SORTIE Java Interface  1
Public Member Functions | Protected Attributes | List of all members
sortie.data.funcgroups.mortality.NCIMort Class Reference

Corresponds to the clNCIMort class. More...

Inheritance diagram for sortie.data.funcgroups.mortality.NCIMort:
sortie.data.funcgroups.Behavior

Public Member Functions

 NCIMort (GUIManager oManager, BehaviorTypeBase oParent, String sDescriptor, String sParFileTag, String sXMLRootString) throws ModelException
 Constructor.
 
void changeOfSpecies (int iOldNumSpecies, int[] p_iIndexer, String[] p_sNewSpecies) throws ModelException
 Overridden to handle lambdas.
 
void validateData (TreePopulation oPop) throws ModelException
 Validates the data.
 
void changeOfSpeciesName (String sOldSpecies, String sNewSpecies)
 Updates the lambda neighbor names when a species name is changed.
 
void copySpecies (int iSpeciesCopyFrom, int iSpeciesCopyTo) throws ModelException
 Updates the lambda when a species is copied.
 
- 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.
 
int getNumberOfDataObjects ()
 Gets the number of managed data objects.
 
ModelData getDataObject (int iInd)
 Gets the managed data object at a particular index.
 
void validate () throws ModelException
 Behavior performs an internal check to make sure its settings are consistent and logical.
 
void setListPosition (int iListPosition)
 Sets the behavior list position.
 
int getListPosition ()
 Gets the behavior list position.
 
String getXMLParametersRoot ()
 Gets the XML parameter root string.
 
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.
 
String getParameterFileBehaviorName ()
 Gets the parameter file name for this behavior.
 
double getVersion ()
 Gets behavior's parameter file version.
 
double getMinimumVersion ()
 Gets behavior's parameter file minimum version.
 
String getDescriptor ()
 Gets the descriptor string.
 
void setDescriptor (String s)
 Sets the descriptor string.
 
int getNumberOfCombos ()
 Gets the number of species/type combos to which this behavior applies.
 
int getNumberOfGrids ()
 Gets the number of grids to which this behavior applies.
 
void deleteSpeciesTypeCombo (int iIndex) throws ModelException
 Deletes the SpeciesTypeCombo at the given index.
 
void clearSpeciesTypeCombos ()
 Empties the species/type combo list.
 
SpeciesTypeCombo getSpeciesTypeCombo (int iIndex) throws ModelException
 Returns the SpeciesTypeCombo at the given index of the species/type combo list.
 
Grid getGrid (int iIndex) throws ModelException
 Returns the Grid at the given index of the grid applies to list.
 
ModelData getRequiredData (int iIndex)
 Returns the required data object at a given index.
 
int getNumberOfRequiredDataObjects ()
 Gets the number of required data objects for this behavior.
 
void addSpeciesTypeCombo (SpeciesTypeCombo oCombo) throws ModelException
 Adds a new species/type combo to the list to which this behavior applies.
 
void addGrid (Grid oGrid)
 Adds a new Grid to the list to which this behavior applies.
 
void addRequiredData (ModelData oData)
 Adds a piece of required data to the list.
 
boolean[] getWhichSpeciesUsed (TreePopulation oPop)
 Returns which species to which this behavior is applied.
 
boolean setVectorValueByXMLTag (String sXMLTag, String sXMLParentTag, Vector< String > p_oData, String[] p_sChildXMLTags, boolean[] p_bAppliesTo, Attributes oParentAttributes, Attributes[] p_oAttributes) throws ModelException
 Sets a data vector's value.
 
void setVectorValues (ModelVector oData, Float[] p_fValuesToSet, boolean[] p_bAppliesTo)
 Sets the values for vector variables.
 
void setVectorValues (ModelVector oData, Float[] p_fValuesToSet)
 Sets the values for vector variables.
 
void setVectorValues (ModelVector oData, Double[] p_fValuesToSet, boolean[] p_bAppliesTo)
 Sets the values for vector variables.
 
void setVectorValues (ModelVector oData, Double[] p_fValuesToSet)
 Sets the values for vector variables.
 
void setVectorValues (ModelVector oData, Integer[] p_iValuesToSet, boolean[] p_bAppliesTo)
 Sets the values for vector variables.
 
void setVectorValues (ModelVector oData, String[] p_sValuesToSet)
 Sets the values for vector variables.
 
void setVectorValues (ModelVector oData, String[] p_sValuesToSet, boolean[] p_bAppliesTo)
 Sets the values for vector variables.
 
void setVectorValues (ModelVector oData, Integer[] p_iValuesToSet)
 Sets the values for vector variables.
 
void setVectorValues (ModelVector p_oData, Vector< String > p_oValuesToSet, boolean[] p_bAppliesTo) throws ModelException
 Sets the values for vector variables.
 
boolean setSingleValueByXMLTag (String sXMLTag, String sXMLParentTag, Attributes oAttributes, Object oData) throws ModelException
 Sets a data object's value.
 
ModelData findObjectByXMLTag (String sXMLTag)
 Finds an object based on its XML tag.
 
void copySpecies (int iSpeciesCopyFrom, int iSpeciesCopyTo) throws ModelException
 Copies one species to another.
 
void writeXML (BufferedWriter jOut, TreePopulation oPop) throws ModelException
 Writes the XML data to a parameter file for the behaviors owned by this object.
 
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.
 
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.
 
void readXMLParentTag (String sXMLTag, Attributes oAttributes) throws ModelException
 Accepts an XML parent tag (empty, no data) from the parser.
 
void changeOfSpeciesName (String sOldSpecies, String sNewSpecies)
 Performs any necessary tasks associated with changing the name of a species.
 
void changeOfSpecies (int iOldNumSpecies, int[] p_iIndexer, String[] p_sNewSpecies) throws ModelException
 Triggered when there is a change in the species list.
 
boolean getAutoDisplayParameters ()
 Gets whether to auto-display this object's parameters.
 
ModelData findObjectByDescriptor (String sDescriptor)
 Finds an object based on its descriptor.
 
void writeBehaviorNode (BufferedWriter out, TreePopulation oPop) throws ModelException
 Writes behavior tags to the parameter file.
 
BehaviorParameterDisplay formatDataForDisplay (TreePopulation oPop)
 Formats data for display in a set of JTables.
 
void readDataFromDisplay (Vector< TableData > p_oData, TreePopulation oPop) throws ModelException
 Reads in data from the parameter display window.
 
boolean canBeDuplicated ()
 Whether or not this behavior can be duplicated in the run.
 
boolean canBeEditedAutomatically ()
 Whether or not this behavior can be edited with the automatic parameter retrieval and editing tools.
 
void endOfParameterFileRead ()
 Called at the end of the parameter file read process.
 
void changeOfPlotResolution (float fOldX, float fOldY, float fNewX, float fNewY) throws ModelException
 Performs any tasks associated with a change of plot resolution.
 

Protected Attributes

ModelVector mp_fNCIMaxCrowdingRadius
 NCI Mortality - Maximum crowding radius.
 
ModelVector mp_fNCINeighDBHEffect
 NCI Mortality - Neighbor DBH effect (alpha) parameter.
 
ModelVector mp_fNCINeighDistanceEffect
 NCI Mortality - Neighbor distance effect (beta) parameter.
 
ModelVector mp_fNCIMinNeighborDBH
 NCI minimum DBH for crowding neighbors, for each species; all species required.
 
ModelVector mp_fNCIShadingEffectCoefficient
 NCI Mortality - Shading coefficient (m)
 
ModelVector mp_fNCIShadingEffectExponent
 NCI Mortality - Shading exponent (n)
 
ModelVector mp_fNCISizeSensToNCI
 NCI Mortality - Size sensitivity to NCI parameter (gamma)
 
ModelVector mp_fNCIMaxProbSurvival
 NCI Mortality - Maximum probability of survival.
 
ModelVector mp_fNCISizeEffectMode
 NCI Mortality - Size effect mode (X0)
 
ModelVector mp_fNCISizeEffectVariance
 NCI Mortality - Size effect variance (Xb)
 
ModelVector mp_fNCISlope
 NCI Mortality - Crowding Effect Slope (C)
 
ModelVector mp_fNCISteepness
 NCI Mortality - Crowding Effect Steepness (D)
 
ModelVector mp_fNCIStormEffectMed
 NCI Mortality - Storm effect - medium damage.
 
ModelVector mp_fNCIStormEffectFull
 NCI Mortality - Storm effect - full damage.
 
ModelVector mp_fNCINeighStormEffMed
 NCI Mortality - Neighbor storm effect - medium damage.
 
ModelVector mp_fNCINeighStormEffFull
 NCI Mortality - Neighbor storm effect - full damage.
 
ModelFloat m_fNCIDbhDivisor
 NCI - NCI DBH divisor.
 
ModelEnum m_iIncludeSnagsInNCI
 NCI - Whether or not to include snags in NCI calculations.
 
- Protected Attributes inherited from sortie.data.funcgroups.Behavior
GUIManager m_oManager
 GUIManager object.
 
BehaviorTypeBase m_oParent
 Parent manager.
 
Vector< ModelDatamp_oAllData = new Vector<ModelData>()
 All data for this object.
 
Vector< SpeciesTypeCombomp_oTreesAppliesTo = new Vector<SpeciesTypeCombo>(0)
 A set of SpeciesTypeCombo objects to which this behavior is applied - or none if it is not applied to trees.
 
Vector< String > mp_oGridsAppliesTo = new Vector<String>(0)
 A set of strings with the name of Grids to which this behavior is applied - or none if it is not applied to grids.
 
Vector< DataMembermp_oNewTreeDataMembers = new Vector<DataMember>(0)
 The new tree data members that this behavior adds, above and beyond the basic tree population data members.
 
boolean m_bCanEditAutomatically = true
 Whether or not this behavior can be edited automatically (true) or must be edited with its own dialog (false)
 
boolean m_bCanBeDuplicated = true
 Whether or not this behavior can have multiple copies in a run or not.
 
boolean m_bAutoDisplayParameters = true
 Whether or not to auto-display this object's parameters.
 
String m_sDescriptor = ""
 This is what will be displayed as the name of a given behavior in the GUI.
 
String m_sParFileTag = ""
 String which is used to identify this behavior in the parameter file.
 
String m_sXMLRootString = ""
 XML tag to surround this behavior's data.
 
String m_sHelpFileString = ""
 Help file topic identifier string.
 
boolean[] mp_bCanApplyToTreeType
 For each tree type, whether or not this behavior can be applied to it.
 
double m_fVersion = 1.0
 Version of this behavior.
 
double m_fMinVersion = 1.0
 Minimum version of this behavior.
 
int m_iListPosition = -1
 This behavior's position in the behavior list.
 

Additional Inherited Members

- Static Public Member Functions inherited from sortie.data.funcgroups.Behavior
static void writeDataToFile (BufferedWriter ojOut, ModelData oData) throws java.io. IOException
 Writes a piece of data to an XML file.
 
static Object[] formatBlankHeaderRow (Object[][] p_oTable)
 Creates a blank header row for a table.
 
static Object[][] formatDataAsComboBox (Object[][] p_oExisting, ModelEnum oToFormat)
 Adds a value with combo box formatting to an Object array for display in a JTable.
 
static String formatComboBoxString (ModelEnum oToFormat)
 Formats a combo box string from a ModelEnum.
 
static void addDataObjectToDisplayArrays (ModelData p_oDataObject, Vector< ModelData > p_oSingles, Vector< Vector< SpeciesSpecific >> p_oSpeciesSpecific, boolean[] p_bAppliesTo)
 Adds a data object to the arrays which will eventually display run parameters in a set of tables.
 
static Object[][] addDataToArray (Object[][] p_oExistingArray, Object[] p_oAddArray)
 Adds an Object array to an existing Object array.
 
static Object[][] formatDataForTable (Object[][] p_oExisting, ModelFloat oToFormat)
 Formats and adds a value into an Object array suitable for placing in a JTable.
 
static Object[][] formatDataForTable (Object[][] p_oExisting, ModelInt oToFormat)
 Formats and adds a value into an Object array suitable for placing in a JTable.
 
static Object[][] formatDataForTable (Object[][] p_oExisting, ModelString oToFormat)
 Formats and adds a value into an Object array suitable for placing in a JTable.
 
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.
 
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.
 
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.
 
- 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.
 
- 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.
 
BehaviorParameterDisplay formatTable (Vector< ModelData > p_oSingles, Vector< Vector< SpeciesSpecific >> p_oSpeciesSpecific, TreePopulation oPop)
 Turns vector groups of data objects into a set of tables for display.
 
- 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.
 

Detailed Description

Corresponds to the clNCIMort class.

Author
lora

Constructor & Destructor Documentation

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

Constructor.

Parameters
oManagerGUIManager object
oParentParent managing object.
sDescriptorThe name of the behavior for the user.
sParFileTagString which is used to identify this behavior in the parameter file.
sXMLRootStringXML tag to surround this behavior's data.
Exceptions
ModelException

Member Function Documentation

void sortie.data.funcgroups.mortality.NCIMort.changeOfSpecies ( int  iOldNumSpecies,
int[]  p_iIndexer,
String[]  p_sNewSpecies 
) throws ModelException

Overridden to handle lambdas.

void sortie.data.funcgroups.mortality.NCIMort.changeOfSpeciesName ( String  sOldSpecies,
String  sNewSpecies 
)

Updates the lambda neighbor names when a species name is changed.

Parameters
sOldSpeciesString Old name of the species, with underscores instead of spaces (like the species names would come from the tree population)
sNewSpeciesString New name of the species, with underscores instead of spaces (like the species names would come from the tree population)
void sortie.data.funcgroups.mortality.NCIMort.copySpecies ( int  iSpeciesCopyFrom,
int  iSpeciesCopyTo 
) throws ModelException

Updates the lambda when a species is copied.

The lambdas for that neighbor are made identical to those being copied as well as entries for species within the lambda.

Parameters
iSpeciesCopyFromint Species to copy.
iSpeciesCopyToint Species that is the copy.
Exceptions
ModelExceptionif there is a problem.
void sortie.data.funcgroups.mortality.NCIMort.validateData ( TreePopulation  oPop) throws ModelException
virtual

Validates the data.

Parameters
oPopTreePopulation
Exceptions
ModelExceptionif:
  • NCI Max. radius of neighbor effects is <= 0 for any species
  • NCI Max growth is <= 0 for any species
  • NCI size effect mode for any species is <= 0
  • NCI Size effect variance = 0 for any species
  • NCI Eta for any species for any damage category is not between 0 and 1
  • NCI Storm Effect parameters for any species for any damage category are not between 0 and 1
  • NCI DBH divisor is <= 0
  • Minimun neighbor DBH value is < 0

Implements sortie.data.funcgroups.Behavior.

Member Data Documentation

ModelFloat sortie.data.funcgroups.mortality.NCIMort.m_fNCIDbhDivisor
protected
Initial value:
= new ModelFloat(1,
"NCI DBH Divisor (q)", "mo_nciDbhDivisor")

NCI - NCI DBH divisor.

ModelEnum sortie.data.funcgroups.mortality.NCIMort.m_iIncludeSnagsInNCI
protected
Initial value:
=
new ModelEnum(new int[] {0, 1},
new String[] {"false", "true"},
"Include Snags in NCI Calculations",
"mo_nciIncludeSnagsInNCI")

NCI - Whether or not to include snags in NCI calculations.

ModelVector sortie.data.funcgroups.mortality.NCIMort.mp_fNCIMaxCrowdingRadius
protected
Initial value:
= new ModelVector(
"NCI Max Radius of Crowding Neighbors, in m",
"mo_nciMaxCrowdingRadius", "mo_nmcrVal", 0, ModelVector.FLOAT)

NCI Mortality - Maximum crowding radius.

ModelVector sortie.data.funcgroups.mortality.NCIMort.mp_fNCIMaxProbSurvival
protected
Initial value:
= new ModelVector(
"NCI Max Survival Probability (0-1)", "mo_nciMaxPotentialSurvival",
"mo_nmpsVal", 0, ModelVector.FLOAT)

NCI Mortality - Maximum probability of survival.

ModelVector sortie.data.funcgroups.mortality.NCIMort.mp_fNCIMinNeighborDBH
protected
Initial value:
= new ModelVector(
"NCI Minimum Neighbor DBH, in cm", "mo_nciMinNeighborDBH",
"mo_nmndVal", 0, ModelVector.FLOAT, true)

NCI minimum DBH for crowding neighbors, for each species; all species required.

ModelVector sortie.data.funcgroups.mortality.NCIMort.mp_fNCINeighDBHEffect
protected
Initial value:
= new ModelVector(
"NCI Neighbor DBH Effect (alpha)", "mo_nciNeighDBHEff",
"mo_nndeVal", 0, ModelVector.FLOAT)

NCI Mortality - Neighbor DBH effect (alpha) parameter.

ModelVector sortie.data.funcgroups.mortality.NCIMort.mp_fNCINeighDistanceEffect
protected
Initial value:
= new ModelVector(
"NCI Neighbor Distance Effect (beta)", "mo_nciNeighDistEff",
"mo_nndseVal", 0, ModelVector.FLOAT)

NCI Mortality - Neighbor distance effect (beta) parameter.

ModelVector sortie.data.funcgroups.mortality.NCIMort.mp_fNCINeighStormEffFull
protected
Initial value:
= new ModelVector(
"NCI Neighbor Storm Damage (eta) - Complete (0-1)",
"mo_nciNeighStormEffFullDmg", "mo_nnsefdVal", 0, ModelVector.FLOAT)

NCI Mortality - Neighbor storm effect - full damage.

ModelVector sortie.data.funcgroups.mortality.NCIMort.mp_fNCINeighStormEffMed
protected
Initial value:
= new ModelVector(
"NCI Neighbor Storm Damage (eta) - Medium (0-1)",
"mo_nciNeighStormEffMedDmg", "mo_nnsemdVal", 0, ModelVector.FLOAT)

NCI Mortality - Neighbor storm effect - medium damage.

ModelVector sortie.data.funcgroups.mortality.NCIMort.mp_fNCIShadingEffectCoefficient
protected
Initial value:
= new ModelVector(
"NCI Shading Effect Coefficient (m)", "mo_nciShadingCoefficient",
"mo_nscVal", 0, ModelVector.FLOAT)

NCI Mortality - Shading coefficient (m)

ModelVector sortie.data.funcgroups.mortality.NCIMort.mp_fNCIShadingEffectExponent
protected
Initial value:
= new ModelVector(
"NCI Shading Effect Exponent (n)", "mo_nciShadingExponent",
"mo_nseVal", 0, ModelVector.FLOAT)

NCI Mortality - Shading exponent (n)

ModelVector sortie.data.funcgroups.mortality.NCIMort.mp_fNCISizeEffectMode
protected
Initial value:
= new ModelVector(
"NCI Size Effect Mode, in cm", "mo_nciSizeEffectMode",
"mo_nsemVal", 0, ModelVector.FLOAT)

NCI Mortality - Size effect mode (X0)

ModelVector sortie.data.funcgroups.mortality.NCIMort.mp_fNCISizeEffectVariance
protected
Initial value:
= new ModelVector(
"NCI Size Effect Variance, in cm", "mo_nciSizeEffectVar",
"mo_nsevVal", 0, ModelVector.FLOAT)

NCI Mortality - Size effect variance (Xb)

ModelVector sortie.data.funcgroups.mortality.NCIMort.mp_fNCISizeSensToNCI
protected
Initial value:
= new ModelVector(
"NCI Size Sensitivity to NCI (gamma)", "mo_nciSizeSensNCI",
"mo_nssnVal", 0, ModelVector.FLOAT)

NCI Mortality - Size sensitivity to NCI parameter (gamma)

ModelVector sortie.data.funcgroups.mortality.NCIMort.mp_fNCISlope
protected
Initial value:
= new ModelVector(
"NCI Crowding Effect Slope (C)", "mo_nciNCISlope", "mo_nnslVal", 0,
ModelVector.FLOAT)

NCI Mortality - Crowding Effect Slope (C)

ModelVector sortie.data.funcgroups.mortality.NCIMort.mp_fNCISteepness
protected
Initial value:
= new ModelVector(
"NCI Crowding Effect Steepness (D)", "mo_nciNCISteepness", "mo_nnstVal",
0, ModelVector.FLOAT)

NCI Mortality - Crowding Effect Steepness (D)

ModelVector sortie.data.funcgroups.mortality.NCIMort.mp_fNCIStormEffectFull
protected
Initial value:
= new ModelVector(
"NCI Storm Effect - Complete Damage (0-1)",
"mo_nciStormEffFullDmg", "mo_nsefdVal", 0, ModelVector.FLOAT)

NCI Mortality - Storm effect - full damage.

ModelVector sortie.data.funcgroups.mortality.NCIMort.mp_fNCIStormEffectMed
protected
Initial value:
= new ModelVector(
"NCI Storm Effect - Medium Damage (0-1)", "mo_nciStormEffMedDmg",
"mo_nsemdVal", 0, ModelVector.FLOAT)

NCI Mortality - Storm effect - medium damage.


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