SiLeBAT/FSK-Lab

/*******************************************************************************
 * Copyright (c) 2015 Federal Institute for Risk Assessment (BfR), Germany
 *
 * This program is free software: you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation, either version 3 of the License, or
 * (at your option) any later version.
 *
 * This program is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with this program.  If not, see <http://www.gnu.org/licenses/>.
 *
 * Contributors:
 *     Department Biological Safety - BfR
 *******************************************************************************/
package de.bund.bfr.knime.pmm.xlsmodelreader;

import java.util.ArrayList;
import java.util.LinkedHashMap;
import java.util.List;
import java.util.Map;

import org.knime.core.node.InvalidSettingsException;
import org.knime.core.node.NodeSettingsRO;
import org.knime.core.node.NodeSettingsWO;

import de.bund.bfr.knime.pmm.common.AgentXml;
import de.bund.bfr.knime.pmm.common.LiteratureItem;
import de.bund.bfr.knime.pmm.common.MatrixXml;
import de.bund.bfr.knime.pmm.common.XmlConverter;
import de.bund.bfr.knime.pmm.common.generictablemodel.KnimeTuple;

public class SettingsHelper {

    public static final String DO_NOT_USE = "Do Not Use";
    public static final String OTHER_PARAMETER = "Select Other";
    public static final String SELECT = "Select";
    public static final String USE_SECONDARY_MODEL = "Use Sec. Model";
    public static final String RELOAD = "Reload";

    private static final String CFG_FILE_NAME = "FileName";
    private static final String CFG_SHEET_NAME = "SheetName";
    private static final String CFG_PRESERVE_IDS = "PreserveIds";
    private static final String CFG_USED_IDS = "UsedIds";
    private static final String CFG_SEC_USED_IDS = "SecUsedIds";
    private static final String CFG_GLOBAL_USED_IDS = "GlobalUsedIds";
    private static final String CFG_MODEL_MAPPINGS = "ModelMappings";
    private static final String CFG_MODEL_DEP_MIN = "ModelDepMin";
    private static final String CFG_MODEL_DEP_MAX = "ModelDepMax";
    private static final String CFG_MODEL_DEP_UNIT = "ModelDepUnit";
    private static final String CFG_MODEL_INDEP_MIN = "ModelIndepMin";
    private static final String CFG_MODEL_INDEP_MAX = "ModelIndepMax";
    private static final String CFG_MODEL_INDEP_UNIT = "ModelIndepUnit";
    private static final String CFG_MODEL_RMSE = "ModelRMSE";
    private static final String CFG_MODEL_R2 = "ModelR2";
    private static final String CFG_MODEL_AIC = "ModelAIC";
    private static final String CFG_MODEL_DATA_POINTS = "ModelDataPoints";
    private static final String CFG_MODEL_PARAM_ERRORS = "ModelParamErrors";
    private static final String CFG_SEC_MODEL_MAPPINGS = "SecModelMappings";
    private static final String CFG_SEC_MODEL_PARAM_ERRORS = "SecModelParamErrors";
    private static final String CFG_SEC_MODEL_INDEP_MINS = "SecModelIndepMins";
    private static final String CFG_SEC_MODEL_INDEP_MAXS = "SecModelIndepMaxs";
    private static final String CFG_SEC_MODEL_INDEP_CATEGORIES = "SecModelIndepCategories";
    private static final String CFG_SEC_MODEL_INDEP_UNITS = "SecModelIndepUnits";
    private static final String CFG_SEC_MODEL_RMSE = "SecModelRMSE";
    private static final String CFG_SEC_MODEL_R2 = "SecModelR2";
    private static final String CFG_SEC_MODEL_AIC = "SecModelAIC";
    private static final String CFG_SEC_MODEL_DATA_POINTS = "SecModelDataPoints";
    private static final String CFG_COLUMN_MAPPINGS = "ColumnMappings";
    private static final String CFG_AGENT_COLUMN = "AgentColumn";
    private static final String CFG_AGENT_MAPPINGS = "AgentMappings";
    private static final String CFG_MATRIX_COLUMN = "MatrixColumn";
    private static final String CFG_MATRIX_MAPPINGS = "MatrixMappings";
    private static final String CFG_MODEL_TUPLE = "ModelTuple";
    private static final String CFG_SEC_MODEL_TUPLES = "SecModelTuples";
    private static final String CFG_AGENT = "Agent";
    private static final String CFG_MATRIX = "Matrix";
    private static final String CFG_LITERATURE = "Literature";

    private String fileName;
    private String sheetName;
    private boolean preserveIds;
    private List<Integer> usedIds;
    private Map<String, List<Integer>> secUsedIds;
    private List<Integer> globalUsedIds;
    private Map<String, String> modelMappings;
    private String modelDepMin;
    private String modelDepMax;
    private String modelDepUnit;
    private String modelIndepMin;
    private String modelIndepMax;
    private String modelIndepUnit;
    private String modelRmse;
    private String modelR2;
    private String modelAic;
    private String modelDataPoints;
    private Map<String, String> modelParamErrors;
    private Map<String, Map<String, String>> secModelMappings;
    private Map<String, Map<String, String>> secModelParamErrors;
    private Map<String, Map<String, String>> secModelIndepMins;
    private Map<String, Map<String, String>> secModelIndepMaxs;
    private Map<String, Map<String, String>> secModelIndepCategories;
    private Map<String, Map<String, String>> secModelIndepUnits;
    private Map<String, String> secModelRmse;
    private Map<String, String> secModelR2;
    private Map<String, String> secModelAic;
    private Map<String, String> secModelDataPoints;
    private Map<String, Object> columnMappings;
    private String agentColumn;
    private Map<String, AgentXml> agentMappings;
    private String matrixColumn;
    private Map<String, MatrixXml> matrixMappings;
    private KnimeTuple modelTuple;
    private Map<String, KnimeTuple> secModelTuples;
    private AgentXml agent;
    private MatrixXml matrix;
    private List<LiteratureItem> literature;

    public SettingsHelper() {
        fileName = null;
        sheetName = null;
        preserveIds = false;
        usedIds = new ArrayList<>();
        secUsedIds = new LinkedHashMap<>();
        globalUsedIds = new ArrayList<>();
        modelTuple = null;
        secModelTuples = new LinkedHashMap<>();
        modelMappings = new LinkedHashMap<>();
        modelDepMin = null;
        modelDepMax = null;
        modelDepUnit = null;
        modelIndepMin = null;
        modelIndepMax = null;
        modelIndepUnit = null;
        modelRmse = null;
        modelR2 = null;
        modelAic = null;
        modelDataPoints = null;
        modelParamErrors = new LinkedHashMap<>();
        secModelMappings = new LinkedHashMap<>();
        secModelParamErrors = new LinkedHashMap<>();
        secModelIndepMins = new LinkedHashMap<>();
        secModelIndepMaxs = new LinkedHashMap<>();
        secModelIndepCategories = new LinkedHashMap<>();
        secModelIndepUnits = new LinkedHashMap<>();
        secModelRmse = new LinkedHashMap<>();
        secModelR2 = new LinkedHashMap<>();
        secModelAic = new LinkedHashMap<>();
        secModelDataPoints = new LinkedHashMap<>();
        columnMappings = new LinkedHashMap<>();
        agentColumn = null;
        agentMappings = new LinkedHashMap<>();
        matrixColumn = null;
        matrixMappings = new LinkedHashMap<>();
        agent = null;
        matrix = null;
        literature = new ArrayList<>();
    }

    public void loadSettings(NodeSettingsRO settings) {
        try {
            fileName = settings.getString(CFG_FILE_NAME);
        } catch (InvalidSettingsException e) {
        }

        try {
            sheetName = settings.getString(CFG_SHEET_NAME);
        } catch (InvalidSettingsException e) {
        }

        try {
            preserveIds = settings.getBoolean(CFG_PRESERVE_IDS);
        } catch (InvalidSettingsException e) {
        }

        try {
            usedIds = XmlConverter.xmlToObject(settings.getString(CFG_USED_IDS), new ArrayList<Integer>());
        } catch (InvalidSettingsException e) {
        }

        try {
            secUsedIds = XmlConverter.xmlToObject(settings.getString(CFG_SEC_USED_IDS),
                    new LinkedHashMap<String, List<Integer>>());
        } catch (InvalidSettingsException e) {
        }

        try {
            globalUsedIds = XmlConverter.xmlToObject(settings.getString(CFG_GLOBAL_USED_IDS), new ArrayList<Integer>());
        } catch (InvalidSettingsException e) {
        }

        try {
            modelTuple = XmlConverter.xmlToTuple(settings.getString(CFG_MODEL_TUPLE));
        } catch (InvalidSettingsException e) {
        }

        try {
            secModelTuples = XmlConverter.xmlToTupleMap(settings.getString(CFG_SEC_MODEL_TUPLES));
        } catch (InvalidSettingsException e) {
        }

        try {
            modelMappings = XmlConverter.xmlToObject(settings.getString(CFG_MODEL_MAPPINGS),
                    new LinkedHashMap<String, String>());
        } catch (InvalidSettingsException e) {
        }

        try {
            modelDepMin = settings.getString(CFG_MODEL_DEP_MIN);
        } catch (InvalidSettingsException e1) {
        }

        try {
            modelDepMax = settings.getString(CFG_MODEL_DEP_MAX);
        } catch (InvalidSettingsException e1) {
        }

        try {
            modelDepUnit = settings.getString(CFG_MODEL_DEP_UNIT);
        } catch (InvalidSettingsException e) {
        }

        try {
            modelIndepMin = settings.getString(CFG_MODEL_INDEP_MIN);
        } catch (InvalidSettingsException e1) {
        }

        try {
            modelIndepMax = settings.getString(CFG_MODEL_INDEP_MAX);
        } catch (InvalidSettingsException e1) {
        }

        try {
            modelIndepUnit = settings.getString(CFG_MODEL_INDEP_UNIT);
        } catch (InvalidSettingsException e1) {
        }

        try {
            modelRmse = settings.getString(CFG_MODEL_RMSE);
        } catch (InvalidSettingsException e1) {
        }

        try {
            modelR2 = settings.getString(CFG_MODEL_R2);
        } catch (InvalidSettingsException e1) {
        }

        try {
            modelAic = settings.getString(CFG_MODEL_AIC);
        } catch (InvalidSettingsException e1) {
        }

        try {
            modelDataPoints = settings.getString(CFG_MODEL_DATA_POINTS);
        } catch (InvalidSettingsException e1) {
        }

        try {
            modelParamErrors = XmlConverter.xmlToObject(settings.getString(CFG_MODEL_PARAM_ERRORS),
                    new LinkedHashMap<String, String>());
        } catch (InvalidSettingsException e) {
        }

        try {
            secModelMappings = XmlConverter.xmlToObject(settings.getString(CFG_SEC_MODEL_MAPPINGS),
                    new LinkedHashMap<String, Map<String, String>>());
        } catch (InvalidSettingsException e) {
        }

        try {
            secModelParamErrors = XmlConverter.xmlToObject(settings.getString(CFG_SEC_MODEL_PARAM_ERRORS),
                    new LinkedHashMap<String, Map<String, String>>());
        } catch (InvalidSettingsException e) {
        }

        try {
            secModelIndepMins = XmlConverter.xmlToObject(settings.getString(CFG_SEC_MODEL_INDEP_MINS),
                    new LinkedHashMap<String, Map<String, String>>());
        } catch (InvalidSettingsException e) {
        }

        try {
            secModelIndepMaxs = XmlConverter.xmlToObject(settings.getString(CFG_SEC_MODEL_INDEP_MAXS),
                    new LinkedHashMap<String, Map<String, String>>());
        } catch (InvalidSettingsException e) {
        }

        try {
            secModelIndepCategories = XmlConverter.xmlToObject(settings.getString(CFG_SEC_MODEL_INDEP_CATEGORIES),
                    new LinkedHashMap<String, Map<String, String>>());
        } catch (InvalidSettingsException e) {
        }

        try {
            secModelIndepUnits = XmlConverter.xmlToObject(settings.getString(CFG_SEC_MODEL_INDEP_UNITS),
                    new LinkedHashMap<String, Map<String, String>>());
        } catch (InvalidSettingsException e) {
        }

        try {
            secModelRmse = XmlConverter.xmlToObject(settings.getString(CFG_SEC_MODEL_RMSE),
                    new LinkedHashMap<String, String>());
        } catch (InvalidSettingsException e) {
        }

        try {
            secModelR2 = XmlConverter.xmlToObject(settings.getString(CFG_SEC_MODEL_R2),
                    new LinkedHashMap<String, String>());
        } catch (InvalidSettingsException e) {
        }

        try {
            secModelAic = XmlConverter.xmlToObject(settings.getString(CFG_SEC_MODEL_AIC),
                    new LinkedHashMap<String, String>());
        } catch (InvalidSettingsException e) {
        }

        try {
            secModelDataPoints = XmlConverter.xmlToObject(settings.getString(CFG_SEC_MODEL_DATA_POINTS),
                    new LinkedHashMap<String, String>());
        } catch (InvalidSettingsException e) {
        }

        try {
            columnMappings = XmlConverter.xmlToObject(settings.getString(CFG_COLUMN_MAPPINGS),
                    new LinkedHashMap<String, Object>());
        } catch (InvalidSettingsException e) {
        }

        try {
            agentColumn = settings.getString(CFG_AGENT_COLUMN);
        } catch (InvalidSettingsException e) {
        }

        try {
            agentMappings = XmlConverter.xmlToObject(settings.getString(CFG_AGENT_MAPPINGS),
                    new LinkedHashMap<String, AgentXml>());
        } catch (InvalidSettingsException e) {
        }

        try {
            matrixColumn = settings.getString(CFG_MATRIX_COLUMN);
        } catch (InvalidSettingsException e) {
        }

        try {
            matrixMappings = XmlConverter.xmlToObject(settings.getString(CFG_MATRIX_MAPPINGS),
                    new LinkedHashMap<String, MatrixXml>());
        } catch (InvalidSettingsException e) {
        }

        try {
            agent = XmlConverter.xmlToObject(settings.getString(CFG_AGENT), null);
        } catch (InvalidSettingsException e) {
        }

        try {
            matrix = XmlConverter.xmlToObject(settings.getString(CFG_MATRIX), null);
        } catch (InvalidSettingsException e) {
        }

        try {
            literature = XmlConverter.xmlToObject(settings.getString(CFG_LITERATURE), new ArrayList<LiteratureItem>());
        } catch (InvalidSettingsException e) {
        }
    }

    public void saveSettings(NodeSettingsWO settings) {
        settings.addString(CFG_FILE_NAME, fileName);
        settings.addString(CFG_SHEET_NAME, sheetName);
        settings.addBoolean(CFG_PRESERVE_IDS, preserveIds);
        settings.addString(CFG_USED_IDS, XmlConverter.objectToXml(usedIds));
        settings.addString(CFG_SEC_USED_IDS, XmlConverter.objectToXml(secUsedIds));
        settings.addString(CFG_GLOBAL_USED_IDS, XmlConverter.objectToXml(globalUsedIds));
        settings.addString(CFG_MODEL_TUPLE, XmlConverter.tupleToXml(modelTuple));
        settings.addString(CFG_SEC_MODEL_TUPLES, XmlConverter.tupleMapToXml(secModelTuples));
        settings.addString(CFG_MODEL_MAPPINGS, XmlConverter.objectToXml(modelMappings));
        settings.addString(CFG_MODEL_DEP_MIN, modelDepMin);
        settings.addString(CFG_MODEL_DEP_MAX, modelDepMax);
        settings.addString(CFG_MODEL_DEP_UNIT, modelDepUnit);
        settings.addString(CFG_MODEL_INDEP_MIN, modelIndepMin);
        settings.addString(CFG_MODEL_INDEP_MAX, modelIndepMax);
        settings.addString(CFG_MODEL_INDEP_UNIT, modelIndepUnit);
        settings.addString(CFG_MODEL_RMSE, modelRmse);
        settings.addString(CFG_MODEL_R2, modelR2);
        settings.addString(CFG_MODEL_AIC, modelAic);
        settings.addString(CFG_MODEL_DATA_POINTS, modelDataPoints);
        settings.addString(CFG_MODEL_PARAM_ERRORS, XmlConverter.objectToXml(modelParamErrors));
        settings.addString(CFG_SEC_MODEL_MAPPINGS, XmlConverter.objectToXml(secModelMappings));
        settings.addString(CFG_SEC_MODEL_PARAM_ERRORS, XmlConverter.objectToXml(secModelParamErrors));
        settings.addString(CFG_SEC_MODEL_INDEP_MINS, XmlConverter.objectToXml(secModelIndepMins));
        settings.addString(CFG_SEC_MODEL_INDEP_MAXS, XmlConverter.objectToXml(secModelIndepMaxs));
        settings.addString(CFG_SEC_MODEL_INDEP_CATEGORIES, XmlConverter.objectToXml(secModelIndepCategories));
        settings.addString(CFG_SEC_MODEL_INDEP_UNITS, XmlConverter.objectToXml(secModelIndepUnits));
        settings.addString(CFG_SEC_MODEL_RMSE, XmlConverter.objectToXml(secModelRmse));
        settings.addString(CFG_SEC_MODEL_R2, XmlConverter.objectToXml(secModelR2));
        settings.addString(CFG_SEC_MODEL_AIC, XmlConverter.objectToXml(secModelAic));
        settings.addString(CFG_SEC_MODEL_DATA_POINTS, XmlConverter.objectToXml(secModelDataPoints));
        settings.addString(CFG_COLUMN_MAPPINGS, XmlConverter.objectToXml(columnMappings));
        settings.addString(CFG_AGENT_COLUMN, agentColumn);
        settings.addString(CFG_AGENT_MAPPINGS, XmlConverter.objectToXml(agentMappings));
        settings.addString(CFG_MATRIX_COLUMN, matrixColumn);
        settings.addString(CFG_MATRIX_MAPPINGS, XmlConverter.objectToXml(matrixMappings));
        settings.addString(CFG_AGENT, XmlConverter.objectToXml(agent));
        settings.addString(CFG_MATRIX, XmlConverter.objectToXml(matrix));
        settings.addString(CFG_LITERATURE, XmlConverter.objectToXml(literature));
    }

    public String getFileName() {
        return fileName;
    }

    public void setFileName(String fileName) {
        this.fileName = fileName;
    }

    public String getSheetName() {
        return sheetName;
    }

    public void setSheetName(String sheetName) {
        this.sheetName = sheetName;
    }

    public boolean isPreserveIds() {
        return preserveIds;
    }

    public void setPreserveIds(boolean preserveIds) {
        this.preserveIds = preserveIds;
    }

    public List<Integer> getUsedIds() {
        return usedIds;
    }

    public void setUsedIds(List<Integer> usedIds) {
        this.usedIds = usedIds;
    }

    public Map<String, List<Integer>> getSecUsedIds() {
        return secUsedIds;
    }

    public void setSecUsedIds(Map<String, List<Integer>> secUsedIds) {
        this.secUsedIds = secUsedIds;
    }

    public List<Integer> getGlobalUsedIds() {
        return globalUsedIds;
    }

    public void setGlobalUsedIds(List<Integer> globalUsedIds) {
        this.globalUsedIds = globalUsedIds;
    }

    public Map<String, String> getModelMappings() {
        return modelMappings;
    }

    public void setModelMappings(Map<String, String> modelMappings) {
        this.modelMappings = modelMappings;
    }

    public String getModelDepMin() {
        return modelDepMin;
    }

    public void setModelDepMin(String modelDepMin) {
        this.modelDepMin = modelDepMin;
    }

    public String getModelDepMax() {
        return modelDepMax;
    }

    public void setModelDepMax(String modelDepMax) {
        this.modelDepMax = modelDepMax;
    }

    public String getModelDepUnit() {
        return modelDepUnit;
    }

    public void setModelDepUnit(String modelDepUnit) {
        this.modelDepUnit = modelDepUnit;
    }

    public String getModelIndepMin() {
        return modelIndepMin;
    }

    public void setModelIndepMin(String modelIndepMin) {
        this.modelIndepMin = modelIndepMin;
    }

    public String getModelIndepMax() {
        return modelIndepMax;
    }

    public void setModelIndepMax(String modelIndepMax) {
        this.modelIndepMax = modelIndepMax;
    }

    public String getModelIndepUnit() {
        return modelIndepUnit;
    }

    public void setModelIndepUnit(String modelIndepUnit) {
        this.modelIndepUnit = modelIndepUnit;
    }

    public String getModelRmse() {
        return modelRmse;
    }

    public void setModelRmse(String modelRmse) {
        this.modelRmse = modelRmse;
    }

    public String getModelR2() {
        return modelR2;
    }

    public void setModelR2(String modelR2) {
        this.modelR2 = modelR2;
    }

    public String getModelAic() {
        return modelAic;
    }

    public void setModelAic(String modelAic) {
        this.modelAic = modelAic;
    }

    public String getModelDataPoints() {
        return modelDataPoints;
    }

    public void setModelDataPoints(String modelDataPoints) {
        this.modelDataPoints = modelDataPoints;
    }

    public Map<String, String> getModelParamErrors() {
        return modelParamErrors;
    }

    public void setModelParamErrors(Map<String, String> modelParamErrors) {
        this.modelParamErrors = modelParamErrors;
    }

    public Map<String, Map<String, String>> getSecModelMappings() {
        return secModelMappings;
    }

    public void setSecModelMappings(Map<String, Map<String, String>> secModelMappings) {
        this.secModelMappings = secModelMappings;
    }

    public Map<String, Map<String, String>> getSecModelParamErrors() {
        return secModelParamErrors;
    }

    public void setSecModelParamErrors(Map<String, Map<String, String>> secModelParamErrors) {
        this.secModelParamErrors = secModelParamErrors;
    }

    public Map<String, Map<String, String>> getSecModelIndepMins() {
        return secModelIndepMins;
    }

    public void setSecModelIndepMins(Map<String, Map<String, String>> secModelIndepMins) {
        this.secModelIndepMins = secModelIndepMins;
    }

    public Map<String, Map<String, String>> getSecModelIndepMaxs() {
        return secModelIndepMaxs;
    }

    public void setSecModelIndepMaxs(Map<String, Map<String, String>> secModelIndepMaxs) {
        this.secModelIndepMaxs = secModelIndepMaxs;
    }

    public Map<String, Map<String, String>> getSecModelIndepCategories() {
        return secModelIndepCategories;
    }

    public void setSecModelIndepCategories(Map<String, Map<String, String>> secModelIndepCategories) {
        this.secModelIndepCategories = secModelIndepCategories;
    }

    public Map<String, Map<String, String>> getSecModelIndepUnits() {
        return secModelIndepUnits;
    }

    public void setSecModelIndepUnits(Map<String, Map<String, String>> secModelIndepUnits) {
        this.secModelIndepUnits = secModelIndepUnits;
    }

    public Map<String, String> getSecModelRmse() {
        return secModelRmse;
    }

    public void setSecModelRmse(Map<String, String> secModelRmse) {
        this.secModelRmse = secModelRmse;
    }

    public Map<String, String> getSecModelR2() {
        return secModelR2;
    }

    public void setSecModelR2(Map<String, String> secModelR2) {
        this.secModelR2 = secModelR2;
    }

    public Map<String, String> getSecModelAic() {
        return secModelAic;
    }

    public void setSecModelAic(Map<String, String> secModelAic) {
        this.secModelAic = secModelAic;
    }

    public Map<String, String> getSecModelDataPoints() {
        return secModelDataPoints;
    }

    public void setSecModelDataPoints(Map<String, String> secModelDataPoints) {
        this.secModelDataPoints = secModelDataPoints;
    }

    public Map<String, Object> getColumnMappings() {
        return columnMappings;
    }

    public void setColumnMappings(Map<String, Object> columnMappings) {
        this.columnMappings = columnMappings;
    }

    public String getAgentColumn() {
        return agentColumn;
    }

    public void setAgentColumn(String agentColumn) {
        this.agentColumn = agentColumn;
    }

    public Map<String, AgentXml> getAgentMappings() {
        return agentMappings;
    }

    public void setAgentMappings(Map<String, AgentXml> agentMappings) {
        this.agentMappings = agentMappings;
    }

    public String getMatrixColumn() {
        return matrixColumn;
    }

    public void setMatrixColumn(String matrixColumn) {
        this.matrixColumn = matrixColumn;
    }

    public Map<String, MatrixXml> getMatrixMappings() {
        return matrixMappings;
    }

    public void setMatrixMappings(Map<String, MatrixXml> matrixMappings) {
        this.matrixMappings = matrixMappings;
    }

    public KnimeTuple getModelTuple() {
        return modelTuple;
    }

    public void setModelTuple(KnimeTuple modelTuple) {
        this.modelTuple = modelTuple;
    }

    public Map<String, KnimeTuple> getSecModelTuples() {
        return secModelTuples;
    }

    public void setSecModelTuples(Map<String, KnimeTuple> secModelTuples) {
        this.secModelTuples = secModelTuples;
    }

    public AgentXml getAgent() {
        return agent;
    }

    public void setAgent(AgentXml agent) {
        this.agent = agent;
    }

    public MatrixXml getMatrix() {
        return matrix;
    }

    public void setMatrix(MatrixXml matrix) {
        this.matrix = matrix;
    }

    public List<LiteratureItem> getLiterature() {
        return literature;
    }

    public void setLiterature(List<LiteratureItem> literature) {
        this.literature = literature;
    }
}