Corresponds to the clDensDepInfestation class. More...

Inheritance diagram for sortie.data.funcgroups.disturbance.DensDepInfestation:

Public Member Functions
	DensDepInfestation (GUIManager oManager, BehaviorTypeBase oParent, String sDescriptor, String sParFileTag, String sXMLRootString) throws ModelException
	Constructor. More...

void	validateData (TreePopulation oPop) throws ModelException
	Validates the data. More...

Public Member Functions inherited from sortie.data.funcgroups.Behavior
GUIManager	getGUIManager ()

	Behavior (GUIManager oManager, BehaviorTypeBase oParent, String sDescriptor, String sParFileTag, String sXMLRootString, String sHelpFileString)
	Constructor. More...

abstract void	validateData (TreePopulation oPop) throws ModelException
	Override this to implement data checking. More...

void	callSetupDialog (JDialog jParent, MainWindow oMain)
	Override this to call a specific setup dialog for this behavior. More...

int	getNumberOfDataObjects ()
	Gets the number of managed data objects. More...

ModelData	getDataObject (int iInd)
	Gets the managed data object at a particular index. More...

void	validate () throws ModelException
	Behavior performs an internal check to make sure its settings are consistent and logical. More...

void	setListPosition (int iListPosition) throws ModelException
	Sets the behavior list position. More...

int	getListPosition ()
	Gets the behavior list position. More...

String	getXMLParametersRoot ()
	Gets the XML parameter root string. More...

int	getNumberNewDataMembers ()

DataMember	getNewTreeDataMember (int iIndex) throws ModelException

void	setCanApplyTo (int iType, boolean bCanApply)
	Sets whether this behavior can apply to a given tree type. More...

String	getParameterFileBehaviorName ()
	Gets the parameter file name for this behavior. More...

double	getVersion ()
	Gets behavior's parameter file version. More...

double	getMinimumVersion ()
	Gets behavior's parameter file minimum version. More...

String	getDescriptor ()
	Gets the descriptor string. More...

String	getHelpFileString ()
	Gets the help file UD. More...

void	setDescriptor (String s)
	Sets the descriptor string. More...

int	getNumberOfCombos ()
	Gets the number of species/type combos to which this behavior applies. More...

int	getNumberOfGrids ()
	Gets the number of grids to which this behavior applies. More...

void	deleteSpeciesTypeCombo (int iIndex) throws ModelException
	Deletes the SpeciesTypeCombo at the given index. More...

void	deleteSpeciesTypeCombo (SpeciesTypeCombo oCombo) throws ModelException
	Deletes a SpeciesTypeCombo. More...

void	clearSpeciesTypeCombos ()
	Empties the species/type combo list. More...

SpeciesTypeCombo	getSpeciesTypeCombo (int iIndex) throws ModelException
	Returns the SpeciesTypeCombo at the given index of the species/type combo list. More...

Grid	getGrid (int iIndex) throws ModelException
	Returns the Grid at the given index of the grid applies to list. More...

ModelData	getRequiredData (int iIndex)
	Returns the required data object at a given index. More...

int	getNumberOfRequiredDataObjects ()
	Gets the number of required data objects for this behavior. More...

void	addSpeciesTypeCombo (SpeciesTypeCombo oCombo) throws ModelException
	Adds a new species/type combo to the list to which this behavior applies. More...

void	addGrid (Grid oGrid, boolean bReplace)
	Adds a new Grid to the list to which this behavior applies. More...

void	addRequiredData (ModelData oData)
	Adds a piece of required data to the list. More...

boolean []	getWhichSpeciesUsed (TreePopulation oPop)
	Returns which species to which this behavior is applied. More...

boolean	setVectorValueByXMLTag (String sXMLTag, String sXMLParentTag, ArrayList< String > p_oData, String[] p_sChildXMLTags, boolean[] p_bAppliesTo, Attributes oParentAttributes, Attributes[] p_oAttributes) throws ModelException
	Sets a data vector's value. More...

boolean	setSingleValueByXMLTag (String sXMLTag, String sXMLParentTag, Attributes oAttributes, Object oData) throws ModelException
	Sets a data object's value. More...

ModelData	findObjectByXMLTag (String sXMLTag)
	Finds an object based on its XML tag. More...

void	copySpecies (int iSpeciesCopyFrom, int iSpeciesCopyTo) throws ModelException
	Copies one species to another. More...

void	writeXML (BufferedWriter jOut, TreePopulation oPop) throws ModelException
	Writes the XML data to a parameter file for the behaviors owned by this object. More...

void	writeSpeciesSpecificValue (BufferedWriter jOut, ModelVector p_oData, TreePopulation oPop) throws java.io.IOException, ModelException
	Writes a set of species-specific float values to a parameter file. More...

void	writeSpeciesSpecificValue (BufferedWriter jOut, ModelVector p_oData, TreePopulation oPop, boolean[] p_bFlags) throws java.io.IOException, ModelException
	Writes a set of species-specific values to a parameter file for a certain subset of species. More...

void	readXMLParentTag (String sXMLTag, Attributes oAttributes) throws ModelException
	Accepts an XML parent tag (empty, no data) from the parser. More...

void	changeOfSpeciesName (String sOldSpecies, String sNewSpecies)
	Performs any necessary tasks associated with changing the name of a species. More...

void	changeOfSpecies (int iOldNumSpecies, int[] p_iIndexer, String[] p_sNewSpecies) throws ModelException
	Triggered when there is a change in the species list. More...

boolean	getMustHaveTrees ()
	Gets whether this behavior must have trees. More...

ModelData	findObjectByDescriptor (String sDescriptor)
	Finds an object based on its descriptor. More...

void	writeBehaviorNode (BufferedWriter out, TreePopulation oPop) throws ModelException
	Writes behavior tags to the parameter file. More...

ArrayList< BehaviorParameterDisplay >	formatDataForDisplay (TreePopulation oPop)
	Formats data for display in a set of JTables. More...

String	getAppliedToForDisplay (TreePopulation oPop)
	Get which species/types this behavior applies to, in a display-friendly format truncated to 250 chars. More...

void	readDataFromDisplay (ArrayList< BehaviorParameterDisplay > oData, TreePopulation oPop) throws ModelException
	Reads in data from the parameter display window. More...

boolean	canBeDuplicated ()
	Whether or not this behavior can be duplicated in the run. More...

void	endOfParameterFileRead ()
	Called at the end of the parameter file read process. More...

void	changeOfPlotResolution (float fOldX, float fOldY, float fNewX, float fNewY) throws ModelException
	Performs any tasks associated with a change of plot resolution. More...

setupType	getSetupType ()

void	writeParametersToTextFile (FileWriter jOut, TreePopulation oPop) throws IOException
	Writes the parameters for the behavior to file, using the same system as the basic parameter display and entry system. More...

Protected Attributes
ModelVector	mp_fMinDBH
	Minimum DBH. More...

ModelVector	mp_fCohortDBH
	Cohort cutoff DBH. More...

ModelVector	mp_fProbResistant
	Probability that a tree is resistant, 0-1. More...

ModelVector	mp_fProbConditionallySusceptible
	Probability that a tree is conditionally susceptible, 0-1. More...

ModelFloat	m_fMax
	Maximum infestation rate parameter. More...

ModelFloat	m_fA
	The "a" parameter. More...

ModelFloat	m_fBx
	The "bx" parameter. More...

ModelFloat	m_fBy
	The "by" parameter. More...

ModelInt	m_iFirstYear
	Year to start infestation. More...

ModelInt	m_iLastYear
	Year to emd infestation. More...

Protected Attributes inherited from sortie.data.funcgroups.Behavior
GUIManager	m_oManager
	GUIManager object. More...

BehaviorTypeBase	m_oParent
	Parent manager. More...

ArrayList< ModelData >	mp_oAllData = new ArrayList<ModelData>()
	All data for this object. More...

ArrayList< SpeciesTypeCombo >	mp_oTreesAppliesTo = new ArrayList<SpeciesTypeCombo>(0)
	A set of SpeciesTypeCombo objects to which this behavior is applied - or none if it is not applied to trees. More...

ArrayList< Integer >	mp_iGridsAppliesTo = new ArrayList<Integer>(0)
	A set of hashcodes of the Grids to which this behavior is applied - or none if it is not applied to grids. More...

ArrayList< DataMember >	mp_oNewTreeDataMembers = new ArrayList<DataMember>(0)
	The new tree data members that this behavior adds, above and beyond the basic tree population data members. More...

boolean	m_bCanBeDuplicated = true
	Whether or not this behavior can have multiple copies in a run or not. More...

String	m_sDescriptor = ""
	This is what will be displayed as the name of a given behavior in the GUI. More...

String	m_sParFileTag = ""
	String which is used to identify this behavior in the parameter file. More...

String	m_sXMLRootString = ""
	XML tag to surround this behavior's data. More...

String	m_sHelpFileString = ""
	Help file topic identifier string. More...

boolean []	mp_bCanApplyToTreeType
	For each tree type, whether or not this behavior can be applied to it. More...

double	m_fVersion = 1.0
	Version of this behavior. More...

double	m_fMinVersion = 1.0
	Minimum version of this behavior. More...

int	m_iListPosition = -1
	This behavior's position in the behavior list. More...

setupType	m_iBehaviorSetupType

Additional Inherited Members
Static Public Member Functions inherited from sortie.data.funcgroups.Behavior
static void	setVectorValues (ModelVector oData, Float[] p_fValuesToSet, boolean[] p_bAppliesTo)
	Sets the values for vector variables. More...

static void	setVectorValues (ModelVector oData, Float[] p_fValuesToSet)
	Sets the values for vector variables. More...

static void	setVectorValues (ModelVector oData, Double[] p_fValuesToSet, boolean[] p_bAppliesTo)
	Sets the values for vector variables. More...

static void	setVectorValues (ModelVector oData, Double[] p_fValuesToSet)
	Sets the values for vector variables. More...

static void	setVectorValues (ModelVector oData, Integer[] p_iValuesToSet, boolean[] p_bAppliesTo)
	Sets the values for vector variables. More...

static void	setVectorValues (ModelVector oData, String[] p_sValuesToSet)
	Sets the values for vector variables. More...

static void	setVectorValues (ModelVector oData, String[] p_sValuesToSet, boolean[] p_bAppliesTo)
	Sets the values for vector variables. More...

static void	setVectorValues (ModelVector oData, Integer[] p_iValuesToSet)
	Sets the values for vector variables. More...

static void	setVectorValues (ModelVector p_oData, ArrayList< String > p_oValuesToSet, boolean[] p_bAppliesTo) throws ModelException
	Sets the values for vector variables. More...

static void	writeDataToFile (BufferedWriter ojOut, ModelData oData) throws java.io. IOException
	Writes a piece of data to an XML file. More...

static Object []	formatBlankHeaderRow (Object[][] p_oTable)
	Creates a blank header row for a table. More...

static Object [][]	formatDataAsComboBox (Object[][] p_oExisting, ModelEnum oToFormat)
	Adds a value with combo box formatting to an Object array for display in a JTable. More...

static String	formatComboBoxString (ModelEnum oToFormat)
	Formats a combo box string from a ModelEnum. More...

static void	addDataObjectToDisplayArrays (ModelData p_oDataObject, ArrayList< ModelData > p_oSingles, ArrayList< ArrayList< SpeciesSpecific >> p_oSpeciesSpecific, boolean[] p_bAppliesTo)
	Adds a data object to the arrays which will eventually display run parameters in a set of tables. More...

static Object [][]	addDataToArray (Object[][] p_oExistingArray, Object[] p_oAddArray)
	Adds an Object array to an existing Object array. More...

static Object [][]	formatDataForTable (Object[][] p_oExisting, ModelFloat oToFormat)
	Formats and adds a value into an Object array suitable for placing in a JTable. More...

static Object [][]	formatDataForTable (Object[][] p_oExisting, ModelInt oToFormat)
	Formats and adds a value into an Object array suitable for placing in a JTable. More...

static Object [][]	formatDataForTable (Object[][] p_oExisting, ModelString oToFormat)
	Formats and adds a value into an Object array suitable for placing in a JTable. More...

static Object [][]	formatDataForTable (Object[][] p_oExisting, ModelVector oToFormat)
	Formats a vector of values into an object array and adds it to another Object array suitable for placing in a JTable. More...

static Object [][]	formatDataForTable (Object[][] p_oExisting, ModelVector oToFormat, boolean[] p_bWhichSpecies)
	Formats a vector of values into a plain vector suitable for placing in a JTable and adds it to a vector of vectors at the end. More...

static Object []	formatSpeciesHeaderRow (boolean[] p_bUsed, TreePopulation oPop)
	Creates an object array of strings consisting of species names, suitable for including in the parameter entry table. More...

static void	ensureSize (ArrayList<?> list, int size)
	Ensure an ArrayList is at least a specific size. More...

Public Attributes inherited from sortie.data.funcgroups.Behavior
boolean	m_bMustHaveTrees = true
	If true, and a tree has no species/type combos, it automatically becomes disabled. More...

Protected Member Functions inherited from sortie.data.funcgroups.Behavior
void	setSingleValue (ModelData oDataMember, Object oData) throws ModelException
	Sets the value of a single data member. More...

BehaviorParameterDisplay	formatTable (ArrayList< ModelData > p_oSingles, ArrayList< ArrayList< SpeciesSpecific >> p_oSpeciesSpecific, TreePopulation oPop)
	Turns vector groups of data objects into a set of tables for display. More...

Static Protected Member Functions inherited from sortie.data.funcgroups.Behavior
static boolean	boolArraysEqual (boolean[] p_bArrayOne, boolean[] p_bArrayTwo)
	Tests two boolean arrays for equality. More...

Detailed Description

Corresponds to the clDensDepInfestation class.

Author: lora

Constructor & Destructor Documentation

◆ DensDepInfestation()

sortie.data.funcgroups.disturbance.DensDepInfestation.DensDepInfestation	(	GUIManager	oManager,
		BehaviorTypeBase	oParent,
		String	sDescriptor,
		String	sParFileTag,
		String	sXMLRootString
	)		throws ModelException

Constructor.

Parameters

oManager	GUIManager object
oParent	Parent managing object.
sDescriptor	The name of the behavior for the user.
sParFileTag	String which is used to identify this behavior in the parameter file.
sXMLRootString	XML tag to surround this behavior's data.

Exceptions

ModelException Won't throw.

Member Function Documentation

◆ validateData()

void sortie.data.funcgroups.disturbance.DensDepInfestation.validateData ( TreePopulation oPop ) throws ModelException

Validates the data.

Parameters

oPop	TreePopulation object

Exceptions

ModelException

if:

Intercepts are not between 0 and 1
Max infestation rates are not between 0 and 1
Any X0 is 0
Minimum DBH values are negative
First infestation timestep is less than 0

Member Data Documentation

◆ m_fA

ModelFloat sortie.data.funcgroups.disturbance.DensDepInfestation.m_fA

protected

Initial value:

= new ModelFloat(0,

"Infestation \"a\"", "di_densDepInfA")

The "a" parameter.

◆ m_fBx

ModelFloat sortie.data.funcgroups.disturbance.DensDepInfestation.m_fBx

protected

Initial value:

= new ModelFloat(0,

"Infestation \"bx\"", "di_densDepInfBx")

The "bx" parameter.

◆ m_fBy

ModelFloat sortie.data.funcgroups.disturbance.DensDepInfestation.m_fBy

protected

Initial value:

= new ModelFloat(0,

"Infestation \"by\"", "di_densDepInfBy")

The "by" parameter.

◆ m_fMax

ModelFloat sortie.data.funcgroups.disturbance.DensDepInfestation.m_fMax

protected

Initial value:

= new ModelFloat(1,

"Infestation Max Rate", "di_densDepInfMaxInfestation")

Maximum infestation rate parameter.

◆ m_iFirstYear

ModelInt sortie.data.funcgroups.disturbance.DensDepInfestation.m_iFirstYear

protected

Initial value:

= new ModelInt(1,

"First Year of Infestation Relative to Start", "di_densDepInfStartYear")

Year to start infestation.

◆ m_iLastYear

ModelInt sortie.data.funcgroups.disturbance.DensDepInfestation.m_iLastYear

protected

Initial value:

= new ModelInt(-1,

"Last Year of Infestation (-1 if no end)", "di_densDepInfEndYear")

Year to emd infestation.

◆ mp_fCohortDBH

ModelVector sortie.data.funcgroups.disturbance.DensDepInfestation.mp_fCohortDBH

protected

Initial value:

= new ModelVector(
    "Infestation Cohort DBH Threshold", "di_densDepInfCohortDBH", "di_ddicdVal",
      0, ModelVector.FLOAT)

Cohort cutoff DBH.

◆ mp_fMinDBH

ModelVector sortie.data.funcgroups.disturbance.DensDepInfestation.mp_fMinDBH

protected

Initial value:

= new ModelVector(
    "Infestation Min DBH", "di_densDepInfMinDBH", "di_ddimdVal",
      0, ModelVector.FLOAT)

Minimum DBH.

◆ mp_fProbConditionallySusceptible

ModelVector sortie.data.funcgroups.disturbance.DensDepInfestation.mp_fProbConditionallySusceptible

protected

Initial value:

= new ModelVector(
      "Proportion of Conditionally Susceptible Trees (0-1)", 
      "di_densDepInfPropCondSusceptible", "di_ddipcsVal", 0, ModelVector.FLOAT)

Probability that a tree is conditionally susceptible, 0-1.

◆ mp_fProbResistant

ModelVector sortie.data.funcgroups.disturbance.DensDepInfestation.mp_fProbResistant

protected

Initial value:

= new ModelVector(
      "Proportion of Resistant Trees (0-1)", "di_densDepInfPropResistant", 
      "di_ddiprVal", 0, ModelVector.FLOAT)

Probability that a tree is resistant, 0-1.

The documentation for this class was generated from the following file:

DensDepInfestation.java

Public Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ DensDepInfestation()

Member Function Documentation

◆ validateData()

Member Data Documentation

◆ m_fA

◆ m_fBx

◆ m_fBy

◆ m_fMax

◆ m_iFirstYear

◆ m_iLastYear

◆ mp_fCohortDBH

◆ mp_fMinDBH

◆ mp_fProbConditionallySusceptible

◆ mp_fProbResistant