AttributeColumnsControllerImpl.java

/*
Copyright 2008-2010 Gephi
Authors : Eduardo Ramos <eduramiba@gmail.com>
Website : http://www.gephi.org

This file is part of Gephi.

Gephi is free software: you can redistribute it and/or modify
it under the terms of the GNU Affero General Public License as
published by the Free Software Foundation, either version 3 of the
License, or (at your option) any later version.

Gephi 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 Affero General Public License for more details.

You should have received a copy of the GNU Affero General Public License
along with Gephi.  If not, see <http://www.gnu.org/licenses/>.
 */
package org.gephi.datalab.impl;

import com.csvreader.CsvReader;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.math.BigDecimal;
import java.nio.charset.Charset;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.Map;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
import org.gephi.data.attributes.api.AttributeColumn;
import org.gephi.data.attributes.api.AttributeController;
import org.gephi.data.attributes.api.AttributeOrigin;
import org.gephi.data.attributes.api.AttributeRow;
import org.gephi.data.attributes.api.AttributeTable;
import org.gephi.data.attributes.api.AttributeType;
import org.gephi.data.attributes.api.AttributeUtils;
import org.gephi.data.attributes.api.AttributeValue;
import org.gephi.data.attributes.type.BooleanList;
import org.gephi.data.attributes.type.DynamicType;
import org.gephi.data.attributes.type.NumberList;
import org.gephi.data.attributes.type.StringList;
import org.gephi.data.properties.PropertiesColumn;
import org.gephi.datalab.api.AttributeColumnsController;
import org.gephi.datalab.api.GraphElementsController;
import org.gephi.dynamic.api.DynamicModel;
import org.gephi.graph.api.Attributes;
import org.gephi.graph.api.Edge;
import org.gephi.graph.api.Graph;
import org.gephi.graph.api.GraphController;
import org.gephi.graph.api.Node;
import org.gephi.utils.StatisticsUtils;
import org.openide.util.Exceptions;
import org.openide.util.Lookup;
import org.openide.util.lookup.ServiceProvider;

/**
 * Implementation of the AttributeColumnsController interface
 * declared in the Data Laboratory API.
 * @author Eduardo Ramos <eduramiba@gmail.com>
 * @see AttributeColumnsController
 */
@ServiceProvider(service = AttributeColumnsController.class)
public class AttributeColumnsControllerImpl implements AttributeColumnsController {

    public boolean setAttributeValue(Object value, Attributes row, AttributeColumn column) {
        AttributeType targetType = column.getType();
        if (value != null && !value.getClass().equals(targetType.getType())) {
            try {
                value = targetType.parse(value.toString());//Try to convert to target type
            } catch (Exception ex) {
                value = null;//Could not parse
            }
        }

        if (value == null && !canClearColumnData(column)) {
            return false;//Do not set a null value when the column can't have a null value.
        } else {
            row.setValue(column.getIndex(), value);
            return true;
        }
    }

    public AttributeColumn addAttributeColumn(AttributeTable table, String title, AttributeType type) {
        if (title == null || title.isEmpty()) {
            return null;
        }
        if (table.hasColumn(title)) {
            return null;
        }
        if (type == AttributeType.TIME_INTERVAL && table.getColumn(DynamicModel.TIMEINTERVAL_COLUMN) == null) {
            return table.addColumn(DynamicModel.TIMEINTERVAL_COLUMN, title, type, AttributeOrigin.PROPERTY, null);
        }
        return table.addColumn(title, title, type, AttributeOrigin.DATA, null);
    }

    public void deleteAttributeColumn(AttributeTable table, AttributeColumn column) {
        if (canDeleteColumn(column)) {
            table.removeColumn(column);
        }
    }

    public AttributeColumn duplicateColumn(AttributeTable table, AttributeColumn column, String title, AttributeType type) {
        AttributeColumn newColumn = addAttributeColumn(table, title, type);
        if (newColumn == null) {
            return null;
        }
        copyColumnDataToOtherColumn(table, column, newColumn);
        return newColumn;
    }

    public void copyColumnDataToOtherColumn(AttributeTable table, AttributeColumn sourceColumn, AttributeColumn targetColumn) {
        if (sourceColumn == targetColumn) {
            throw new IllegalArgumentException("Source and target columns can't be equal");
        }

        final int sourceColumnIndex = sourceColumn.getIndex();
        final int targetColumnIndex = targetColumn.getIndex();
        AttributeType targetType = targetColumn.getType();
        if (targetType != sourceColumn.getType()) {
            Object value;
            for (Attributes row : getTableAttributeRows(table)) {
                value = row.getValue(sourceColumnIndex);
                setAttributeValue(value, row, targetColumn);
            }
        } else {
            for (Attributes row : getTableAttributeRows(table)) {
                row.setValue(targetColumnIndex, row.getValue(sourceColumnIndex));
            }
        }
    }

    public void fillColumnWithValue(AttributeTable table, AttributeColumn column, String value) {
        if (canChangeColumnData(column)) {
            for (Attributes row : getTableAttributeRows(table)) {
                setAttributeValue(value, row, column);
            }
        }
    }

    public void clearColumnData(AttributeTable table, AttributeColumn column) {
        if (canClearColumnData(column)) {
            final int columnIndex = column.getIndex();
            for (Attributes attributes : getTableAttributeRows(table)) {
                attributes.setValue(columnIndex, null);
            }
        }
    }

    public Map<Object, Integer> calculateColumnValuesFrequencies(AttributeTable table, AttributeColumn column) {
        Map<Object, Integer> valuesFrequencies = new HashMap<Object, Integer>();
        Object value;
        for (Attributes row : getTableAttributeRows(table)) {
            value = row.getValue(column.getIndex());
            if (valuesFrequencies.containsKey(value)) {
                valuesFrequencies.put(value, new Integer(valuesFrequencies.get(value) + 1));
            } else {
                valuesFrequencies.put(value, new Integer(1));
            }
        }

        return valuesFrequencies;
    }

    public AttributeColumn createBooleanMatchesColumn(AttributeTable table, AttributeColumn column, String newColumnTitle, Pattern pattern) {
        if (pattern != null) {
            AttributeColumn newColumn = addAttributeColumn(table, newColumnTitle, AttributeType.BOOLEAN);
            if (newColumn == null) {
                return null;
            }
            Matcher matcher;
            Object value;
            for (Attributes row : getTableAttributeRows(table)) {
                value = row.getValue(column.getIndex());
                if (value != null) {
                    matcher = pattern.matcher(value.toString());
                } else {
                    matcher = pattern.matcher("");
                }
                row.setValue(newColumn.getIndex(), matcher.matches());
            }
            return newColumn;
        } else {
            return null;
        }
    }

    public void negateBooleanColumn(AttributeTable table, AttributeColumn column) {
        AttributeUtils attributeUtils = AttributeUtils.getDefault();
        if (attributeUtils.isColumnOfType(column, AttributeType.BOOLEAN)) {
            negateColumnBooleanType(table, column);
        } else if (attributeUtils.isColumnOfType(column, AttributeType.LIST_BOOLEAN)) {
            negateColumnListBooleanType(table, column);
        } else {
            throw new IllegalArgumentException();
        }
    }

    public AttributeColumn createFoundGroupsListColumn(AttributeTable table, AttributeColumn column, String newColumnTitle, Pattern pattern) {
        if (pattern != null) {
            AttributeColumn newColumn = addAttributeColumn(table, newColumnTitle, AttributeType.LIST_STRING);
            if (newColumn == null) {
                return null;
            }
            Matcher matcher;
            Object value;
            ArrayList<String> foundGroups = new ArrayList<String>();
            for (Attributes attributes : getTableAttributeRows(table)) {
                value = attributes.getValue(column.getIndex());
                if (value != null) {
                    matcher = pattern.matcher(value.toString());
                } else {
                    matcher = pattern.matcher("");
                }
                while (matcher.find()) {
                    foundGroups.add(matcher.group());
                }
                if (foundGroups.size() > 0) {
                    attributes.setValue(newColumn.getIndex(), new StringList(foundGroups.toArray(new String[0])));
                    foundGroups.clear();
                } else {
                    attributes.setValue(newColumn.getIndex(), null);
                }
            }
            return newColumn;
        } else {
            return null;
        }
    }

    public void clearNodeData(Node node, AttributeColumn[] columnsToClear) {
        clearRowData((AttributeRow) node.getNodeData().getAttributes(), columnsToClear);
    }

    public void clearNodesData(Node[] nodes, AttributeColumn[] columnsToClear) {
        for (Node n : nodes) {
            clearNodeData(n, columnsToClear);
        }
    }

    public void clearEdgeData(Edge edge, AttributeColumn[] columnsToClear) {
        clearRowData((AttributeRow) edge.getEdgeData().getAttributes(), columnsToClear);
    }

    public void clearEdgesData(Edge[] edges, AttributeColumn[] columnsToClear) {
        for (Edge e : edges) {
            clearEdgeData(e, columnsToClear);
        }
    }

    public void clearRowData(Attributes row, AttributeColumn[] columnsToClear) {
        AttributeRow attributeRow = (AttributeRow) row;
        if (columnsToClear != null) {
            for (AttributeColumn column : columnsToClear) {
                //Clear all except id and computed attributes:
                if (canClearColumnData(column)) {
                    row.setValue(column.getIndex(), null);
                }
            }
        } else {
            AttributeValue[] values = attributeRow.getValues();
            for (int i = 0; i < values.length; i++) {
                //Clear all except id and computed attributes:
                if (canClearColumnData(values[i].getColumn())) {
                    row.setValue(i, null);
                }
            }
        }
    }

    public void copyNodeDataToOtherNodes(Node node, Node[] otherNodes, AttributeColumn[] columnsToCopy) {
        Attributes row = node.getNodeData().getAttributes();
        Attributes[] otherRows = new Attributes[otherNodes.length];
        for (int i = 0; i < otherNodes.length; i++) {
            otherRows[i] = otherNodes[i].getNodeData().getAttributes();
        }

        copyRowDataToOtherRows(row, otherRows, columnsToCopy);
    }

    public void copyEdgeDataToOtherEdges(Edge edge, Edge[] otherEdges, AttributeColumn[] columnsToCopy) {
        Attributes row = edge.getEdgeData().getAttributes();
        Attributes[] otherRows = new Attributes[otherEdges.length];
        for (int i = 0; i < otherEdges.length; i++) {
            otherRows[i] = otherEdges[i].getEdgeData().getAttributes();
        }

        copyRowDataToOtherRows(row, otherRows, columnsToCopy);
    }

    public void copyRowDataToOtherRows(Attributes row, Attributes[] otherRows, AttributeColumn[] columnsToCopy) {
        AttributeRow attributeRow = (AttributeRow) row;
        if (columnsToCopy != null) {
            for (AttributeColumn column : columnsToCopy) {
                //Copy all except id and computed attributes:
                if (canChangeColumnData(column)) {
                    for (Attributes otherRow : otherRows) {
                        otherRow.setValue(column.getIndex(), row.getValue(column.getIndex()));
                    }
                }
            }
        } else {
            AttributeColumn column;
            AttributeValue[] values = attributeRow.getValues();
            for (int i = 0; i < values.length; i++) {
                column = values[i].getColumn();
                //Copy all except id and computed attributes:
                if (canChangeColumnData(column)) {
                    for (Attributes otherRow : otherRows) {
                        otherRow.setValue(column.getIndex(), row.getValue(column.getIndex()));
                    }
                }
            }
        }
    }

    public Attributes[] getTableAttributeRows(AttributeTable table) {
        Attributes[] attributes;
        if (isNodeTable(table)) {
            Node[] nodes = getNodesArray();
            attributes = new Attributes[nodes.length];
            for (int i = 0; i < nodes.length; i++) {
                attributes[i] = nodes[i].getNodeData().getAttributes();
            }
        } else {
            Edge[] edges = getEdgesArray();
            attributes = new Attributes[edges.length];
            for (int i = 0; i < edges.length; i++) {
                attributes[i] = edges[i].getEdgeData().getAttributes();
            }
        }
        return attributes;
    }

    public int getTableRowsCount(AttributeTable table) {
        if (isNodeTable(table)) {
            return Lookup.getDefault().lookup(GraphElementsController.class).getNodesCount();
        } else {
            return Lookup.getDefault().lookup(GraphElementsController.class).getEdgesCount();
        }
    }

    public boolean isNodeTable(AttributeTable table) {
        AttributeController ac = Lookup.getDefault().lookup(AttributeController.class);
        return table == ac.getModel().getNodeTable();
    }

    public boolean isEdgeTable(AttributeTable table) {
        AttributeController ac = Lookup.getDefault().lookup(AttributeController.class);
        return table == ac.getModel().getEdgeTable();
    }

    public boolean canDeleteColumn(AttributeColumn column) {
        return column.getOrigin() != AttributeOrigin.PROPERTY;
    }

    public boolean canChangeColumnData(AttributeColumn column) {
        AttributeUtils au = Lookup.getDefault().lookup(AttributeUtils.class);
        if (au.isNodeColumn(column)) {
            return canChangeGenericColumnData(column) && column.getIndex() != PropertiesColumn.NODE_ID.getIndex();
        } else if (au.isEdgeColumn(column)) {
            return canChangeGenericColumnData(column) && column.getIndex() != PropertiesColumn.EDGE_ID.getIndex();
        } else {
            return canChangeGenericColumnData(column);
        }
    }

    public boolean canClearColumnData(AttributeColumn column) {
        AttributeUtils au = Lookup.getDefault().lookup(AttributeUtils.class);
        if (au.isNodeColumn(column)) {
            return canChangeGenericColumnData(column) && column.getIndex() != PropertiesColumn.NODE_ID.getIndex();
        } else if (au.isEdgeColumn(column)) {
            return canChangeGenericColumnData(column) && column.getIndex() != PropertiesColumn.EDGE_ID.getIndex() && column.getIndex() != PropertiesColumn.EDGE_WEIGHT.getIndex();
        } else {
            return canChangeGenericColumnData(column);
        }
    }

    public BigDecimal[] getNumberOrNumberListColumnStatistics(AttributeTable table, AttributeColumn column) {
        return StatisticsUtils.getAllStatistics(getColumnNumbers(table, column));
    }

    public Number[] getColumnNumbers(AttributeTable table, AttributeColumn column) {
        AttributeUtils attributeUtils = AttributeUtils.getDefault();
        if (!attributeUtils.isNumberOrNumberListColumn(column)) {
            throw new IllegalArgumentException("The column has to be a number or number list column");
        }

        ArrayList<Number> numbers = new ArrayList<Number>();
        final int columnIndex = column.getIndex();
        Number number;
        if (attributeUtils.isNumberColumn(column)) {//Number column
            for (Attributes row : getTableAttributeRows(table)) {
                number = (Number) row.getValue(columnIndex);
                if (number != null) {
                    numbers.add(number);
                }
            }
        } else {//Number list column
            for (Attributes row : getTableAttributeRows(table)) {
                numbers.addAll(getNumberListColumnNumbers(row, column));
            }
        }

        return numbers.toArray(new Number[0]);
    }

    public Number[] getRowNumbers(Attributes row, AttributeColumn[] columns) {
        AttributeUtils attributeUtils = AttributeUtils.getDefault();
        checkColumnsAreNumberOrNumberList(columns);

        ArrayList<Number> numbers = new ArrayList<Number>();
        Number number;
        for (AttributeColumn column : columns) {
            if (attributeUtils.isNumberColumn(column)) {//Single number column:
                number = (Number) row.getValue(column.getIndex());
                if (number != null) {
                    numbers.add(number);
                }
            } else if (attributeUtils.isNumberListColumn(column)) {//Number list column:
                numbers.addAll(getNumberListColumnNumbers(row, column));
            } else if (attributeUtils.isDynamicNumberColumn(column)) {//Dynamic number column
                numbers.addAll(getDynamicNumberColumnNumbers(row, column));
            }
        }

        return numbers.toArray(new Number[0]);
    }

    public void importCSVToNodesTable(File file, Character separator, Charset charset, String[] columnNames, AttributeType[] columnTypes, boolean assignNewNodeIds) {
        if (columnNames == null || columnNames.length == 0) {
            return;
        }

        if (columnTypes == null || columnNames.length != columnTypes.length) {
            throw new IllegalArgumentException("Column names length must be the same as column types lenght");
        }

        CsvReader reader = null;
        try {
            //Prepare attribute columns for the column names, creating the not already existing columns:
            AttributeTable nodesTable = Lookup.getDefault().lookup(AttributeController.class).getModel().getNodeTable();
            String idColumn = null;
            ArrayList<AttributeColumn> columnsList = new ArrayList<AttributeColumn>();
            for (int i = 0; i < columnNames.length; i++) {
                //Separate first id column found from the list to use as id. If more are found later, the will not be in the list and be ignored.
                if (columnNames[i].equalsIgnoreCase("id")) {
                    if (idColumn == null) {
                        idColumn = columnNames[i];
                    }
                } else if (nodesTable.hasColumn(columnNames[i])) {
                    columnsList.add(nodesTable.getColumn(columnNames[i]));
                } else {
                    columnsList.add(addAttributeColumn(nodesTable, columnNames[i], columnTypes[i]));
                }
            }

            //Create nodes:
            GraphElementsController gec = Lookup.getDefault().lookup(GraphElementsController.class);
            Graph graph = Lookup.getDefault().lookup(GraphController.class).getModel().getGraph();
            String id = null;
            Node node;
            Attributes nodeAttributes;
            reader = new CsvReader(new FileInputStream(file), separator, charset);
            reader.readHeaders();
            while (reader.readRecord()) {
                //Prepare the correct node to assign the attributes:
                if (idColumn != null) {
                    id = reader.get(idColumn);
                    if (id == null || id.isEmpty()) {
                        node = gec.createNode(null);//id null or empty, assign one
                    } else {
                        graph.readLock();
                        node = graph.getNode(id);
                        graph.readUnlock();
                        if (node != null) {//Node with that id already in graph
                            if (assignNewNodeIds) {
                                node = gec.createNode(null);
                            }
                        } else {
                            node = gec.createNode(null, id);//New id in the graph
                        }
                    }
                } else {
                    node = gec.createNode(null);
                }
                //Assign attributes to the current node:
                nodeAttributes = node.getNodeData().getAttributes();
                for (AttributeColumn column : columnsList) {
                    setAttributeValue(reader.get(column.getTitle()), nodeAttributes, column);
                }
            }
        } catch (FileNotFoundException ex) {
            Exceptions.printStackTrace(ex);
        } catch (IOException ex) {
            Exceptions.printStackTrace(ex);
        } finally {
            reader.close();
        }
    }

    public void importCSVToEdgesTable(File file, Character separator, Charset charset, String[] columnNames, AttributeType[] columnTypes, boolean createNewNodes) {
        if (columnNames == null || columnNames.length == 0) {
            return;
        }

        if (columnTypes == null || columnNames.length != columnTypes.length) {
            throw new IllegalArgumentException("Column names length must be the same as column types lenght");
        }

        CsvReader reader = null;
        try {
            //Prepare attribute columns for the column names, creating the not already existing columns:
            AttributeTable edges = Lookup.getDefault().lookup(AttributeController.class).getModel().getEdgeTable();
            String idColumn = null;
            String sourceColumn = null;
            String targetColumn = null;
            String typeColumn = null;
            ArrayList<AttributeColumn> columnsList = new ArrayList<AttributeColumn>();
            for (int i = 0; i < columnNames.length; i++) {
                //Separate first id column found from the list to use as id. If more are found later, the will not be in the list and be ignored.
                if (columnNames[i].equalsIgnoreCase("id")) {
                    if (idColumn == null) {
                        idColumn = columnNames[i];
                    }
                } else if (columnNames[i].equalsIgnoreCase("source") && sourceColumn == null) {//Separate first source column found from the list to use as source node id
                    sourceColumn = columnNames[i];
                } else if (columnNames[i].equalsIgnoreCase("target") && targetColumn == null) {//Separate first target column found from the list to use as target node id
                    targetColumn = columnNames[i];
                } else if (columnNames[i].equalsIgnoreCase("type") && typeColumn == null) {//Separate first type column found from the list to use as edge type (directed/undirected)
                    typeColumn = columnNames[i];
                } else if (edges.hasColumn(columnNames[i])) {
                    columnsList.add(edges.getColumn(columnNames[i]));
                } else {
                    columnsList.add(addAttributeColumn(edges, columnNames[i], columnTypes[i]));
                }
            }

            //Create edges:
            GraphElementsController gec = Lookup.getDefault().lookup(GraphElementsController.class);
            Graph graph = Lookup.getDefault().lookup(GraphController.class).getModel().getGraph();
            String id = null;
            Edge edge;
            String sourceId, targetId;
            Node source, target;
            String type;
            boolean directed;
            Attributes edgeAttributes;
            reader = new CsvReader(new FileInputStream(file), separator, charset);
            reader.readHeaders();
            while (reader.readRecord()) {
                sourceId = reader.get(sourceColumn);
                targetId = reader.get(targetColumn);

                if (sourceId == null || sourceId.isEmpty() || targetId == null || targetId.isEmpty()) {
                    continue;//No correct source and target ids were provided, ignore row
                }

                graph.readLock();
                source = graph.getNode(sourceId);
                graph.readUnlock();

                if (source == null) {
                    if (createNewNodes) {//Create new nodes when they don't exist already and option is enabled
                        if (source == null) {
                            source = gec.createNode(null, sourceId);
                        }
                    } else {
                        continue;//Ignore this edge row, since no new nodes should be created.
                    }
                }

                graph.readLock();
                target = graph.getNode(targetId);
                graph.readUnlock();

                if (target == null) {
                    if (createNewNodes) {//Create new nodes when they don't exist already and option is enabled
                        if (target == null) {
                            target = gec.createNode(null, targetId);
                        }
                    } else {
                        continue;//Ignore this edge row, since no new nodes should be created.
                    }
                }

                if (typeColumn != null) {
                    type = reader.get(typeColumn);
                    //Undirected if indicated correctly, otherwise always directed:
                    if (type != null) {
                        directed = !type.equalsIgnoreCase("undirected");
                    } else {
                        directed = true;
                    }
                } else {
                    directed = true;//Directed by default when not indicated
                }

                //Prepare the correct edge to assign the attributes:
                if (idColumn != null) {
                    id = reader.get(idColumn);
                    if (id == null || id.isEmpty()) {
                        edge = gec.createEdge(source, target, directed);//id null or empty, assign one
                    } else {
                        edge = gec.createEdge(id, source, target, directed);
                        if (edge == null) {//Edge with that id already in graph
                            edge = gec.createEdge(source, target, directed);
                        }
                    }
                } else {
                    edge = gec.createEdge(source, target, directed);
                }

                if (edge != null) {//Edge could be created because it does not already exist:
                    //Assign attributes to the current edge:
                    edgeAttributes = edge.getEdgeData().getAttributes();
                    for (AttributeColumn column : columnsList) {
                        setAttributeValue(reader.get(column.getTitle()), edgeAttributes, column);
                    }
                }
            }
        } catch (FileNotFoundException ex) {
            Exceptions.printStackTrace(ex);
        } catch (IOException ex) {
            Exceptions.printStackTrace(ex);
        } finally {
            reader.close();
        }
    }

    /************Private methods : ************/
    /**
     * Used for iterating through all nodes of the graph
     * @return Array with all graph nodes
     */
    private Node[] getNodesArray() {
        return Lookup.getDefault().lookup(GraphController.class).getModel().getHierarchicalGraph().getNodesTree().toArray();
    }

    /**
     * Used for iterating through all edges of the graph
     * @return Array with all graph edges
     */
    private Edge[] getEdgesArray() {
        return Lookup.getDefault().lookup(GraphController.class).getModel().getHierarchicalGraph().getEdges().toArray();
    }

    /**
     * Only checks that a column is not <code>COMPUTED</code> or <code>DELEGATE</code>
     */
    private boolean canChangeGenericColumnData(AttributeColumn column) {
        return column.getOrigin() != AttributeOrigin.COMPUTED && column.getOrigin() != AttributeOrigin.DELEGATE;
    }

    /**
     * Used to negate the values of a single boolean column.
     */
    private void negateColumnBooleanType(AttributeTable table, AttributeColumn column) {
        final int columnIndex = column.getIndex();
        Object value;
        Boolean newValue;
        for (Attributes row : getTableAttributeRows(table)) {
            value = row.getValue(columnIndex);
            if (value != null) {
                newValue = !((Boolean) value);
                row.setValue(columnIndex, newValue);
            }
        }
    }

    /**
     * Used to negate all values of a list of boolean values column.
     */
    private void negateColumnListBooleanType(AttributeTable table, AttributeColumn column) {
        final int columnIndex = column.getIndex();
        Object value;
        BooleanList list;
        Boolean[] newValues;
        for (Attributes row : getTableAttributeRows(table)) {
            value = row.getValue(columnIndex);
            if (value != null) {
                list = (BooleanList) value;
                newValues = new Boolean[list.size()];
                for (int i = 0; i < list.size(); i++) {
                    newValues[i] = !list.getItem(i);
                }
                row.setValue(columnIndex, new BooleanList(newValues));
            }
        }
    }

    /**
     * Used for obtaining a list of the numbers of row of a number list column.
     */
    private ArrayList<Number> getNumberListColumnNumbers(Attributes row, AttributeColumn column) {
        if (!AttributeUtils.getDefault().isNumberListColumn(column)) {
            throw new IllegalArgumentException("Column must be a number list column");
        }

        ArrayList<Number> numbers = new ArrayList<Number>();
        NumberList list = (NumberList) row.getValue(column.getIndex());
        if (list == null) {
            return numbers;
        }
        Number n;
        for (int i = 0; i < list.size(); i++) {
            n = (Number) list.getItem(i);
            if (n != null) {
                numbers.add((Number) n);
            }
        }
        return numbers;
    }

    /**
     * Used for obtaining a list of the numbers of row of a dynamic number column.
     */
    private ArrayList<Number> getDynamicNumberColumnNumbers(Attributes row, AttributeColumn column) {
        if (!AttributeUtils.getDefault().isDynamicNumberColumn(column)) {
            throw new IllegalArgumentException("Column must be a dynamic number column");
        }
        ArrayList<Number> numbers = new ArrayList<Number>();
        DynamicType dynamicList = (DynamicType) row.getValue(column.getIndex());
        if (dynamicList == null) {
            return numbers;
        }
        Number[] dynamicNumbers;
        dynamicNumbers = (Number[]) dynamicList.getValues().toArray(new Number[0]);
        Number n;
        for (int i = 0; i < dynamicNumbers.length; i++) {
            n = (Number) dynamicNumbers[i];
            if (n != null) {
                numbers.add((Number) n);
            }
        }
        return numbers;
    }

    private void checkColumnsAreNumberOrNumberList(AttributeColumn[] columns) {
        if (columns == null || (!AttributeUtils.getDefault().areAllNumberOrNumberListColumns(columns) && !AttributeUtils.getDefault().areAllDynamicNumberColumns(columns))) {
            throw new IllegalArgumentException("All columns have to be number or number list columns and can't be null");
        }
    }
}