editing NCI functions |
    NCIParameterEdit | This class displays the dialog for editing NCI parameters, with a button for editing the function choices |
    ParameterEdit | Window used to trigger the parameter editing process |
    QuickScrollingPanel | This class creates a JPanel that scrolls at a normal speed through a JScrollPane |
    StormParameterEdit | This class displays the dialog for editing Storm parameters, with a button for scheduling storms |
    TableData | For packaging header data in a typesafe way |
   components | |
    FileOpenFilter | This provides a file filter which shows all potential SORTIE file types: .xml, .hvr, .txt, and .gz.tar files |
    ModelFileChooser | Manages directories for SORTIE |
    ModelIcon | Creates different icons needed by the model |
    MultilineLabel | Renders a multi-line "JLabel" |
    OKCancelButtonPanel | A panel containing OK, Cancel, and Help buttons |
    OutFileFilter | File filter for short output files |
    OutputFileFilter | This provides a filter for output files - .out and .gz.tar files |
    SORTIEComboBox< T > | Improves the basic combo box by allowing the popup area to be bigger than the box itself |
    SortieFont | The common font for all GUI elements |
    SortieLabel | Wrapper class for labels which set them up with the correct font |
    SortieMenuItem | This class wraps the JMenuItem class to set some things we always want to set in the constructor as a convenience |
    TextFileFilter | File filter for text files |
    XMLFileFilter | This filters to only XML files for file choosers |
   harvepplant | |
    Diam10Edit | For editing initial diam10s for planting |
    DisplayWindowBase | Provides a base class with common methods for display of current specifications for harvest, episodic mortality, and planting |
     windowType | |
    EditWindowBase | Base class for windows for disturbance and planting event editing |
    EpisodicEventsMouseListener | Class for interpreting mouse clicks on the chart for selecting cells for episodic event editing |
    HarvestDisplayWindow | Displays harvest events and allows for editing |
    HarvestEdit | Window for harvest editing |
    MortalityEpisodeDisplayWindow | Displays episodic events and allows for editing |
    MortalityEpisodeEdit | Window for mortality episode editing |
    PlantEdit | Window for planting editing |
    PlantingDisplayWindow | Displays planting events and allows for editing |
   BatchSetup | Window for working with batch files |
   ChartFrameInfo | This class bundles information and methods handy when dealing with chart frames |
   DetailedOutputDeadTreeSetup | Window used by the user to set up detailed output output options for dead trees |
   DetailedOutputFileCopy | This window will rename a detailed output file |
   DetailedOutputFileFilter | This provides a filter for data files - .gz.tar files |
   DetailedOutputFileSetup | Window that the user uses to set up detailed output options |
   DetailedOutputGridSetup | Window the user uses to set up detailed output options for grids |
   DetailedOutputTreeSetup | Window used by the user to set up detailed output tree output options |
   DisplayBehaviorComboEdit | Displays an edit window for editing the tree species/type combos to which a single behavior applies |
   ErrorGUI | This class handles all error message writing |
   GridCellEditor | This is a simple dialog box which will allow editing of grid cell resolution for a single grid |
   GridSetup | Displays grid settings for editing |
   GridValueEditor | Window for editing grid values in a spreadsheet-like format |
   GUIManager | The GUI manager provides all behind-the-scenes functionality for the Main Window |
   MainWindow | Main application window |
   MainWindowStateSetter | The purpose of this class is to control the states of the main window - all the enabling and disabling, etc |
   ManageTreeMap | Allows management of tree maps |
   ModelFlowSetup | Allows users to make changes to the model flow and behavior order |
    BehaviorPackager | Class for tracking behaviors |
    DisplayBehaviorComboEdit | Displays an edit window for editing the tree species/type combos to which a single behavior applies |
    DisplayBehaviorEdit | Displays the edit window for editing behavior order |
    DisplayComboEdit | Displays the edit window for editing behavior flow for a tree species/ type combo |
   OutputSetup | Window used by the user to start setting up run output options |
   ScheduledStormInfo | Holds data for scheduled storms grouped together |
   ScheduledStormSetup | This is a window allowing scheduling of storms for the storm behavior |
   ShortOutputFileSetup | Window used by the user to set up summary (short) output files |
   SizeClassEditor | Displays dialog for entering size class data |
   SubplotEdit | Window for editing subplot information |
   TreeSpeciesSetup | Dialog allowing the user to set up basic tree information |
    CopySpeciesEditor | This class creates an interface for copying species |
  parfile | |
   Interface | Interface between the Java GUI and the C++ application core |
   Model | Main class that's called to start the application |
   ParFileHelpers | |
   SwingWorker | |
    ThreadVar | Class to maintain reference to current worker thread under separate synchronization control |
  sax | |
   ParameterFileParser | SAX parameter file parse handler |
   SaxParseTools | |
  tools | |
   batchoutput | |
    BatchDetailedOutput | This class allows the user to set up batch extraction of data from detailed output files |
    BatchOptionsDialog | This class collects options needed for a data request for batch writing |
    ChartInfo | |
    FileAnalysisBackgroundProcess | This class performs the file analysis of output files in a background thread so that it can be reported on with the progress bar or canceled |
    FileChoosingWindow | Shows the window for choosing a set of detailed output files - step 1 of the wizard |
    FileWritingBackgroundProcess | This class triggers the writing of the chosen output in a background thread so that it can be reported on with the progress bar or canceled |
    OptionChoosingWindow | Shows the window for choosing save options - step 2 of the wizard |
    PopupListener | |
    ProgressChangeListener | This class listens for published progress reports and updates the progress dialog accordingly |
    ProgressDialog | A small progress dialog to inform the user of file option extraction progress |
   parfileupdater | |
    AnalysisBehaviors | Manages analysis behaviors and data |
    Behavior | Represents a single behavior in the core |
    DisperseBehaviors | This is the organizer class for all disperse behaviors |
    DisturbanceBehaviors | |
    EpiphyticEstablishmentBehaviors | |
    EstablishmentBehaviors | |
    GroupBase | |
    GrowthBehaviors | |
    LightBehaviors | |
    ManagementBehaviors | |
    ModelData | This is a base class for packaging data values with additional information |
    MortalityBehaviors | |
    MortalityUtilitiesBehaviors | |
    OldParFileParser | SAX parameter file parse handler |
    OutputBehaviors | |
    PlantingBehaviors | |
    SeedPredationBehaviors | |
    SnagDynamicsBehaviors | |
    StateChangeBehaviors | |
    SubstrateBehaviors | |