sortie.data.funcgroups.nci.NCIMasterGrowth Class Reference

Corresponds to the clNCIMasterGrowth class. More...

Inheritance diagram for sortie.data.funcgroups.nci.NCIMasterGrowth:

Public Member Functions
	NCIMasterGrowth (GUIManager oManager, BehaviorTypeBase oParent, String sDescriptor, String sParFileTag, String sXMLRootString) throws ModelException
	Constructor. More...
boolean	setVectorValueByXMLTag (String sXMLTag, String sXMLParentTag, ArrayList< String > p_oData, String[] p_sChildXMLTags, boolean[] p_bAppliesTo, Attributes oParentAttributes, Attributes[] p_oAttributes) throws ModelException
	Overridden to capture pre-integration tags. More...
void	validateData (TreePopulation oPop) throws ModelException
	Validates the data. More...
ArrayList< BehaviorParameterDisplay >	formatDataForDisplay (TreePopulation oPop)
	Formats data for display in a set of JTables. More...
Public Member Functions inherited from sortie.data.funcgroups.nci.NCIMasterBase
	NCIMasterBase (GUIManager oManager, BehaviorTypeBase oParent, String sDescriptor, String sParFileTag, String sXMLRootString, String sHelpString) throws ModelException
	Constructor. More...
boolean	usesIndividuals ()
boolean	setSingleValueByXMLTag (String sXMLTag, String sXMLParentTag, Attributes oAttributes, Object oData) throws ModelException
	Overridden to capture effects choices. More...
boolean	setVectorValueByXMLTag (String sXMLTag, String sXMLParentTag, ArrayList< String > p_oData, String[] p_sChildXMLTags, boolean[] p_bAppliesTo, Attributes oParentAttributes, Attributes[] p_oAttributes) throws ModelException
	Overridden to allow effects to read parameters as well. More...
void	validateData (TreePopulation oPop) throws ModelException
	Validates the data. More...
void	writeXML (BufferedWriter jOut, TreePopulation oPop) throws ModelException
	Overridden to allow effects to write their parameters. More...
void	deleteSpeciesTypeCombo (int iIndex) throws ModelException
	Override to give effects behaviors the same instructions. More...
void	clearSpeciesTypeCombos ()
	Override to give effects behaviors the same instructions. More...
void	addSpeciesTypeCombo (SpeciesTypeCombo oCombo) throws ModelException
	Override to give effects behaviors the same instructions. More...
void	copySpecies (int iSpeciesCopyFrom, int iSpeciesCopyTo) throws ModelException
	Override to give effects behaviors the same instructions. More...
void	changeOfSpeciesName (String sOldSpecies, String sNewSpecies)
	Override to give effects behaviors the same instructions. More...
void	changeOfSpecies (int iOldNumSpecies, int[] p_iIndexer, String[] p_sNewSpecies) throws ModelException
	Override to give effects behaviors the same instructions. More...
void	setupLikeOldNCI () throws ModelException
	For backwards compatibility with the old NCI behavior. More...
void	setupLikeOldWeibullClimate () throws ModelException
	For backwards compatibility with the old weibull climate behavior. More...
void	setupLikeOldWeibullClimateQuadrat () throws ModelException
	For backwards compatibility with the old weibull climate quadrat behavior. More...
void	setupLikeOldBANCI () throws ModelException
	For backwards compatibility with the old BA NCI behavior. More...
void	setupLikeOldNCIJuvenile () throws ModelException
	For backwards compatibility with the old NCI Juvenile growth behavior. More...
void	callSetupDialog (JDialog jParent, MainWindow oMain)
	Override to call NCI's dialog. More...
ArrayList< BehaviorParameterDisplay >	formatEffectsDataForDisplay (TreePopulation oPop)
	Formats effects data for display in a set of JTables. More...
void	readDataFromDisplay (ArrayList< BehaviorParameterDisplay > oData, TreePopulation oPop) throws ModelException
	Overriden to give effects their shot at the parameters as well. More...
String []	getSizeEffectChoices (boolean all)
String []	getShadingEffectChoices (boolean all)
String []	getCrowdingEffectChoices (boolean all)
String []	getNCITermChoices (boolean all)
String []	getDamageEffectChoices (boolean all)
String []	getTemperatureEffectChoices (boolean all)
String []	getPrecipitationEffectChoices (boolean all)
String []	getNitrogenEffectChoices (boolean all)
String []	getInfectionEffectChoices (boolean all)
int	getSizeEffectChoice ()
int	getShadingEffectChoice ()
int	getCrowdingEffectChoice ()
int	getNCITermChoice ()
int	getDamageEffectChoice ()
int	getTemperatureEffectChoice ()
int	getPrecipitationEffectChoice ()
int	getNitrogenEffectChoice ()
int	getInfectionEffectChoice ()
void	setSizeEffect (String sChoice) throws ModelException
	Sets the choice of size effect options, and updates the effects list accordingly. More...
void	setShadingEffect (String sChoice) throws ModelException
	Sets the choice of shading effect options, and updates the effects list accordingly. More...
void	setCrowdingEffect (String sChoice) throws ModelException
	Sets the choice of crowding effect options, and updates the effects list accordingly. More...
void	setNCITerm (String sChoice) throws ModelException
	Sets the choice of NCI term options, and updates the effects list accordingly. More...
void	setDamageEffect (String sChoice) throws ModelException
	Sets the choice of damage effect options, and updates the effects list accordingly. More...
void	setPrecipitationEffect (String sChoice) throws ModelException
	Sets the choice of precipitation effect options, and updates the effects list accordingly. More...
void	setTemperatureEffect (String sChoice) throws ModelException
	Sets the choice of temperature effect options, and updates the effects list accordingly. More...
void	setNitrogenEffect (String sChoice) throws ModelException
	Sets the choice of nitrogen effect options, and updates the effects list accordingly. More...
void	setInfectionEffect (String sChoice) throws ModelException
	Sets the choice of infection effect options, and updates the effects list accordingly. 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_fNCIMaxPotentialGrowth
	NCI max potential growth for each species. More...
ModelVector	mp_fRandParameter
	Standard deviation if normal or lognormal distribution is desired. More...
ModelEnum	m_iStochasticGrowthMethod
	Which growth adjustment. More...
Protected Attributes inherited from sortie.data.funcgroups.nci.NCIMasterBase
ArrayList< NCIEffect >	mp_iShadingEffects = new ArrayList<NCIEffect>(0)
	Set of possible shading effects. More...
ModelInt	m_iShadingEffect = new ModelInt("Shading Effect", "nciWhichShadingEffect")
	Which shading effect. More...
ArrayList< NCIEffect >	mp_iCrowdingEffects = new ArrayList<NCIEffect>(0)
	Set of possible crowding effects. More...
ModelInt	m_iCrowdingEffect = new ModelInt("Crowding Effect", "nciWhichCrowdingEffect")
	Which crowding effect. More...
ArrayList< NCIEffect >	mp_iNCITerms = new ArrayList<NCIEffect>(0)
	Set of possible NCI terms. More...
ModelInt	m_iNCITerm = new ModelInt("NCI Term", "nciWhichNCITerm")
	Which NCI term. More...
ArrayList< NCIEffect >	mp_iSizeEffects = new ArrayList<NCIEffect>(0)
	Set of possible size effects. More...
ModelInt	m_iSizeEffect = new ModelInt("Size Effect", "nciWhichSizeEffect")
	Which size effect. More...
ArrayList< NCIEffect >	mp_iDamageEffects = new ArrayList<NCIEffect>(0)
	Set of possible damage effects. More...
ModelInt	m_iDamageEffect = new ModelInt("Damage Effect", "nciWhichDamageEffect")
	Which damage effect. More...
ArrayList< NCIEffect >	mp_iPrecipEffects = new ArrayList<NCIEffect>(0)
	Set of possible precipitation effects. More...
ModelInt	m_iPrecipEffect = new ModelInt("Precipitation Effect", "nciWhichPrecipitationEffect")
	Which precipitation effect. More...
ArrayList< NCIEffect >	mp_iTempEffects = new ArrayList<NCIEffect>(0)
	Set of possible temperature effects. More...
ModelInt	m_iTempEffect = new ModelInt("Temperature Effect", "nciWhichTemperatureEffect")
	Which temperature effect. More...
ArrayList< NCIEffect >	mp_iNEffects = new ArrayList<NCIEffect>(0)
	Set of possible nitrogen effects. More...
ModelInt	m_iNEffect = new ModelInt("Nitrogen Effect", "nciWhichNitrogenEffect")
	Which nitrogen effect. More...
ArrayList< NCIEffect >	mp_iInfectionEffects = new ArrayList<NCIEffect>(0)
	Set of possible infection effects. More...
ModelInt	m_iInfectionEffect = new ModelInt("Infection Effect", "nciWhichInfectionEffect")
	Which infection effect. More...
ArrayList< Behavior >	mp_oEffects
	The multiplicative effects assigned. More...
boolean	m_bUsesIndividuals = true
	Whether or not the NCI behavior uses individuals and therefore will have target diameters available. 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 clNCIMasterGrowth class.

This is newly updated with the more flexible NCI system allowing the user to choose any combination of multiplicative effects.

Author

lora

Constructor & Destructor Documentation

NCIMasterGrowth()

sortie.data.funcgroups.nci.NCIMasterGrowth.NCIMasterGrowth	(	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

Member Function Documentation

formatDataForDisplay()

ArrayList<BehaviorParameterDisplay> sortie.data.funcgroups.nci.NCIMasterGrowth.formatDataForDisplay

(

TreePopulation

oPop

)

Formats data for display in a set of JTables.

This is overridden so that only those values appropriate to the effects functions that have been chosen are used.

Parameters

oPop	TreePopulation object.

Returns

Vector of vectors suitable for creating a set of JTables, or null if there is no data to display.

setVectorValueByXMLTag()

boolean sortie.data.funcgroups.nci.NCIMasterGrowth.setVectorValueByXMLTag	(	String	sXMLTag,
		String	sXMLParentTag,
		ArrayList< String >	p_oData,
		String []	p_sChildXMLTags,
		boolean []	p_bAppliesTo,
		Attributes	oParentAttributes,
		Attributes []	p_oAttributes
	)		throws ModelException

Overridden to capture pre-integration tags.

validateData()

void sortie.data.funcgroups.nci.NCIMasterGrowth.validateData

(

TreePopulation

oPop

)

throws ModelException

Validates the data.

Parameters

oPop	TreePopulation object.

Exceptions

ModelException

if NCI Max growth is <= 0 for any species.

Member Data Documentation

m_iStochasticGrowthMethod

ModelEnum sortie.data.funcgroups.nci.NCIMasterGrowth.m_iStochasticGrowthMethod

protected

Initial value:

= new ModelEnum(new int[] { 0, 3, 2 },
      new String[] { "None", 
                     "Normal",
                     "Lognormal"},
       "Growth Increment Adjustment PDF", "gr_stochGrowthMethod")

Which growth adjustment.

mp_fNCIMaxPotentialGrowth

ModelVector sortie.data.funcgroups.nci.NCIMasterGrowth.mp_fNCIMaxPotentialGrowth

protected

Initial value:

= new ModelVector(
      "NCI Maximum Potential Growth, cm/yr",
      "gr_nciMaxPotentialGrowth",
      "gr_nmpgVal", 0,
      ModelVector.FLOAT)

NCI max potential growth for each species.

mp_fRandParameter

ModelVector sortie.data.funcgroups.nci.NCIMasterGrowth.mp_fRandParameter

protected

Initial value:

= new ModelVector("Std Deviation for Normal or Lognormal Adjustment", 
      "gr_standardDeviation", "gr_sdVal", 0, ModelVector.FLOAT)

Standard deviation if normal or lognormal distribution is desired.

One for each species.

---

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

• NCIMasterGrowth.java