Revize b07f6ea7

re #7885 #8134re #8154 re #8136 added comments and connected switch to allow user to set if he wants to see empty rows or columns in the final table

src/main/java/vldc/aswi/model/table/BooleanWrapper.java

@@ -1 +1 @@
 package vldc.aswi.model.table;
 
+/**
+ * Class used to wrap a boolean value
+ */
 public class BooleanWrapper {
 
+    /**
+     * Boolean value that is wrapped in this class
+     */
     private boolean value;
 
+    /**
+     * Constructor of the boolean wrapper
+     * @param value boolean value to be saved
+     */
     public BooleanWrapper(boolean value) {
         this.value = value;
     }
 
+    /**
+     * Returns the wrapped value
+     * @return wrapped value
+     */
     public boolean isValue() {
         return value;
     }
 
+    /**
+     * Sets the wrapped value
+     * @param value value to be wrapped
+     */
     public void setValue(boolean value) {
         this.value = value;
     }

src/main/java/vldc/aswi/model/table/DoubleWrapper.java

@@ -1 +1 @@
 package vldc.aswi.model.table;
 
+/**
+ * Class used to wrap a double value
+ */
 public class DoubleWrapper {
 
+    /**
+     * Value that is wrapped in this class
+     */
     private double value;
 
+    /**
+     * Constructor of the double wrapper
+     * @param value double value to be saved
+     */
     public DoubleWrapper(double value) {
         this.value = value;
     }
 
+    /**
+     * Returns the wrapped value
+     * @return wrapped value
+     */
     public double getValue() {
         return value;
     }
 
+    /**
+     * Sets the wrapped value
+     * @param value value to be wrapped
+     */
     public void setValue(double value) {
         this.value = value;
     }

src/main/java/vldc/aswi/model/table/Node.java

@@ -8 +8 @@
  */
 public class Node {
 
+    /**
+     * Result of COUNT function.
+     */
     private double totalResult;
 
+    /**
+     * Result of count of AVG function.
+     */
     private double totalResultAvg;
 
+    /**
+     * Result of sum of AVG function.
+     */
     private double totalResultAvgSum;
 
+    /**
+     * Result of SUM function.
+     */
     private double totalResultSum;
 
+    /**
+     * Result of MIN function.
+     */
     private double totalMin;
 
+    /**
+     * Result of MAX function.
+     */
     private double totalMax;
 
+    /**
+     * Tells if the counted value is the first value of the MIN function.
+     */
     private boolean isFirstMin;
 
+    /**
+     * Tells if the counted value is the first value of the MAX function.
+     */
     private boolean isFirstMax;
 
+    /**
+     * Tells if the node is usable if it represents a column.
+     */
     private boolean isUsable;
 
+    /**
+     * Tells if total value of a column is filled.
+     */
     private boolean isFilledTotalValue = false;
 
     /**
@@ -70 +100 @@
         this.values = values;
     }
 
+    /**
+     * Gets the total result of COUNT function if this node represents a column.
+     * @return Total result of COUNT function if this node represents a column.
+     */
     public double getTotalResult() {
         return totalResult;
     }
 
+    /**
+     * Sets the total result of COUNT function if this node represents a column.
+     * @param totalResult Total result to be set if this node represents a column.
+     */
     public void setTotalResult(double totalResult) {
         this.totalResult = totalResult;
     }
 
+    /**
+     * Gets the total result of count of AVG function if this node represents a column.
+     * @return Total result of count of AVG function if this node represents a column.
+     */
     public double getTotalResultAvg() {
         return totalResultAvg;
     }
 
+    /**
+     * Sets the total result of of count of AVG function if this node represents a column.
+     * @param totalResultAvg Total result to be set if this node represents a column.
+     */
     public void setTotalResultAvg(double totalResultAvg) {
         this.totalResultAvg = totalResultAvg;
     }
 
+    /**
+     * Gets the total result of sum of AVG function if this node represents a column.
+     * @return Total result of of sum of AVG function if this node represents a column.
+     */
     public double getTotalResultAvgSum() {
         return totalResultAvgSum;
     }
 
+    /**
+     * Sets the total result of of sum of AVG function if this node represents a column.
+     * @param totalResultAvgSum Total result to be set if this node represents a column.
+     */
     public void setTotalResultAvgSum(double totalResultAvgSum) {
         this.totalResultAvgSum = totalResultAvgSum;
     }
 
+    /**
+     * Gets the total result of SUM function if this node represents a column.
+     * @return Total result of SUM function if this node represents a column.
+     */
     public double getTotalResultSum() {
         return totalResultSum;
     }
 
+    /**
+     * Sets the total result of SUM function if this node represents a column.
+     * @param totalResultSum Total result to be set if this node represents a column.
+     */
     public void setTotalResultSum(double totalResultSum) {
         this.totalResultSum = totalResultSum;
     }
 
+    /**
+     * Gets the total result of MIN function if this node represents a column.
+     * @return Total result of MIN function if this node represents a column.
+     */
     public double getTotalMin() {
         return totalMin;
     }
 
+    /**
+     * Sets the total result of MIN function if this node represents a column.
+     * @param totalMin Total result to be set if this node represents a column.
+     */
     public void setTotalMin(double totalMin) {
         this.totalMin = totalMin;
     }
 
+    /**
+     * Gets the total result of MAX function if this node represents a column.
+     * @return Total result of MAX function if this node represents a column.
+     */
     public double getTotalMax() {
         return totalMax;
     }
 
+    /**
+     * Sets the total result of MAX function if this node represents a column.
+     * @param totalMax Total result to be set if this node represents a column.
+     */
     public void setTotalMax(double totalMax) {
         this.totalMax = totalMax;
     }
 
+    /**
+     * Checks if the value if MIN function has been set if this node represents a column.
+     * @return True of the value of MIN function has been set.
+     */
     public boolean isFirstMin() {
         return isFirstMin;
     }
 
+    /**
+     * Set information that first MIN total value jas been set if this node represents a column.
+     * @param firstMin Value whether total MIN value is set if this node represents a column.
+     */
     public void setFirstMin(boolean firstMin) {
         isFirstMin = firstMin;
     }
 
+    /**
+     * Checks if the value if MAX function has been set if this node represents a column.
+     * @return True of the value of MAX function has been set.
+     */
     public boolean isFirstMax() {
         return isFirstMax;
     }
 
+    /**
+     * Set information that first MAX total value jas been set if this node represents a column.
+     * @param firstMax Value whether total MAX value is set if this node represents a column.
+     */
     public void setFirstMax(boolean firstMax) {
         isFirstMax = firstMax;
     }
 
+    /**
+     * Checks if a column this node represents is usable (has some values).
+     * @return True if a column has some values.
+     */
     public boolean isUsable() {
         return isUsable;
     }
 
+    /**
+     * Sets if a column this node represents is usable (has some values).
+     * @param usable Value whether a column this node represents is usable (has some values).
+     */
     public void setUsable(boolean usable) {
         isUsable = usable;
     }
 
+    /**
+     * Checks if a total value of a column this node represents is set.
+     * @return True if one of the total values is set.
+     */
     public boolean isFilledTotalValue() {
         return isFilledTotalValue;
     }
 
+    /**
+     * Sets if a total value of a column this node represents is set.
+     * @param filledTotalValue Value whether a total value of a column this node represents is set.
+     */
     public void setFilledTotalValue(boolean filledTotalValue) {
         isFilledTotalValue = filledTotalValue;
     }

src/main/java/vldc/aswi/model/table/ValueFunction.java

@@ -6 +6 @@
  */
 public class ValueFunction {
 
+    /**
+     * Result of COUNT function.
+     */
     private double totalResult = 0.0;
 
+    /**
+     * Result of count of AVG function.
+     */
     private double totalResultAvg;
 
+    /**
+     * Result of sum of AVG function.
+     */
     private double totalResultAvgSum;
 
+    /**
+     * Result of SUM function.
+     */
     private double totalResultSum;
 
+    /**
+     * Result of MIN function.
+     */
     private double totalMin;
 
+    /**
+     * Result of MAX function.
+     */
     private double totalMax;
 
+    /**
+     * Tells if the counted value is the first value of the MIN function.
+     */
     private boolean isFirstMin = true;
 
+    /**
+     * Tells if the counted value is the first value of the MAX function.
+     */
     private boolean isFirstMax = true;
 
+    /**
+     * Tells if total value of a column is filled.
+     */
     private boolean isFilledTotalValue = false;
 
     /**
-     * Value
+     * Name of chosen value row in the original table.
      */
     private String nameOfSelect;
 
-    private String name;
+    /**
+     * Name of the value's parameter..
+     */
+    private String parameterName;
 
     /**
-     * Function
+     * Name of function this class represents.
      */
     private String function;
 
+    /**
+     * Type of the value (number, date, etc.).
+     */
     private String type;
 
     /**
@@ -43 +76 @@
      * @param nameOfSelect value
      * @param function function
      */
-    public ValueFunction(String nameOfSelect, String name, String function, String type) {
+    public ValueFunction(String nameOfSelect, String parameterName, String function, String type) {
         this.nameOfSelect = nameOfSelect;
-        this.name = name;
+        this.parameterName = parameterName;
         this.function = function;
         this.type = type;
     }
 
     /**
-     * Gets value.
-     * @return value
+     * Gets name of chosen value row in the original table.
+     * @return Name of chosen value row in the original table.
      */
     public String getNameOfSelect() {
         return nameOfSelect;
     }
 
     /**
-     * Sets value.
-     * @param nameOfSelect value
+     * Sets name of chosen value row in the original table.
+     * @param nameOfSelect Name of chosen value row in the original table.
      */
     public void setNameOfSelect(String nameOfSelect) {
         this.nameOfSelect = nameOfSelect;
     }
 
-    public String getName() {
-        return name;
+    /**
+     * Gets the name of the value's parameter.
+     * @return Name of the value's parameter.
+     */
+    public String getParameterName() {
+        return parameterName;
     }
 
-    public void setName(String name) {
-        this.name = name;
+    public void setParameterName(String parameterName) {
+        this.parameterName = parameterName;
     }
 
     /**
-     * Gets function.
-     * @return function
+     * Gets name of function this class represents.
+     * @return Name of function this class represents.
      */
     public String getFunction() {
         return function;
     }
 
     /**
-     * Sets function.
-     * @param function function.
+     * Sets name of function this class represents.
+     * @param function Name of function this class represents.
      */
     public void setFunction(String function) {
         this.function = function;
     }
 
+    /**
+     * Gets the type of the value (number, date, etc.).
+     * @return Type of the value.
+     */
     public String getType() {
         return type;
     }
 
+    /**
+     * Sets the type of the value (number, date, etc.).
+     * @param type Type of the value.
+     */
     public void setType(String type) {
         this.type = type;
     }
 
+    /**
+     * Gets the total result of COUNT function if this node represents a column.
+     * @return Total result of COUNT function if this node represents a column.
+     */
     public double getTotalResult() {
         return totalResult;
     }
 
+    /**
+     * Sets the total result of COUNT function if this node represents a column.
+     * @param totalResult Total result to be set if this node represents a column.
+     */
     public void setTotalResult(double totalResult) {
         this.totalResult = totalResult;
     }
 
+    /**
+     * Gets the total result of count of AVG function if this node represents a column.
+     * @return Total result of count of AVG function if this node represents a column.
+     */
     public double getTotalResultAvg() {
         return totalResultAvg;
     }
 
+    /**
+     * Sets the total result of of count of AVG function if this node represents a column.
+     * @param totalResultAvg Total result to be set if this node represents a column.
+     */
     public void setTotalResultAvg(double totalResultAvg) {
         this.totalResultAvg = totalResultAvg;
     }
 
+    /**
+     * Gets the total result of sum of AVG function if this node represents a column.
+     * @return Total result of of sum of AVG function if this node represents a column.
+     */
     public double getTotalResultAvgSum() {
         return totalResultAvgSum;
     }
 
+    /**
+     * Sets the total result of of sum of AVG function if this node represents a column.
+     * @param totalResultAvgSum Total result to be set if this node represents a column.
+     */
     public void setTotalResultAvgSum(double totalResultAvgSum) {
         this.totalResultAvgSum = totalResultAvgSum;
     }
 
+    /**
+     * Gets the total result of SUM function if this node represents a column.
+     * @return Total result of SUM function if this node represents a column.
+     */
     public double getTotalResultSum() {
         return totalResultSum;
     }
 
+    /**
+     * Sets the total result of SUM function if this node represents a column.
+     * @param totalResultSum Total result to be set if this node represents a column.
+     */
     public void setTotalResultSum(double totalResultSum) {
         this.totalResultSum = totalResultSum;
     }
 
+    /**
+     * Gets the total result of MIN function if this node represents a column.
+     * @return Total result of MIN function if this node represents a column.
+     */
     public double getTotalMin() {
         return totalMin;
     }
 
+    /**
+     * Sets the total result of MIN function if this node represents a column.
+     * @param totalMin Total result to be set if this node represents a column.
+     */
     public void setTotalMin(double totalMin) {
         this.totalMin = totalMin;
     }
 
+    /**
+     * Gets the total result of MAX function if this node represents a column.
+     * @return Total result of MAX function if this node represents a column.
+     */
     public double getTotalMax() {
         return totalMax;
     }
 
+    /**
+     * Sets the total result of MAX function if this node represents a column.
+     * @param totalMax Total result to be set if this node represents a column.
+     */
     public void setTotalMax(double totalMax) {
         this.totalMax = totalMax;
     }
 
+    /**
+     * Checks if the value if MIN function has been set if this node represents a column.
+     * @return True of the value of MIN function has been set.
+     */
     public boolean isFirstMin() {
         return isFirstMin;
     }
 
+    /**
+     * Set information that first MIN total value jas been set if this node represents a column.
+     * @param firstMin Value whether total MIN value is set if this node represents a column.
+     */
     public void setFirstMin(boolean firstMin) {
         isFirstMin = firstMin;
     }
 
+    /**
+     * Checks if the value if MAX function has been set if this node represents a column.
+     * @return True of the value of MAX function has been set.
+     */
     public boolean isFirstMax() {
         return isFirstMax;
     }
 
+    /**
+     * Set information that first MAX total value jas been set if this node represents a column.
+     * @param firstMax Value whether total MAX value is set if this node represents a column.
+     */
     public void setFirstMax(boolean firstMax) {
         isFirstMax = firstMax;
     }
 
+    /**
+     * Checks if a total value of a column this node represents is set.
+     * @return True if one of the total values is set.
+     */
     public boolean isFilledTotalValue() {
         return isFilledTotalValue;
     }
 
+    /**
+     * Sets if a total value of a column this node represents is set.
+     * @param filledTotalValue Value whether a total value of a column this node represents is set.
+     */
     public void setFilledTotalValue(boolean filledTotalValue) {
         isFilledTotalValue = filledTotalValue;
     }

src/main/java/vldc/aswi/model/table/contingencyTable/ContingencyTableRowCell.java

@@ -46 +46 @@
         return "(" + value + ", " + colSpan + ")";
     }
 
+    /**
+     * Sets the colspan of a cell.
+     * @param colSpan Colspan of a cell.
+     */
     public void setColSpan(int colSpan) {
         this.colSpan = colSpan;
     }

src/main/java/vldc/aswi/service/SqlQueryManager.java

@@ -1 +1 @@
 package vldc.aswi.service;
 
+import vldc.aswi.domain.Assembly;
 import vldc.aswi.domain.Configuration;
 import vldc.aswi.domain.parameter.ParameterInConfiguration;
 import vldc.aswi.model.table.contingencyTable.ContingencyTableRow;
@@ -13 +14 @@
 
     /**
      * Get list of  contingencyTableRow.
+     * @param assembly Assembly from which configuration was created.
+     * @param parametersInConfiguration Parameters in configuration with their locations and operators.
+     * @param isNotRemoveEmpty Sets if empty rows and columns should not be removed.
      * @return List of contingencyTableRow.
      */
-    List<ContingencyTableRow> getContingencyTableRow(Configuration configuration);
+    List<ContingencyTableRow> getContingencyTableRow(Assembly assembly,
+                                                     List<ParameterInConfiguration> parametersInConfiguration,
+                                                     boolean isNotRemoveEmpty);
 
     /**
      * Validate given SQL query.

src/main/java/vldc/aswi/service/SqlQueryManagerImpl.java

@@ -4 +4 @@
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.stereotype.Service;
 import vldc.aswi.database.DatabaseInterface;
+import vldc.aswi.domain.Assembly;
 import vldc.aswi.domain.Configuration;
 import vldc.aswi.domain.Function;
 import vldc.aswi.domain.parameter.ParameterInConfiguration;
@@ -31 +32 @@
 
     /**
      * Get list of  contingencyTableRow.
-     *
-     * @param configuration - configuration from which table will be created.
+     * @param assembly Assembly from which configuration was created.
+     * @param parametersInConfiguration Parameters in configuration with their locations and operators.
+     * @param isNotRemoveEmpty Sets if empty rows and columns should not be removed.
      * @return List of contingencyTableRow.
      */
     @Override
-    public List<ContingencyTableRow> getContingencyTableRow(Configuration configuration) {
+    public List<ContingencyTableRow> getContingencyTableRow(Assembly assembly,
+                                                            List<ParameterInConfiguration> parametersInConfiguration,
+                                                            boolean isNotRemoveEmpty) {
         long startTime = System.nanoTime();
 
         Map<String, TableColumn> tableColumns = this.databaseInterface.executeQueryAndReturnTableColumns(
-                generateFullSQLQuery(configuration.getAssembly().getSQLQuery(), configuration.getParametersInConfiguration())
+                generateFullSQLQuery(assembly.getSQLQuery(), parametersInConfiguration)
         );
 
         long stopTime = System.nanoTime();
@@ -50 +54 @@
         List<ValueFunction> valueFunctions = new ArrayList<>();
 
         // Create a copy of list.
-        List<ParameterInConfiguration> copiedParametersInConfiguration = new ArrayList<>(configuration.getParametersInConfiguration());
+        List<ParameterInConfiguration> copiedParametersInConfiguration = new ArrayList<>(parametersInConfiguration);
 
         // sort parameters in configuration to have them in order set by user
         Collections.sort(copiedParametersInConfiguration);
 
         initializeContingencyTableDataLists(rowNames, columnNames, valueFunctions, copiedParametersInConfiguration);
 
-        Converter converter = new Converter(tableColumns, rowNames, columnNames, valueFunctions, true);
+        Converter converter = new Converter(tableColumns, rowNames, columnNames, valueFunctions, isNotRemoveEmpty);
         return converter.convertTableColumnsToContingencyTableRows();
     }
 
@@ -83 +87 @@
     private void initializeContingencyTableDataLists(List<NameUserName> rowNames, List<NameUserName> columnNames,
                                                      List<ValueFunction> valueFunctions, List<ParameterInConfiguration> parametersInConfiguration) {
         for (ParameterInConfiguration parameterInConfiguration : parametersInConfiguration) {
-            if (parameterInConfiguration.getLocation() != null && parameterInConfiguration.getLocation().getName().equals("Řádek")) {
-                rowNames.add(new NameUserName(parameterInConfiguration.getParameter().getNameOfSelect().toUpperCase(),
-                        parameterInConfiguration.getColumnName()));
-            } else if (parameterInConfiguration.getLocation() != null && parameterInConfiguration.getLocation().getName().equals("Sloupec")) {
-                columnNames.add(new NameUserName(parameterInConfiguration.getParameter().getNameOfSelect().toUpperCase(),
-                        parameterInConfiguration.getColumnName()));
-            } else if (parameterInConfiguration.getLocation() != null && parameterInConfiguration.getLocation().getName().equals("Hodnota")) {
+            if (parameterInConfiguration.getLocation().getName() != null && parameterInConfiguration.getLocation().getName().equals("Řádek")) {
+                if (parameterInConfiguration.getColumnName() != null && !parameterInConfiguration.getColumnName().equals("")) {
+                    rowNames.add(new NameUserName(parameterInConfiguration.getParameter().getNameOfSelect().toUpperCase(),
+                            parameterInConfiguration.getColumnName()));
+                }
+                else {
+                    rowNames.add(new NameUserName(parameterInConfiguration.getParameter().getNameOfSelect().toUpperCase(),
+                            parameterInConfiguration.getParameter().getName()));
+                }
+            } else if (parameterInConfiguration.getLocation().getName() != null && parameterInConfiguration.getLocation().getName().equals("Sloupec")) {
+                if (parameterInConfiguration.getColumnName() != null && !parameterInConfiguration.getColumnName().equals("")) {
+                    columnNames.add(new NameUserName(parameterInConfiguration.getParameter().getNameOfSelect().toUpperCase(),
+                            parameterInConfiguration.getColumnName()));
+                }
+                else {
+                    columnNames.add(new NameUserName(parameterInConfiguration.getParameter().getNameOfSelect().toUpperCase(),
+                            parameterInConfiguration.getParameter().getName()));
+                }
+            } else if (parameterInConfiguration.getLocation().getName() != null && parameterInConfiguration.getLocation().getName().equals("Hodnota")) {
                 for (Function function : parameterInConfiguration.getFunctions()) {
                     valueFunctions.add(new ValueFunction(parameterInConfiguration.getParameter().getNameOfSelect().toUpperCase(),
                             parameterInConfiguration.getParameter().getName(), function.getName().toUpperCase(),
@@ -108 +124 @@
         }
     }
 
+    /**
+     * Generates full SQL query with all the filters
+     * @param basicSQLQuery SQL query saved in assembly
+     * @param parametersInConfiguration Parameters in configuration.
+     * @return SQL query with filters.
+     */
     private String generateFullSQLQuery(String basicSQLQuery, List<ParameterInConfiguration> parametersInConfiguration) {
         StringBuilder finalSQLQuery = new StringBuilder("SELECT * FROM (");
         finalSQLQuery.append(basicSQLQuery);
@@ -128 +150 @@
         return finalSQLQuery.toString();
     }
 
+    /**
+     * Precesses listing (enum) type.
+     * @param parameterInConfiguration Listing type parameter iin configuration.
+     * @param finalSQLQuery Resulting SQL query.
+     * @param isWhereDefined Variable storing information if WHERE clause was defined in the resulting SQL query.
+     * @return Information that WHERE clause was defined.
+     */
     private boolean processListing(ParameterInConfiguration parameterInConfiguration, StringBuilder finalSQLQuery, boolean isWhereDefined) {
         if (!isWhereDefined) {
             finalSQLQuery.append(" WHERE ");
@@ -142 +171 @@
         return true;
     }
 
+    /**
+     * Process filter of parameter in configuration.
+     * @param parameterInConfiguration Parameter in configuration.
+     * @param finalSQLQuery Resulting SQL query.
+     * @param isWhereDefined Variable storing information if WHERE clause was defined in the resulting SQL query.
+     * @return Information that WHERE clause was defined
+     */
     private boolean processFilter(ParameterInConfiguration parameterInConfiguration, StringBuilder finalSQLQuery, boolean isWhereDefined) {
         String[] values = parameterInConfiguration.getOperatorValue().split(";");
         if (!isWhereDefined) {
@@ -179 +215 @@
         return true;
     }
 
+    /**
+     * Validate LIKE and NOT LIKE operator.
+     * @param values Values set by user.
+     * @param type Type of the parameter.
+     * @return String to be added to SQL query.
+     */
     private String likeNotLike(String[] values, String type) {
         StringBuilder SQLQueryPart = new StringBuilder();
         addQuotes(type, SQLQueryPart);
@@ -188 +230 @@
         return SQLQueryPart.toString();
     }
 
+    /**
+     * Validate IN and NOT IN operator.
+     * @param values Values set by user.
+     * @param type Type of the parameter.
+     * @return String to be added to SQL query.
+     */
     private String inNotIn(String[] values, String type) {
         StringBuilder SQLQueryPart = new StringBuilder();
         SQLQueryPart.append("(");
@@ -204 +252 @@
         return SQLQueryPart.toString();
     }
 
+    /**
+     * Validate BETWEEN and NOT BETWEEN operator.
+     * @param values Values set by user.
+     * @param type Type of the parameter.
+     * @return String to be added to SQL query.
+     */
     private String betweenNotBetween(String[] values, String type) {
         StringBuilder SQLQueryPart = new StringBuilder();
 
@@ -220 +274 @@
         return SQLQueryPart.toString();
     }
 
+    /**
+     * Validate other operators.
+     * @param values Values set by user.
+     * @param type Type of the parameter.
+     * @return String to be added to SQL query.
+     */
     private String otherOperators(String[] values, String type) {
         StringBuilder SQLQueryPart = new StringBuilder();
 
@@ -230 +290 @@
         return SQLQueryPart.toString();
     }
 
+    /**
+     * Adds quote to the value.
+     * @param type Type Type of the parameter.
+     * @param SQLQueryPart Appends quote to the final SQL query.
+     */
     private void addQuotes(String type, StringBuilder SQLQueryPart) {
         if (type.equals("Text") || type.equals("Datum")) {
             SQLQueryPart.append("'");

src/main/java/vldc/aswi/service/parameter/ParameterManager.java

@@ -36 +36 @@
      * @return true if all parameters was successfully deleted, false if not.
      */
     boolean deleteParameters(Long assemblyId);
+
+    /**
+     * Gets a parameter by its ID
+     * @param id ID of the parameter
+     * @return parameter with selected ID
+     */
+    Parameter getParameterById(Long id);
 }

src/main/java/vldc/aswi/service/parameter/ParameterManagerImpl.java

@@ -494 +494 @@
             return false;
         }
     }
+
+    /**
+     * Gets a parameter by its ID
+     * @param id ID of the parameter
+     * @return parameter with selected ID
+     */
+    public Parameter getParameterById(Long id) {
+        return parameterRepository.getById(id);
+    }
 }

src/main/java/vldc/aswi/utils/Converter.java

@@ -11 +11 @@
 import java.util.concurrent.TimeUnit;
 
 /**
- * Class for converting classes.
+ * Class used to convert original table to contingency table.
  */
 public class Converter {
 
+    /**
+     * Stores information about whether user set switch to show empty rows and columns to ON.
+     */
     private final boolean isNotRemoveEmpty;
 
+    /**
+     * Map of original table.
+     */
     private final Map<String, TableColumn> tableColumns;
+
+    /**
+     * List of names and user names of selected rows.
+     */
     private final List<NameUserName> rowNames;
+
+    /**
+     * List of names and user names of selected columns.
+     */
     private final List<NameUserName> columnNames;
+
+    /**
+     * List of information about selected value and functions.
+     */
     private final List<ValueFunction> valueFunctions;
 
+    /**
+     * List of columns node of contingency table going from left to right.
+     */
     private List<Node> columnNodes;
+
+    /**
+     * Formatter of the cell content.
+     */
     private final DecimalFormat decimalFormat = new DecimalFormat("0.###");
 
+    /**
+     * Creates and initializes converter.
+     * @param tableColumns Map of original table.
+     * @param rowNames List of names and user names of selected rows.
+     * @param columnNames List of names and user names of selected columns.
+     * @param valueFunctions List of information about selected value and functions.
+     * @param isNotRemoveEmpty Stores information about whether user set switch to show empty rows and columns to ON.
+     */
     public Converter(Map<String, TableColumn> tableColumns, List<NameUserName> rowNames, List<NameUserName> columnNames,
                      List<ValueFunction> valueFunctions, boolean isNotRemoveEmpty) {
         this.tableColumns = tableColumns;
@@ -126 +159 @@
         List<String> prevValues = new ArrayList<>();
         int prevSize = 0;
         for (ValueFunction valueFunction : valueFunctions) {
-            headerRows.get(0).addTableRowCell(new ContingencyTableRowCell(valueFunction.getFunction() + " z " + valueFunction.getName(), 0));
+            headerRows.get(0).addTableRowCell(new ContingencyTableRowCell(valueFunction.getFunction() + " z " + valueFunction.getParameterName(), 0));
             for (Node columnNode : columnNodes) {
                 for (int i = 0; i < columnNode.getValues().size(); i++) {
                     String value = columnNode.getValues().get(i);
@@ -162 +195 @@
                 headerRows.get(i).addTableRowCell(new ContingencyTableRowCell("", 1));
             }
             headerRows.get(0).addTableRowCell(new ContingencyTableRowCell("Celkový " + valueFunction.getFunction() +
-                    " z " + valueFunction.getName(), 1));
+                    " z " + valueFunction.getParameterName(), 1));
         }
 
         return headerRows;
@@ -315 +348 @@
         }
 
         DoubleWrapper[] totals = new DoubleWrapper[valueFunctions.size()];
-        initializeWrapperField(totals);
+        initializeDoubleWrapperField(totals);
 
         DoubleWrapper[] totalsAvgSum = new DoubleWrapper[valueFunctions.size()];
-        initializeWrapperField(totalsAvgSum);
+        initializeDoubleWrapperField(totalsAvgSum);
 
         boolean[] isFilledValueCells = new boolean[valueFunctions.size()];
         //hodnota
@@ -419 +452 @@
         return ids;
     }
 
+    /**
+     * Checks if column is usable by going through all values of columns of a node in the original table.
+     * @param columnNodeValues Values of a column node.
+     * @return True if all values of a node are present in the original table columns.
+     */
     private boolean checkIfColumnIsUsable(List<String> columnNodeValues) {
         for (int i = 0; i < tableColumns.get(columnNames.get(0).getName()).getValues().size(); i++) {
             boolean isUsable = true;
@@ -437 +475 @@
         return false;
     }
 
+    /**
+     * Computes value of the cell in regards to function.
+     * @param valueFunction Function that should be computed for a cell.
+     * @param result Variable to which result is saved.
+     * @param resultAvgSum Variable to which sum is saved of a function is AVG.
+     * @param columnNode Column node of a cell.
+     * @param isFirstMinMax Tells if the counted value is the first value of the MIN or MAX function.
+     * @param usableID ID of the row in the original table.
+     * @param isValueTotal Tells if a value is total value for the given function.
+     * @param isSingleValueRow Tells whether a row only has single value (only represents one column of the original table).
+     */
     private void computeValues(ValueFunction valueFunction, DoubleWrapper result, DoubleWrapper resultAvgSum, Node columnNode,
                                BooleanWrapper isFirstMinMax, int usableID, boolean isValueTotal, boolean isSingleValueRow) {
         switch (valueFunction.getFunction()) {
@@ -458 +507 @@
         }
     }
 
+    /**
+     * Generates a cell with filled data.
+     * @param function Name of the function.
+     * @param totalResult Result of COUNT function to be saved.
+     * @param totalResultSum Result of SUM function to be saved.
+     * @param totalMin Result of MIN function to be saved.
+     * @param totalMax Result of MAX function to be saved.
+     * @param totalResultAvgSum Result of sum of AVG function to be saved.
+     * @param totalResultAvg Result of count of AVG function to be saved.
+     * @return Generated and filled cell.
+     */
     private ContingencyTableRowCell generateFilledCell(String function, double totalResult, double totalResultSum,
                                                        double totalMin, double totalMax, double totalResultAvgSum,
                                                        double totalResultAvg) {
@@ -487 +547 @@
         return cell;
     }
 
-    private void initializeWrapperField(DoubleWrapper[] field) {
+    /**
+     * Initializes a filled of the values of a DoubleWrapper type.
+     * @param field Field to be initialized.
+     */
+    private void initializeDoubleWrapperField(DoubleWrapper[] field) {
         for (int i = 0; i < field.length; i++) {
             field[i] = new DoubleWrapper(0);
         }
     }
 
+    /**
+     * Calculates COUNT function.
+     * @param valueFunction Function that should be computed for a cell.
+     * @param result Variable to which result is saved.
+     * @param columnNode Column node of a cell.
+     * @param isValueTotal Tells if a value is total value for the given function.
+     * @param isSingleValueRow Tells whether a row only has single value (only represents one column of the original table).
+     */
     private void count(ValueFunction valueFunction, DoubleWrapper result, Node columnNode, boolean isValueTotal,
                        boolean isSingleValueRow) {
         result.setValue(result.getValue() + 1);
@@ -504 +576 @@
         }
     }
 
+    /**
+     * Calculates SUM function.
+     * @param valueFunction Function that should be computed for a cell.
+     * @param result Variable to which result is saved.
+     * @param columnNode Column node of a cell.
+     * @param usableID ID of the row in the original table.
+     * @param isValueTotal Tells if a value is total value for the given function.
+     * @param isSingleValueRow Tells whether a row only has single value (only represents one column of the original table).
+     */
     private void sum(ValueFunction valueFunction, DoubleWrapper result, Node columnNode, int usableID, boolean isValueTotal,
                      boolean isSingleValueRow) {
         if (valueFunction.getType().equals("Číslo")) {
@@ -517 +598 @@
         }
     }
 
+    /**
+     * Calculates MIN function.
+     * @param valueFunction Function that should be computed for a cell.
+     * @param result Variable to which result is saved.
+     * @param columnNode Column node of a cell.
+     * @param isFirstMinMax Tells if the counted value is the first value of the MIN or MAX function.
+     * @param usableID ID of the row in the original table.
+     * @param isValueTotal Tells if a value is total value for the given function.
+     * @param isSingleValueRow Tells whether a row only has single value (only represents one column of the original table).
+     */
     private void min(ValueFunction valueFunction, DoubleWrapper result, Node columnNode, BooleanWrapper isFirstMinMax,
                      int usableID, boolean isValueTotal, boolean isSingleValueRow) {
         if (valueFunction.getType().equals("Číslo")) {
@@ -546 +637 @@
         }
     }
 
+    /**
+     * Calculates MAX function.
+     * @param valueFunction Function that should be computed for a cell.
+     * @param result Variable to which result is saved.
+     * @param columnNode Column node of a cell.
+     * @param isFirstMinMax Tells if the counted value is the first value of the MIN or MAX function.
+     * @param usableID ID of the row in the original table.
+     * @param isValueTotal Tells if a value is total value for the given function.
+     * @param isSingleValueRow Tells whether a row only has single value (only represents one column of the original table).
+     */
     private void max(ValueFunction valueFunction, DoubleWrapper result, Node columnNode, BooleanWrapper isFirstMinMax,
                      int usableID, boolean isValueTotal, boolean isSingleValueRow) {
         if (valueFunction.getType().equals("Číslo")) {
@@ -575 +676 @@
         }
     }
 
+    /**
+     * Calculates AVG function.
+     * @param valueFunction Function that should be computed for a cell.
+     * @param result Variable to which count result is saved.
+     * @param resultAvgSum Variable to which sum result is saved.
+     * @param columnNode Column node of a cell.
+     * @param usableID ID of the row in the original table.
+     * @param isValueTotal Tells if a value is total value for the given function.
+     * @param isSingleValueRow Tells whether a row only has single value (only represents one column of the original table).
+     */
     private void average(ValueFunction valueFunction, DoubleWrapper result, DoubleWrapper resultAvgSum, Node columnNode,
                          int usableID, boolean isValueTotal, boolean isSingleValueRow) {
         if (valueFunction.getType().equals("Číslo")) {
@@ -591 +702 @@
         }
     }
 
+    /**
+     * Generates a final row, with total values of columns.
+     * @return Final row filled with data.
+     */
     private ContingencyTableRow createFinalRow() {
         ContingencyTableRow finalRow = new ContingencyTableRow(false, 0);
         finalRow.addTableRowCell(new ContingencyTableRowCell("Celkem", 1));

src/main/java/vldc/aswi/validators/ConfigurationValidator.java

@@ -29 +29 @@
         return Configuration.class.isAssignableFrom(aClass);
     }
 
+    /**
+     * Validates the given configuration object.
+     * @param obj Configuration object to be validated.
+     * @param errors Errors variable where errors are stored.
+     */
     @Override
     public void validate(Object obj, Errors errors) {
         Configuration configuration = (Configuration) obj;
@@ -56 +61 @@
 
     }
 
+    /**
+     * Validates BETWEEN and NOT BETWEEN operator.
+     * @param parameterInConfiguration Parameter in configuration to be validated.
+     * @param errors Errors variable where errors are stored.
+     * @param i Index of the parameter.
+     * @param operator Operator of the parameter in configuration.
+     */
     private void validateBETWEEN(ParameterInConfiguration parameterInConfiguration, Errors errors, int i, String operator) {
         if (!parameterInConfiguration.getOperatorValue().matches("\\w+;\\w+")) {
             errors.rejectValue("parametersInConfiguration[" + i + "].operatorValue", "Nesprávně oddělené hodnoty" +
@@ -66 +78 @@
         }
     }
 
+    /**
+     * Validates values in list.
+     * @param parameterInConfiguration Parameter in configuration to be validated.
+     * @param errors Errors variable where errors are stored.
+     * @param i Index of the parameter.
+     * @param operator Operator of the parameter in configuration.
+     */
     private void validateValuesInList(ParameterInConfiguration parameterInConfiguration, Errors errors, int i, String operator) {
         String[] values = parameterInConfiguration.getOperatorValue().split(";");
         for (String value : values) {
@@ -78 +97 @@
         }
     }
 
+    /**
+     * Validates IN and NOT IN operator.
+     * @param parameterInConfiguration Parameter in configuration to be validated.
+     * @param errors Errors variable where errors are stored.
+     * @param i Index of the parameter.
+     * @param operator Operator of the parameter in configuration.
+     */
     private void validateIN(ParameterInConfiguration parameterInConfiguration, Errors errors, int i, String operator) {
         if (!parameterInConfiguration.getOperatorValue().matches("\\w+(;\\w+)*$")) {
             errors.rejectValue("parametersInConfiguration[" + i + "].operatorValue", "Špatně zadaná hodnota" +
@@ -88 +114 @@
         }
     }
 
+    /**
+     * Validates other operators.
+     * @param parameterInConfiguration Parameter in configuration to be validated.
+     * @param errors Errors variable where errors are stored.
+     * @param i Index of the parameter.
+     * @param operator Operator of the parameter in configuration.
+     */
     private void validateOthersExceptLIKE(ParameterInConfiguration parameterInConfiguration, Errors errors, int i, String operator) {
         if (parameterInConfiguration.getParameter().getParameterType().getName().equals("Datum")) {
             validateDate(parameterInConfiguration.getOperatorValue(), errors, i, operator);
@@ -97 +130 @@
         }
     }
 
+    /**
+     * Validates numeric value.
+     * @param value Value to be validated.
+     * @param errors Errors variable where errors are stored.
+     * @param i Index of hte parameter.
+     * @param operator operator Operator of the parameter in configuration.
+     */
     private void validateNumber(String value, Errors errors, int i, String operator) {
         if (!value.matches("-?\\d+(\\.\\d+)?")) {
             errors.rejectValue("parametersInConfiguration[" + i + "].operatorValue", "Špatně zadaná hodnota" +
@@ -104 +144 @@
         }
     }
 
+    /**
+     * Validates date value.
+     * @param value Value to be validated.
+     * @param errors Errors variable where errors are stored.
+     * @param i Index of hte parameter.
+     * @param operator operator Operator of the parameter in configuration.
+     */
     private void validateDate(String value, Errors errors, int i, String operator) {
         try {
             new SimpleDateFormat("yyyy-MM-dd").parse(value);

src/main/java/vldc/aswi/web/controller/AssemblyController.java

@@ -6 +6 @@
 import org.springframework.validation.BeanPropertyBindingResult;
 import org.springframework.validation.BindingResult;
 import org.springframework.web.bind.WebDataBinder;
-import org.springframework.web.bind.annotation.GetMapping;
-import org.springframework.web.bind.annotation.InitBinder;
-import org.springframework.web.bind.annotation.ModelAttribute;
-import org.springframework.web.bind.annotation.PostMapping;
-import org.springframework.web.bind.annotation.RequestParam;
+import org.springframework.web.bind.annotation.*;
 import org.springframework.web.servlet.ModelAndView;
 import org.springframework.web.servlet.mvc.support.RedirectAttributes;
 import vldc.aswi.domain.*;
 import vldc.aswi.domain.parameter.Parameter;
 import vldc.aswi.domain.parameter.ParameterInConfiguration;
+import vldc.aswi.model.table.BooleanWrapper;
 import vldc.aswi.model.table.contingencyTable.ContingencyTableRow;
 import vldc.aswi.service.*;
 import vldc.aswi.service.parameter.ParameterManager;
@@ -26 +23 @@
 import vldc.aswi.validators.ConfigurationValidator;
 
 import javax.validation.Valid;
-import java.util.ArrayList;
-import java.util.Comparator;
-import java.util.List;
-import java.util.Set;
+import java.util.*;
 import java.util.stream.Collectors;
 
 /**
@@ -46 +40 @@
     @Autowired
     private AssemblyManager assemblyManager;
 
+    /** Autowired parameter manager. */
+    @Autowired
+    private ParameterManager parameterManager;
+
     /** Autowired configuration manager */
     @Autowired
     private ConfigurationManager configurationManager;
@@ -70 +68 @@
     @Autowired
     private LocationManager locationManager;
 
-    /** Autowired parameter manager. */
-    @Autowired
-    private ParameterManager parameterManager;
-
     /** Autowired assembly validator */
     @Autowired
     private AssemblyValidator assemblyValidator;
@@ -148 +142 @@
 
         Comparator<ParameterInConfiguration> comparator = Comparator.comparingInt(o -> o.getParameter().getParameterOrder());
 
+        boolean isNotRemoveEmpty = false;
+        modelMap.addAttribute("isNotRemoveEmpty", isNotRemoveEmpty);
         modelMap.addAttribute("configuration", configuration);
         modelMap.addAttribute("comparator", comparator);
         modelMap.addAttribute("formAction", "/assembly?assemblyID=" + assembly.getId());
@@ -167 +163 @@
     public ModelAndView assemblyPost(Configuration newConfiguration,
                                      BindingResult bindingResult,
                                      RedirectAttributes atts,
+                                     @RequestParam("isNotRemoveEmpty") String isNotRemoveEmptyString,
                                      @RequestParam("assemblyID") String id,
                                      @RequestParam(required=false, value="generateTable") String generateTable,
                                      @RequestParam(required=false, value="exportXls") String exportXls,
@@ -207 +204 @@
                 modelMap.addAttribute(assemblyTitleName, generateTableTitleText + " " + newConfiguration.getName());
             }
             else {
-                List<ContingencyTableRow> rows = this.sqlQueryManager.getContingencyTableRow(newConfiguration);
+                boolean isNotRemoveEmpty = isNotRemoveEmptyString == null || !isNotRemoveEmptyString.equals("");
+                List<ContingencyTableRow> rows = this.sqlQueryManager.getContingencyTableRow(newConfiguration.getAssembly(),
+                        newConfiguration.getParametersInConfiguration(), isNotRemoveEmpty);
 
                 System.out.println("Generuj tabulku");
                 modelMap.addAttribute("configurationID", id);
                 modelMap.addAttribute("contingencyTableRows", rows);
+                modelMap.addAttribute("isNotRemoveEmpty", isNotRemoveEmpty);
                 addConfigurationDataIntoModelAndView(newConfiguration, modelAndView, modelMap);
             }
         }
@@ -254 +254 @@
  */
     }
 
+    /**
+     * Adds configuration and other data to modelAndView.
+     * @param newConfiguration Configuration to be added to the modelAndView.
+     * @param modelAndView ModelAndView to which to which modelMap belongs.
+     * @param modelMap ModelMap to which data is added.
+     */
     private void addConfigurationDataIntoModelAndView(Configuration newConfiguration, ModelAndView modelAndView, ModelMap modelMap) {
         Comparator<ParameterInConfiguration> comparator = Comparator.comparingInt(o -> o.getParameter().getParameterOrder());
         initializeFields(newConfiguration);
@@ -454 +460 @@
 
         for(int i = 0; i < configuration.getParametersInConfiguration().size(); i++) {
             ParameterInConfiguration parameterInConfiguration = configuration.getParametersInConfiguration().get(i);
-            parameterInConfiguration.setParameter(assembly.getParameters().get(i));
+            parameterInConfiguration.setParameter(parameterManager.getParameterById(parameterInConfiguration.getParameter().getId()));
             if (parameterInConfiguration.getLocation() != null) {
                 parameterInConfiguration.setLocation(locationManager.getLocationById(parameterInConfiguration.getLocation().getId()));
+            } else {
+                parameterInConfiguration.setLocation(new Location());
             }
+            parameterInConfiguration.setConfiguration(configuration);
         }
+
+        Comparator<ParameterInConfiguration> comparator = Comparator.comparingInt(o -> o.getParameter().getParameterOrder());
+        configuration.getParametersInConfiguration().sort(comparator);
     }
 }

src/main/java/vldc/aswi/web/controller/ConfigurationController.java

@@ -19 +19 @@
 import vldc.aswi.service.ConfigurationManager;
 import vldc.aswi.service.LocationManager;
 import vldc.aswi.service.SqlQueryManager;
+import vldc.aswi.service.parameter.ParameterManager;
 import vldc.aswi.utils.AuthControl;
 import vldc.aswi.utils.Utils;
 import vldc.aswi.validators.AssemblyValidator;
@@ -47 +48 @@
     @Autowired
     private SqlQueryManager sqlQueryManager;
 
+    /** Autowired parameter manager. */
+    @Autowired
+    private ParameterManager parameterManager;
+
     /** Autowired configuration manager */
     @Autowired
     private ConfigurationManager configurationManager;
@@ -114 +119 @@
     @PostMapping("/configuration")
     public ModelAndView configurationPost(@Valid Configuration newConfiguration,
                                            BindingResult bindingResult,
+                                           @RequestParam("isNotRemoveEmpty") String isNotRemoveEmptyString,
                                            @RequestParam("configurationID") String id,
                                            @RequestParam(required=false, value="generateTable") String generateTable,
                                            @RequestParam(required=false, value="exportXls") String exportXls,
@@ -144 +150 @@
                 modelMap.addAttribute(assemblyTitleName, generateTableTitleText + " " + newConfiguration.getName());
             }
             else {
-                List<ContingencyTableRow> rows = this.sqlQueryManager.getContingencyTableRow(newConfiguration);
+                boolean isNotRemoveEmpty = isNotRemoveEmptyString == null || !isNotRemoveEmptyString.equals("");
+                List<ContingencyTableRow> rows = this.sqlQueryManager.getContingencyTableRow(newConfiguration.getAssembly(),
+                        newConfiguration.getParametersInConfiguration(), isNotRemoveEmpty);
                 System.out.println("Generuj tabulku");
                 modelMap.addAttribute("configurationID", id);
                 modelMap.addAttribute("contingencyTableRows", rows);
@@ -232 +240 @@
 
         for(int i = 0; i < configuration.getParametersInConfiguration().size(); i++) {
             ParameterInConfiguration parameterInConfiguration = configuration.getParametersInConfiguration().get(i);
+            parameterInConfiguration.setParameter(parameterManager.getParameterById(parameterInConfiguration.getParameter().getId()));
             parameterInConfiguration.setParameter(assembly.getParameters().get(i));
             if (parameterInConfiguration.getLocation() != null) {
                 parameterInConfiguration.setLocation(locationManager.getLocationById(parameterInConfiguration.getLocation().getId()));
+            } else {
+                parameterInConfiguration.setLocation(new Location());
             }
+            parameterInConfiguration.setConfiguration(configuration);
         }
+
+        Comparator<ParameterInConfiguration> comparator = Comparator.comparingInt(o -> o.getParameter().getParameterOrder());
+        configuration.getParametersInConfiguration().sort(comparator);
     }
 
+    /**
+     * Adds configuration and other data to modelAndView.
+     * @param newConfiguration Configuration to be added to the modelAndView.
+     * @param modelAndView ModelAndView to which to which modelMap belongs.
+     * @param modelMap ModelMap to which data is added.
+     */
     private void addConfigurationDataIntoModelAndView(Configuration newConfiguration, ModelAndView modelAndView, ModelMap modelMap) {
         Comparator<ParameterInConfiguration> comparator = Comparator.comparingInt(o -> o.getParameter().getParameterOrder());
         initializeFields(newConfiguration);

src/main/webapp/WEB-INF/templates/assembly.html

@@ -19 +19 @@
 
         <form th:object="${configuration}" method="post" th:action="@{${formAction}}">
             <input type="hidden" th:field="*{assembly.id}" th:value="${configuration.assembly?.getId()}"/>
+            <input type="hidden" name="isNotRemoveEmpty"/>
             <div class="container box">
                 <div class="col-md-12">
                     <div class="col-md-12 form-group row">
@@ -37 +38 @@
                             </tr>
                             </thead>
                             <tbody>
-                            <tr th:each="parameterInConfiguration, itemStat : ${#lists.sort(configuration.parametersInConfiguration, comparator)}" class="parameter-row">
-                               <input type="hidden" class="parameterIndex" th:value="${itemStat.index}">
+                            <tr th:each="parameterInConfiguration, itemStat : ${configuration.parametersInConfiguration}" class="parameter-row">
+                                <input type="hidden" class="parameterIndex" th:value="${itemStat.index}">
+                                <input type="hidden" th:field="${configuration.parametersInConfiguration[__${itemStat.index}__].parameter.id}"/>
                                 <td>
                                     <span class="select-text-padding parameter-name"
                                           th:text="${parameterInConfiguration.parameter.name}"></span>
@@ -200 +202 @@
                     </div>
 
                     <div class="custom-control custom-switch form-group">
-                        <input type="checkbox" class="custom-control-input" id="customSwitch1" checked>
+                        <input type="checkbox" class="custom-control-input" id="customSwitch1" th:checked="${isNotRemoveEmpty}" name="isNotRemoveEmpty">
                         <label class="custom-control-label" for="customSwitch1">Zobrazovat prázdné řádky</label>
                     </div>