Examples with Document dna.dataStructures.Document used on opensource projects

Example 1 with Document

use of dna.dataStructures.Document in project dna by leifeld.

the class Exporter method exportGEFX.

private void exportGEFX(Matrix mt, boolean twoMode, StatementType statementType, String outfile, String var1, String var2, int[] frequencies1, int[] frequencies2, ArrayList<AttributeVector> attributes, String qualifierAggregation, boolean qualifierBinary) {
    // extract attributes
    String[] rn = mt.getRownames();
    String[] cn = mt.getColnames();
    String[] names;
    String[] variables;
    int[] frequencies;
    if (twoMode == true) {
        names = new String[rn.length + cn.length];
        variables = new String[names.length];
        frequencies = new int[names.length];
    } else {
        names = new String[rn.length];
        variables = new String[rn.length];
        frequencies = new int[rn.length];
    }
    for (int i = 0; i < rn.length; i++) {
        names[i] = rn[i];
        variables[i] = var1;
        frequencies[i] = frequencies1[i];
    }
    if (twoMode == true) {
        for (int i = 0; i < cn.length; i++) {
            names[i + rn.length] = cn[i];
            variables[i + rn.length] = var2;
            frequencies[i + rn.length] = frequencies2[i];
        }
    }
    int[] id = new int[names.length];
    java.awt.Color[] color = new java.awt.Color[names.length];
    String[] type = new String[names.length];
    String[] alias = new String[names.length];
    String[] notes = new String[names.length];
    for (int i = 0; i < attributes.size(); i++) {
        if (attributes.get(i).getStatementTypeId() == statementType.getId() && attributes.get(i).getVariable().equals(var1)) {
            for (int j = 0; j < rn.length; j++) {
                if (rn[j].equals(attributes.get(i).getValue())) {
                    id[j] = attributes.get(i).getId();
                    color[j] = attributes.get(i).getColor();
                    type[j] = attributes.get(i).getType();
                    alias[j] = attributes.get(i).getAlias();
                    notes[j] = attributes.get(i).getNotes();
                }
            }
        } else if (attributes.get(i).getStatementTypeId() == statementType.getId() && attributes.get(i).getVariable().equals(var2) && twoMode == true) {
            for (int j = 0; j < cn.length; j++) {
                if (cn[j].equals(attributes.get(i).getValue())) {
                    id[j + rn.length] = attributes.get(i).getId();
                    color[j + rn.length] = attributes.get(i).getColor();
                    type[j + rn.length] = attributes.get(i).getType();
                    alias[j + rn.length] = attributes.get(i).getAlias();
                    notes[j + rn.length] = attributes.get(i).getNotes();
                }
            }
        }
    }
    DocType dt = new DocType("xml");
    org.jdom.Document document = new org.jdom.Document();
    document.setDocType(dt);
    // gexf element with schema information
    Element gexfElement = new Element("gexf");
    gexfElement.setAttribute(new Attribute("xmlns", "http://www.gexf.net/1.2draft"));
    gexfElement.setAttribute(new Attribute("xmlns:viz", "http://www.gexf.net/1.2draft/viz"));
    gexfElement.setAttribute(new Attribute("xmlns:xsi", "http://www.w3.org/2001/XMLSchema-instance"));
    gexfElement.setAttribute(new Attribute("xsi:schemaLocation", "http://www.gexf.net/1.2draft/gexf.xsd"));
    gexfElement.setAttribute(new Attribute("version", "1.2"));
    document.addContent(gexfElement);
    // meta data
    Element meta = new Element("meta");
    DateFormat df = new SimpleDateFormat("yyyy.MM.dd");
    Date today = new Date();
    meta.setAttribute(new Attribute("lastmodifieddate", df.format(today)));
    Element creator = new Element("creator");
    creator.setText("Discourse Network Analyzer (DNA)");
    meta.addContent(creator);
    Element description = new Element("description");
    if (twoMode == true) {
        description.setText("Two-mode network");
    } else {
        description.setText("One-mode network");
    }
    meta.addContent(description);
    gexfElement.addContent(meta);
    // graph element with node and edge attribute definitions
    Element graphElement = new Element("graph");
    graphElement.setAttribute(new Attribute("mode", "static"));
    graphElement.setAttribute(new Attribute("defaultedgetype", "undirected"));
    Element attributesElement = new Element("attributes");
    attributesElement.setAttribute(new Attribute("class", "node"));
    Element at0 = new Element("attribute");
    at0.setAttribute(new Attribute("id", "0"));
    at0.setAttribute(new Attribute("title", "type"));
    at0.setAttribute(new Attribute("type", "string"));
    attributesElement.addContent(at0);
    Element at1 = new Element("attribute");
    at1.setAttribute(new Attribute("id", "1"));
    at1.setAttribute(new Attribute("title", "alias"));
    at1.setAttribute(new Attribute("type", "string"));
    attributesElement.addContent(at1);
    Element at2 = new Element("attribute");
    at2.setAttribute(new Attribute("id", "2"));
    at2.setAttribute(new Attribute("title", "notes"));
    at2.setAttribute(new Attribute("type", "string"));
    attributesElement.addContent(at2);
    /*
		<attributes class="node">
	      <attribute id="0" title="url" type="string"/>
	      <attribute id="1" title="indegree" type="float"/>
	      <attribute id="2" title="frog" type="boolean">
	        <default>true</default>
	      </attribute>
	    </attributes>
		*/
    // add nodes
    Element nodes = new Element("nodes");
    for (int i = 0; i < names.length; i++) {
        Element node = new Element("node");
        node.setAttribute(new Attribute("id", "" + id[i]));
        node.setAttribute(new Attribute("label", "" + names[i]));
        Element attvaluesElement = new Element("attvalues");
        Element attvalueElement0 = new Element("attvalue");
        attvalueElement0.setAttribute(new Attribute("for", "0"));
        attvalueElement0.setAttribute(new Attribute("value", type[i]));
        attvaluesElement.addContent(attvalueElement0);
        Element attvalueElement1 = new Element("attvalue");
        attvalueElement1.setAttribute(new Attribute("for", "1"));
        attvalueElement1.setAttribute(new Attribute("value", alias[i]));
        attvaluesElement.addContent(attvalueElement1);
        Element attvalueElement2 = new Element("attvalue");
        attvalueElement2.setAttribute(new Attribute("for", "2"));
        attvalueElement2.setAttribute(new Attribute("value", notes[i]));
        attvaluesElement.addContent(attvalueElement2);
        Element attvalueElement3 = new Element("attvalue");
        attvalueElement3.setAttribute(new Attribute("for", "3"));
        attvalueElement3.setAttribute(new Attribute("value", variables[i]));
        attvaluesElement.addContent(attvalueElement3);
        Element attvalueElement4 = new Element("attvalue");
        attvalueElement4.setAttribute(new Attribute("for", "4"));
        attvalueElement4.setAttribute(new Attribute("value", String.valueOf(frequencies[i])));
        attvaluesElement.addContent(attvalueElement4);
        node.addContent(attvaluesElement);
        Element vizColor = new Element("viz:color");
        vizColor.setAttribute(new Attribute("r", "" + color[i].getRed()));
        vizColor.setAttribute(new Attribute("g", "" + color[i].getGreen()));
        vizColor.setAttribute(new Attribute("b", "" + color[i].getBlue()));
        vizColor.setAttribute(new Attribute("a", "" + color[i].getAlpha()));
        node.addContent(vizColor);
        Element vizShape = new Element("viz:shape");
        if (i < rn.length) {
            vizShape.setAttribute(new Attribute("value", "disc"));
        } else {
            vizShape.setAttribute(new Attribute("value", "square"));
        }
        node.addContent(vizShape);
        nodes.addContent(node);
    }
    graphElement.addContent(nodes);
    // add edges
    Element edges = new Element("edges");
    graphElement.addContent(edges);
    gexfElement.addContent(graphElement);
    // write to file
    File dnaFile = new File(outfile);
    try {
        FileOutputStream outStream = new FileOutputStream(dnaFile);
        XMLOutputter outToFile = new XMLOutputter();
        Format format = Format.getPrettyFormat();
        format.setEncoding("utf-8");
        outToFile.setFormat(format);
        outToFile.output(document, outStream);
        outStream.flush();
        outStream.close();
    } catch (IOException e) {
        System.err.println("Cannot save \"" + dnaFile + "\":" + e.getMessage());
    }
}

Example 2 with Document

use of dna.dataStructures.Document in project dna by leifeld.

the class Exporter method eventCSV.

/**
 * This function is supposed to convert a rank back into a binary vector, but it does not seem to work properly.
 *
 * Source: https://cw.fel.cvut.cz/wiki/_media/courses/b4m33pal/pal06.pdf
 *
 * @param rank  The integer rank
 * @param n     Length of the binary vector
 * @return      Binary vector of length n
 */
/*
	private int[] lexUnrank(int rank, int n) {
		int[] binaryVector = new int[n];
		for (int i = n; i > 0; i--) {
			if (rank % 2 == 1) {
				binaryVector[i - 1] = 1;
				rank = (int) Math.floor(rank / 2);
			}
		}
		return binaryVector;
	}
	*/
/**
 * This function accepts a list of statements that should be included in the relational event export,
 * and it exports the variables of all statements to a CSV file, along with the statement ID and a
 * date/time stamp. There is one statement per row, and the number of columns is the number of variables
 * present in the statement type.
 *
 * @param statements	 An array list of {@link Statement}s (of the same statement type) that should be exported.
 * @param documents      An array list of {@link Document}s in which the statements are embedded.
 * @param statementType  The statement type corresponding to the statements.
 * @param fileName		 String with the file name of the CSV file to which the event list will be exported.
 */
private void eventCSV(ArrayList<Statement> statements, ArrayList<Document> documents, StatementType statementType, String fileName) {
    String key, value;
    int statementId;
    Date d;
    SimpleDateFormat dateFormat;
    int statementTypeId = statementType.getId();
    for (int i = 0; i < statements.size(); i++) {
        if (statements.get(i).getStatementTypeId() != statementTypeId) {
            throw new IllegalArgumentException("More than one statement type was selected. Cannot export to a spreadsheet!");
        }
    }
    // HashMap for fast lookup of document indices by ID
    HashMap<Integer, Integer> docMap = new HashMap<Integer, Integer>();
    for (int i = 0; i < documents.size(); i++) {
        docMap.put(documents.get(i).getId(), i);
    }
    HashMap<String, String> variables = statementType.getVariables();
    Iterator<String> keyIterator;
    try {
        BufferedWriter out = new BufferedWriter(new OutputStreamWriter(new FileOutputStream(fileName), "UTF-8"));
        keyIterator = variables.keySet().iterator();
        out.write("\"statement ID\";\"time\";\"document ID\";\"document title\";\"author\";\"source\";\"section\";\"type\";\"text\"");
        while (keyIterator.hasNext()) {
            out.write(";\"" + keyIterator.next() + "\"");
        }
        for (int i = 0; i < statements.size(); i++) {
            out.newLine();
            statementId = statements.get(i).getId();
            String stringId = new Integer(statementId).toString();
            out.write(stringId);
            d = statements.get(i).getDate();
            dateFormat = new SimpleDateFormat("yyyy-MM-dd hh:mm:ss");
            out.write(";" + dateFormat.format(d));
            Document doc = documents.get(docMap.get(statements.get(i).getDocumentId()));
            out.write(";" + doc.getId());
            out.write(";\"" + doc.getTitle().replaceAll(";", ",").replaceAll("\"", "'") + "\"");
            out.write(";\"" + doc.getAuthor().replaceAll(";", ",").replaceAll("\"", "'") + "\"");
            out.write(";\"" + doc.getSource().replaceAll(";", ",").replaceAll("\"", "'") + "\"");
            out.write(";\"" + doc.getSection().replaceAll(";", ",").replaceAll("\"", "'") + "\"");
            out.write(";\"" + doc.getType().replaceAll(";", ",").replaceAll("\"", "'") + "\"");
            out.write(";\"" + doc.getText().substring(statements.get(i).getStart(), statements.get(i).getStop()).replaceAll(";", ",").replaceAll("\"", "'") + "\"");
            keyIterator = variables.keySet().iterator();
            while (keyIterator.hasNext()) {
                key = keyIterator.next();
                value = variables.get(key);
                if (value.equals("short text") || value.equals("long text")) {
                    out.write(";\"" + ((String) statements.get(i).getValues().get(key)).replaceAll(";", ",").replaceAll("\"", "'") + "\"");
                } else if (value.equals("boolean") || value.equals("integer")) {
                    out.write(";" + statements.get(i).getValues().get(key));
                }
            }
        }
        out.close();
        System.out.println("Event list has been exported to \"" + fileName + "\".");
    } catch (IOException e) {
        System.err.println("Error while saving CSV file: " + e);
    }
}

Example 3 with Document

use of dna.dataStructures.Document in project dna by leifeld.

the class DocumentPanel method documentFilter.

public void documentFilter() {
    RowFilter<DocumentTableModel, Integer> documentFilter = new RowFilter<DocumentTableModel, Integer>() {

        public boolean include(Entry<? extends DocumentTableModel, ? extends Integer> entry) {
            DocumentTableModel dtm = entry.getModel();
            Document d = dtm.get(entry.getIdentifier());
            int documentId = d.getId();
            boolean[] b = Dna.data.getActiveDocumentPermissions(documentId);
            if (b[0] == true) {
                return true;
            }
            return false;
        }
    };
    sorter.setRowFilter(documentFilter);
}

Example 4 with Document

use of dna.dataStructures.Document in project dna by leifeld.

the class Exporter method eventListR.

/**
 * This function accepts a list of statements that should be included in the relational event export,
 * and it returns the variables of all statements, along with the statement ID and a date/time stamp.
 * There is one statement per row, and the number of columns is the number of variables present in
 * the statement type plus 8 columns that represent statement ID and document-level variables.
 *
 * @param statements	 An array list of {@link Statement}s (of the same statement type) that should be exported.
 * @param documents      An array list of {@link Document}s in which the statements are embedded.
 * @param statementType  The statement type corresponding to the statements.
 */
private Object[] eventListR(ArrayList<Statement> statements, ArrayList<Document> documents, StatementType statementType) {
    String key, value;
    Document doc;
    int statementTypeId = statementType.getId();
    for (int i = 0; i < statements.size(); i++) {
        if (statements.get(i).getStatementTypeId() != statementTypeId) {
            throw new IllegalArgumentException("More than one statement type was selected. Cannot export to a spreadsheet!");
        }
    }
    // HashMap for fast lookup of document indices by ID
    HashMap<Integer, Integer> docMap = new HashMap<Integer, Integer>();
    for (int i = 0; i < documents.size(); i++) {
        docMap.put(documents.get(i).getId(), i);
    }
    // Get variable names and types of current statement type
    HashMap<String, String> variables = statementType.getVariables();
    Iterator<String> keyIterator;
    ArrayList<String> variableNames = new ArrayList<String>();
    ArrayList<String> variableTypes = new ArrayList<String>();
    keyIterator = variables.keySet().iterator();
    while (keyIterator.hasNext()) {
        key = keyIterator.next();
        value = variables.get(key);
        variableNames.add(key);
        variableTypes.add(value);
    }
    columnNames = new String[variableNames.size()];
    columnTypes = new String[variableTypes.size()];
    for (int i = 0; i < variableNames.size(); i++) {
        columnNames[i] = variableNames.get(i);
        columnTypes[i] = variableTypes.get(i);
    }
    // create array of columns and populate document-level and statement-level columns; leave out variables for now
    Object[] columns = new Object[variableNames.size() + 8];
    int[] ids = new int[statements.size()];
    long[] time = new long[statements.size()];
    int[] docId = new int[statements.size()];
    String[] docTitle = new String[statements.size()];
    String[] author = new String[statements.size()];
    String[] source = new String[statements.size()];
    String[] section = new String[statements.size()];
    String[] type = new String[statements.size()];
    for (int i = 0; i < statements.size(); i++) {
        ids[i] = statements.get(i).getId();
        // convert milliseconds to seconds (since 1/1/1970)
        time[i] = statements.get(i).getDate().getTime() / 1000;
        docId[i] = statements.get(i).getDocumentId();
        doc = documents.get(docMap.get(docId[i]));
        docTitle[i] = doc.getTitle();
        author[i] = doc.getAuthor();
        source[i] = doc.getSource();
        section[i] = doc.getSection();
        type[i] = doc.getType();
    }
    columns[0] = ids;
    columns[1] = time;
    columns[2] = docId;
    columns[3] = docTitle;
    columns[4] = author;
    columns[5] = source;
    columns[6] = section;
    columns[7] = type;
    // Now add the variables to the columns array
    for (int i = 0; i < variableNames.size(); i++) {
        if (columnTypes[i].equals("short text") || columnTypes[i].equals("long text")) {
            columns[i + 8] = new String[statements.size()];
        } else {
            columns[i + 8] = new int[statements.size()];
        }
    }
    for (int i = 0; i < statements.size(); i++) {
        for (int j = 0; j < variableNames.size(); j++) {
            if (columnTypes[j].equals("short text") || columnTypes[j].equals("long text")) {
                String[] temp = ((String[]) columns[j + 8]);
                temp[i] = (String) statements.get(i).getValues().get(columnNames[j]);
                columns[j + 8] = temp;
            } else {
                int[] temp = ((int[]) columns[j + 8]);
                temp[i] = (int) statements.get(i).getValues().get(columnNames[j]);
                columns[j + 8] = temp;
            }
        }
    }
    return columns;
}

Example 5 with Document

use of dna.dataStructures.Document in project dna by leifeld.

the class Exporter method exportGraphml.

/**
 * Export filter for graphML files.
 *
 * @param matrix                 Input {@link Matrix}.
 * @param twoMode                Indicates whether the network is a two-mode network.
 * @param statementType          The statement type on which the network is based.
 * @param outfile                Name of the output file.
 * @param var1                   Name of the first variable (the rows of the matrix).
 * @param var2                   Name of the second variable (the columns of the matrix).
 * @param frequencies1           The number of statements in which the row node is involved (after filtering).
 * @param frequencies2           The number of statements in which the column node is involved (after filtering).
 * @param attributes             An ArrayList of {@link AttributeVector}s containing all attribute vectors in the database.
 * @param qualifierAggregation   A String denoting the qualifier aggregation. Valid values are "ignore", "combine", "subtract", "congruence", and "conflict".
 * @param qualifierBinary        Indicates whether the qualifier is a binary variable.
 */
private void exportGraphml(Matrix mt, boolean twoMode, StatementType statementType, String outfile, String var1, String var2, int[] frequencies1, int[] frequencies2, ArrayList<AttributeVector> attributes, String qualifierAggregation, boolean qualifierBinary) {
    // extract attributes
    String[] rn = mt.getRownames();
    String[] cn = mt.getColnames();
    String[] names;
    String[] variables;
    int[] frequencies;
    if (twoMode == true) {
        names = new String[rn.length + cn.length];
        variables = new String[names.length];
        frequencies = new int[names.length];
    } else {
        names = new String[rn.length];
        variables = new String[rn.length];
        frequencies = new int[rn.length];
    }
    for (int i = 0; i < rn.length; i++) {
        names[i] = rn[i];
        variables[i] = var1;
        frequencies[i] = frequencies1[i];
    }
    if (twoMode == true) {
        for (int i = 0; i < cn.length; i++) {
            names[i + rn.length] = cn[i];
            variables[i + rn.length] = var2;
            frequencies[i + rn.length] = frequencies2[i];
        }
    }
    int[] id = new int[names.length];
    String[] color = new String[names.length];
    String[] type = new String[names.length];
    String[] alias = new String[names.length];
    String[] notes = new String[names.length];
    for (int i = 0; i < attributes.size(); i++) {
        if (attributes.get(i).getStatementTypeId() == statementType.getId() && attributes.get(i).getVariable().equals(var1)) {
            for (int j = 0; j < rn.length; j++) {
                if (rn[j].equals(attributes.get(i).getValue())) {
                    id[j] = attributes.get(i).getId();
                    color[j] = String.format("#%02X%02X%02X", attributes.get(i).getColor().getRed(), attributes.get(i).getColor().getGreen(), attributes.get(i).getColor().getBlue());
                    type[j] = attributes.get(i).getType();
                    alias[j] = attributes.get(i).getAlias();
                    notes[j] = attributes.get(i).getNotes();
                }
            }
        } else if (attributes.get(i).getStatementTypeId() == statementType.getId() && attributes.get(i).getVariable().equals(var2) && twoMode == true) {
            for (int j = 0; j < cn.length; j++) {
                if (cn[j].equals(attributes.get(i).getValue())) {
                    id[j + rn.length] = attributes.get(i).getId();
                    color[j + rn.length] = String.format("#%02X%02X%02X", attributes.get(i).getColor().getRed(), attributes.get(i).getColor().getGreen(), attributes.get(i).getColor().getBlue());
                    type[j + rn.length] = attributes.get(i).getType();
                    alias[j + rn.length] = attributes.get(i).getAlias();
                    notes[j + rn.length] = attributes.get(i).getNotes();
                }
            }
        }
    }
    // set up graph structure
    Namespace xmlns = Namespace.getNamespace("http://graphml.graphdrawing.org/xmlns");
    Element graphml = new Element("graphml", xmlns);
    Namespace visone = Namespace.getNamespace("visone", "http://visone.info/xmlns");
    graphml.addNamespaceDeclaration(visone);
    Namespace xsi = Namespace.getNamespace("xsi", "http://www.w3.org/2001/XMLSchema-instance");
    graphml.addNamespaceDeclaration(xsi);
    Namespace yNs = Namespace.getNamespace("y", "http://www.yworks.com/xml/graphml");
    graphml.addNamespaceDeclaration(yNs);
    Attribute attSchema = new Attribute("schemaLocation", "http://graphml.graphdrawing.org/xmlns/graphml http://www.yworks.com/xml/schema/graphml/1.0/ygraphml.xsd ", xsi);
    graphml.setAttribute(attSchema);
    org.jdom.Document document = new org.jdom.Document(graphml);
    Comment dataSchema = new Comment(" data schema ");
    graphml.addContent(dataSchema);
    Element keyVisoneNode = new Element("key", xmlns);
    keyVisoneNode.setAttribute(new Attribute("for", "node"));
    keyVisoneNode.setAttribute(new Attribute("id", "d0"));
    keyVisoneNode.setAttribute(new Attribute("yfiles.type", "nodegraphics"));
    graphml.addContent(keyVisoneNode);
    Element keyVisoneEdge = new Element("key", xmlns);
    keyVisoneEdge.setAttribute(new Attribute("for", "edge"));
    keyVisoneEdge.setAttribute(new Attribute("id", "e0"));
    keyVisoneEdge.setAttribute(new Attribute("yfiles.type", "edgegraphics"));
    graphml.addContent(keyVisoneEdge);
    Element keyVisoneGraph = new Element("key", xmlns);
    keyVisoneGraph.setAttribute(new Attribute("for", "graph"));
    keyVisoneGraph.setAttribute(new Attribute("id", "prop"));
    keyVisoneGraph.setAttribute(new Attribute("visone.type", "properties"));
    graphml.addContent(keyVisoneGraph);
    Element keyId = new Element("key", xmlns);
    keyId.setAttribute(new Attribute("id", "id"));
    keyId.setAttribute(new Attribute("for", "node"));
    keyId.setAttribute(new Attribute("attr.name", "id"));
    keyId.setAttribute(new Attribute("attr.type", "string"));
    graphml.addContent(keyId);
    Element keyName = new Element("key", xmlns);
    keyName.setAttribute(new Attribute("id", "name"));
    keyName.setAttribute(new Attribute("for", "node"));
    keyName.setAttribute(new Attribute("attr.name", "name"));
    keyName.setAttribute(new Attribute("attr.type", "string"));
    graphml.addContent(keyName);
    Element keyType = new Element("key", xmlns);
    keyType.setAttribute(new Attribute("id", "type"));
    keyType.setAttribute(new Attribute("for", "node"));
    keyType.setAttribute(new Attribute("attr.name", "type"));
    keyType.setAttribute(new Attribute("attr.type", "string"));
    graphml.addContent(keyType);
    Element keyAlias = new Element("key", xmlns);
    keyAlias.setAttribute(new Attribute("id", "alias"));
    keyAlias.setAttribute(new Attribute("for", "node"));
    keyAlias.setAttribute(new Attribute("attr.name", "alias"));
    keyAlias.setAttribute(new Attribute("attr.type", "string"));
    graphml.addContent(keyAlias);
    Element keyNote = new Element("key", xmlns);
    keyNote.setAttribute(new Attribute("id", "note"));
    keyNote.setAttribute(new Attribute("for", "node"));
    keyNote.setAttribute(new Attribute("attr.name", "note"));
    keyNote.setAttribute(new Attribute("attr.type", "string"));
    graphml.addContent(keyNote);
    Element keyVariable = new Element("key", xmlns);
    keyVariable.setAttribute(new Attribute("id", "variable"));
    keyVariable.setAttribute(new Attribute("for", "node"));
    keyVariable.setAttribute(new Attribute("attr.name", "variable"));
    keyVariable.setAttribute(new Attribute("attr.type", "string"));
    graphml.addContent(keyVariable);
    Element keyFrequency = new Element("key", xmlns);
    keyFrequency.setAttribute(new Attribute("id", "frequency"));
    keyFrequency.setAttribute(new Attribute("for", "node"));
    keyFrequency.setAttribute(new Attribute("attr.name", "frequency"));
    keyFrequency.setAttribute(new Attribute("attr.type", "int"));
    graphml.addContent(keyFrequency);
    Element keyWeight = new Element("key", xmlns);
    keyWeight.setAttribute(new Attribute("id", "weight"));
    keyWeight.setAttribute(new Attribute("for", "edge"));
    keyWeight.setAttribute(new Attribute("attr.name", "weight"));
    keyWeight.setAttribute(new Attribute("attr.type", "double"));
    graphml.addContent(keyWeight);
    Element graphElement = new Element("graph", xmlns);
    graphElement.setAttribute(new Attribute("edgedefault", "undirected"));
    graphElement.setAttribute(new Attribute("id", "DNA"));
    int numEdges = rn.length * cn.length;
    if (twoMode == false) {
        numEdges = (numEdges / 2) - rn.length;
    }
    int numNodes = rn.length;
    if (twoMode == true) {
        numNodes = numNodes + cn.length;
    }
    graphElement.setAttribute(new Attribute("parse.edges", String.valueOf(numEdges)));
    graphElement.setAttribute(new Attribute("parse.nodes", String.valueOf(numNodes)));
    graphElement.setAttribute(new Attribute("parse.order", "free"));
    Element properties = new Element("data", xmlns);
    properties.setAttribute(new Attribute("key", "prop"));
    Element labelAttribute = new Element("labelAttribute", visone);
    labelAttribute.setAttribute("edgeLabel", "weight");
    labelAttribute.setAttribute("nodeLabel", "name");
    properties.addContent(labelAttribute);
    graphElement.addContent(properties);
    // add nodes
    Comment nodes = new Comment(" nodes ");
    graphElement.addContent(nodes);
    for (int i = 0; i < names.length; i++) {
        Element node = new Element("node", xmlns);
        node.setAttribute(new Attribute("id", "n" + id[i]));
        Element idElement = new Element("data", xmlns);
        idElement.setAttribute(new Attribute("key", "id"));
        idElement.setText(String.valueOf(id[i]));
        node.addContent(idElement);
        Element nameElement = new Element("data", xmlns);
        nameElement.setAttribute(new Attribute("key", "name"));
        nameElement.setText(names[i]);
        node.addContent(nameElement);
        Element typeElement = new Element("data", xmlns);
        typeElement.setAttribute(new Attribute("key", "type"));
        typeElement.setText(type[i]);
        node.addContent(typeElement);
        Element aliasElement = new Element("data", xmlns);
        aliasElement.setAttribute(new Attribute("key", "alias"));
        aliasElement.setText(alias[i]);
        node.addContent(aliasElement);
        Element notesElement = new Element("data", xmlns);
        notesElement.setAttribute(new Attribute("key", "notes"));
        notesElement.setText(notes[i]);
        node.addContent(notesElement);
        Element variableElement = new Element("data", xmlns);
        variableElement.setAttribute(new Attribute("key", "variable"));
        variableElement.setText(variables[i]);
        node.addContent(variableElement);
        Element frequency = new Element("data", xmlns);
        frequency.setAttribute(new Attribute("key", "frequency"));
        frequency.setText(String.valueOf(frequencies[i]));
        node.addContent(frequency);
        Element vis = new Element("data", xmlns);
        vis.setAttribute(new Attribute("key", "d0"));
        Element visoneShapeNode = new Element("shapeNode", visone);
        Element yShapeNode = new Element("ShapeNode", yNs);
        Element geometry = new Element("Geometry", yNs);
        geometry.setAttribute(new Attribute("height", "20.0"));
        geometry.setAttribute(new Attribute("width", "20.0"));
        geometry.setAttribute(new Attribute("x", String.valueOf(Math.random() * 800)));
        geometry.setAttribute(new Attribute("y", String.valueOf(Math.random() * 600)));
        yShapeNode.addContent(geometry);
        Element fill = new Element("Fill", yNs);
        fill.setAttribute(new Attribute("color", color[i]));
        fill.setAttribute(new Attribute("transparent", "false"));
        yShapeNode.addContent(fill);
        Element borderStyle = new Element("BorderStyle", yNs);
        borderStyle.setAttribute(new Attribute("color", "#000000"));
        borderStyle.setAttribute(new Attribute("type", "line"));
        borderStyle.setAttribute(new Attribute("width", "1.0"));
        yShapeNode.addContent(borderStyle);
        Element nodeLabel = new Element("NodeLabel", yNs);
        nodeLabel.setAttribute(new Attribute("alignment", "center"));
        nodeLabel.setAttribute(new Attribute("autoSizePolicy", "content"));
        nodeLabel.setAttribute(new Attribute("backgroundColor", "#FFFFFF"));
        nodeLabel.setAttribute(new Attribute("fontFamily", "Dialog"));
        nodeLabel.setAttribute(new Attribute("fontSize", "12"));
        nodeLabel.setAttribute(new Attribute("fontStyle", "plain"));
        nodeLabel.setAttribute(new Attribute("hasLineColor", "false"));
        nodeLabel.setAttribute(new Attribute("height", "19.0"));
        nodeLabel.setAttribute(new Attribute("modelName", "eight_pos"));
        nodeLabel.setAttribute(new Attribute("modelPosition", "n"));
        nodeLabel.setAttribute(new Attribute("textColor", "#000000"));
        nodeLabel.setAttribute(new Attribute("visible", "true"));
        nodeLabel.setText(names[i]);
        yShapeNode.addContent(nodeLabel);
        Element shape = new Element("Shape", yNs);
        if (i < rn.length) {
            shape.setAttribute(new Attribute("type", "ellipse"));
        } else {
            shape.setAttribute(new Attribute("type", "roundrectangle"));
        }
        yShapeNode.addContent(shape);
        visoneShapeNode.addContent(yShapeNode);
        vis.addContent(visoneShapeNode);
        node.addContent(vis);
        graphElement.addContent(node);
    }
    // add edges
    double[][] m = mt.getMatrix();
    Comment edges = new Comment(" edges ");
    graphElement.addContent(edges);
    for (int i = 0; i < rn.length; i++) {
        for (int j = 0; j < cn.length; j++) {
            if (m[i][j] != 0.0 && (twoMode == true || (twoMode == false && i < j))) {
                // only lower triangle is used for one-mode networks
                Element edge = new Element("edge", xmlns);
                int currentId = id[i];
                edge.setAttribute(new Attribute("source", "n" + String.valueOf(currentId)));
                if (twoMode == true) {
                    currentId = id[j + rn.length];
                } else {
                    currentId = id[j];
                }
                edge.setAttribute(new Attribute("target", "n" + String.valueOf(currentId)));
                Element weight = new Element("data", xmlns);
                weight.setAttribute(new Attribute("key", "weight"));
                weight.setText(String.valueOf(m[i][j]));
                edge.addContent(weight);
                Element visEdge = new Element("data", xmlns);
                visEdge.setAttribute("key", "e0");
                Element visPolyLineEdge = new Element("polyLineEdge", visone);
                Element yPolyLineEdge = new Element("PolyLineEdge", yNs);
                Element yLineStyle = new Element("LineStyle", yNs);
                if (qualifierAggregation.equals("combine") && qualifierBinary == true) {
                    if (m[i][j] == 1.0) {
                        yLineStyle.setAttribute("color", "#00ff00");
                    } else if (m[i][j] == 2.0) {
                        yLineStyle.setAttribute("color", "#ff0000");
                    } else if (m[i][j] == 3.0) {
                        yLineStyle.setAttribute("color", "#0000ff");
                    }
                } else if (qualifierAggregation.equals("subtract")) {
                    if (m[i][j] < 0) {
                        yLineStyle.setAttribute("color", "#ff0000");
                    } else if (m[i][j] > 0) {
                        yLineStyle.setAttribute("color", "#00ff00");
                    }
                } else if (qualifierAggregation.equals("conflict")) {
                    yLineStyle.setAttribute("color", "#ff0000");
                } else if (qualifierAggregation.equals("congruence")) {
                    yLineStyle.setAttribute("color", "#00ff00");
                } else {
                    yLineStyle.setAttribute("color", "#000000");
                }
                yLineStyle.setAttribute(new Attribute("type", "line"));
                yLineStyle.setAttribute(new Attribute("width", "2.0"));
                yPolyLineEdge.addContent(yLineStyle);
                visPolyLineEdge.addContent(yPolyLineEdge);
                visEdge.addContent(visPolyLineEdge);
                edge.addContent(visEdge);
                graphElement.addContent(edge);
            }
        }
    }
    graphml.addContent(graphElement);
    // write to file
    File dnaFile = new File(outfile);
    try {
        FileOutputStream outStream = new FileOutputStream(dnaFile);
        XMLOutputter outToFile = new XMLOutputter();
        Format format = Format.getPrettyFormat();
        format.setEncoding("utf-8");
        outToFile.setFormat(format);
        outToFile.output(document, outStream);
        outStream.flush();
        outStream.close();
    } catch (IOException e) {
        System.err.println("Cannot save \"" + dnaFile + "\":" + e.getMessage());
    }
}