Examples with Text nu.xom.Text used on opensource projects

Example 6 with Text

use of nu.xom.Text in project tetrad by cmu-phil.

the class BayesXmlRenderer method getCptsElement.

private static Element getCptsElement(BayesIm bayesIm) {
    Element cpts = new Element("cpts");
    cpts.addAttribute(new Attribute("rowSumTolerance", "0.0001"));
    for (int i = 0; i < bayesIm.getNumNodes(); i++) {
        Element cpt = new Element("cpt");
        cpts.appendChild(cpt);
        String varName = bayesIm.getNode(i).getName();
        int numRows = bayesIm.getNumRows(i);
        int numCols = bayesIm.getNumColumns(i);
        cpt.addAttribute(new Attribute("variable", varName));
        cpt.addAttribute(new Attribute("numRows", "" + numRows));
        cpt.addAttribute(new Attribute("numCols", "" + numCols));
        for (int j = 0; j < numRows; j++) {
            Element row = new Element("row");
            cpt.appendChild(row);
            StringBuilder buf = new StringBuilder();
            for (int k = 0; k < numCols; k++) {
                double probability = bayesIm.getProbability(i, j, k);
                buf.append(NumberFormatUtil.getInstance().getNumberFormat().format(probability)).append(" ");
            }
            String s = buf.toString();
            row.appendChild(new Text(s.trim()));
        }
    }
    return cpts;
}

Example 7 with Text

use of nu.xom.Text in project tetrad by cmu-phil.

the class GraphUtils method convertToXml.

/**
 * @return an XML element representing the given graph. (Well, only a basic
 * graph for now...)
 */
public static Element convertToXml(Graph graph) {
    Element element = new Element("graph");
    Element variables = new Element("variables");
    element.appendChild(variables);
    for (Node node : graph.getNodes()) {
        Element variable = new Element("variable");
        Text text = new Text(node.getName());
        variable.appendChild(text);
        variables.appendChild(variable);
    }
    Element edges = new Element("edges");
    element.appendChild(edges);
    for (Edge edge : graph.getEdges()) {
        Element _edge = new Element("edge");
        Text text = new Text(edge.toString());
        _edge.appendChild(text);
        edges.appendChild(_edge);
    }
    Set<Triple> ambiguousTriples = graph.getAmbiguousTriples();
    if (!ambiguousTriples.isEmpty()) {
        Element underlinings = new Element("ambiguities");
        element.appendChild(underlinings);
        for (Triple triple : ambiguousTriples) {
            Element underlining = new Element("ambiguities");
            Text text = new Text(niceTripleString(triple));
            underlining.appendChild(text);
            underlinings.appendChild(underlining);
        }
    }
    Set<Triple> underlineTriples = graph.getUnderLines();
    if (!underlineTriples.isEmpty()) {
        Element underlinings = new Element("underlines");
        element.appendChild(underlinings);
        for (Triple triple : underlineTriples) {
            Element underlining = new Element("underline");
            Text text = new Text(niceTripleString(triple));
            underlining.appendChild(text);
            underlinings.appendChild(underlining);
        }
    }
    Set<Triple> dottedTriples = graph.getDottedUnderlines();
    if (!dottedTriples.isEmpty()) {
        Element dottedUnderlinings = new Element("dottedUnderlines");
        element.appendChild(dottedUnderlinings);
        for (Triple triple : dottedTriples) {
            Element dottedUnderlining = new Element("dottedUnderline");
            Text text = new Text(niceTripleString(triple));
            dottedUnderlining.appendChild(text);
            dottedUnderlinings.appendChild(dottedUnderlining);
        }
    }
    return element;
}

Example 8 with Text

use of nu.xom.Text in project tetrad by cmu-phil.

the class BayesXmlParser method makeBayesIm.

private static BayesIm makeBayesIm(BayesPm bayesPm, Element element2) {
    if (!"cpts".equals(element2.getQualifiedName())) {
        throw new IllegalArgumentException("Expecting 'cpts' element.");
    }
    MlBayesIm bayesIm = new MlBayesIm(bayesPm);
    Elements elements2 = element2.getChildElements();
    for (int nodeIndex = 0; nodeIndex < elements2.size(); nodeIndex++) {
        Element e1 = elements2.get(nodeIndex);
        if (!"cpt".equals(e1.getQualifiedName())) {
            throw new IllegalArgumentException("Expecting 'cpt' element.");
        }
        String numRowsString = e1.getAttributeValue("numRows");
        String numColsString = e1.getAttributeValue("numCols");
        int numRows = Integer.parseInt(numRowsString);
        int numCols = Integer.parseInt(numColsString);
        Elements e1Elements = e1.getChildElements();
        if (e1Elements.size() != numRows) {
            throw new IllegalArgumentException("Element cpt claimed " + +numRows + " rows, but there are only " + e1Elements.size() + " rows in the file.");
        }
        for (int rowIndex = 0; rowIndex < numRows; rowIndex++) {
            Element e2 = e1Elements.get(rowIndex);
            if (!"row".equals(e2.getQualifiedName())) {
                throw new IllegalArgumentException("Expecting 'parent' element.");
            }
            Text rowNode = (Text) e2.getChild(0);
            String rowString = rowNode.getValue();
            StringTokenizer t = new StringTokenizer(rowString);
            for (int colIndex = 0; colIndex < numCols; colIndex++) {
                String token = t.nextToken();
                try {
                    double value = Double.parseDouble(token);
                    bayesIm.setProbability(nodeIndex, rowIndex, colIndex, value);
                } catch (NumberFormatException e) {
                // Skip.
                }
            }
            if (t.hasMoreTokens()) {
                throw new IllegalArgumentException("Element cpt claimed " + numCols + " columnns , but there are more that that " + "in the file.");
            }
        }
    }
    return bayesIm;
}

Example 9 with Text

use of nu.xom.Text in project cdk by cdk.

the class RssWriter method write.

/**
 * Writes a IChemObject to the MDL molfile formated output.
 *
 * @param object Best choice is a set of molecules
 */
/*
     * (non-Javadoc)
     * @see
     * org.openscience.cdk.io.IChemObjectWriter#write(org.openscience.cdk.interfaces
     * .IChemObject)
     */
@Override
public void write(IChemObject object) throws CDKException {
    try {
        ProcessingInstruction processingInstruction = new ProcessingInstruction("xml-stylesheet", "href=\"http://www.w3.org/2000/08/w3c-synd/style.css\" type=\"text/css\"");
        Element rdfElement = new Element("rdf:RDF", NS_RDF);
        rdfElement.addNamespaceDeclaration("", NS_RSS10);
        rdfElement.addNamespaceDeclaration("mn", "http://usefulinc.com/rss/manifest/");
        rdfElement.addNamespaceDeclaration("dc", NS_DCELEMENTS);
        rdfElement.addNamespaceDeclaration("cml", Convertor.NS_CML);
        Document doc = new Document(rdfElement);
        doc.insertChild(processingInstruction, 0);
        Element channelElement = new Element("channel", NS_RSS10);
        Element titleElement = new Element("title", NS_RSS10);
        titleElement.appendChild(new Text(title));
        channelElement.appendChild(titleElement);
        Element linkElement = new Element("link", NS_RSS10);
        linkElement.appendChild(new Text(link));
        channelElement.appendChild(linkElement);
        Element descriptionElement = new Element("description", NS_RSS10);
        descriptionElement.appendChild(new Text(description));
        channelElement.appendChild(descriptionElement);
        Element publisherElement = new Element("dc:publisher", NS_DCELEMENTS);
        publisherElement.appendChild(new Text(publisher));
        channelElement.appendChild(publisherElement);
        Element creatorElement = new Element("dc:creator", NS_DCELEMENTS);
        creatorElement.appendChild(new Text(creator));
        channelElement.appendChild(creatorElement);
        Element imageElement = new Element("image", NS_RSS10);
        imageElement.addAttribute(new Attribute("rdf:resource", NS_RDF, imagelink));
        channelElement.appendChild(imageElement);
        Element itemsElement = new Element("items", NS_RSS10);
        Element seqElement = new Element("rdf:Seq", NS_RDF);
        itemsElement.appendChild(seqElement);
        channelElement.appendChild(itemsElement);
        channelElement.addAttribute(new Attribute("rdf:about", NS_RDF, about));
        rdfElement.appendChild(channelElement);
        List<IChemObject> list = new ArrayList<>();
        if (object instanceof IAtomContainerSet) {
            for (int i = 0; i < ((IAtomContainerSet) object).getAtomContainerCount(); i++) {
                list.add(((IAtomContainerSet) object).getAtomContainer(i));
            }
        } else {
            list.add(object);
        }
        for (IChemObject iChemObject : list) {
            IChemObject chemObject = iChemObject;
            Element itemElement = new Element("item", NS_RSS10);
            String easylink = (String) linkmap.get(chemObject);
            if (easylink != null)
                itemElement.addAttribute(new Attribute("rdf:about", NS_RDF, easylink));
            Element link2Element = new Element("link", NS_RSS10);
            link2Element.appendChild(new Text(easylink));
            itemElement.appendChild(link2Element);
            String title = (String) chemObject.getProperties().get(CDKConstants.TITLE);
            if (titlemap.get(chemObject) != null) {
                Element title2Element = new Element("title", NS_RSS10);
                title2Element.appendChild(new Text((String) titlemap.get(chemObject)));
                itemElement.appendChild(title2Element);
            }
            if (title != null) {
                Element description2Element = new Element("description", NS_RSS10);
                description2Element.appendChild(new Text(title));
                itemElement.appendChild(description2Element);
                Element subjectElement = new Element("dc:subject", NS_DCELEMENTS);
                subjectElement.appendChild(new Text(title));
                itemElement.appendChild(subjectElement);
            }
            if (datemap.get(chemObject) != null) {
                Element dateElement = new Element("dc:date", NS_DCELEMENTS);
                SimpleDateFormat formatter = new SimpleDateFormat("yyyy-MM-dd'T'HH:mm:ss", Locale.ROOT);
                dateElement.appendChild(new Text(formatter.format((Date) datemap.get(chemObject)) + timezone));
                itemElement.appendChild(dateElement);
            }
            Element creator2Element = new Element("dc:creator", NS_DCELEMENTS);
            creator2Element.appendChild(new Text((String) creatormap.get(chemObject)));
            itemElement.appendChild(creator2Element);
            // add the InChI to the CMLRSS feed
            if (inchimap.get(chemObject) != null) {
                Element inchiElement = new Element("cml:identifier", "http://www.xml-cml.org/schema/cml2/core/");
                inchiElement.appendChild(new Text((String) inchimap.get(chemObject)));
                itemElement.appendChild(inchiElement);
            }
            Element root;
            Convertor convertor = new Convertor(true, null);
            object = iChemObject;
            if (object instanceof ICrystal) {
                root = convertor.cdkCrystalToCMLMolecule((ICrystal) object);
            } else if (object instanceof IAtomContainer) {
                root = convertor.cdkAtomContainerToCMLMolecule((IAtomContainer) object);
            } else if (object instanceof IAtom) {
                root = convertor.cdkAtomToCMLAtom(null, (IAtom) object);
            } else if (object instanceof IBond) {
                root = convertor.cdkBondToCMLBond((IBond) object);
            } else if (object instanceof IReaction) {
                root = convertor.cdkReactionToCMLReaction((IReaction) object);
            } else if (object instanceof IReactionSet) {
                root = convertor.cdkReactionSetToCMLReactionList((IReactionSet) object);
            } else if (object instanceof IAtomContainerSet) {
                root = convertor.cdkAtomContainerSetToCMLList((IAtomContainerSet) object);
            } else if (object instanceof IChemSequence) {
                root = convertor.cdkChemSequenceToCMLList((IChemSequence) object);
            } else if (object instanceof IChemModel) {
                root = convertor.cdkChemModelToCMLList((IChemModel) object);
            } else if (object instanceof IChemFile) {
                root = convertor.cdkChemFileToCMLList((IChemFile) object);
            } else {
                throw new CDKException("Unsupported chemObject: " + object.getClass().getName());
            }
            itemElement.appendChild(root);
            if (multiMap.get(chemObject) != null) {
                Collection coll = (Collection) multiMap.get(chemObject);
                for (Object o : coll) {
                    itemElement.appendChild((Element) o);
                }
            }
            rdfElement.appendChild(itemElement);
            Element imageElement2 = new Element("rdf:li", NS_RDF);
            imageElement2.addAttribute(new Attribute("rdf:resource", NS_RDF, (String) linkmap.get(chemObject)));
            seqElement.appendChild(imageElement2);
        }
        writer.write(doc.toXML());
        writer.flush();
    } catch (IOException ex) {
        throw new CDKException(ex.getMessage(), ex);
    }
}

Example 10 with Text

use of nu.xom.Text in project meico by cemfi.

the class Comment method parseData.

/**
 * parse the comment element and set the according class variables
 * @param xml
 * @throws Exception
 */
@Override
protected void parseData(Element xml) throws Exception {
    if (xml == null)
        throw new Exception("Cannot generate Comment object. XML Element is null.");
    this.setXml(xml);
    if ((xml.getChildCount() == 0) || !(xml.getChild(0) instanceof Text)) {
        // if no text node is given in the xml source
        // generate a placeholder text node
        this.text = new Text("");
        // add it to the xml
        xml.appendChild(this.text);
    } else
        this.text = (Text) xml.getChild(0);
    this.id = Helper.getAttribute("id", xml);
}