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SORTIE Java Interface
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| This class is used by the DetailedOutputFileManager class to manage open requests for data | |
| Produces a table of carbon value results | |
| Produces a line graph of foliar chemistry results (one component - i.e | |
| Produces a table of foliar chemistry results | |
| This controls the drawing of a histogram for all species at once for a grid for those grids that display values by species | |
| Draws a map for a single grid's data member | |
| This controls the drawing of a histogram for a single piece of grid information | |
| Produces a table of harvest or mortality episode results | |
| This controls the drawing of a histogram for a single piece of information | |
| Creates different types of line graphs for detailed output files | |
| Produces a table of merchantable timber value results | |
| Writes an overview table for a detailed output file (basal area and density for each life history stage) | |
| Produces a line graph of partitioned biomass results (one component - i.e | |
| Produces a table of partitioned biomass results | |
| Produces a line graph of Relative Neighborhood Density grid results | |
| Produces a line graph of Ripley's K results | |
| Produces a table of dispersed seeds | |
| Writes a stand table for a detailed output file (basal area or density for each life history stage throughout the run) | |
| Produces a table of state variable results | |
| Writes a stock table for a detailed output file | |
| Produces a table of storm results | |
| Produces a table of partitioned biomass results | |
| This class will write a complete tree list for any desired time step | |
| This class manages the data for, and draws, tree maps | |
| This class manages the data for, and draws, tree maps | |
| Produces a table of windstorm results | |
| Writes an overview table for a detailed output file (basal area and density for each life history stage) | |
| Writes a stand table for a detailed output file (basal area or density for each life history stage throughout the run) | |
| Displays an edit window for editing the tree species/type combos to which a single behavior applies | |
| Displays grid settings for editing | |
| Window for editing grid values in a spreadsheet-like format | |
| This class allows the user to set up batch extraction of data from detailed output files | |
| Represents a single behavior in the core | |
| This holds all data relating to allometry | |
| Corresponds to the clBoleVolumeCalculator class | |
| Corresponds to the clCarbonValueCalculator class | |
| Corresponds to the clConditOmegaCalculator class | |
| Corresponds to the clDimensionAnalysis class | |
| Corresponds to the clFoliarChemistry class | |
| Corresponds to the clMerchValueCalculator class | |
| Corresponds to the clPartitionedBiomass class | |
| Corresponds to the clPartitionedBiomass class | |
| Corresponds to the clRipleysKCalculator class | |
| Corresponds to the clStateReporter class | |
| Corresponds to the clStormKilledPartitionedBiomass class | |
| Corresponds to the clStormKilledPartitionedBiomass class | |
| Corresponds to the clTreeAgeCalculator class | |
| Corresponds to the clVolumeCalculator class | |
| Corresponds to the clMastingNonSpatialDisperse class | |
| Corresponds to the clNonSpatialDispersal class | |
| Corresponds to the clSpatialDispersal class | |
| Corresponds to the clSpatialDispersal class | |
| Corresponds to the clMastingSpatialDisperse class | |
| Corresponds to the clSpatialDispersal class | |
| Corresponds to the clTemperatureDependentNeighborhoodDisperse class | |
| Corresponds to the clStochDoubleLogTempDepNeighDisperse class | |
| Corresponds to the clCompetitionHarvest class | |
| Corresponds to the clDensDepInfestation class | |
| Corresponds to the clDisturbance class | |
| Corresponds to the clGeneralizedHarvestRegime class | |
| Corresponds to the clDisturbance class | |
| Corresponds to the clHarvestInterface class | |
| Corresponds to the clInsectInfestation class | |
| Corresponds to the clRandomBrowse class | |
| Corresponds to the clSelectionHarvest class | |
| Corresponds to the clStorm class | |
| Corresponds to the clStormDamageApplier class | |
| Corresponds to the clStormKiller class | |
| Corresponds to the clStormDirectKiller class | |
| Corresponds to the clWindstorm class | |
| Corresponds to the clEpiphyticEstablishment class | |
| Corresponds to the clDensitySeedSurvival class | |
| Corresponds to the clDensitySeedSurvival class | |
| Corresponds to the clEstablishment class | |
| Corresponds to the clLightDepSeedSurvival class | |
| Corresponds to the clMicroEstablishment class | |
| Corresponds to the clSubstrateDepSeedSurvival class | |
| Corresponds to the clGermination class | |
| Corresponds to the clLightDepSeedSurvival class | |
| Corresponds to the clSubstrateDepSeedSurvival class | |
| Corresponds to the clSubstrateDepSeedSurvival class | |
| Corresponds to the clAbsoluteGrowth class | |
| Corresponds to the clAbsoluteGrowth class | |
| Corresponds to the clAbsoluteGrowth class | |
| Corresponds to the clAllometricGrowthIncrementer class | |
| Corresponds to the clAllometricGrowthIncrementer class | |
| Corresponds to the clBrowsedRelativeGrowth class | |
| Corresponds to the clConstantBAGrowth class | |
| Corresponds to the clConstantBAGrowth class | |
| Corresponds to the clDoubleMMRelGrowth class | |
| Corresponds to the clLaggedPostHarvestGrowth class | |
| Corresponds to the clLinearBiLevelGrowth class | |
| Corresponds to the clLogBiLevelGrowth class | |
| Corresponds to the clLogisticGrowth class | |
| Corresponds to the clLogisticGrowth class | |
| Corresponds to the clLognormalGrowth class | |
| Corresponds to the clLognormalGrowth class | |
| Corresponds to the clMichMenNegGrowth class | |
| Corresponds to the clMichMenPhotoinhibition class | |
| Corresponds to the clPowerHeightGrowth class | |
| Corresponds to the clPRSemiStochGrowth class | |
| Corresponds to the clPRStormBiLevelGrowth class | |
| Corresponds to the clRelativeGrowth class | |
| Corresponds to the clRelativeGrowth class | |
| Corresponds to the clRelativeGrowth class | |
| Corresponds to the clRelativeGrowth class | |
| Corresponds to the clShadedLinearGrowth class | |
| Corresponds to the clShadedLinearGrowth class | |
| Corresponds to the clSimpleLinearGrowth class | |
| Corresponds to the clSimpleLinearGrowth class | |
| Corresponds to the clSizeDepLogisticGrowth class | |
| Corresponds to the clSizeDepLogisticGrowth class | |
| Corresponds to the clStochasticGapGrowth class | |
| Corresponds to the clAverageLight class | |
| Corresponds to the clBasalAreaLight class | |
| Corresponds to the clConstantGLI class | |
| Corresponds to the clGapLight class | |
| Corresponds to the class | |
| Corresponds to the clGLILight class | |
| Corresponds to the clGLIMap class | |
| Corresponds to the clGLIPoints class | |
| Corresponds to the clQuadratGLILight class | |
| Corresponds to the clSailLight class | |
| Corresponds to the clLightFilter class | |
| Corresponds to the clStormLight class | |
| Corresponds to the clQualityVigorClassifier class | |
| Corresponds to the clAggregatedMortality class | |
| Corresponds to the clBCMort class | |
| Corresponds to the clBrowsedStochasticMortality class | |
| Corresponds to the clClimateCompDepNeighborhoodSurvival class | |
| Corresponds to the clCompetitionMort class | |
| Corresponds to the clDensitySelfThinning class | |
| Corresponds to the clDensitySelfThinningGompertz class | |
| Corresponds to the clExpResourceMortality class | |
| Corresponds to the clGMFMort class | |
| Corresponds to the clResourceMortality class | |
| Corresponds to the clHeightGLIWeibullMortality class | |
| Corresponds to the clInsectInfestationMortality class | |
| Corresponds to the clLogisticBiLevelMortality class | |
| Corresponds to the clPostHarvestSkiddingMort class | |
| Corresponds to the clSelfThinMort class | |
| Corresponds to the clSenescenceMort class | |
| Corresponds to the clSizeDependentLogisticMortality class | |
| Corresponds to the clStochasticBiLevelMortality class | |
| Corresponds to the clStochasticMort class | |
| Corresponds to the clSuppressionDurationMort class | |
| Corresponds to the clTempDependentNeighborhoodSurvival class | |
| Corresponds to the clWeibullSnagMort class | |
| Corresponds to the clTreeRemover class | |
| This class calculates a crowding effect | |
| This class calculates a crowding effect with no size term | |
| This class calculates a crowding effect using the function: | |
| This returns the damage effect due to storms | |
| This class calculates an infection effect according to the term:
where T is the time in years that an individual tree has been infested, and a and b are parameters | |
| This class calculates an infection effect according to the term:
where | |
| 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 | |
| The base for behaviors using the flexible NCI system allowing the user to choose any combination of multiplicative effects | |
| Corresponds to the clNCIMasterGrowth class | |
| Corresponds to the clNCIGrowth class | |
| Corresponds to the clNCIMasterQuadratGrowth class | |
| The NCI term is the sum of BA of neighbors | |
| NCIi is calculated using basal area ratio | |
| NCIi is calculated using basal area ratio, using a single default value for target tree size | |
NCIi is calculated as follows (simplifying the notation):
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NCIi is calculated as follows (simplifying the notation):
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NCIi is calculated as follows (simplifying the notation):
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NCIi is calculated as follows (simplifying the notation):
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NCIi is calculated as follows (simplifying the notation):
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NCIi is calculated as follows (simplifying the notation):
Note that eta is per target species, not per neighbor (like lambda) | |
| This is an NCI term which allows seedlings to compete | |
| This class calculates a nitrogen effect according to the term:
where: | |
| This represents precipitation effect in NCI behaviors calculated with a double logistic function | |
| This represents the default Weibull precipitation effect in NCI growth | |
| This represents the default shading effect in NCI growth | |
| This represents the default size effect in NCI growth | |
| This represents the default size effect in NCI growth | |
| This represents the default size effect in NCI growth | |
| This represents the default size effect in NCI growth | |
| This represents a size effect in NCI growth that uses a shifted lognormal function | |
| This represents temperature effect in NCI behaviors calculated with a double logistic function | |
| This represents the default Weibull temperature effect in NCI behaviors | |
| Corresponds to detailed output | |
| Corresponds to short output | |
| Corresponds to the clPlant class | |
| Holds clPlot data | |
| Corresponds to the clFuncResponseSeedPredation class | |
| Corresponds to the clFuncResponseSeedPredation class | |
| Corresponds to the clNeighborhoodSeedPredation class | |
| Corresponds to the clNeighborhoodSeedPredation class | |
| Corresponds to the clSnagDecomp class | |
| Corresponds to the clClimateChange class | |
| Corresponds to the clSeasonalWaterDeficit class | |
| Corresponds to the clClimateChange class | |
| Corresponds to the clDetailedSubstrate class | |
| Corresponds to the clSubstrate class | |
| Holds clTreePopulation data | |
| Represents a single behavior in the core | |
| Contains information for behavior instantiation | |
| Class for tracking behaviors | |
| Packages all the information needed for displaying a behavior's parameters | |
| This class functions as an organizer for model-level behaviors | |
| Manages analysis behaviors and data | |
| This is the organizer class for all disperse behaviors | |
| This class manages data for disturbance behaviors | |
| Manages treefern establishment | |
| This is the organizer class for all establishment behaviors | |
| Controls the data relating to growth behaviors | |
| Manages data for the light behaviors | |
| Manages management behaviors and data | |
| Manages mortality behaviors and data | |
| This is the organizer class for the dead remover behavor | |
| Manages output behaviors and data | |
| Manages planting behaviors and data | |
| Plot object | |
| This class organizes the seed predation behaviors | |
| Manages snag dynamics data and behaviors | |
| Manages state change behaviors | |
| Manages substrate data and behaviors | |
| This holds all data relating to the tree population | |
| This class holds a set of grid cell coordinates | |
| This class bundles information and methods handy when dealing with chart frames | |
| Class for interpreting mouse clicks on the chart for selecting cells for episodic event editing | |
| An object of this class represents a data member from a grid or tree | |
| Captures the output settings for a single grid | |
| This class packages together a set of tree settings | |
| This is a hack of the HistogramDataset in JFreeChart | |
| A renderer that draws a circle at each data point | |
| Combines a text description of species/type combos with the actual data, for display in lists | |
| 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 | |
| Flag values for which crowding effect term is desired | |
| Flag values for which damage effect term is desired | |
| This class manages a single data file for the data visualizer | |
| Controls the data visualization for a single detailed output file | |
| Manages all the data visualization for a single short output file | |
| Objects of this class can create graphs of various kinds, given data | |
| Abstract class holding data member-based data, such as trees or grid values | |
| Class for holding the data for a single grid cell | |
| Class for holding the data for a single package | |
| Represents a single tree's data | |
| This class takes care of managing data visualization | |
| Base class for detailed output settings | |
| Captures the output settings for a single grid | |
| This class packages together a set of tree settings | |
| Identifier for different types of effects | |
| Interface for classes wishing to use the EnhancedTable class | |
| Makes a window for editing tree allometry functions | |
| This class displays the dialog for editing Allometry parameters, with a button for editing the function choices | |
| This class displays the default dialog for editing the parameters for a single behavior | |
| This class displays the dialog for editing NCI parameters, with a button for editing the function choices | |
| This class displays the dialog for editing Storm parameters, with a button for scheduling storms | |
| Window for editing grid values in a spreadsheet-like format | |
| This class handles all error message writing | |
| This provides a file filter which shows all potential SORTIE file types: .xml, .hvr, .txt, and .gz.tar files | |
| File filter for short output files | |
| This provides a filter for output files - .out and .gz.tar files | |
| File filter for text files | |
| This filters to only XML files for file choosers | |
| This provides a filter for data files - .gz.tar files | |
| Provides extensions and customizations for JTable | |
| This class represents grids in the core model | |
| Manages analysis behaviors and data | |
| This is the organizer class for all disperse behaviors | |
| The GUI manager provides all behind-the-scenes functionality for the Main Window | |
| This class encapsulates the data for a single harvest event - being for one timestep, for one cut type | |
| Copied from HistogramBin in JFreeChart by Jelai Wang with some modifications | |
| Flag values for which infection effect term is desired | |
| Interface between the Java GUI and the C++ application core | |
| The purpose of this class is to control the states of the main window - all the enabling and disabling, etc | |
| Main class that's called to start the application | |
| This is a base class for packaging data values with additional information | |
| Packages a data value with other information | |
| This class packages float values with additional information | |
| This class packages integer values with additional data | |
| Packages a String value together with additional data | |
| This class packages vector data with other pieces of information important to the model | |
| This is a base class for packaging data values with additional information | |
| This provides common file-reading functions for reading tab-delimited files | |
| Structure for message passing | |
| Class for interpreting mouse clicks on the chart for selecting cells for episodic event editing | |
| Class for interpreting mouse clicks on the chart for selecting cells for episodic event editing | |
| Flag values for which NCI term is desired | |
| This class provides a class for NCI effects with organizing information | |
| Flag values for which nitrogen effect term is desired | |
| The TarArchive class implements the concept of a tar archive | |
| This class encapsulates the data for a single planting event - being for one species, for one timestep | |
| Flag values for which precipitation effect term is desired | |
| Holds data for scheduled storms grouped together | |
| How this behavior's setup interface is handled | |
| Flag values for which shading effect term is desired | |
| Flag values for which size effect term is desired | |
| This class will package together a data member and an array of booleans on which species uses it | |
| 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 | |
| This rolls up a set of cell coordinates into a defined subplot | |
| 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 | |
| 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 | |
| For packaging header data in a typesafe way | |
| Functions for working with tarballs (.gz.tar files) | |
| Flag values for which temperature effect term is desired | |
| Class to maintain reference to current worker thread under separate synchronization control | |
| Model exception class | |
| This collects tree saving information for short output for one tree type | |
| Main application window | |
| Represents one (x, y, z) data item for an xyz-series | |
| This is a hack of the HistogramDataset in JFreeChart | |
| This class fills in map cell rectangles on a plot | |
| This class fills in map cell rectangles on a plot | |
| A renderer that draws a circle at each data point | |
| A simple implementation of the jorg.jfree.data.xyXYZDataset interface that stores data values in arrays of bool primitives | |
| 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 | |
| This extends the legend class and adds some features specific to the viewing of detailed output files - specifically the ability to step through timesteps | |
| This controls the drawing of a histogram for all species at once for a grid for those grids that display values by species | |
| This controls the drawing of a histogram for a single piece of grid information | |
| This controls the drawing of a histogram for a single piece of information | |
| This is an internal frame which displays a color legend for species-based charts | |
| This extends the legend class and adds some features specific to the viewing of detailed output files - specifically the ability to step through timesteps | |
| Writes a stock table for a detailed output file | |
| This class manages the data for, and draws, tree maps | |
| This class manages the data for, and draws, tree maps | |
| Window for working with batch files | |
| Makes a window for editing tree allometry functions | |
| This class displays the dialog for editing Allometry parameters, with a button for editing the function choices | |
| This class displays the default dialog for editing the parameters for a single behavior | |
| Provides extensions and customizations for JTable | |
| This is a window allowing setup of the Harvest Interface behavior | |
| Dialog for choosing new file columns | |
| Makes a window for editing NCI functions | |
| This class displays the dialog for editing NCI parameters, with a button for editing the function choices | |
| Window used to trigger the parameter editing process | |
| This class displays the dialog for editing Storm parameters, with a button for scheduling storms | |
| Window used by the user to set up detailed output output options for dead trees | |
| This window will rename a detailed output file | |
| Window that the user uses to set up detailed output options | |
| Window the user uses to set up detailed output options for grids | |
| Window used by the user to set up detailed output tree output options | |
| This is a simple dialog box which will allow editing of grid cell resolution for a single grid | |
| For editing initial diam10s for planting | |
| Provides a base class with common methods for display of current specifications for harvest, episodic mortality, and planting | |
| Displays harvest events and allows for editing | |
| Displays episodic events and allows for editing | |
| Displays planting events and allows for editing | |
| Base class for windows for disturbance and planting event editing | |
| Window for harvest editing | |
| Window for mortality episode editing | |
| Window for planting editing | |
| Displays harvest events and allows for editing | |
| Window for harvest editing | |
| Displays episodic events and allows for editing | |
| Window for mortality episode editing | |
| Window for planting editing | |
| Displays planting events and allows for editing | |
| Main application window | |
| Allows management of tree maps | |
| Allows users to make changes to the model flow and behavior order | |
| Displays an edit window for editing the tree species/type combos to which a single behavior applies | |
| Displays the edit window for editing behavior order | |
| Displays the edit window for editing behavior flow for a tree species/ type combo | |
| Window used by the user to start setting up run output options | |
| This is a window allowing scheduling of storms for the storm behavior | |
| Window used by the user to set up summary (short) output files | |
| Displays dialog for entering size class data | |
| Window for editing subplot information | |
| Dialog allowing the user to set up basic tree information | |
| This class creates an interface for copying species | |
| This class collects options needed for a data request for batch writing | |
| Shows the window for choosing a set of detailed output files - step 1 of the wizard | |
| Shows the window for choosing save options - step 2 of the wizard | |
| A small progress dialog to inform the user of file option extraction progress | |
| Plugs into the Xerces SAX parser to handle the incoming data when the detailed output setup XML file is parsed | |
| An object of this class will parse detailed output timestep files and pass the data to a DetailedOutputFileManager object | |
| SAX parameter file parse handler | |
| SAX parameter file parse handler | |
| The common font for all GUI elements | |
| Creates different icons needed by the model | |
| Main application window | |
| This is a hack of the HistogramDataset in JFreeChart | |
| Improves the basic combo box by allowing the popup area to be bigger than the box itself | |
| Window for working with batch files | |
| Makes a window for editing tree allometry functions | |
| This class displays the dialog for editing Allometry parameters, with a button for editing the function choices | |
| This class displays the default dialog for editing the parameters for a single behavior | |
| This is a window allowing setup of the Harvest Interface behavior | |
| Dialog for choosing new file columns | |
| Makes a window for editing NCI functions | |
| This class displays the dialog for editing NCI parameters, with a button for editing the function choices | |
| Window used to trigger the parameter editing process | |
| This class displays the dialog for editing Storm parameters, with a button for scheduling storms | |
| Window used by the user to set up detailed output output options for dead trees | |
| Window that the user uses to set up detailed output options | |
| Window the user uses to set up detailed output options for grids | |
| Window used by the user to set up detailed output tree output options | |
| Displays an edit window for editing the tree species/type combos to which a single behavior applies | |
| This is a simple dialog box which will allow editing of grid cell resolution for a single grid | |
| Displays grid settings for editing | |
| Window for editing grid values in a spreadsheet-like format | |
| For editing initial diam10s for planting | |
| Provides a base class with common methods for display of current specifications for harvest, episodic mortality, and planting | |
| Base class for windows for disturbance and planting event editing | |
| Allows management of tree maps | |
| Allows users to make changes to the model flow and behavior order | |
| Displays an edit window for editing the tree species/type combos to which a single behavior applies | |
| Displays the edit window for editing behavior order | |
| Displays the edit window for editing behavior flow for a tree species/ type combo | |
| Window used by the user to start setting up run output options | |
| This is a window allowing scheduling of storms for the storm behavior | |
| Window used by the user to set up summary (short) output files | |
| Displays dialog for entering size class data | |
| Window for editing subplot information | |
| Dialog allowing the user to set up basic tree information | |
| This class creates an interface for copying species | |
| This class collects options needed for a data request for batch writing | |
| Shows the window for choosing a set of detailed output files - step 1 of the wizard | |
| Shows the window for choosing save options - step 2 of the wizard | |
| A small progress dialog to inform the user of file option extraction progress | |
| Manages directories for SORTIE | |
| This window will rename a detailed output file | |
| Main application window | |
| This is an internal frame which displays a color legend for species-based charts | |
| Ensures consistent behavior across graph windows | |
| Wrapper class for labels which set them up with the correct font | |
| This class wraps the JMenuItem class to set some things we always want to set in the constructor as a convenience | |
| This class creates a JPanel that scrolls at a normal speed through a JScrollPane | |
| A panel containing OK, Cancel, and Help buttons | |
| Provides extensions and customizations for JTable | |
| Renders a multi-line "JLabel" | |
| This class listens for published progress reports and updates the progress dialog accordingly | |
| This class creates a JPanel that scrolls at a normal speed through a JScrollPane | |
| Allows users to make changes to the model flow and behavior order | |
| This class fills in map cell rectangles on a plot | |
| This class fills in map cell rectangles on a plot | |
| A renderer that draws a circle at each data point | |
| A simple implementation of the jorg.jfree.data.xyXYZDataset interface that stores data values in arrays of bool primitives | |
| Provides a more informative tooltip string for cell values | |
| Provides a more informative tooltip string for cell values |
1.8.2