| javawrapper.Allometry | This holds all data relating to allometry |
| javawrapper.AllometryFunctionEditor | Makes a window for editing tree allometry functions |
| javawrapper.AnalysisBehaviors | Manages analysis behaviors and data |
| javawrapper.BatchFileParser | SAX batch file parse handler |
| javawrapper.BatchParFile | Encapsulates a parameter file and the number of times to run it |
| javawrapper.BatchSetup | Window for working with batch files |
| javawrapper.Behavior | Represents a single behavior in the core |
| javawrapper.BehaviorTypeBase | This class functions as an organizer for model-level behaviors |
| datavisualizer.CarbonValueDataRequest | Produces a table of carbon value results |
| javawrapper.Cell | This class holds a set of grid cell coordinates |
| javawrapper.ComboBoxRenderer | This limits values displayed in the file choices combo box to 50 characters (the last 50, so filenames are displayed) |
| javawrapper.ComboDisplay | Combines a text description of species/type combos with the actual data, for display in lists |
| javawrapper.CutRange | This class defines a cut range for a harvest event |
| datavisualizer.DataFileFilter | This provides a filter for data files - .out, .xml, and .gz files |
| uihelpers.DataFileFilter | This provides a filter for data files - .out, .xml, and .gz files |
| datavisualizer.DataFileManager | This class manages a single data file for the data visualizer |
| datavisualizer.DataGrapher | Objects of this class can create graphs of various kinds, given data |
| javawrapper.DataMember | An object of this class represents a data member from a grid or tree |
| javawrapper.DataMemberData | Abstract class holding data member-based data, such as trees or grid values |
| datavisualizer.DataRequest | This class is used by the DetailedOutputFileManager class to manage open requests for data |
| javawrapper.DataVisualizerManager | This class takes care of managing data visualization |
| datavisualizer.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 |
| javawrapper.DetailedGridSettings | Captures the output settings for a single grid |
| javawrapper.DetailedOutputDeadTreeSetup | Window used by the user to set up detailed output output options for dead trees |
| datavisualizer.DetailedOutputFileManager | Controls the data visualization for a single detailed output file |
| javawrapper.DetailedOutputFileSetup | Window that the user uses to set up detailed output options |
| javawrapper.DetailedOutputFileSetup_this_windowAdapter | Triggers refresh of save information on window focus |
| datavisualizer.DetailedOutputFileSetupParseHandler | Plugs into the Xerces SAX parser to handle the incoming data when the detailed output setup XML file is parsed |
| javawrapper.DetailedOutputGridRenderer | This renders choices in a JList so that, if they have a prepended "(p)" string, it is not shown to the user |
| javawrapper.DetailedOutputGridSetup | Window the user uses to set up detailed output options for grids |
| datavisualizer.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 |
| javawrapper.DetailedOutputSettings | Base class for detailed output settings |
| datavisualizer.DetailedOutputTimestepParseHandler | An object of this class will parse detailed output timestep files and pass the data to a DetailedOutputFileManager object |
| javawrapper.DetailedOutputTreeSetup | Window used by the user to set up detailed output tree output options |
| javawrapper.DetailedTreeSettings | This class packages together a set of tree settings |
| javawrapper.Diam10Edit | For editing initial diam10s for planting |
| javawrapper.DisperseBehaviors | This is the organizer class for all disperse behaviors |
| javawrapper.DisplayBehaviorComboEdit | Displays an edit window for editing the tree species/type combos to which a single behavior applies |
| javawrapper.DisplayParameters | Displays a window with parameter data for the user to edit |
| javawrapper.DisturbanceBehaviors | This class manages data for disturbance behaviors |
| javawrapper.EnhancedTable | Provides extensions and customizations for JTable |
| javawrapper.EnhancedTableWindow | Interface for classes wishing to use the EnhancedTable class |
| javawrapper.EpiphyticEstablishmentBehaviors | Manages treefern establishment |
| javawrapper.EpisodicEventsEdit | Base class for windows for episodic event editing |
| javawrapper.EpisodicEventsMouseListener | Class for interpreting mouse clicks on the chart for selecting cells for episodic event editing |
| javawrapper.EpisodicEventsWindow | Displays episodic events and allows for editing |
| javawrapper.ErrorGUI | This class handles all error message writing |
| javawrapper.EstablishmentBehaviors | This is the organizer class for all establishment behaviors |
| uihelpers.FileOpenFilter | This provides a file filter which shows all potential SORTIE file types: .xml, .hvr, .txt, and .gz.tar files |
| datavisualizer.FoliarChemistryLineGraphDataRequest | Produces a line graph of foliar chemistry results (one component - i.e |
| datavisualizer.FoliarChemistryTableDataRequest | Produces a table of foliar chemistry results |
| datavisualizer.GrayscaleListener | Performs the action when the checkbox for using logarithmic axis is checked on a histogram |
| javawrapper.Grid | This class represents grids in the core model |
| datavisualizer.GridAllSpeciesHistogramDataRequest | This controls the drawing of a histogram for all species at once for a grid for those grids that display values by species |
| datavisualizer.GridDataRequest | Draws a map for a single grid's data member |
| datavisualizer.GridHistogramDataRequest | This controls the drawing of a histogram for a single piece of grid information |
| javawrapper.GridSetup | Displays grid settings for editing |
| javawrapper.GridValue | Class for holding the data for a single grid cell |
| javawrapper.GridValueEditor | Window for editing grid values in a spreadsheet-like format |
| javawrapper.GrowthBehaviors | Controls the data relating to growth behaviors |
| javawrapper.GUIManager | The GUI manager provides all behind-the-scenes functionality for the Main Window |
| javawrapper.HarvestData | This class encapsulates the data for a single harvest event - being for one timestep, for one cut type |
| datavisualizer.HarvestDataRequest | Produces a table of harvest or mortality episode results |
| javawrapper.HarvestEdit | Window for harvest editing |
| javawrapper.HarvestInterfaceSetup | This is a window allowing setup of the Harvest Interface behavior |
| javawrapper.HarvestInterfaceSetup.FileColumnsChooser | Dialog for choosing new file columns |
| datavisualizer.HistogramBin | Copied from HistogramBin in JFreeChart by Jelai Wang with some modifications |
| datavisualizer.HistogramDataRequest | This controls the drawing of a histogram for a single piece of information |
| javawrapper.Interface | Interface between the Java GUI and the C++ application core |
| datavisualizer.Legend | This is an internal frame which displays a color legend for species-based charts |
| datavisualizer.Legend_CheckBox_actionAdapter | Triggers species changes when the user clicks species checkboxes |
| datavisualizer.Legend_ColorChooserButton_actionAdapter | Triggered when the user clicks a color button |
| javawrapper.LightBehaviors | Manages data for the light behaviors |
| datavisualizer.LineGraphDataRequest | Creates different types of line graphs for detailed output files |
| javawrapper.MainWindow | Main application window |
| javawrapper.MainWindow.RunListener | Runs the window's timer code while the C++ core is running |
| javawrapper.MainWindowStateSetter | The purpose of this class is to control the states of the main window - all the enabling and disabling, etc |
| javawrapper.ManageTreeMap | Allows management of tree maps |
| datavisualizer.MerchValueDataRequest | Produces a table of merchantable timber value results |
| javawrapper.Model | Main class that's called to start the application |
| javawrapper.ModelData | This is a base class for packaging data values with additional information |
| datavisualizer.ModelDataset | This encapsulates any kind of a chart dataset with a string to match it to its chart window |
| javawrapper.ModelEnum | Packages a data value with other information |
| javawrapper.ModelException | Model exception class |
| javawrapper.ModelFileChooser | Manages directories for SORTIE |
| javawrapper.ModelFileFunctions | This provides common file-reading functions for reading tab-delimited files |
| javawrapper.ModelFloat | This class packages float values with additional information |
| javawrapper.ModelFlowSetup | Allows users to make changes to the model flow and behavior order |
| javawrapper.ModelFlowSetup.BehaviorIndexer | Class which packages individual behavior names with an index number |
| javawrapper.ModelFlowSetup.DisplayBehaviorComboEdit | Displays an edit window for editing the tree species/type combos to which a single behavior applies |
| javawrapper.ModelFlowSetup.DisplayBehaviorEdit | Displays the edit window for editing behavior order |
| javawrapper.ModelFlowSetup.DisplayBehaviorEdit.AddFloatClicker | This class implements the float-click so that float-clicking on behavior names adds the behavior to the list |
| javawrapper.ModelFlowSetup.DisplayBehaviorEdit.ModifyFloatClicker | This class implements the float-click so that float-clicking on behavior names launches the behavior combo editor |
| javawrapper.ModelFlowSetup.DisplayComboEdit | Displays the edit window for editing behavior flow for a tree species/ type combo |
| javawrapper.ModelFlowSetup.DisplayComboEdit.AddFloatClicker | This class implements the float-click so that float-clicking on behavior names adds the behavior to the list |
| javawrapper.ModelFlowSetup.ListRenderer | Provides multi-line text wrapping to our list boxes Copyright: Copyright (c) Charles D |
| javawrapper.ModelFlowSetup.TreeNodeInfo | Objects set in tree nodes to give information about what to do when the user clicks a node |
| datavisualizer.ModelHistogramDataset | This is a hack of the HistogramDataset in JFreeChart |
| javawrapper.ModelIcon | Creates different icons needed by the model |
| javawrapper.ModelInt | This class packages integer values with additional data |
| datavisualizer.ModelInternalFrame | Ensures consistent behavior across graph windows |
| javawrapper.ModelMessage | Structure for message passing |
| javawrapper.ModelString | Packages a String value together with additional data |
| javawrapper.ModelVector | This class packages vector data with other pieces of information important to the model |
| javawrapper.MortalityBehaviors | Manages mortality behaviors and data |
| javawrapper.MortalityEpisodeEdit | Window for mortality episode editing |
| javawrapper.MortalityUtilitiesBehaviors | This is the organizer class for the dead remover behavor |
| uihelpers.MultilineLabel | Renders a multi-line "JLabel" |
| javawrapper.OKCancelButtonPanel | A panel containing OK, Cancel, and Help buttons |
| uihelpers.OutFileFilter | File filter for short output files |
| javawrapper.OutputBehaviors | Manages output behaviors and data |
| javawrapper.OutputSetup | Window used by the user to start setting up run output options |
| javawrapper.OutputSetup_this_windowAdapter | Allows us to refresh the saving information on window focus |
| datavisualizer.OverviewTableDataRequest | Writes an overview table for a detailed output file (basal area and density for each life history stage) |
| javawrapper.PackageGridValue | Class for holding the data for a single package |
| javawrapper.ParameterCellEditor | Handles the editing for the file parameter table |
| javawrapper.ParameterEdit | Window used to trigger the parameter editing process |
| javawrapper.ParameterFileParser | SAX parameter file parse handler |
| javawrapper.ParameterTableModel | Table model for the parameter data table |
| javawrapper.ParameterTextRenderer | Renders the first column values in a table to bold font with word wrapping to multiple lines |
| javawrapper.ParseReader | Processes SAX parser output |
| datavisualizer.PartitionedBiomassLineGraphDataRequest | Produces a line graph of partitioned biomass results (one component - i.e |
| datavisualizer.PartitionedBiomassTableDataRequest | Produces a table of partitioned biomass results |
| javawrapper.PlantEdit | Window for planting editing |
| javawrapper.PlantingBehaviors | Manages planting behaviors and data |
| javawrapper.PlantingData | This class encapsulates the data for a single planting event - being for one species, for one timestep |
| javawrapper.PlantingData.PlantingAbundance | This encapsulates a species with its planting abundance |
| javawrapper.Plot | Plot object |
| javawrapper.Points | For listing points for GLI points calculations |
| javawrapper.QuickScrollingPanel | This class creates a JPanel that scrolls at a normal speed through a JScrollPane |
| datavisualizer.RelativeNeighborhoodDensityDataRequest | Produces a line graph of Relative Neighborhood Density grid results |
| datavisualizer.RelativeNeighborhoodDensityDataRequest.SpInc | This class bundles together a species number and increment number |
| datavisualizer.RelativeNeighborhoodDensityDataRequest.ValCode | This class bundles together a grid value and its associated grid data member code |
| javawrapper.RenamePair | This class holds information about species renaming and copying |
| datavisualizer.RipleysKDataRequest | Produces a line graph of Ripley's K results |
| datavisualizer.RipleysKDataRequest.SpInc | This class bundles together a species number and increment number |
| datavisualizer.RipleysKDataRequest.ValCode | This class bundles together a grid value and its associated grid data member code |
| javawrapper.SaxParseTools | |
| javawrapper.ScheduledStormInfo | Holds data for scheduled storms grouped together |
| javawrapper.ScheduledStormSetup | This is a window allowing scheduling of storms for the storm behavior |
| javawrapper.SeedPredationBehaviors | This class organizes the seed predation behaviors |
| datavisualizer.SeedTableDataRequest | Produces a table of dispersed seeds |
| datavisualizer.ShortOutputFileManager | Manages all the data visualization for a single short output file |
| datavisualizer.ShortOutputFileManager.LineGraphFileWriter | Takes care of writing out a line graph's data |
| datavisualizer.ShortOutputFileManager.TableFileWriter | Writes out table data to file |
| datavisualizer.ShortOutputFileManager.TotalUpdater | Handles it when a "Show Total" checkbox is checked |
| javawrapper.ShortOutputFileSetup | Window used by the user to set up summary (short) output files |
| javawrapper.SizeClassEditor | Displays dialog for entering size class data |
| javawrapper.SnagDynamicsBehaviors | Manages snag dynamics data and behaviors |
| uihelpers.SORTIEComboBox | Improves the basic combo box by allowing the popup area to be bigger than the box itself |
| uihelpers.SortieFont | The common font for all GUI elements |
| uihelpers.SortieLabel | Wrapper class for labels which set them up with the correct font |
| javawrapper.SpeciesSpecific | This class will package together a data member and an array of booleans on which species uses it |
| javawrapper.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 |
| javawrapper.SpringUtilities | A 1.4 file that provides utility methods for creating form- or grid-style layouts with SpringLayout |
| datavisualizer.StandTableDataRequest | Writes a stand table for a detailed output file (basal area or density for each life history stage throughout the run) |
| javawrapper.StateChangeBehaviors | Manages state change behaviors |
| datavisualizer.StateVariableTableDataRequest | Produces a table of state variable results |
| datavisualizer.StockTableDataRequest | Writes a stock table for a detailed output file |
| datavisualizer.StormDataRequest | Produces a table of storm results |
| datavisualizer.StormKilledPartitionedBiomassDataRequest | Produces a table of partitioned biomass results |
| javawrapper.Subplot | This rolls up a set of cell coordinates into a defined subplot |
| javawrapper.SubplotEdit | Window for editing subplot information |
| javawrapper.SubplotEdit.SubplotCellResolutionPicker | A small window for changing subplot resolution |
| javawrapper.SubplotEdit.SubplotMouseListener | Class for interpreting mouse clicks on the chart for selecting cells for subplot editing |
| javawrapper.SubstrateBehaviors | Manages substrate data and behaviors |
| javawrapper.SwingWorker | * This is the 3rd version of SwingWorker (also known as SwingWorker 3), an abstract class that you subclass to perform GUI-related work in a dedicated thread |
| javawrapper.SwingWorker.ThreadVar | Class to maintain reference to current worker thread under separate synchronization control |
| javawrapper.TableData | For packaging header data in a typesafe way |
| datavisualizer.TableUpdater | Responds to the buttons in the overview table windows |
| javawrapper.TarArchive | The TarArchive class implements the concept of a tar archive |
| javawrapper.Tarball | Functions for working with tarballs (.gz.tar files) |
| uihelpers.TextFileFilter | File filter for text files |
| javawrapper.Tree | Represents a single tree's data |
| datavisualizer.TreeListWriter | This class will write a complete tree list for any desired time step |
| datavisualizer.TreeMapCrownRadDataRequest | This class manages the data for, and draws, tree maps |
| datavisualizer.TreeMapDataRequest | This class manages the data for, and draws, tree maps |
| javawrapper.TreeOutputSaveInfo | This collects tree saving information for short output for one tree type |
| javawrapper.TreePopulation | This holds all data relating to the tree population |
| javawrapper.TreeSpeciesSetup | Dialog allowing the user to set up basic tree information |
| javawrapper.TreeSpeciesSetup.CopySpeciesEditor | This class creates an interface for copying species |
| datavisualizer.WindstormDataRequest | Produces a table of windstorm results |
| javawrapper.WorkerBase | This class contains methods common to all objects that contain data |
| uihelpers.XMLFileFilter | This filters to only XML files for file choosers |
| datavisualizer.XYCellRenderer | This class fills in map cell rectangles on a plot |
| datavisualizer.XYCellRenderer.CellTooltipGenerator | Provides a more informative tooltip string for cell values |
| datavisualizer.XYSimpleCellRenderer | This class fills in map cell rectangles on a plot |
| datavisualizer.XYTreeRenderer | A renderer that draws a circle at each data point |
| datavisualizer.XYTreeRenderer.TreeTooltipGenerator | Provides a more informative tooltip string for cell values |
| datavisualizer.XYZDataItem | Represents one (x, y, z) data item for an xyz-series |
| datavisualizer.XYZSimpleDataset | A simple implementation of the jorg.jfree.data.xyXYZDataset interface that stores data values in arrays of bool primitives |