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| | NCIMasterMortality (GUIManager oManager, BehaviorTypeBase oParent, String sDescriptor, String sParFileTag, String sXMLRootString) throws ModelException |
| | Constructor.
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| 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.
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| void | validateData (TreePopulation oPop) throws ModelException |
| | Validates the data.
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ArrayList
< BehaviorParameterDisplay > | formatDataForDisplay (TreePopulation oPop) |
| | Formats data for display in a set of JTables.
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| | NCIMasterBase (GUIManager oManager, BehaviorTypeBase oParent, String sDescriptor, String sParFileTag, String sXMLRootString, String sHelpString) throws ModelException |
| | Constructor.
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| boolean | usesIndividuals () |
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| boolean | setSingleValueByXMLTag (String sXMLTag, String sXMLParentTag, Attributes oAttributes, Object oData) throws ModelException |
| | Overridden to capture effects choices.
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| 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.
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| void | writeXML (BufferedWriter jOut, TreePopulation oPop) throws ModelException |
| | Overridden to allow effects to write their parameters.
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| void | deleteSpeciesTypeCombo (int iIndex) throws ModelException |
| | Override to give effects behaviors the same instructions.
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| void | clearSpeciesTypeCombos () |
| | Override to give effects behaviors the same instructions.
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| void | addSpeciesTypeCombo (SpeciesTypeCombo oCombo) throws ModelException |
| | Override to give effects behaviors the same instructions.
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| void | copySpecies (int iSpeciesCopyFrom, int iSpeciesCopyTo) throws ModelException |
| | Override to give effects behaviors the same instructions.
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| void | changeOfSpeciesName (String sOldSpecies, String sNewSpecies) |
| | Override to give effects behaviors the same instructions.
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| void | changeOfSpecies (int iOldNumSpecies, int[] p_iIndexer, String[] p_sNewSpecies) throws ModelException |
| | Override to give effects behaviors the same instructions.
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| void | setupLikeOldNCI () throws ModelException |
| | For backwards compatibility with the old NCI behavior.
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| void | setupLikeOldWeibullClimate () throws ModelException |
| | For backwards compatibility with the old weibull climate behavior.
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| void | setupLikeOldWeibullClimateQuadrat () throws ModelException |
| | For backwards compatibility with the old weibull climate quadrat behavior.
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| void | setupLikeOldBANCI () throws ModelException |
| | For backwards compatibility with the old BA NCI behavior.
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| void | setupLikeOldNCIJuvenile () throws ModelException |
| | For backwards compatibility with the old NCI Juvenile growth behavior.
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| void | callSetupDialog (JDialog jParent, MainWindow oMain) |
| | Override to call NCI's dialog.
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ArrayList
< BehaviorParameterDisplay > | formatEffectsDataForDisplay (TreePopulation oPop) |
| | Formats effects data for display in a set of JTables.
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| void | readDataFromDisplay (ArrayList< BehaviorParameterDisplay > oData, TreePopulation oPop) throws ModelException |
| | Overriden to give effects their shot at the parameters as well.
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| String[] | getSizeEffectChoices (boolean all) |
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| String[] | getShadingEffectChoices (boolean all) |
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| String[] | getCrowdingEffectChoices (boolean all) |
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| String[] | getNCITermChoices (boolean all) |
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| String[] | getDamageEffectChoices (boolean all) |
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| String[] | getTemperatureEffectChoices (boolean all) |
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| String[] | getPrecipitationEffectChoices (boolean all) |
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| String[] | getNitrogenEffectChoices (boolean all) |
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| String[] | getInfectionEffectChoices (boolean all) |
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| int | getSizeEffectChoice () |
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| int | getShadingEffectChoice () |
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| int | getCrowdingEffectChoice () |
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| int | getNCITermChoice () |
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| int | getDamageEffectChoice () |
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| int | getTemperatureEffectChoice () |
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| int | getPrecipitationEffectChoice () |
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| int | getNitrogenEffectChoice () |
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| int | getInfectionEffectChoice () |
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| void | setSizeEffect (String sChoice) throws ModelException |
| | Sets the choice of size effect options, and updates the effects list accordingly.
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| void | setShadingEffect (String sChoice) throws ModelException |
| | Sets the choice of shading effect options, and updates the effects list accordingly.
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| void | setCrowdingEffect (String sChoice) throws ModelException |
| | Sets the choice of crowding effect options, and updates the effects list accordingly.
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| void | setNCITerm (String sChoice) throws ModelException |
| | Sets the choice of NCI term options, and updates the effects list accordingly.
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| void | setDamageEffect (String sChoice) throws ModelException |
| | Sets the choice of damage effect options, and updates the effects list accordingly.
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| void | setPrecipitationEffect (String sChoice) throws ModelException |
| | Sets the choice of precipitation effect options, and updates the effects list accordingly.
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| void | setTemperatureEffect (String sChoice) throws ModelException |
| | Sets the choice of temperature effect options, and updates the effects list accordingly.
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| void | setNitrogenEffect (String sChoice) throws ModelException |
| | Sets the choice of nitrogen effect options, and updates the effects list accordingly.
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| void | setInfectionEffect (String sChoice) throws ModelException |
| | Sets the choice of infection effect options, and updates the effects list accordingly.
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| GUIManager | getGUIManager () |
| |
| | Behavior (GUIManager oManager, BehaviorTypeBase oParent, String sDescriptor, String sParFileTag, String sXMLRootString, String sHelpFileString) |
| | Constructor.
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| void | callSetupDialog (JDialog jParent, MainWindow oMain) |
| | Override this to call a specific setup dialog for this behavior.
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| int | getNumberOfDataObjects () |
| | Gets the number of managed data objects.
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| ModelData | getDataObject (int iInd) |
| | Gets the managed data object at a particular index.
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| void | validate () throws ModelException |
| | Behavior performs an internal check to make sure its settings are consistent and logical.
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| void | setListPosition (int iListPosition) |
| | Sets the behavior list position.
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| int | getListPosition () |
| | Gets the behavior list position.
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| String | getXMLParametersRoot () |
| | Gets the XML parameter root string.
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| int | getNumberNewDataMembers () |
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| DataMember | getNewTreeDataMember (int iIndex) throws ModelException |
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| void | setCanApplyTo (int iType, boolean bCanApply) |
| | Sets whether this behavior can apply to a given tree type.
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| String | getParameterFileBehaviorName () |
| | Gets the parameter file name for this behavior.
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| double | getVersion () |
| | Gets behavior's parameter file version.
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| double | getMinimumVersion () |
| | Gets behavior's parameter file minimum version.
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| String | getDescriptor () |
| | Gets the descriptor string.
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| String | getHelpFileString () |
| | Gets the help file UD.
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| void | setDescriptor (String s) |
| | Sets the descriptor string.
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| int | getNumberOfCombos () |
| | Gets the number of species/type combos to which this behavior applies.
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| int | getNumberOfGrids () |
| | Gets the number of grids to which this behavior applies.
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| void | deleteSpeciesTypeCombo (int iIndex) throws ModelException |
| | Deletes the SpeciesTypeCombo at the given index.
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| void | deleteSpeciesTypeCombo (SpeciesTypeCombo oCombo) throws ModelException |
| | Deletes a SpeciesTypeCombo.
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| void | clearSpeciesTypeCombos () |
| | Empties the species/type combo list.
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| SpeciesTypeCombo | getSpeciesTypeCombo (int iIndex) throws ModelException |
| | Returns the SpeciesTypeCombo at the given index of the species/type combo list.
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| Grid | getGrid (int iIndex) throws ModelException |
| | Returns the Grid at the given index of the grid applies to list.
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| ModelData | getRequiredData (int iIndex) |
| | Returns the required data object at a given index.
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| int | getNumberOfRequiredDataObjects () |
| | Gets the number of required data objects for this behavior.
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| void | addSpeciesTypeCombo (SpeciesTypeCombo oCombo) throws ModelException |
| | Adds a new species/type combo to the list to which this behavior applies.
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| void | addGrid (Grid oGrid) |
| | Adds a new Grid to the list to which this behavior applies.
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| void | addRequiredData (ModelData oData) |
| | Adds a piece of required data to the list.
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| boolean[] | getWhichSpeciesUsed (TreePopulation oPop) |
| | Returns which species to which this behavior is applied.
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| 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.
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| boolean | setSingleValueByXMLTag (String sXMLTag, String sXMLParentTag, Attributes oAttributes, Object oData) throws ModelException |
| | Sets a data object's value.
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| ModelData | findObjectByXMLTag (String sXMLTag) |
| | Finds an object based on its XML tag.
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| void | copySpecies (int iSpeciesCopyFrom, int iSpeciesCopyTo) throws ModelException |
| | Copies one species to another.
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| void | writeXML (BufferedWriter jOut, TreePopulation oPop) throws ModelException |
| | Writes the XML data to a parameter file for the behaviors owned by this object.
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| 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.
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| 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.
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| void | readXMLParentTag (String sXMLTag, Attributes oAttributes) throws ModelException |
| | Accepts an XML parent tag (empty, no data) from the parser.
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| void | changeOfSpeciesName (String sOldSpecies, String sNewSpecies) |
| | Performs any necessary tasks associated with changing the name of a species.
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| void | changeOfSpecies (int iOldNumSpecies, int[] p_iIndexer, String[] p_sNewSpecies) throws ModelException |
| | Triggered when there is a change in the species list.
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| boolean | getMustHaveTrees () |
| | Gets whether this behavior must have trees.
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| ModelData | findObjectByDescriptor (String sDescriptor) |
| | Finds an object based on its descriptor.
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| void | writeBehaviorNode (BufferedWriter out, TreePopulation oPop) throws ModelException |
| | Writes behavior tags to the parameter file.
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ArrayList
< BehaviorParameterDisplay > | formatDataForDisplay (TreePopulation oPop) |
| | Formats data for display in a set of JTables.
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| String | getAppliedToForDisplay (TreePopulation oPop) |
| | Get which species/types this behavior applies to, in a display-friendly format truncated to 250 chars.
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| void | readDataFromDisplay (ArrayList< BehaviorParameterDisplay > oData, TreePopulation oPop) throws ModelException |
| | Reads in data from the parameter display window.
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| boolean | canBeDuplicated () |
| | Whether or not this behavior can be duplicated in the run.
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| void | endOfParameterFileRead () |
| | Called at the end of the parameter file read process.
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| void | changeOfPlotResolution (float fOldX, float fOldY, float fNewX, float fNewY) throws ModelException |
| | Performs any tasks associated with a change of plot resolution.
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| setupType | getSetupType () |
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| 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.
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| ModelVector | mp_fNCIMaxProbSurvival |
| | NCI Mortality - Maximum probability of survival.
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| ModelFloat | m_fParamPeriod |
| | Parameter period - default to 1.
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| ArrayList< NCIEffect > | mp_iShadingEffects = new ArrayList<NCIEffect>(0) |
| | Set of possible shading effects.
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| ModelInt | m_iShadingEffect = new ModelInt("Shading Effect", "nciWhichShadingEffect") |
| | Which shading effect.
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| ArrayList< NCIEffect > | mp_iCrowdingEffects = new ArrayList<NCIEffect>(0) |
| | Set of possible crowding effects.
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| ModelInt | m_iCrowdingEffect = new ModelInt("Crowding Effect", "nciWhichCrowdingEffect") |
| | Which crowding effect.
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| ArrayList< NCIEffect > | mp_iNCITerms = new ArrayList<NCIEffect>(0) |
| | Set of possible NCI terms.
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| ModelInt | m_iNCITerm = new ModelInt("NCI Term", "nciWhichNCITerm") |
| | Which NCI term.
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| ArrayList< NCIEffect > | mp_iSizeEffects = new ArrayList<NCIEffect>(0) |
| | Set of possible size effects.
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| ModelInt | m_iSizeEffect = new ModelInt("Size Effect", "nciWhichSizeEffect") |
| | Which size effect.
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| ArrayList< NCIEffect > | mp_iDamageEffects = new ArrayList<NCIEffect>(0) |
| | Set of possible damage effects.
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| ModelInt | m_iDamageEffect = new ModelInt("Damage Effect", "nciWhichDamageEffect") |
| | Which damage effect.
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| ArrayList< NCIEffect > | mp_iPrecipEffects = new ArrayList<NCIEffect>(0) |
| | Set of possible precipitation effects.
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| ModelInt | m_iPrecipEffect = new ModelInt("Precipitation Effect", "nciWhichPrecipitationEffect") |
| | Which precipitation effect.
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| ArrayList< NCIEffect > | mp_iTempEffects = new ArrayList<NCIEffect>(0) |
| | Set of possible temperature effects.
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| ModelInt | m_iTempEffect = new ModelInt("Temperature Effect", "nciWhichTemperatureEffect") |
| | Which temperature effect.
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| ArrayList< NCIEffect > | mp_iNEffects = new ArrayList<NCIEffect>(0) |
| | Set of possible nitrogen effects.
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| ModelInt | m_iNEffect = new ModelInt("Nitrogen Effect", "nciWhichNitrogenEffect") |
| | Which nitrogen effect.
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| ArrayList< NCIEffect > | mp_iInfectionEffects = new ArrayList<NCIEffect>(0) |
| | Set of possible infection effects.
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| ModelInt | m_iInfectionEffect = new ModelInt("Infection Effect", "nciWhichInfectionEffect") |
| | Which infection effect.
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| ArrayList< Behavior > | mp_oEffects |
| | The multiplicative effects assigned.
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| boolean | m_bUsesIndividuals = true |
| | Whether or not the NCI behavior uses individuals and therefore will have target diameters available.
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| GUIManager | m_oManager |
| | GUIManager object.
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| BehaviorTypeBase | m_oParent |
| | Parent manager.
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| ArrayList< ModelData > | mp_oAllData = new ArrayList<ModelData>() |
| | All data for this object.
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| 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.
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| ArrayList< String > | mp_oGridsAppliesTo = new ArrayList<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.
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| 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.
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| boolean | m_bCanBeDuplicated = true |
| | Whether or not this behavior can have multiple copies in a run or not.
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| String | m_sDescriptor = "" |
| | This is what will be displayed as the name of a given behavior in the GUI.
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| String | m_sParFileTag = "" |
| | String which is used to identify this behavior in the parameter file.
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| String | m_sXMLRootString = "" |
| | XML tag to surround this behavior's data.
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| String | m_sHelpFileString = "" |
| | Help file topic identifier string.
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| boolean[] | mp_bCanApplyToTreeType |
| | For each tree type, whether or not this behavior can be applied to it.
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| double | m_fVersion = 1.0 |
| | Version of this behavior.
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| double | m_fMinVersion = 1.0 |
| | Minimum version of this behavior.
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| int | m_iListPosition = -1 |
| | This behavior's position in the behavior list.
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| setupType | m_iBehaviorSetupType |
| |
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| static void | setVectorValues (ModelVector oData, Float[] p_fValuesToSet, boolean[] p_bAppliesTo) |
| | Sets the values for vector variables.
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| static void | setVectorValues (ModelVector oData, Float[] p_fValuesToSet) |
| | Sets the values for vector variables.
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| static void | setVectorValues (ModelVector oData, Double[] p_fValuesToSet, boolean[] p_bAppliesTo) |
| | Sets the values for vector variables.
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| static void | setVectorValues (ModelVector oData, Double[] p_fValuesToSet) |
| | Sets the values for vector variables.
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| static void | setVectorValues (ModelVector oData, Integer[] p_iValuesToSet, boolean[] p_bAppliesTo) |
| | Sets the values for vector variables.
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| static void | setVectorValues (ModelVector oData, String[] p_sValuesToSet) |
| | Sets the values for vector variables.
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| static void | setVectorValues (ModelVector oData, String[] p_sValuesToSet, boolean[] p_bAppliesTo) |
| | Sets the values for vector variables.
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| static void | setVectorValues (ModelVector oData, Integer[] p_iValuesToSet) |
| | Sets the values for vector variables.
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| static void | setVectorValues (ModelVector p_oData, ArrayList< String > p_oValuesToSet, boolean[] p_bAppliesTo) throws ModelException |
| | Sets the values for vector variables.
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| static void | writeDataToFile (BufferedWriter ojOut, ModelData oData) throws java.io. IOException |
| | Writes a piece of data to an XML file.
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| static Object[] | formatBlankHeaderRow (Object[][] p_oTable) |
| | Creates a blank header row for a table.
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| static Object[][] | formatDataAsComboBox (Object[][] p_oExisting, ModelEnum oToFormat) |
| | Adds a value with combo box formatting to an Object array for display in a JTable.
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| static String | formatComboBoxString (ModelEnum oToFormat) |
| | Formats a combo box string from a ModelEnum.
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| 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.
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| static Object[][] | addDataToArray (Object[][] p_oExistingArray, Object[] p_oAddArray) |
| | Adds an Object array to an existing Object array.
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| static Object[][] | formatDataForTable (Object[][] p_oExisting, ModelFloat oToFormat) |
| | Formats and adds a value into an Object array suitable for placing in a JTable.
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| static Object[][] | formatDataForTable (Object[][] p_oExisting, ModelInt oToFormat) |
| | Formats and adds a value into an Object array suitable for placing in a JTable.
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| static Object[][] | formatDataForTable (Object[][] p_oExisting, ModelString oToFormat) |
| | Formats and adds a value into an Object array suitable for placing in a JTable.
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| 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.
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| 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.
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| 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.
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| static void | ensureSize (ArrayList<?> list, int size) |
| | Ensure an ArrayList is at least a specific size.
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| boolean | m_bMustHaveTrees = true |
| | If true, and a tree has no species/type combos, it automatically becomes disabled.
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| void | setSingleValue (ModelData oDataMember, Object oData) throws ModelException |
| | Sets the value of a single data member.
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| 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.
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| static boolean | boolArraysEqual (boolean[] p_bArrayOne, boolean[] p_bArrayTwo) |
| | Tests two boolean arrays for equality.
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