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